supplementary figures and tables · 10/1/2015 · supplementary figures and tables ... otx2

Disease Models & Mechanisms 8: doi:10.1242/dmm.020594: Supplementary information

Supplementary Figures and Tables:

Supplementary Figure 1: Overexpression of OTX2 in Daoy and hEN does not significantly affect viability in adherent cultures. (A-D) Representative flow plots and quantification of Annexin V staining in Daoy

(A-B) and hEN (C-D) cells in control and OTX2-overexpressing cultures. For both

cell lines, no significant changes in dying (Annexin V+/7AAD-) and dead (Annexin

V+/7AAD+) cells were observed. Error Bars: s.e.m.

(E). Representative dot plots of BrdU incorporation and DNA content (7AAD)

from Daoy adherent cultures following OTX2 overexpression. Inset: 7AAD only

control.

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Supplementary Figure 2: Overexpression of OTX2 in Daoy and hEN tumorspheres results in decreased cell viability. (A-B) OTX2 overexpression decreases cell viability in OTX2 Daoy (A) and OTX2

hEN (B) spheres between passages as measured by Trypan Blue staining. Error

Bars: s.e.m. P<0.05*, P<0.01**.

(C-J) Annexin V staining demonstrates significant decreases in cell viability in

both OTX2 Daoy (C-F) and OTX2 hEN (G-J) spheres relative to controls over

subsequent passage. Increases in both dying (Annexin V+/7AAD-) and dead

(Annexin V+/7AAD+) cells were evident for both cell lines. For all paired

comparisons of dead/dying cells, P<0.001***, expect for dying cells in p1 hEN

spheres which were not significantly different. Error Bars: s.e.m.

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Supplementary Figure 3: Overexpression of OTX2 decreases the frequency of cells in S phase and increases the frequency of G0/G1 and apoptotic cells in sphere culture. Representative dot plots of BrdU incorporation and DNA content (7AAD) from

Daoy tumorspheres following OTX2 overexpression. Inset: 7AAD only control.

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Supplementary Figure 4: OTX2 overexpression decreases levels of both proliferation and migration transcripts. (A) Validation of proliferation transcript downregulation in hENs (upper) and Daoy

(lower) following OTX2 overexpression by qPCR. Error Bars: s.e.m. N=3

independent biological replicates.

(B) Validation of migration transcript downregulation in hENs (upper) and Daoy

(lower) following OTX2 overexpression by qPCR. Error Bars: s.e.m. N=3

independent biological replicates.

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Supplementary Figure 5: Representative brightfield and fluorescent images of D283, trans-hEN and D341 cells following transfection with a Block IT ™ Red Fluorescent control. (A-B). Representative brightfield (A) and fluorescent (B) images of adherent

D283 cells following transfection with a Block IT ™ Red Fluorescent control to

determine transduction efficiency. Scale bar: 200 µm.

(C-D). Representative brightfield (C) and fluorescent (D) images of trans-hEN

neurospheres cells following transfection with a Block IT ™ Red Fluorescent

control to determine transduction efficiency. Scale bar: 400 µm.

(E-F). Representative brightfield (E) and fluorescent (F) images of D341 spheres

following transfection with a Block IT ™ Red Fluorescent control to determine

transduction efficiency. Scale bar: 400 µm.

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Supplementary Figure 6: Knockdown of OTX2 decreases the frequency of cells in S phase and increases the frequency of apoptotic cells.

(A) Representative dot plots of BrdU incorporation and DNA content (7AAD) in

D283 tumorspheres following OTX2 knockdown. Inset: 7AAD only control. For

clarity, results from the 3 siRNA sequences were pooled and presented as the

mean ± s.e.m. N=2 independent biological replicates for each sequence.

(B) Representative dot plots of BrdU incorporation and DNA content (7AAD) in

trans-hEN neurospheres following OTX2 knockdown. Inset: 7AAD only control.

For clarity, results from the 3 siRNA sequences were pooled and presented as

the mean ± s.e.m. N=2 independent biological replicates for each sequence. Dis

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Supplementary Figure 7: OTX2 knockdown significantly inhibits self-renewal and viability in D341 MB cells. (A). Western Blot validation of OTX2 knockdown in 3 independent siRNA

sequences relative to scramble siRNA and untransduced cells. β-actin serves as

a loading control.

(B). Representative images of D341 MB cells in sphere culture or stem cell

enriched conditions following 6 days knockdown of OTX2. Scale bar: 400 µm.

(C-E). Tumorsphere formation, cell viability and self-renewal capacity were

significantly inhibited following OTX2 knockdown in D341 cells. Error bars:

s.e.m. P<0.05*, P<0.01**, P<0.001***.

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Supplementary Figure 8: OTX2 knockdown results in only modest changes in hESC gene epxresssion levels in D283 and trans-hENs. (A-D). hESC pluripotency factor transcript levels in D283 (black bars) and trans-

hEN (grey bars) following OTX2 knockdown by qPCR. Error Bars: s.e.m.

P<0.05*. N=3 biological replicates for each cell line. (E). Western Blot of OTX2 knockdown in 2 independent shRNA sequences

relative to scramble shRNA. β-actin serves as a loading control.

(F-K). Quantification of total cell number (F,H) and cell viability (G,I) in D283 (F-

G) and trans-hENs (H-I) following knockdown of OTX2 over 4 days. (J-K).

Sphere formation following OTX2 knockdown in D283 (J) and trans-hENs (K).

Error bars: s.e.m. P<0.05*, P<0.01**, P<0.001***.

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Column # Transcript ID gene_assignmentGene SymbolRefSeq mrna_assignmentp-‐value(type)p-‐value(OTX2 hEN vs. hEN)Ratio(OTX2 hEN vs. hEN)Fold-‐Change(OTX2 hEN vs. hEN) F(type) SS(type) SS(Error) F(Error)52978 17125282 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ 0.022355 0.022355 7.40057 7.40057 13.1052 12.5077 3.81762 146946 17094667 AK098218 // PGM5-‐AS1 // PGM5 antisense RNA 1 (non-‐protein coding) // 9q13 // 572558PGM5-‐AS1 AK098218 AK098218 // GenBank // Homo sapiens cDNA FLJ40899 fis, clone UTERU2003126. // chr9 // 80.0484786 0.0484786 7.25139 7.25139 7.87767 12.2545 6.22238 128035 16902037 -‐-‐-‐ -‐-‐-‐ TCONS_l2_00014823-‐XLOC_l2_008214 // Broad TUCP // linc-‐PAX8-‐1 chr2:-‐:114286363-‐114293430.0477426 0.0477426 6.99003 6.99003 7.96233 11.8046 5.9302 146928 17094498 -‐-‐-‐ -‐-‐-‐ TCONS_l2_00029975-‐XLOC_l2_015216 // Broad TUCP // linc-‐FAM75A7-‐32 chr9:-‐:69082535-‐691080.0330381 0.0330381 4.57727 4.57727 10.2121 7.22365 2.82946 140205 17023799 NM_145176 // SLC2A12 // solute carrier family 2 (facilitated glucose transporter), membSLC2A12 NM_145176 NM_145176 // RefSeq // Homo sapiens solute carrier family 2 (facilitated glucose transp0.0244244 0.0244244 4.22078 4.22078 12.3986 6.47408 2.08865 128669 16909482 NM_000867 // HTR2B // 5-‐hydroxytryptamine (serotonin) receptor 2B, G protein-‐coupled //HTR2B NM_000867 NM_000867 // RefSeq // Homo sapiens 5-‐hydroxytryptamine (serotonin) receptor 2B, G prot0.0117491 0.0117491 3.01384 3.01384 19.3042 3.7998 0.787353 145300 17078592 ENST00000256104 // FABP4 // fatty acid binding protein 4, adipocyte // 8q21 // 2167 ///FABP4 ENST00000256104ENST00000256104 // ENSEMBL // cdna:known chromosome:GRCh37:8:82390654:82395498:-‐1 gene:0.0475545 0.0475545 2.8927 2.8927 7.98429 3.52246 1.76469 127548 16897834 NM_001039348 // EFEMP1 // EGF containing fibulin-‐like extracellular matrix protein 1 //EFEMP1 NM_001039348NM_001039348 // RefSeq // Homo sapiens EGF containing fibulin-‐like extracellular matrix0.0097099 0.0097099 2.83274 2.83274 21.5604 3.3849 0.627986 121832 16841137 NM_201433 // GAS7 // growth arrest-‐specific 7 // 17p13.1 // 8522 /// NM_001130831 // GAGAS7 NM_201433 NM_201433 // RefSeq // Homo sapiens growth arrest-‐specific 7 (GAS7), transcript variant0.0459384 0.0459384 2.54604 2.54604 8.1785 2.72668 1.33358 139616 17017205 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // pos_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.00496703 0.00496703 2.4551 2.4551 31.4475 2.51857 0.320352 14323 16664828 NM_001199080 // PODN // podocan // 1p32.3 // 127435 /// ENST00000371500 // PODN // podoPODN NM_001199080NM_001199080 // RefSeq // Homo sapiens podocan (PODN), transcript variant 2, mRNA. // c0.0101091 0.0101091 2.2385 2.2385 21.0653 2.02721 0.384938 11129 16652349 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0100807 0.0100807 2.22566 2.22566 21.0996 1.99838 0.378848 147463 17099703 NR_039695 // MIR3689E // microRNA 3689e // -‐-‐-‐ // 100616460MIR3689E NR_039695 NR_039695 // RefSeq // Homo sapiens microRNA 3689e (MIR3689E), microRNA. // chr9 // 1000.0327028 0.0327028 2.20272 2.20272 10.2806 1.94695 0.757525 113171 16755908 NM_018370 // DRAM1 // DNA-‐damage regulated autophagy modulator 1 // 12q23.2 // 55332 //DRAM1 NM_018370 NM_018370 // RefSeq // Homo sapiens DNA-‐damage regulated autophagy modulator 1 (DRAM1),0.00373664 0.00373664 2.16841 2.16841 36.7597 1.87032 0.203518 142547 17051553 NM_016352 // CPA4 // carboxypeptidase A4 // 7q32 // 51200 /// NM_001163446 // CPA4 // cCPA4 NM_016352 NM_016352 // RefSeq // Homo sapiens carboxypeptidase A4 (CPA4), transcript variant 1, m0.0254871 0.0254871 2.12041 2.12041 12.0697 1.7637 0.584502 15958 16681827 NM_004753 // DHRS3 // dehydrogenase/reductase (SDR family) member 3 // 1p36.1 // 9249 /DHRS3 NM_004753 NM_004753 // RefSeq // Homo sapiens dehydrogenase/reductase (SDR family) member 3 (DHRS0.00159987 0.00159987 2.0849 2.0849 57.9203 1.68534 0.11639 138585 17008092 NM_002648 // PIM1 // pim-‐1 oncogene // 6p21.2 // 5292 /// NM_001243186 // PIM1 // pim-‐1PIM1 NM_002648 NM_002648 // RefSeq // Homo sapiens pim-‐1 oncogene (PIM1), transcript variant 1, mRNA. 0.0314848 0.0314848 2.01803 2.01803 10.5387 1.53909 0.584168 146746 17092936 ENST00000543880 // IZUMO3 // IZUMO family member 3 // -‐-‐-‐ // -‐-‐-‐IZUMO3 ENST00000543880TCONS_l2_00029227-‐XLOC_l2_015134 // Broad TUCP // linc-‐ELAVL2-‐2 chr9:-‐:24542983-‐24546050.012618 0.012618 2.00209 2.00209 18.5138 1.50452 0.32506 12561 16655325 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0285017 0.0285017 1.95883 1.95883 11.2395 1.41132 0.502273 1568 16651171 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0436576 0.0436576 1.91462 1.91462 8.47084 1.31712 0.621956 1

17935 16800680 ENST00000260324 // SQRDL // sulfide quinone reductase-‐like (yeast) // 15q15 // 58472 //SQRDL ENST00000260324ENST00000260324 // ENSEMBL // cdna:known chromosome:GRCh37:15:45926938:45983492:1 gene:0.0495743 0.0495743 1.89567 1.89567 7.75515 1.27709 0.658708 11553 16653241 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.00735663 0.00735663 1.85353 1.85353 25.2559 1.18889 0.188295 1156 16650305 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0413606 0.0413606 1.82653 1.82653 8.78951 1.13302 0.515623 1

46991 17095056 NM_015225 // PRUNE2 // prune homolog 2 (Drosophila) // 9q21.2 // 158471 /// ENST0000037PRUNE2 NM_015225 NM_015225 // RefSeq // Homo sapiens prune homolog 2 (Drosophila) (PRUNE2), mRNA. // chr0.0161249 0.0161249 1.79042 1.79042 16.0031 1.05914 0.264734 114690 16771532 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // pos_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0471907 0.0471907 1.77535 1.77535 8.02714 1.02863 0.512576 11039 16652155 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0014175 0.0014175 1.76167 1.76167 61.7398 1.0011 0.0648595 116955 16791810 NR_027263 // ARHGAP5-‐AS1 // ARHGAP5 antisense RNA 1 (non-‐protein coding) // 14q12 // 84ARHGAP5-‐AS1NR_027263 NR_027263 // RefSeq // Homo sapiens ARHGAP5 antisense RNA 1 (non-‐protein coding) (ARHGA0.0224123 0.0224123 1.76065 1.76065 13.0843 0.999055 0.30542 110208 16724751 NM_001004739 // OR5L2 // olfactory receptor, family 5, subfamily L, member 2 // 11q11 /OR5L2 NM_001004739NM_001004739 // RefSeq // Homo sapiens olfactory receptor, family 5, subfamily L, membe0.0389379 0.0389379 1.75811 1.75811 9.15591 0.993946 0.434231 124632 16867784 NM_000064 // C3 // complement component 3 // 19p13.3-‐p13.2 // 718 /// ENST00000245907 /C3 NM_000064 NM_000064 // RefSeq // Homo sapiens complement component 3 (C3), mRNA. // chr19 // 100 0.0457878 0.0457878 1.75602 1.75602 8.19713 0.989771 0.482984 13141 16656515 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0341407 0.0341407 1.75419 1.75419 9.99397 0.986101 0.394678 12554 16655311 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.03802 0.03802 1.74124 1.74124 9.30384 0.960285 0.412855 145348 17078995 -‐-‐-‐ -‐-‐-‐ ENST00000517884 // ENSEMBL // cdna:known chromosome:GRCh37:8:91818702:91871468:-‐1 gene:0.026826 0.026826 1.74116 1.74116 11.6837 0.960117 0.328704 133570 16960911 NM_020169 // LXN // latexin // 3q25.32 // 56925 /// ENST00000264265 // LXN // latexin /LXN NM_020169 NM_020169 // RefSeq // Homo sapiens latexin (LXN), mRNA. // chr3 // 100 // 85 // 22 // 0.0357047 0.0357047 1.73663 1.73663 9.70216 0.951122 0.392128 124482 16866289 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // pos_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0188526 0.0188526 1.73376 1.73376 14.5573 0.945418 0.259779 11107 16652301 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0222873 0.0222873 1.71774 1.71774 13.13 0.913799 0.278386 11677 16653495 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0438602 0.0438602 1.71533 1.71533 8.44395 0.90907 0.430637 1687 16651411 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0434573 0.0434573 1.71039 1.71039 8.49761 0.89936 0.423348 1

12076 16744205 NM_020809 // ARHGAP20 // Rho GTPase activating protein 20 // 11q23.1 // 57569 /// ENST0ARHGAP20 NM_020809 NM_020809 // RefSeq // Homo sapiens Rho GTPase activating protein 20 (ARHGAP20), transc0.00754399 0.00754399 1.70962 1.70962 24.8995 0.897856 0.144237 143423 17060317 NM_001256497 // CYP3A7-‐CYP3AP1 // CYP3A7-‐CYP3AP1 readthrough // 7q // 100861540 /// NM_CYP3A7-‐CYP3AP1NM_001256497NM_001256497 // RefSeq // Homo sapiens CYP3A7-‐CYP3AP1 readthrough (CYP3A7-‐CYP3AP1), mRN0.0344384 0.0344384 1.69972 1.69972 9.93688 0.878525 0.353642 131225 16934243 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // pos_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0390548 0.0390548 1.68965 1.68965 9.13745 0.858955 0.376015 11161 16652417 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.00306457 0.00306457 1.68796 1.68796 40.9339 0.855664 0.0836143 136716 16991180 ENST00000526627 // C5orf62 // chromosome 5 open reading frame 62 // 5q33.1 // 85027 ///C5orf62 ENST00000526627ENST00000526627 // ENSEMBL // cdna:known chromosome:GRCh37:5:150157508:150176296:1 gene0.0174466 0.0174466 1.68597 1.68597 15.2601 0.851831 0.223283 1818 16651683 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0372551 0.0372551 1.68412 1.68412 9.4313 0.848247 0.359758 1

18259 16804165 NM_001267536 // GOLGA6L4 // golgin A6 family-‐like 4 // 15q25.2 // 643707 /// BC101293 /GOLGA6L4 NM_001267536NM_001267536 // RefSeq // Homo sapiens golgin A6 family-‐like 4 (GOLGA6L4), mRNA. // chr0.0374169 0.0374169 1.65951 1.65951 9.40401 0.801014 0.340711 150186 17119520 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ 0.0331199 0.0331199 1.65614 1.65614 10.1955 0.794598 0.311744 13249 16656739 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.00053544 0.00053544 1.64517 1.64517 102.532 0.773793 0.0301875 12143 16654461 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0404161 0.0404161 1.64319 1.64319 8.92841 0.77005 0.344988 13500 16657259 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0233246 0.0233246 1.62756 1.62756 12.7624 0.740712 0.232154 1

Supplementary Table 1: Differentially expressed transcripts in OTX2 hEN

vs. hEN cells. All transcripts are significantly and differentially expressed.

P<0.05 is considered significant. N=3 independent, biological replicates.


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15657 16779956 NR_037438 // MIR3665 // microRNA 3665 // -‐-‐-‐ // 100500861MIR3665 NR_037438 NR_037438 // RefSeq // Homo sapiens microRNA 3665 (MIR3665), microRNA. // chr13 // 100 0.0413784 0.0413784 1.62581 1.62581 8.78694 0.737433 0.335695 139748 17018720 NM_001162900 // TMEM217 // transmembrane protein 217 // 6p21.2 // 221468 /// NM_145316 TMEM217 NM_001162900NM_001162900 // RefSeq // Homo sapiens transmembrane protein 217 (TMEM217), transcript 0.00910656 0.00910656 1.6191 1.6191 22.3694 0.724932 0.129629 110210 16724755 NM_032681 // TRIM51 // tripartite motif-‐containing 51 // 11q11 // 84767 /// ENST0000044TRIM51 NM_032681 NM_032681 // RefSeq // Homo sapiens tripartite motif-‐containing 51 (TRIM51), mRNA. // c0.0107441 0.0107441 1.61556 1.61556 20.3356 0.718374 0.141304 129473 16917444 -‐-‐-‐ -‐-‐-‐ ENST00000390863 // ENSEMBL // ncrna:snoRNA chromosome:GRCh37:20:16963477:16963678:-‐1 ge0.0480024 0.0480024 1.60904 1.60904 7.93223 0.706315 0.356175 111723 16740576 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // pos_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0384238 0.0384238 1.60237 1.60237 9.23811 0.694021 0.300503 143984 17066083 NM_006207 // PDGFRL // platelet-‐derived growth factor receptor-‐like // 8p22-‐p21.3 // 51PDGFRL NM_006207 NM_006207 // RefSeq // Homo sapiens platelet-‐derived growth factor receptor-‐like (PDGFR0.00880368 0.00880368 1.5978 1.5978 22.8066 0.685643 0.120253 114898 16773160 -‐-‐-‐ -‐-‐-‐ TCONS_00021731-‐XLOC_010311 // Rinn lincRNA // linc-‐TNFRSF19-‐1 chr13:+:24079514-‐240996230.00411465 0.00411465 1.5874 1.5874 34.8758 0.666659 0.076461 143322 17059044 NM_012301 // MAGI2 // membrane associated guanylate kinase, WW and PDZ domain containinMAGI2 NM_012301 NM_012301 // RefSeq // Homo sapiens membrane associated guanylate kinase, WW and PDZ do0.00925276 0.00925276 1.58339 1.58339 22.1661 0.659384 0.11899 116427 16787065 -‐-‐-‐ -‐-‐-‐ TCONS_00022565-‐XLOC_010884 // Rinn lincRNA // linc-‐TSHR-‐1 chr14:+:80931125-‐80938379 // 0.0128374 0.0128374 1.58299 1.58299 18.327 0.658661 0.143757 11569 16653275 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0334278 0.0334278 1.5809 1.5809 10.1337 0.654875 0.258493 13773 16659357 ENST00000288048 // C1orf158 // chromosome 1 open reading frame 158 // 1p36.21 // 93190 C1orf158 ENST00000288048ENST00000288048 // ENSEMBL // cdna:known chromosome:GRCh37:1:12806163:12823847:1 gene:E0.0136993 0.0136993 1.58088 1.58088 17.6373 0.654845 0.148514 141853 17044177 ENST00000404625 // IL6 // interleukin 6 (interferon, beta 2) // 7p21 // 3569 /// NM_000IL6 ENST00000404625ENST00000404625 // ENSEMBL // cdna:known chromosome:GRCh37:7:22765503:22771621:1 gene:E0.00570425 0.00570425 1.57084 1.57084 29.1257 0.636757 0.0874494 113624 16761185 -‐-‐-‐ -‐-‐-‐ ENST00000391043 // ENSEMBL // ncrna:snRNA chromosome:GRCh37:12:9776718:9776824:-‐1 gene:0.0142742 0.0142742 1.56539 1.56539 17.2125 0.626991 0.145706 19859 16721375 NM_000543 // SMPD1 // sphingomyelin phosphodiesterase 1, acid lysosomal // 11p15.4-‐p15.SMPD1 NM_000543 NM_000543 // RefSeq // Homo sapiens sphingomyelin phosphodiesterase 1, acid lysosomal (0.0467994 0.0467994 1.56523 1.56523 8.07377 0.626703 0.310489 129638 16918722 ENST00000374372 // GDF5 // growth differentiation factor 5 // 20q11.2 // 8200 /// NM_00GDF5 ENST00000374372ENST00000374372 // ENSEMBL // cdna:known chromosome:GRCh37:20:34021145:34042568:-‐1 gene0.0147723 0.0147723 1.56356 1.56356 16.8647 0.62371 0.147933 12942 16656109 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0222485 0.0222485 1.55372 1.55372 13.1442 0.606229 0.184485 150070 17119106 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ 0.0135996 0.0135996 1.54639 1.54639 17.7138 0.593284 0.133971 11924 16654003 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0391495 0.0391495 1.54611 1.54611 9.12256 0.592791 0.259923 121220 16835037 NM_001007532 // STH // saitohin // 17q21.1 // 246744 /// ENST00000537309 // STH // saitSTH NM_001007532NM_001007532 // RefSeq // Homo sapiens saitohin (STH), mRNA. // chr17 // 100 // 100 // 0.012331 0.012331 1.54531 1.54531 18.7656 0.591386 0.126057 137794 17000650 NM_198282 // TMEM173 // transmembrane protein 173 // 5q31.2 // 340061 /// ENST000003307TMEM173 NM_198282 NM_198282 // RefSeq // Homo sapiens transmembrane protein 173 (TMEM173), nuclear gene e0.0310249 0.0310249 1.54061 1.54061 10.64 0.583125 0.219219 141579 17040626 ENST00000425724 // HCG22 // HLA complex group 22 (non-‐protein coding) // -‐-‐-‐ // -‐-‐-‐HCG22 ENST00000425724TCONS_00030010-‐XLOC_014494 // Rinn lincRNA // linc-‐PTER-‐1 chr6_ssto_hap7:+:2356965-‐23620.0264696 0.0264696 1.54048 1.54048 11.7836 0.582898 0.197868 151690 17122696 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ 0.0272427 0.0272427 1.53856 1.53856 11.5694 0.579536 0.200369 119280 16815355 ENST00000526464 // IL32 // interleukin 32 // 16p13.3 // 9235 /// NM_001012631 // IL32 /IL32 ENST00000526464ENST00000526464 // ENSEMBL // cdna:known chromosome:GRCh37:16:3115370:3119544:1 gene:EN0.0356672 0.0356672 1.53752 1.53752 9.70893 0.577729 0.23802 17066 16693652 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // pos_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0302863 0.0302863 1.53168 1.53168 10.8077 0.567554 0.210055 142953 17055786 BC027978 // LOC541472 // uncharacterized LOC541472 // 7p21 // 541472 /// ENST0000032504LOC541472 BC027978 BC027978 // GenBank // Homo sapiens hypothetical LOC541472, mRNA (cDNA clone IMAGE:34630.0315025 0.0315025 1.52266 1.52266 10.5348 0.55194 0.209568 139296 17014798 NM_022138 // SMOC2 // SPARC related modular calcium binding 2 // 6q27 // 64094 /// ENSTSMOC2 NM_022138 NM_022138 // RefSeq // Homo sapiens SPARC related modular calcium binding 2 (SMOC2), tr0.0226582 0.0226582 1.52221 1.52221 12.9956 0.551161 0.169645 120451 16827227 NM_001128850 // RRAD // Ras-‐related associated with diabetes // 16q22 // 6236 /// NM_00RRAD NM_001128850NM_001128850 // RefSeq // Homo sapiens Ras-‐related associated with diabetes (RRAD), tra0.0425352 0.0425352 1.51212 1.51212 8.62331 0.533842 0.247628 114700 16771546 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // pos_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0258819 0.0258819 1.5116 1.5116 11.9528 0.532953 0.178353 138667 17009219 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // pos_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0296895 0.0296895 1.51078 1.51078 10.9478 0.531564 0.194219 17504 16698419 -‐-‐-‐ -‐-‐-‐ ENST00000517137 // ENSEMBL // ncrna:snoRNA chromosome:GRCh37:1:204873875:204873946:-‐1 g0.0315562 0.0315562 1.50585 1.50585 10.5231 0.523169 0.198865 116947 16791734 NM_015473 // HEATR5A // HEAT repeat containing 5A // 14q12 // 25938 /// ENST00000543095HEATR5A NM_015473 NM_015473 // RefSeq // Homo sapiens HEAT repeat containing 5A (HEATR5A), mRNA. // chr140.0496059 0.0496059 1.50516 1.50516 7.75167 0.522003 0.269363 137541 16998309 NM_012081 // ELL2 // elongation factor, RNA polymerase II, 2 // 5q15 // 22936 /// ENST0ELL2 NM_012081 NM_012081 // RefSeq // Homo sapiens elongation factor, RNA polymerase II, 2 (ELL2), mRN0.0264736 0.0264736 1.50256 1.50256 11.7824 0.517596 0.175718 135282 16977346 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // pos_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0306861 0.0306861 0.665964 -‐1.50158 10.7162 0.515947 0.192586 114962 16773727 NM_130806 // RXFP2 // relaxin/insulin-‐like family peptide receptor 2 // 13q13.1 // 1220RXFP2 NM_130806 NM_130806 // RefSeq // Homo sapiens relaxin/insulin-‐like family peptide receptor 2 (RXF0.00405888 0.00405888 0.665788 -‐1.50198 35.1371 0.516615 0.0588114 128267 16904324 NM_004460 // FAP // fibroblast activation protein, alpha // 2q23 // 2191 /// ENST000001FAP NM_004460 NM_004460 // RefSeq // Homo sapiens fibroblast activation protein, alpha (FAP), mRNA. /0.031904 0.031904 0.664013 -‐1.506 10.4482 0.52342 0.200388 148175 17105847 NM_017416 // IL1RAPL2 // interleukin 1 receptor accessory protein-‐like 2 // Xq22 // 262IL1RAPL2 NM_017416 NM_017416 // RefSeq // Homo sapiens interleukin 1 receptor accessory protein-‐like 2 (IL0.0248004 0.0248004 0.663727 -‐1.50664 12.2798 0.524519 0.170856 16607 16689113 ENST00000370571 // COL24A1 // collagen, type XXIV, alpha 1 // 1p22.3 // 255631 /// NM_1COL24A1 ENST00000370571ENST00000370571 // ENSEMBL // cdna:known chromosome:GRCh37:1:86194916:86622446:-‐1 gene:0.00925222 0.00925222 0.663581 -‐1.50697 22.1669 0.525082 0.0947509 122158 16844585 NM_001165252 // LOC730755 // keratin associated protein 2-‐4-‐like // -‐-‐-‐ // 730755 /// ELOC730755 NM_001165252NM_001165252 // RefSeq // Homo sapiens keratin associated protein 2-‐4-‐like (LOC730755),0.00345873 0.00345873 0.662935 -‐1.50844 38.3376 0.527582 0.0550459 18269 16705295 NM_178011 // LRRTM3 // leucine rich repeat transmembrane neuronal 3 // 10q21.3 // 34773LRRTM3 NM_178011 NM_178011 // RefSeq // Homo sapiens leucine rich repeat transmembrane neuronal 3 (LRRTM0.00124693 0.00124693 0.66288 -‐1.50857 66.0463 0.527794 0.0319651 150596 17120506 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ 0.00799474 0.00799474 0.662217 -‐1.51008 24.0939 0.530365 0.0880497 151102 17121518 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ 0.0146527 0.0146527 0.661702 -‐1.51125 16.9466 0.532369 0.125658 18502 16707468 NM_004523 // KIF11 // kinesin family member 11 // 10q24.1 // 3832 /// ENST00000260731 /KIF11 NM_004523 NM_004523 // RefSeq // Homo sapiens kinesin family member 11 (KIF11), mRNA. // chr10 //0.0470245 0.0470245 0.660985 -‐1.51289 8.04688 0.535171 0.266027 114954 16773662 NM_001204406 // ALOX5AP // arachidonate 5-‐lipoxygenase-‐activating protein // 13q12 // 2ALOX5AP NM_001204406NM_001204406 // RefSeq // Homo sapiens arachidonate 5-‐lipoxygenase-‐activating protein (0.0132965 0.0132965 0.660236 -‐1.51461 17.9513 0.538103 0.119903 131690 16939503 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // pos_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0436358 0.0436358 0.660182 -‐1.51473 8.47374 0.538316 0.25411 135139 16975969 -‐-‐-‐ -‐-‐-‐ ENST00000384655 // ENSEMBL // ncrna:snRNA chromosome:GRCh37:4:54131628:54131734:-‐1 gene0.0228066 0.0228066 0.658454 -‐1.51871 12.9428 0.545132 0.168474 15486 16677425 NM_016343 // CENPF // centromere protein F, 350/400kDa (mitosin) // 1q32-‐q41 // 1063 //CENPF NM_016343 NM_016343 // RefSeq // Homo sapiens centromere protein F, 350/400kDa (mitosin) (CENPF),0.0110401 0.0110401 0.658279 -‐1.51911 20.0173 0.545828 0.109071 123983 16861457 NR_040027 // ZNF790-‐AS1 // ZNF790 antisense RNA 1 (non-‐protein coding) // 19q13.13 // 2ZNF790-‐AS1 NR_040027 NR_040027 // RefSeq // Homo sapiens ZNF790 antisense RNA 1 (non-‐protein coding) (ZNF7900.00909688 0.00909688 0.656882 -‐1.52234 22.3831 0.551387 0.0985365 16876 16691969 -‐-‐-‐ -‐-‐-‐ ENST00000466343 // ENSEMBL // cdna:known chromosome:GRCh37:1:144833168:144835867:-‐1 gen0.0201475 0.0201475 0.656734 -‐1.52269 13.9763 0.551979 0.157976 134968 16974315 ENST00000411154 // RN5S155 // RNA, 5S ribosomal 155 // -‐-‐-‐ // -‐-‐-‐RN5S155 ENST00000411154ENST00000411154 // ENSEMBL // ncrna:rRNA chromosome:GRCh37:4:10117380:10117508:-‐1 gene:0.0459863 0.0459863 0.656655 -‐1.52287 8.1726 0.552298 0.270317 126586 16887675 ENST00000361725 // DLX1 // distal-‐less homeobox 1 // 2q32 // 1745 /// NM_178120 // DLX1DLX1 ENST00000361725ENST00000361725 // ENSEMBL // cdna:known chromosome:GRCh37:2:172949954:172954405:1 gene0.0255939 0.0255939 0.655465 -‐1.52563 12.0378 0.557069 0.185106 114388 16769481 NM_001034173 // ALDH1L2 // aldehyde dehydrogenase 1 family, member L2 // 12q23.3 // 160ALDH1L2 NM_001034173NM_001034173 // RefSeq // Homo sapiens aldehyde dehydrogenase 1 family, member L2 (ALDH0.0186276 0.0186276 0.654229 -‐1.52852 14.6643 0.56206 0.153313 128872 16911463 ENST00000405977 // BTBD3 // BTB (POZ) domain containing 3 // 20p12.2 // 22903 /// NM_01BTBD3 ENST00000405977ENST00000405977 // ENSEMBL // cdna:known chromosome:GRCh37:20:11871476:11907257:1 gene:0.034876 0.034876 0.653388 -‐1.53048 9.85432 0.565472 0.229532 11733 16653611 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.00584079 0.00584079 0.653302 -‐1.53069 28.7447 0.565823 0.0787375 12154 16654483 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0193576 0.0193576 0.650173 -‐1.53805 14.3237 0.578656 0.161594 122130 16844312 NM_001067 // TOP2A // topoisomerase (DNA) II alpha 170kDa // 17q21-‐q22 // 7153 /// ENSTTOP2A NM_001067 NM_001067 // RefSeq // Homo sapiens topoisomerase (DNA) II alpha 170kDa (TOP2A), mRNA. 0.023613 0.023613 0.648457 -‐1.54212 12.6645 0.585782 0.185015 138306 17005578 ENST00000356530 // HIST1H2BC // histone cluster 1, H2bc // 6p22.1 // 8347 /// ENST00000HIST1H2BC ENST00000356530ENST00000356530 // ENSEMBL // cdna:known chromosome:GRCh37:6:26183958:26184454:1 gene:E0.0392814 0.0392814 0.647693 -‐1.54394 9.1019 0.588976 0.258837 1


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36662 16990461 -‐-‐-‐ -‐-‐-‐ TCONS_l2_00023557-‐XLOC_l2_011793 // Broad TUCP // linc-‐SPRY4-‐BP chr5:+:141704857-‐1418430.015197 0.015197 0.646612 -‐1.54652 16.5818 0.593516 0.143173 127704 16899357 NM_032603 // LOXL3 // lysyl oxidase-‐like 3 // 2p13 // 84695 /// ENST00000264094 // LOXLLOXL3 NM_032603 NM_032603 // RefSeq // Homo sapiens lysyl oxidase-‐like 3 (LOXL3), mRNA. // chr2 // 100 0.0185142 0.0185142 0.646503 -‐1.54678 14.719 0.593972 0.161416 131956 16942743 NM_002942 // ROBO2 // roundabout, axon guidance receptor, homolog 2 (Drosophila) // 3p1ROBO2 NM_002942 NM_002942 // RefSeq // Homo sapiens roundabout, axon guidance receptor, homolog 2 (Dros0.0143428 0.0143428 0.646343 -‐1.54717 17.1636 0.594649 0.138584 114279 16768341 NM_001001323 // ATP2B1 // ATPase, Ca++ transporting, plasma membrane 1 // 12q21.3 // 49ATP2B1 NM_001001323NM_001001323 // RefSeq // Homo sapiens ATPase, Ca++ transporting, plasma membrane 1 (AT0.0191678 0.0191678 0.646091 -‐1.54777 14.4104 0.59571 0.165355 112424 16747852 NM_024865 // NANOG // Nanog homeobox // 12p13.31 // 79923 /// ENST00000229307 // NANOG NANOG NM_024865 NM_024865 // RefSeq // Homo sapiens Nanog homeobox (NANOG), mRNA. // chr12 // 100 // 630.0235273 0.0235273 0.644659 -‐1.55121 12.6934 0.60178 0.189635 113970 16764724 NM_001031628 // SMAGP // small cell adhesion glycoprotein // 12q13.13 // 57228 /// ENSTSMAGP NM_001031628NM_001031628 // RefSeq // Homo sapiens small cell adhesion glycoprotein (SMAGP), transc0.0392597 0.0392597 0.644521 -‐1.55154 9.10529 0.602366 0.264623 138818 17010552 ENST00000509894 // TTK // TTK protein kinase // 6q13-‐q21 // 7272 /// ENST00000230510 //TTK ENST00000509894ENST00000509894 // ENSEMBL // cdna:novel chromosome:GRCh37:6:80713604:80752244:1 gene:E0.0481009 0.0481009 0.644284 -‐1.55211 7.92088 0.603375 0.304701 12361 16654913 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0454714 0.0454714 0.642269 -‐1.55698 8.23655 0.612004 0.297214 13878 16660436 NM_000478 // ALPL // alkaline phosphatase, liver/bone/kidney // 1p36.12 // 249 /// ENSTALPL NM_000478 NM_000478 // RefSeq // Homo sapiens alkaline phosphatase, liver/bone/kidney (ALPL), tra0.00740907 0.00740907 0.642216 -‐1.55711 25.1548 0.612233 0.0973544 133646 16961685 -‐-‐-‐ -‐-‐-‐ TCONS_00006710-‐XLOC_003330 // Rinn lincRNA // linc-‐SPATA16-‐2 chr3:-‐:176018235-‐1760371660.00977488 0.00977488 0.641834 -‐1.55803 21.4777 0.613877 0.114328 121385 16836732 -‐-‐-‐ -‐-‐-‐ TCONS_00025946-‐XLOC_012269 // Rinn lincRNA // linc-‐TBX2 chr17:+:59475312-‐59476820 // ch0.0203051 0.0203051 0.640195 -‐1.56202 13.9094 0.620978 0.178578 136664 16990478 -‐-‐-‐ -‐-‐-‐ TCONS_l2_00022558-‐XLOC_l2_011798 // Broad TUCP // linc-‐ARHGAP26-‐1 chr5:+:142095840-‐14210.0309543 0.0309543 0.638532 -‐1.56609 10.6558 0.628242 0.235831 110850 16731965 -‐-‐-‐ -‐-‐-‐ ENST00000384456 // ENSEMBL // ncrna:snRNA chromosome:GRCh37:11:118464703:118464808:1 ge0.0456032 0.0456032 0.636714 -‐1.57056 8.22008 0.636252 0.309609 128027 16901957 NM_152515 // CKAP2L // cytoskeleton associated protein 2-‐like // 2q13 // 150468 /// AK3CKAP2L NM_152515 NM_152515 // RefSeq // Homo sapiens cytoskeleton associated protein 2-‐like (CKAP2L), mR0.0347702 0.0347702 0.635811 -‐1.5728 9.87413 0.640262 0.259369 128987 16912379 NM_012112 // TPX2 // TPX2, microtubule-‐associated, homolog (Xenopus laevis) // 20q11.2 TPX2 NM_012112 NM_012112 // RefSeq // Homo sapiens TPX2, microtubule-‐associated, homolog (Xenopus laev0.011835 0.011835 0.635577 -‐1.57337 19.2222 0.641301 0.13345 145333 17078856 -‐-‐-‐ -‐-‐-‐ ENST00000517711 // ENSEMBL // cdna:known chromosome:GRCh37:8:88578398:88746071:-‐1 gene:0.00256268 0.00256268 0.634121 -‐1.57699 45.0714 0.64781 0.0574919 16690 16690019 ENST00000370188 // LPPR5 // lipid phosphate phosphatase-‐related protein type 5 // 1p21.LPPR5 ENST00000370188ENST00000370188 // ENSEMBL // cdna:known chromosome:GRCh37:1:99355806:99470588:-‐1 gene:0.00455531 0.00455531 0.633374 -‐1.57885 32.9831 0.651166 0.0789697 12155 16654485 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0258096 0.0258096 0.631847 -‐1.58266 11.974 0.658068 0.219832 120463 16827344 NM_016140 // TPPP3 // tubulin polymerization-‐promoting protein family member 3 // 16q22TPPP3 NM_016140 NM_016140 // RefSeq // Homo sapiens tubulin polymerization-‐promoting protein family mem0.047533 0.047533 0.631397 -‐1.58379 7.98681 0.660111 0.330601 131284 16934609 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // pos_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0214218 0.0214218 0.630764 -‐1.58538 13.457 0.662992 0.197071 117095 16793225 NM_014750 // DLGAP5 // discs, large (Drosophila) homolog-‐associated protein 5 // 14q22.DLGAP5 NM_014750 NM_014750 // RefSeq // Homo sapiens discs, large (Drosophila) homolog-‐associated protei0.0086067 0.0086067 0.630468 -‐1.58612 23.1033 0.664347 0.115022 128632 16908977 NM_003469 // SCG2 // secretogranin II // 2q35-‐q36 // 7857 /// ENST00000305409 // SCG2 /SCG2 NM_003469 NM_003469 // RefSeq // Homo sapiens secretogranin II (SCG2), mRNA. // chr2 // 100 // 680.0176558 0.0176558 0.630361 -‐1.58639 15.1502 0.664834 0.175531 151104 17121522 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ 0.00021149 0.00021149 0.628283 -‐1.59164 165.107 0.674384 0.0163381 113612 16761012 ENST00000318602 // A2M // alpha-‐2-‐macroglobulin // 12p13.31 // 2 /// NM_000014 // A2M /A2M ENST00000318602ENST00000318602 // ENSEMBL // cdna:known chromosome:GRCh37:12:9220308:9268753:-‐1 gene:E0.00222815 0.00222815 0.627778 -‐1.59292 48.5756 0.676716 0.0557248 134636 16971414 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // pos_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0258282 0.0258282 0.626634 -‐1.59583 11.9685 0.68203 0.227941 121386 16836735 NM_005994 // TBX2 // T-‐box 2 // 17q23.2 // 6909 /// ENST00000240328 // TBX2 // T-‐box 2 TBX2 NM_005994 NM_005994 // RefSeq // Homo sapiens T-‐box 2 (TBX2), mRNA. // chr17 // 100 // 84 // 16 /0.00937224 0.00937224 0.625859 -‐1.5978 22.0035 0.685649 0.124644 141877 17044414 NM_004289 // NFE2L3 // nuclear factor (erythroid-‐derived 2)-‐like 3 // 7p15.2 // 9603 //NFE2L3 NM_004289 NM_004289 // RefSeq // Homo sapiens nuclear factor (erythroid-‐derived 2)-‐like 3 (NFE2L30.00298896 0.00298896 0.624558 -‐1.60113 41.4898 0.691748 0.0666909 145125 17077004 ENST00000396822 // SNAI2 // snail homolog 2 (Drosophila) // 8q11 // 6591 /// NM_003068 SNAI2 ENST00000396822ENST00000396822 // ENSEMBL // cdna:known chromosome:GRCh37:8:49830327:49834299:-‐1 gene:0.0347471 0.0347471 0.622689 -‐1.60594 9.87848 0.700586 0.283682 152409 17124138 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ 0.030019 0.030019 0.622613 -‐1.60613 10.8699 0.700946 0.25794 151338 17121990 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ 0.0433011 0.0433011 0.622477 -‐1.60649 8.51862 0.701597 0.329442 11147 16652387 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0224511 0.0224511 0.620304 -‐1.61211 13.0702 0.711984 0.217895 115259 16776103 NM_007129 // ZIC2 // Zic family member 2 // 13q32 // 7546 /// ENST00000376335 // ZIC2 /ZIC2 NM_007129 NM_007129 // RefSeq // Homo sapiens Zic family member 2 (ZIC2), mRNA. // chr13 // 100 /0.00272545 0.00272545 0.620294 -‐1.61214 43.6048 0.71203 0.0653166 115393 16777527 NR_026730 // TPTE2P1 // transmembrane phosphoinositide 3-‐phosphatase and tensin homologTPTE2P1 NR_026730 NR_026730 // RefSeq // Homo sapiens transmembrane phosphoinositide 3-‐phosphatase and te0.0443359 0.0443359 0.620204 -‐1.61237 8.38152 0.712466 0.340017 135401 16978568 NM_001813 // CENPE // centromere protein E, 312kDa // 4q24-‐q25 // 1062 /// ENST00000265CENPE NM_001813 NM_001813 // RefSeq // Homo sapiens centromere protein E, 312kDa (CENPE), mRNA. // chr40.00932871 0.00932871 0.618903 -‐1.61576 22.0624 0.71874 0.13031 115593 16779472 NM_007015 // LECT1 // leukocyte cell derived chemotaxin 1 // 13q14.3 // 11061 /// NM_00LECT1 NM_007015 NM_007015 // RefSeq // Homo sapiens leukocyte cell derived chemotaxin 1 (LECT1), transc0.0163195 0.0163195 0.617193 -‐1.62024 15.888 0.727054 0.183045 135727 16981582 -‐-‐-‐ -‐-‐-‐ TCONS_l2_00022056-‐XLOC_l2_011361 // Broad TUCP // linc-‐MORF4-‐4 chr4:-‐:175056205-‐17507570.00166424 0.00166424 0.616951 -‐1.62087 56.7245 0.728235 0.0513524 16531 16688386 NM_001114120 // DEPDC1 // DEP domain containing 1 // 1p31.2 // 55635 /// ENST0000045631DEPDC1 NM_001114120NM_001114120 // RefSeq // Homo sapiens DEP domain containing 1 (DEPDC1), transcript var0.0409518 0.0409518 0.616454 -‐1.62218 8.84904 0.730669 0.330282 11467 16653067 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0435203 0.0435203 0.615966 -‐1.62347 8.48917 0.733065 0.345412 111659 16739979 NM_005609 // PYGM // phosphorylase, glycogen, muscle // 11q12-‐q13.2 // 5837 /// NM_0011PYGM NM_005609 NM_005609 // RefSeq // Homo sapiens phosphorylase, glycogen, muscle (PYGM), transcript 0.0214231 0.0214231 0.615889 -‐1.62367 13.4564 0.733444 0.21802 136748 16991582 NM_001099287 // NIPAL4 // NIPA-‐like domain containing 4 // 5q33.3 // 348938 /// NM_0011NIPAL4 NM_001099287NM_001099287 // RefSeq // Homo sapiens NIPA-‐like domain containing 4 (NIPAL4), transcri0.00017095 0.00017095 0.614459 -‐1.62745 184.016 0.740494 0.0160963 13360 16656971 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.00829048 0.00829048 0.613884 -‐1.62897 23.6015 0.743344 0.125983 13465 16657183 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0393556 0.0393556 0.613759 -‐1.6293 9.09032 0.743966 0.327366 128856 16911330 AK128046 // LOC100128668 // uncharacterized LOC100128668 // 20p12.3 // 100128668LOC100128668AK128046 AK128046 // GenBank // Homo sapiens cDNA FLJ46166 fis, clone TESTI4002889. // chr20 // 0.02234 0.02234 0.612742 -‐1.63201 13.1107 0.749026 0.228524 152310 17123938 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ 0.0299615 0.0299615 0.610791 -‐1.63722 10.8834 0.758811 0.278888 137993 17002667 NM_001129891 // FAM196B // family with sequence similarity 196, member B // 5q35.1 // 1FAM196B NM_001129891NM_001129891 // RefSeq // Homo sapiens family with sequence similarity 196, member B (F0.0124956 0.0124956 0.60991 -‐1.63959 18.6201 0.763261 0.163965 145336 17078870 ENST00000286614 // MMP16 // matrix metallopeptidase 16 (membrane-‐inserted) // 8q21.3 //MMP16 ENST00000286614ENST00000286614 // ENSEMBL // cdna:known chromosome:GRCh37:8:89044237:89339717:-‐1 gene:0.00728422 0.00728422 0.608047 -‐1.64461 25.3974 0.77274 0.121704 1

25 16650033 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0202549 0.0202549 0.607289 -‐1.64666 13.9307 0.776615 0.222994 147993 17104236 -‐-‐-‐ -‐-‐-‐ TCONS_00017426-‐XLOC_008001 // Rinn lincRNA // linc-‐ZC3H12B-‐1 chrX:+:64586533-‐64588866 /0.0356199 0.0356199 0.607242 -‐1.64679 9.71748 0.776861 0.319779 145245 17078134 NM_172058 // EYA1 // eyes absent homolog 1 (Drosophila) // 8q13.3 // 2138 /// NM_000503EYA1 NM_172058 NM_172058 // RefSeq // Homo sapiens eyes absent homolog 1 (Drosophila) (EYA1), transcri0.0483598 0.0483598 0.605216 -‐1.6523 7.8912 0.787303 0.399079 130296 16924620 NM_007038 // ADAMTS5 // ADAM metallopeptidase with thrombospondin type 1 motif, 5 // 21ADAMTS5 NM_007038 NM_007038 // RefSeq // Homo sapiens ADAM metallopeptidase with thrombospondin type 1 mo0.0335828 0.0335828 0.604583 -‐1.65403 10.103 0.790589 0.313012 125249 16874298 NM_020309 // SLC17A7 // solute carrier family 17 (sodium-‐dependent inorganic phosphate SLC17A7 NM_020309 NM_020309 // RefSeq // Homo sapiens solute carrier family 17 (sodium-‐dependent inorgani0.00444742 0.00444742 0.604524 -‐1.65419 33.4203 0.790893 0.0946601 111069 16734355 NR_002196 // H19 // H19, imprinted maternally expressed transcript (non-‐protein coding)H19 NR_002196 NR_002196 // RefSeq // Homo sapiens H19, imprinted maternally expressed transcript (non0.0146265 0.0146265 0.603027 -‐1.6583 16.9647 0.798704 0.188322 145845 17084130 NM_000459 // TEK // TEK tyrosine kinase, endothelial // 9p21 // 7010 /// ENST0000038003TEK NM_000459 NM_000459 // RefSeq // Homo sapiens TEK tyrosine kinase, endothelial (TEK), mRNA. // ch0.0436714 0.0436714 0.602396 -‐1.66004 8.469 0.802018 0.378801 12396 16654987 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.00519281 0.00519281 0.602266 -‐1.6604 30.6841 0.802698 0.10464 151385 17122086 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ 0.0384581 0.0384581 0.600443 -‐1.66544 9.23258 0.812325 0.351938 148127 17105321 NM_022144 // TNMD // tenomodulin // Xq21.33-‐q23 // 64102 /// ENST00000373031 // TNMD //TNMD NM_022144 NM_022144 // RefSeq // Homo sapiens tenomodulin (TNMD), mRNA. // chrX // 100 // 88 // 20.0490656 0.0490656 0.598172 -‐1.67176 7.81152 0.824438 0.422166 1


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11714 16740566 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // pos_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0180291 0.0180291 0.597951 -‐1.67238 14.9589 0.825624 0.220771 1286 16650573 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0348636 0.0348636 0.597679 -‐1.67314 9.85663 0.827087 0.335647 1

42557 17051659 -‐-‐-‐ -‐-‐-‐ TCONS_00013599-‐XLOC_006253 // Rinn lincRNA // linc-‐MKLN1-‐1 chr7:+:130610772-‐130618587 /0.00572547 0.00572547 0.596621 -‐1.6761 29.0656 0.832789 0.114608 144118 17067729 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ 0.0135539 0.0135539 0.596248 -‐1.67715 17.7491 0.834807 0.188135 148755 17111858 NM_032803 // SLC7A3 // solute carrier family 7 (cationic amino acid transporter, y+ sysSLC7A3 NM_032803 NM_032803 // RefSeq // Homo sapiens solute carrier family 7 (cationic amino acid transp0.00323418 0.00323418 0.59476 -‐1.68135 39.7585 0.842895 0.0848015 12895 16656015 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0123598 0.0123598 0.59437 -‐1.68245 18.7399 0.845026 0.180369 135541 16979875 NM_019035 // PCDH18 // protocadherin 18 // 4q31 // 54510 /// ENST00000344876 // PCDH18 PCDH18 NM_019035 NM_019035 // RefSeq // Homo sapiens protocadherin 18 (PCDH18), mRNA. // chr4 // 100 // 0.00125199 0.00125199 0.593089 -‐1.68609 65.9059 0.852047 0.0517129 144476 17070949 NM_017697 // ESRP1 // epithelial splicing regulatory protein 1 // 8q22.1 // 54845 /// NESRP1 NM_017697 NM_017697 // RefSeq // Homo sapiens epithelial splicing regulatory protein 1 (ESRP1), t0.0201966 0.0201966 0.591824 -‐1.68969 13.9554 0.859028 0.246221 129476 16917466 -‐-‐-‐ -‐-‐-‐ ENST00000365390 // ENSEMBL // ncrna:misc_RNA chromosome:GRCh37:20:17556851:17557155:-‐1 0.00388972 0.00388972 0.591646 -‐1.6902 35.9637 0.860012 0.0956533 112546 16748888 NM_001256470 // PLEKHA5 // pleckstrin homology domain containing, family A member 5 // PLEKHA5 NM_001256470NM_001256470 // RefSeq // Homo sapiens pleckstrin homology domain containing, family A 0.0257272 0.0257272 0.590189 -‐1.69437 11.9983 0.868113 0.289412 143536 17061759 ENST00000379028 // NRCAM // neuronal cell adhesion molecule // 7q31 // 4897 /// NM_0011NRCAM ENST00000379028ENST00000379028 // ENSEMBL // cdna:known chromosome:GRCh37:7:107788082:108096826:-‐1 gen0.0496011 0.0496011 0.589241 -‐1.6971 7.75221 0.873412 0.450665 113047 16754880 ENST00000316824 // ALX1 // ALX homeobox 1 // 12q21.31 // 8092 /// NM_006982 // ALX1 // ALX1 ENST00000316824ENST00000316824 // ENSEMBL // cdna:known chromosome:GRCh37:12:85673885:85695562:1 gene:0.00587069 0.00587069 0.589234 -‐1.69712 28.6631 0.873456 0.121893 116137 16783473 NM_006194 // PAX9 // paired box 9 // 14q13.3 // 5083 /// ENST00000402703 // PAX9 // paiPAX9 NM_006194 NM_006194 // RefSeq // Homo sapiens paired box 9 (PAX9), mRNA. // chr14 // 100 // 43 //0.00139238 0.00139238 0.588441 -‐1.69941 62.3239 0.87791 0.056345 128314 16905108 ENST00000234198 // DLX2 // distal-‐less homeobox 2 // 2q32 // 1746 /// NM_004405 // DLX2DLX2 ENST00000234198ENST00000234198 // ENSEMBL // cdna:known chromosome:GRCh37:2:172964167:172967628:-‐1 gen0.0168789 0.0168789 0.585273 -‐1.7086 15.5685 0.895871 0.230176 152497 17124314 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ 0.0104542 0.0104542 0.581826 -‐1.71873 20.6606 0.915738 0.177292 127708 16899401 NM_001058 // TACR1 // tachykinin receptor 1 // 2p12 // 6869 /// NM_015727 // TACR1 // tTACR1 NM_001058 NM_001058 // RefSeq // Homo sapiens tachykinin receptor 1 (TACR1), transcript variant l0.0410298 0.0410298 0.579142 -‐1.72669 8.83761 0.931439 0.421579 117131 16793613 NM_005982 // SIX1 // SIX homeobox 1 // 14q23.1 // 6495 /// ENST00000247182 // SIX1 // SSIX1 NM_005982 NM_005982 // RefSeq // Homo sapiens SIX homeobox 1 (SIX1), mRNA. // chr14 // 100 // 45 0.00215384 0.00215384 0.579091 -‐1.72684 49.4628 0.931741 0.0753488 110723 16730427 -‐-‐-‐ -‐-‐-‐ ENST00000411337 // ENSEMBL // ncrna:misc_RNA chromosome:GRCh37:11:98990906:98991220:1 g0.0142579 0.0142579 0.577803 -‐1.73069 17.2242 0.939351 0.218147 16265 16685330 NM_000831 // GRIK3 // glutamate receptor, ionotropic, kainate 3 // 1p34.3 // 2899 /// EGRIK3 NM_000831 NM_000831 // RefSeq // Homo sapiens glutamate receptor, ionotropic, kainate 3 (GRIK3),0.0192495 0.0192495 0.576623 -‐1.73424 14.373 0.94637 0.263375 17961 16702571 NM_182751 // MCM10 // minichromosome maintenance complex component 10 // 10p13 // 55388MCM10 NM_182751 NM_182751 // RefSeq // Homo sapiens minichromosome maintenance complex component 10 (MC0.0495083 0.0495083 0.575375 -‐1.738 7.76242 0.953829 0.491511 1225 16650445 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.00807345 0.00807345 0.574164 -‐1.74166 23.9602 0.961118 0.160453 1

43546 17061879 -‐-‐-‐ -‐-‐-‐ ENST00000459130 // ENSEMBL // ncrna:snoRNA chromosome:GRCh37:7:110749324:110749413:-‐1 g0.00943012 0.00943012 0.573855 -‐1.7426 21.9259 0.962983 0.17568 18751 16710126 NM_002775 // HTRA1 // HtrA serine peptidase 1 // 10q26.3 // 5654 /// ENST00000368984 //HTRA1 NM_002775 NM_002775 // RefSeq // Homo sapiens HtrA serine peptidase 1 (HTRA1), mRNA. // chr10 // 0.0314453 0.0314453 0.573632 -‐1.74328 10.5473 0.96433 0.365717 152499 17124318 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ 0.00991763 0.00991763 0.569774 -‐1.75508 21.299 0.987891 0.185528 126720 16889160 NM_006226 // PLCL1 // phospholipase C-‐like 1 // 2q33 // 5334 /// ENST00000428675 // PLCPLCL1 NM_006226 NM_006226 // RefSeq // Homo sapiens phospholipase C-‐like 1 (PLCL1), mRNA. // chr2 // 100.0463081 0.0463081 0.568631 -‐1.75861 8.13318 0.994957 0.489332 112547 16748933 -‐-‐-‐ -‐-‐-‐ BX537654 // GenBank // Homo sapiens mRNA; cDNA DKFZp686I1890 (from clone DKFZp686I1890)0.0134762 0.0134762 0.567438 -‐1.76231 17.8095 1.00238 0.225133 112548 16748936 -‐-‐-‐ -‐-‐-‐ ENST00000541575 // ENSEMBL // havana:sense_intronic chromosome:GRCh37:12:19411205:194120.0222649 0.0222649 0.567318 -‐1.76268 13.1382 1.00312 0.305406 152312 17123942 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ 0.0041926 0.0041926 0.566901 -‐1.76398 34.5194 1.00573 0.116541 135533 16979836 -‐-‐-‐ -‐-‐-‐ TCONS_00007838-‐XLOC_004085 // Rinn lincRNA // linc-‐PABPC4L-‐5 chr4:-‐:136034059-‐1360448920.0393075 0.0393075 0.566793 -‐1.76431 9.09782 1.0064 0.442481 17230 16695741 NM_015441 // OLFML2B // olfactomedin-‐like 2B // 1q23.3 // 25903 /// ENST00000294794 // OLFML2B NM_015441 NM_015441 // RefSeq // Homo sapiens olfactomedin-‐like 2B (OLFML2B), mRNA. // chr1 // 100.00158895 0.00158895 0.565252 -‐1.76912 58.1303 1.01608 0.0699172 112566 16749139 ENST00000256969 // C12orf39 // chromosome 12 open reading frame 39 // 12p12.1 // 80763 C12orf39 ENST00000256969ENST00000256969 // ENSEMBL // cdna:known chromosome:GRCh37:12:21679241:21685457:1 gene:0.0249307 0.0249307 0.561568 -‐1.78073 12.2393 1.0395 0.339726 129005 16912597 NM_006892 // DNMT3B // DNA (cytosine-‐5-‐)-‐methyltransferase 3 beta // 20q11.2 // 1789 //DNMT3B NM_006892 NM_006892 // RefSeq // Homo sapiens DNA (cytosine-‐5-‐)-‐methyltransferase 3 beta (DNMT3B)0.0197483 0.0197483 0.561143 -‐1.78208 14.1493 1.04223 0.294639 1633 16651303 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0334702 0.0334702 0.560285 -‐1.78481 10.1253 1.04776 0.413918 1

47811 17102559 -‐-‐-‐ -‐-‐-‐ ENST00000567273 // ENSEMBL // cdna:known chromosome:GRCh37:X:37765400:37808658:1 gene:E0.017054 0.017054 0.559489 -‐1.78735 15.4717 1.05291 0.272216 131736 16939960 NM_020242 // KIF15 // kinesin family member 15 // 3p21.31 // 56992 /// ENST00000326047 KIF15 NM_020242 NM_020242 // RefSeq // Homo sapiens kinesin family member 15 (KIF15), mRNA. // chr3 // 0.0311632 0.0311632 0.55743 -‐1.79395 10.6093 1.06632 0.402032 136742 16991472 NM_000337 // SGCD // sarcoglycan, delta (35kDa dystrophin-‐associated glycoprotein) // 5SGCD NM_000337 NM_000337 // RefSeq // Homo sapiens sarcoglycan, delta (35kDa dystrophin-‐associated gly0.0346131 0.0346131 0.555854 -‐1.79903 9.90372 1.07668 0.434858 148619 17110365 NR_029635 // MIR221 // microRNA 221 // Xp11.3 // 407006MIR221 NR_029635 NR_029635 // RefSeq // Homo sapiens microRNA 221 (MIR221), microRNA. // chrX // 100 // 0.0140136 0.0140136 0.555382 -‐1.80056 17.4019 1.07979 0.248201 136798 16991948 NM_001122679 // ODZ2 // odz, odd Oz/ten-‐m homolog 2 (Drosophila) // 5q34 // 57451 /// EODZ2 NM_001122679NM_001122679 // RefSeq // Homo sapiens odz, odd Oz/ten-‐m homolog 2 (Drosophila) (ODZ2),0.0108006 0.0108006 0.554444 -‐1.80361 20.2739 1.08601 0.214268 113017 16754471 NM_014903 // NAV3 // neuron navigator 3 // 12q14.3 // 89795 /// ENST00000536525 // NAV3NAV3 NM_014903 NM_014903 // RefSeq // Homo sapiens neuron navigator 3 (NAV3), mRNA. // chr12 // 100 //0.0151354 0.0151354 0.550455 -‐1.81668 16.6221 1.11277 0.26778 143138 17057478 NM_001013398 // IGFBP3 // insulin-‐like growth factor binding protein 3 // 7p13-‐p12 // 3IGFBP3 NM_001013398NM_001013398 // RefSeq // Homo sapiens insulin-‐like growth factor binding protein 3 (IG0.0164609 0.0164609 0.548898 -‐1.82183 15.8057 1.12335 0.284289 134364 16968878 ENST00000394980 // MMRN1 // multimerin 1 // 4q22 // 22915 /// NM_007351 // MMRN1 // mulMMRN1 ENST00000394980ENST00000394980 // ENSEMBL // cdna:known chromosome:GRCh37:4:90800683:90875780:1 gene:E0.012983 0.012983 0.54694 -‐1.82835 18.2057 1.13677 0.249761 145218 17077826 NM_001080416 // MYBL1 // v-‐myb myeloblastosis viral oncogene homolog (avian)-‐like 1 // MYBL1 NM_001080416NM_001080416 // RefSeq // Homo sapiens v-‐myb myeloblastosis viral oncogene homolog (avi0.00218124 0.00218124 0.546935 -‐1.82837 49.1304 1.13681 0.0925543 143595 17062311 NM_001024613 // FEZF1 // FEZ family zinc finger 1 // 7q31.32 // 389549 /// ENST00000442FEZF1 NM_001024613NM_001024613 // RefSeq // Homo sapiens FEZ family zinc finger 1 (FEZF1), transcript var0.0415833 0.0415833 0.546142 -‐1.83103 8.75746 1.14228 0.521742 118288 16804506 NM_013227 // ACAN // aggrecan // 15q26.1 // 176 /// ENST00000439576 // ACAN // aggrecanACAN NM_013227 NM_013227 // RefSeq // Homo sapiens aggrecan (ACAN), transcript variant 2, mRNA. // chr0.00381521 0.00381521 0.545737 -‐1.83239 36.3452 1.14509 0.126024 138912 17011255 NM_001004317 // LIN28B // lin-‐28 homolog B (C. elegans) // 6q21 // 389421 /// ENST00000LIN28B NM_001004317NM_001004317 // RefSeq // Homo sapiens lin-‐28 homolog B (C. elegans) (LIN28B), mRNA. //0.0395356 0.0395356 0.544273 -‐1.83731 9.06238 1.15527 0.509919 132509 16948461 NM_003106 // SOX2 // SRY (sex determining region Y)-‐box 2 // 3q26.3-‐q27 // 6657 /// ENSSOX2 NM_003106 NM_003106 // RefSeq // Homo sapiens SRY (sex determining region Y)-‐box 2 (SOX2), mRNA. 0.00025181 0.00025181 0.543515 -‐1.83987 151.035 1.16056 0.0307362 12310 16654811 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0329707 0.0329707 0.543491 -‐1.83996 10.2258 1.16073 0.454043 1492 16651005 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.00695776 0.00695776 0.540624 -‐1.84971 26.0622 1.18096 0.181252 1

50812 17120938 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ 0.0186714 0.0186714 0.538212 -‐1.85801 14.6434 1.1982 0.327301 137629 16999083 NM_020796 // SEMA6A // sema domain, transmembrane domain (TM), and cytoplasmic domain,SEMA6A NM_020796 NM_020796 // RefSeq // Homo sapiens sema domain, transmembrane domain (TM), and cytopla0.0314197 0.0314197 0.538037 -‐1.85861 10.5529 1.19945 0.454645 120061 16823250 ENST00000396925 // CLDN6 // claudin 6 // 16p13.3 // 9074 /// NM_021195 // CLDN6 // clauCLDN6 ENST00000396925ENST00000396925 // ENSEMBL // cdna:known chromosome:GRCh37:16:3064713:3070072:-‐1 gene:E0.0252172 0.0252172 0.537119 -‐1.86178 12.1513 1.20607 0.397017 123002 16852938 NM_033646 // CDH7 // cadherin 7, type 2 // 18q22.1 // 1005 /// ENST00000323011 // CDH7 CDH7 NM_033646 NM_033646 // RefSeq // Homo sapiens cadherin 7, type 2 (CDH7), transcript variant a, mR0.00299313 0.00299313 0.536383 -‐1.86434 41.4586 1.2114 0.116878 18351 16706233 -‐-‐-‐ -‐-‐-‐ ENST00000416076 // ENSEMBL // havana:sense_intronic chromosome:GRCh37:10:75764895:757870.005065 0.005065 0.532733 -‐1.87711 31.11 1.2381 0.159191 14396 16665439 NM_001164835 // L1TD1 // LINE-‐1 type transposase domain containing 1 // 1p31.3 // 54596L1TD1 NM_001164835NM_001164835 // RefSeq // Homo sapiens LINE-‐1 type transposase domain containing 1 (L1T0.0093289 0.0093289 0.532034 -‐1.87958 22.0621 1.24327 0.225412 134462 16969817 ENST00000309733 // C4orf32 // chromosome 4 open reading frame 32 // 4q25 // 132720 /// C4orf32 ENST00000309733ENST00000309733 // ENSEMBL // cdna:known chromosome:GRCh37:4:113066553:113110237:1 gene0.00358856 0.00358856 0.52901 -‐1.89032 37.5777 1.26583 0.134743 18680 16709358 -‐-‐-‐ -‐-‐-‐ AK025137 // GenBank // Homo sapiens cDNA: FLJ21484 fis, clone COL05256. // chr10 // 95 0.0454972 0.0454972 0.528055 -‐1.89374 8.23332 1.27302 0.618474 1


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18983 16812406 ENST00000302824 // STARD5 // StAR-‐related lipid transfer (START) domain containing 5 //STARD5 ENST00000302824ENST00000302824 // ENSEMBL // cdna:known chromosome:GRCh37:15:81601394:81616466:-‐1 gene0.0345344 0.0345344 0.527313 -‐1.89641 9.91863 1.27863 0.515649 124050 16862427 NM_030622 // CYP2S1 // cytochrome P450, family 2, subfamily S, polypeptide 1 // 19q13.1CYP2S1 NM_030622 NM_030622 // RefSeq // Homo sapiens cytochrome P450, family 2, subfamily S, polypeptide0.00082115 0.00082115 0.526586 -‐1.89902 82.1564 1.28415 0.0625224 110722 16730393 NM_014361 // CNTN5 // contactin 5 // 11q21-‐q22.2 // 53942 /// ENST00000524871 // CNTN5 CNTN5 NM_014361 NM_014361 // RefSeq // Homo sapiens contactin 5 (CNTN5), transcript variant 1, mRNA. //0.0192508 0.0192508 0.525744 -‐1.90207 14.3724 1.29057 0.359181 152311 17123940 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ 0.0458314 0.0458314 0.523482 -‐1.91029 8.19172 1.30794 0.638666 150622 17120558 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ 0.00847817 0.00847817 0.522614 -‐1.91346 23.3024 1.31465 0.225669 129145 16914395 NM_004994 // MMP9 // matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa tMMP9 NM_004994 NM_004994 // RefSeq // Homo sapiens matrix metallopeptidase 9 (gelatinase B, 92kDa gela0.00049642 0.00049642 0.521143 -‐1.91886 106.614 1.3261 0.0497536 1438 16650891 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0162595 0.0162595 0.52091 -‐1.91972 15.9233 1.32792 0.333579 1

11994 16743403 NR_031630 // MIR548L // microRNA 548l // -‐-‐-‐ // 100302275MIR548L NR_031630 NR_031630 // RefSeq // Homo sapiens microRNA 548l (MIR548L), microRNA. // chr11 // 100 0.0257742 0.0257742 0.520902 -‐1.91975 11.9844 1.32799 0.443237 12111 16654395 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.032269 0.032269 0.519484 -‐1.92499 10.3708 1.3391 0.51649 142437 17050350 NM_001099660 // LRRN3 // leucine rich repeat neuronal 3 // 7q31.1 // 54674 /// ENST0000LRRN3 NM_001099660NM_001099660 // RefSeq // Homo sapiens leucine rich repeat neuronal 3 (LRRN3), transcri0.0145819 0.0145819 0.518977 -‐1.92687 16.9955 1.3431 0.316107 124128 16863287 NM_006732 // FOSB // FBJ murine osteosarcoma viral oncogene homolog B // 19q13.32 // 23FOSB NM_006732 NM_006732 // RefSeq // Homo sapiens FBJ murine osteosarcoma viral oncogene homolog B (F0.00482816 0.00482816 0.51897 -‐1.9269 31.9434 1.34316 0.168193 135350 16978010 -‐-‐-‐ -‐-‐-‐ TCONS_00007796-‐XLOC_004018 // Rinn lincRNA // linc-‐TMSL3 chr4:-‐:93189917-‐93198226 // ch0.00070308 0.00070308 0.517979 -‐1.93058 89.0551 1.351 0.0606816 152643 17124612 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ 0.0465074 0.0465074 0.517791 -‐1.93128 8.10896 1.35249 0.667158 132738 16950825 NM_003256 // TIMP4 // TIMP metallopeptidase inhibitor 4 // 3p25 // 7079 /// ENST0000028TIMP4 NM_003256 NM_003256 // RefSeq // Homo sapiens TIMP metallopeptidase inhibitor 4 (TIMP4), mRNA. //0.0281135 0.0281135 0.511738 -‐1.95413 11.3388 1.40125 0.494321 14496 16666545 ENST00000359929 // LPHN2 // latrophilin 2 // 1p31.1 // 23266 /// ENST00000319517 // LPHLPHN2 ENST00000359929ENST00000359929 // ENSEMBL // cdna:known chromosome:GRCh37:1:82165455:82458107:1 gene:E0.00992046 0.00992046 0.510699 -‐1.9581 21.2955 1.40977 0.2648 136310 16987125 NM_006467 // POLR3G // polymerase (RNA) III (DNA directed) polypeptide G (32kD) // 5q14POLR3G NM_006467 NM_006467 // RefSeq // Homo sapiens polymerase (RNA) III (DNA directed) polypeptide G (0.0204875 0.0204875 0.510389 -‐1.95929 13.833 1.41231 0.408391 142471 17050797 NM_024913 // CPED1 // cadherin-‐like and PC-‐esterase domain containing 1 // 7q31.31 // 7CPED1 NM_024913 NM_024913 // RefSeq // Homo sapiens cadherin-‐like and PC-‐esterase domain containing 1 (0.00190685 0.00190685 0.510264 -‐1.95977 52.776 1.41334 0.10712 126484 16886491 NM_007115 // TNFAIP6 // tumor necrosis factor, alpha-‐induced protein 6 // 2q23.3 // 713TNFAIP6 NM_007115 NM_007115 // RefSeq // Homo sapiens tumor necrosis factor, alpha-‐induced protein 6 (TNF0.0440668 0.0440668 0.508915 -‐1.96497 8.41672 1.42449 0.67698 126550 16887167 -‐-‐-‐ -‐-‐-‐ TCONS_00003044-‐XLOC_001742 // Rinn lincRNA // linc-‐B3GALT1 chr2:+:168149680-‐168414843 /0.0324944 0.0324944 0.508571 -‐1.96629 10.3237 1.42734 0.553034 116284 16784938 -‐-‐-‐ -‐-‐-‐ ENST00000517205 // ENSEMBL // ncrna:snoRNA chromosome:GRCh37:14:61073785:61073883:1 gen0.0400865 0.0400865 0.507563 -‐1.9702 8.97805 1.43573 0.639662 15444 16676965 ENST00000009105 // CAMK1G // calcium/calmodulin-‐dependent protein kinase IG // 1q32-‐q41CAMK1G ENST00000009105ENST00000009105 // ENSEMBL // cdna:known chromosome:GRCh37:1:209757062:209787283:1 gene0.00026401 0.00026401 0.507522 -‐1.97036 147.425 1.43607 0.0389639 135418 16978779 NM_014421 // DKK2 // dickkopf 2 homolog (Xenopus laevis) // 4q25 // 27123 /// ENST00000DKK2 NM_014421 NM_014421 // RefSeq // Homo sapiens dickkopf 2 homolog (Xenopus laevis) (DKK2), mRNA. /0.00653156 0.00653156 0.507154 -‐1.97179 27.0042 1.43915 0.213174 141474 17039262 ENST00000383524 // POU5F1 // POU class 5 homeobox 1 // 6p21.31 // 5460 /// ENST00000437POU5F1 ENST00000383524ENST00000383524 // ENSEMBL // cdna:known chromosome:GRCh37:HSCHR6_MHC_QBL:31124569:31130.00026252 0.00026252 0.504085 -‐1.98379 147.854 1.46499 0.0396335 141657 17041763 ENST00000383524 // POU5F1 // POU class 5 homeobox 1 // 6p21.31 // 5460 /// ENST00000437POU5F1 ENST00000383524ENST00000383524 // ENSEMBL // cdna:known chromosome:GRCh37:HSCHR6_MHC_QBL:31124569:31130.00026252 0.00026252 0.504085 -‐1.98379 147.854 1.46499 0.0396335 147813 17102566 ENST00000357972 // SYTL5 // synaptotagmin-‐like 5 // Xp21.1 // 94122 /// NM_001163335 //SYTL5 ENST00000357972ENST00000357972 // ENSEMBL // cdna:known chromosome:GRCh37:X:37865835:37988072:1 gene:E0.021218 0.021218 0.503131 -‐1.98755 13.5369 1.4731 0.435286 136681 16990703 NR_038902 // JAKMIP2-‐AS1 // JAKMIP2 antisense RNA 1 (non-‐protein coding) // 5q32 // 153JAKMIP2-‐AS1NR_038902 NR_038902 // RefSeq // Homo sapiens JAKMIP2 antisense RNA 1 (non-‐protein coding) (JAKMI0.0160852 0.0160852 0.501972 -‐1.99214 16.0268 1.48301 0.370132 133745 16962705 NM_198152 // UTS2D // urotensin 2 domain containing // 3q28 // 257313 /// ENST000003405UTS2D NM_198152 NM_198152 // RefSeq // Homo sapiens urotensin 2 domain containing (UTS2D), mRNA. // chr0.0366251 0.0366251 0.494595 -‐2.02186 9.53928 1.54741 0.648859 135447 16979108 NR_029860 // MIR367 // microRNA 367 // 4q25 // 442912MIR367 NR_029860 NR_029860 // RefSeq // Homo sapiens microRNA 367 (MIR367), microRNA. // chr4 // 100 // 0.00738247 0.00738247 0.484087 -‐2.06574 25.206 1.64325 0.260772 145477 17080082 ENST00000297450 // ANGPT1 // angiopoietin 1 // 8q23.1 // 284 /// NM_001146 // ANGPT1 //ANGPT1 ENST00000297450ENST00000297450 // ENSEMBL // cdna:novel chromosome:GRCh37:8:108261721:108510283:-‐1 gen0.0163079 0.0163079 0.480854 -‐2.07963 15.8949 1.67374 0.421204 135677 16981099 NM_000909 // NPY1R // neuropeptide Y receptor Y1 // 4q31.3-‐q32 // 4886 /// ENST00000296NPY1R NM_000909 NM_000909 // RefSeq // Homo sapiens neuropeptide Y receptor Y1 (NPY1R), mRNA. // chr4 /0.00710603 0.00710603 0.48004 -‐2.08316 25.7546 1.68151 0.261158 1432 16650879 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0277995 0.0277995 0.479255 -‐2.08657 11.4207 1.68901 0.591562 1

15198 16775686 -‐-‐-‐ -‐-‐-‐ TCONS_00021577-‐XLOC_010455 // Rinn lincRNA // linc-‐SLITRK5-‐8 chr13:+:81617804-‐81618577 0.0174773 0.0174773 0.477987 -‐2.09211 15.2438 1.7012 0.446397 148135 17105428 ENST00000395209 // DRP2 // dystrophin related protein 2 // Xq22 // 1821 /// NM_001939 /DRP2 ENST00000395209ENST00000395209 // ENSEMBL // cdna:known chromosome:GRCh37:X:100474775:100519486:1 gene0.0338619 0.0338619 0.47594 -‐2.1011 10.0481 1.72104 0.685119 123368 16855673 ENST00000398117 // BCL2 // B-‐cell CLL/lymphoma 2 // 18q21.3 // 596 /// NM_000633 // BCLBCL2 ENST00000398117ENST00000398117 // ENSEMBL // cdna:known chromosome:GRCh37:18:60790579:60987361:-‐1 gene0.011417 0.011417 0.470828 -‐2.12392 19.6299 1.77147 0.360974 1415 16650841 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0026408 0.0026408 0.468203 -‐2.13582 44.3506 1.79786 0.16215 1

40701 17028984 ENST00000429603 // POU5F1 // POU class 5 homeobox 1 // 6p21.31 // 5460 /// ENST00000434POU5F1 ENST00000429603ENST00000429603 // ENSEMBL // cdna:known chromosome:GRCh37:HSCHR6_MHC_COX:31124663:31130.0001473 0.0001473 0.467821 -‐2.13757 198.497 1.80173 0.0363074 140898 17031762 ENST00000429603 // POU5F1 // POU class 5 homeobox 1 // 6p21.31 // 5460 /// ENST00000434POU5F1 ENST00000429603ENST00000429603 // ENSEMBL // cdna:known chromosome:GRCh37:HSCHR6_MHC_COX:31124663:31130.0001473 0.0001473 0.467821 -‐2.13757 198.497 1.80173 0.0363074 134724 16972108 NR_038825 // LOC100506013 // uncharacterized LOC100506013 // 4q32 // 100506013LOC100506013NR_038825 NR_038825 // RefSeq // Homo sapiens uncharacterized LOC100506013 (LOC100506013), non-‐co0.00254973 0.00254973 0.466185 -‐2.14507 45.194 1.81838 0.16094 138830 17010703 NM_001170423 // PRSS35 // protease, serine, 35 // 6q14.2 // 167681 /// NM_153362 // PRSPRSS35 NM_001170423NM_001170423 // RefSeq // Homo sapiens protease, serine, 35 (PRSS35), transcript varian0.0256373 0.0256373 0.464651 -‐2.15215 12.0249 1.83413 0.610108 113843 16763373 -‐-‐-‐ -‐-‐-‐ BX648207 // GenBank // Homo sapiens mRNA; cDNA DKFZp686E16168 (from clone DKFZp686E16160.033169 0.033169 0.462448 -‐2.1624 10.1856 1.85694 0.729241 141094 17034217 ENST00000454714 // POU5F1 // POU class 5 homeobox 1 // 6p21.31 // 5460 /// ENST00000433POU5F1 ENST00000454714ENST00000454714 // ENSEMBL // cdna:known chromosome:GRCh37:HSCHR6_MHC_MANN:31177061:3110.00044361 0.00044361 0.461015 -‐2.16913 112.972 1.87192 0.0662788 141273 17036467 ENST00000454714 // POU5F1 // POU class 5 homeobox 1 // 6p21.31 // 5460 /// ENST00000433POU5F1 ENST00000454714ENST00000454714 // ENSEMBL // cdna:known chromosome:GRCh37:HSCHR6_MHC_MANN:31177061:3110.00044361 0.00044361 0.461015 -‐2.16913 112.972 1.87192 0.0662788 115690 16780133 ENST00000400286 // SLITRK6 // SLIT and NTRK-‐like family, member 6 // 13q31.1 // 84189 /SLITRK6 ENST00000400286ENST00000400286 // ENSEMBL // cdna:known chromosome:GRCh37:13:86366925:86373623:-‐1 gene0.0362545 0.0362545 0.458084 -‐2.18301 9.60411 1.90289 0.79253 128714 16909828 NM_004369 // COL6A3 // collagen, type VI, alpha 3 // 2q37 // 1293 /// ENST00000295550 /COL6A3 NM_004369 NM_004369 // RefSeq // Homo sapiens collagen, type VI, alpha 3 (COL6A3), transcript var0.0342174 0.0342174 0.456587 -‐2.19016 9.97919 1.91887 0.769147 142252 17047985 NM_021722 // ADAM22 // ADAM metallopeptidase domain 22 // 7q21 // 53616 /// ENST0000039ADAM22 NM_021722 NM_021722 // RefSeq // Homo sapiens ADAM metallopeptidase domain 22 (ADAM22), transcrip0.0371459 0.0371459 0.453571 -‐2.20473 9.44982 1.95145 0.826025 134036 16965750 -‐-‐-‐ -‐-‐-‐ TCONS_00007495-‐XLOC_003484 // Rinn lincRNA // linc-‐PCDH7-‐9 chr4:+:27219100-‐27283847 // 0.00690549 0.00690549 0.452168 -‐2.21157 26.173 1.96678 0.300581 142014 17045806 NM_021116 // ADCY1 // adenylate cyclase 1 (brain) // 7p13-‐p12 // 107 /// ENST0000029732ADCY1 NM_021116 NM_021116 // RefSeq // Homo sapiens adenylate cyclase 1 (brain) (ADCY1), mRNA. // chr7 0.00202165 0.00202165 0.451507 -‐2.21481 51.1606 1.97404 0.15434 126551 16887171 NM_020981 // B3GALT1 // UDP-‐Gal:betaGlcNAc beta 1,3-‐galactosyltransferase, polypeptide B3GALT1 NM_020981 NM_020981 // RefSeq // Homo sapiens UDP-‐Gal:betaGlcNAc beta 1,3-‐galactosyltransferase,0.014967 0.014967 0.451093 -‐2.21684 16.7335 1.97859 0.472965 127414 16896396 -‐-‐-‐ -‐-‐-‐ ENST00000516947 // ENSEMBL // ncrna:snRNA chromosome:GRCh37:2:37094541:37094638:-‐1 gene0.0475148 0.0475148 0.450227 -‐2.2211 7.98895 1.98815 0.99545 148867 17112918 NM_018476 // BEX1 // brain expressed, X-‐linked 1 // Xq21-‐q23|Xq22 // 55859 /// ENST0000BEX1 NM_018476 NM_018476 // RefSeq // Homo sapiens brain expressed, X-‐linked 1 (BEX1), mRNA. // chrX /0.0409755 0.0409755 0.448962 -‐2.22736 8.84557 2.00219 0.9054 114368 16769250 NM_001111283 // IGF1 // insulin-‐like growth factor 1 (somatomedin C) // 12q23.2 // 3479IGF1 NM_001111283NM_001111283 // RefSeq // Homo sapiens insulin-‐like growth factor 1 (somatomedin C) (IG0.0162086 0.0162086 0.43623 -‐2.29237 15.9534 2.14864 0.538729 144197 17068610 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // pos_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.00896612 0.00896612 0.42509 -‐2.35244 22.5694 2.28472 0.404924 139510 17016499 NM_005322 // HIST1H1B // histone cluster 1, H1b // 6p22.1 // 3009 /// ENST00000331442 /HIST1H1B NM_005322 NM_005322 // RefSeq // Homo sapiens histone cluster 1, H1b (HIST1H1B), mRNA. // chr6 //0.0152815 0.0152815 0.424996 -‐2.35296 16.5269 2.2859 0.553255 135449 16979112 NR_029835 // MIR302A // microRNA 302a // 4q25 // 407028MIR302A NR_029835 NR_029835 // RefSeq // Homo sapiens microRNA 302a (MIR302A), microRNA. // chr4 // 100 /0.0227869 0.0227869 0.423414 -‐2.36175 12.9498 2.30587 0.712249 116394 16786587 NM_005252 // FOS // FBJ murine osteosarcoma viral oncogene homolog // 14q24.3 // 2353 /FOS NM_005252 NM_005252 // RefSeq // Homo sapiens FBJ murine osteosarcoma viral oncogene homolog (FOS0.00495705 0.00495705 0.421404 -‐2.37302 31.4824 2.33148 0.296226 144245 17068867 ENST00000522124 // SNTG1 // syntrophin, gamma 1 // 8q11-‐q12 // 54212 /// ENST0000051886SNTG1 ENST00000522124ENST00000522124 // ENSEMBL // cdna:known chromosome:GRCh37:8:50824233:51706678:1 gene:E0.00477965 0.00477965 0.421373 -‐2.3732 32.1217 2.33188 0.290381 1


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7549 16698801 NM_001773 // CD34 // CD34 molecule // 1q32 // 947 /// ENST00000356522 // CD34 // CD34 mCD34 NM_001773 NM_001773 // RefSeq // Homo sapiens CD34 molecule (CD34), transcript variant 2, mRNA. /0.0384423 0.0384423 0.420406 -‐2.37866 9.23514 2.3443 1.01538 126861 16890207 ENST00000360351 // MAP2 // microtubule-‐associated protein 2 // 2q34-‐q35 // 4133 /// NM_MAP2 ENST00000360351ENST00000360351 // ENSEMBL // cdna:known chromosome:GRCh37:2:210444145:210598842:1 gene0.0275579 0.0275579 0.414778 -‐2.41093 11.4847 2.41779 0.842092 128716 16909887 -‐-‐-‐ -‐-‐-‐ TCONS_00003518-‐XLOC_002531 // Rinn lincRNA // linc-‐COL6A3-‐2 chr2:-‐:238337562-‐238343465 0.0351358 0.0351358 0.413003 -‐2.42129 9.80604 2.44141 0.995881 141821 17043791 -‐-‐-‐ -‐-‐-‐ TCONS_00013351-‐XLOC_005991 // Rinn lincRNA // linc-‐LOC100129335-‐2 chr7:+:15728025-‐157360.00134213 0.00134213 0.412128 -‐2.42643 63.5412 2.45313 0.154428 119647 16819161 NM_020988 // GNAO1 // guanine nucleotide binding protein (G protein), alpha activating GNAO1 NM_020988 NM_020988 // RefSeq // Homo sapiens guanine nucleotide binding protein (G protein), alp0.00993313 0.00993313 0.409012 -‐2.44492 21.2799 2.49532 0.469048 115197 16775683 -‐-‐-‐ -‐-‐-‐ TCONS_00021860-‐XLOC_010454 // Rinn lincRNA // linc-‐SLITRK5-‐9 chr13:+:81592376-‐81592799 0.0478526 0.0478526 0.402043 -‐2.48729 7.94956 2.59217 1.30431 140024 17021792 NM_004440 // EPHA7 // EPH receptor A7 // 6q16.1 // 2045 /// ENST00000369303 // EPHA7 //EPHA7 NM_004440 NM_004440 // RefSeq // Homo sapiens EPH receptor A7 (EPHA7), mRNA. // chr6 // 100 // 960.0373148 0.0373148 0.401642 -‐2.48978 9.42122 2.59786 1.10298 135459 16979182 ENST00000264363 // NDST4 // N-‐deacetylase/N-‐sulfotransferase (heparan glucosaminyl) 4 /NDST4 ENST00000264363ENST00000264363 // ENSEMBL // cdna:known chromosome:GRCh37:4:115748919:116035032:-‐1 gen0.0443388 0.0443388 0.400681 -‐2.49575 8.38115 2.61152 1.24638 14809 16669850 NM_003637 // ITGA10 // integrin, alpha 10 // 1q21 // 8515 /// ENST00000369304 // ITGA10ITGA10 NM_003637 NM_003637 // RefSeq // Homo sapiens integrin, alpha 10 (ITGA10), mRNA. // chr1 // 100 /0.00125424 0.00125424 0.400597 -‐2.49627 65.8439 2.61272 0.158722 143691 17063420 NM_080660 // ZC3HAV1L // zinc finger CCCH-‐type, antiviral 1-‐like // 7q34 // 92092 /// EZC3HAV1L NM_080660 NM_080660 // RefSeq // Homo sapiens zinc finger CCCH-‐type, antiviral 1-‐like (ZC3HAV1L),0.00213907 0.00213907 0.400224 -‐2.4986 49.6447 2.61804 0.210942 134275 16967831 NM_001013442 // EPGN // epithelial mitogen homolog (mouse) // 4q13.3 // 255324 /// ENSTEPGN NM_001013442NM_001013442 // RefSeq // Homo sapiens epithelial mitogen homolog (mouse) (EPGN), mRNA.0.0164392 0.0164392 0.399123 -‐2.50549 15.8183 2.63382 0.666017 148326 17107349 NM_003413 // ZIC3 // Zic family member 3 // Xq26.2 // 7547 /// ENST00000287538 // ZIC3 ZIC3 NM_003413 NM_003413 // RefSeq // Homo sapiens Zic family member 3 (ZIC3), mRNA. // chrX // 100 //0.00091499 0.00091499 0.397996 -‐2.51259 77.6554 2.65006 0.136504 145226 17077974 NM_020361 // CPA6 // carboxypeptidase A6 // 8q13.2 // 57094 /// ENST00000297770 // CPA6CPA6 NM_020361 NM_020361 // RefSeq // Homo sapiens carboxypeptidase A6 (CPA6), mRNA. // chr8 // 100 //0.00971314 0.00971314 0.391747 -‐2.55267 21.5562 2.74189 0.508788 135498 16979613 -‐-‐-‐ -‐-‐-‐ TCONS_00008568-‐XLOC_004061 // Rinn lincRNA // linc-‐NUDT6-‐2 chr4:-‐:124946453-‐124949512 /0.00122139 0.00122139 0.388819 -‐2.57189 66.7675 2.78596 0.166905 116585 16788475 ENST00000341267 // DLK1 // delta-‐like 1 homolog (Drosophila) // 14q32 // 8788 /// NM_00DLK1 ENST00000341267ENST00000341267 // ENSEMBL // cdna:known chromosome:GRCh37:14:101193164:101201539:1 gen0.0483836 0.0483836 0.38495 -‐2.59774 7.88849 2.84526 1.44274 144119 17067739 ENST00000523320 // NRG1-‐IT2 // NRG1 intronic transcript 2 (non-‐protein coding) // -‐-‐-‐ /NRG1-‐IT2 ENST00000523320ENST00000523320 // ENSEMBL // havana:sense_intronic chromosome:GRCh37:8:32078444:3214490.0345823 0.0345823 0.384924 -‐2.59791 9.90955 2.84565 1.14865 148167 17105775 -‐-‐-‐ -‐-‐-‐ TCONS_00017449-‐XLOC_008039 // Rinn lincRNA // linc-‐PLP1 chrX:+:102997791-‐103001839 // c0.00211447 0.00211447 0.384622 -‐2.59996 49.9518 2.85034 0.228247 19958 16722278 NM_006108 // SPON1 // spondin 1, extracellular matrix protein // 11p15.2 // 10418 /// ESPON1 NM_006108 NM_006108 // RefSeq // Homo sapiens spondin 1, extracellular matrix protein (SPON1), mR0.0359484 0.0359484 0.383666 -‐2.60643 9.65842 2.8652 1.18661 128715 16909882 -‐-‐-‐ -‐-‐-‐ ENST00000409162 // ENSEMBL // cdna:putative chromosome:GRCh37:2:238330063:238333919:-‐1 0.00272343 0.00272343 0.383105 -‐2.61025 43.6222 2.87397 0.263532 142315 17048694 ENST00000319273 // TAC1 // tachykinin, precursor 1 // 7q21-‐q22 // 6863 /// NM_003182 //TAC1 ENST00000319273ENST00000319273 // ENSEMBL // cdna:known chromosome:GRCh37:7:97361220:97369784:1 gene:E0.0007596 0.0007596 0.379336 -‐2.63619 85.5517 2.9335 0.137157 149610 17117888 -‐-‐-‐ -‐-‐-‐ AK098835 // GenBank // Homo sapiens cDNA FLJ25969 fis, clone CBR02250. // chr2 // 100 /0.00317885 0.00317885 0.377039 -‐2.65225 40.1316 2.97038 0.296064 130311 16924761 ENST00000399907 // GRIK1 // glutamate receptor, ionotropic, kainate 1 // 21q22.11 // 28GRIK1 ENST00000399907ENST00000399907 // ENSEMBL // cdna:known chromosome:GRCh37:21:30925573:31312230:-‐1 gene0.00098104 0.00098104 0.355848 -‐2.81019 74.882 3.33313 0.178047 136003 16983652 NM_004932 // CDH6 // cadherin 6, type 2, K-‐cadherin (fetal kidney) // 5p13.3 // 1004 //CDH6 NM_004932 NM_004932 // RefSeq // Homo sapiens cadherin 6, type 2, K-‐cadherin (fetal kidney) (CDH60.00751446 0.00751446 0.348157 -‐2.87227 24.9548 3.47559 0.557103 135358 16978054 NM_003728 // UNC5C // unc-‐5 homolog C (C. elegans) // 4q21-‐q23 // 8633 /// ENST00000453UNC5C NM_003728 NM_003728 // RefSeq // Homo sapiens unc-‐5 homolog C (C. elegans) (UNC5C), mRNA. // chr40.0227382 0.0227382 0.345237 -‐2.89656 12.9671 3.53131 1.08932 144974 17075553 NM_003155 // STC1 // stanniocalcin 1 // 8p21-‐p11.2 // 6781 /// ENST00000290271 // STC1 STC1 NM_003155 NM_003155 // RefSeq // Homo sapiens stanniocalcin 1 (STC1), mRNA. // chr8 // 100 // 86 0.0063481 0.0063481 0.33591 -‐2.97699 27.4386 3.71552 0.541648 137488 16997802 NM_001884 // HAPLN1 // hyaluronan and proteoglycan link protein 1 // 5q14.3 // 1404 ///HAPLN1 NM_001884 NM_001884 // RefSeq // Homo sapiens hyaluronan and proteoglycan link protein 1 (HAPLN1)0.00059095 0.00059095 0.329113 -‐3.03847 97.4376 3.85608 0.158299 128350 16905441 -‐-‐-‐ -‐-‐-‐ TCONS_l2_00016032-‐XLOC_l2_008363 // Broad TUCP // linc-‐EVX2-‐5 chr2:-‐:177626135-‐177684030.031599 0.031599 0.329091 -‐3.03867 10.5138 3.85654 1.46723 137261 16996017 NM_021072 // HCN1 // hyperpolarization activated cyclic nucleotide-‐gated potassium chanHCN1 NM_021072 NM_021072 // RefSeq // Homo sapiens hyperpolarization activated cyclic nucleotide-‐gated0.0153394 0.0153394 0.322628 -‐3.09954 16.4896 3.99541 0.969195 132332 16946707 NM_031850 // AGTR1 // angiotensin II receptor, type 1 // 3q24 // 185 /// ENST0000054228AGTR1 NM_031850 NM_031850 // RefSeq // Homo sapiens angiotensin II receptor, type 1 (AGTR1), transcript0.005543 0.005543 0.322299 -‐3.10271 29.5937 4.00261 0.541009 122524 16848173 NM_080283 // ABCA9 // ATP-‐binding cassette, sub-‐family A (ABC1), member 9 // 17q24.2 //ABCA9 NM_080283 NM_080283 // RefSeq // Homo sapiens ATP-‐binding cassette, sub-‐family A (ABC1), member 90.0124092 0.0124092 0.321796 -‐3.10756 18.6961 4.01367 0.858716 134209 16967238 -‐-‐-‐ -‐-‐-‐ ENST00000365299 // ENSEMBL // ncrna:misc_RNA chromosome:GRCh37:4:62772031:62772126:1 ge0.00514406 0.00514406 0.318231 -‐3.14237 30.8446 4.09294 0.530781 148912 17113346 NM_001143981 // CHRDL1 // chordin-‐like 1 // Xq23 // 91851 /// NM_001143982 // CHRDL1 //CHRDL1 NM_001143981NM_001143981 // RefSeq // Homo sapiens chordin-‐like 1 (CHRDL1), transcript variant 1, m0.00914873 0.00914873 0.311745 -‐3.20775 22.3103 4.24148 0.760453 142474 17050847 NM_002851 // PTPRZ1 // protein tyrosine phosphatase, receptor-‐type, Z polypeptide 1 // PTPRZ1 NM_002851 NM_002851 // RefSeq // Homo sapiens protein tyrosine phosphatase, receptor-‐type, Z poly0.00437063 0.00437063 0.309425 -‐3.2318 33.7414 4.29602 0.509288 114137 16766946 NM_000706 // AVPR1A // arginine vasopressin receptor 1A // 12q14-‐q15 // 552 /// ENST000AVPR1A NM_000706 NM_000706 // RefSeq // Homo sapiens arginine vasopressin receptor 1A (AVPR1A), mRNA. //0.00327505 0.00327505 0.304848 -‐3.28032 39.4891 4.40586 0.446287 122523 16848123 NM_007168 // ABCA8 // ATP-‐binding cassette, sub-‐family A (ABC1), member 8 // 17q24 // 1ABCA8 NM_007168 NM_007168 // RefSeq // Homo sapiens ATP-‐binding cassette, sub-‐family A (ABC1), member 80.0427842 0.0427842 0.293949 -‐3.40195 8.58896 4.68004 2.17956 134347 16968680 NM_001251830 // SPP1 // secreted phosphoprotein 1 // 4q22.1 // 6696 /// NM_001040058 //SPP1 NM_001251830NM_001251830 // RefSeq // Homo sapiens secreted phosphoprotein 1 (SPP1), transcript var0.00269601 0.00269601 0.292757 -‐3.41581 43.8602 4.71118 0.429654 118195 16803492 NM_004378 // CRABP1 // cellular retinoic acid binding protein 1 // 15q24 // 1381 /// ENCRABP1 NM_004378 NM_004378 // RefSeq // Homo sapiens cellular retinoic acid binding protein 1 (CRABP1),9.85E-‐05 9.85E-‐05 0.283977 -‐3.52141 243.501 4.94761 0.0812747 129671 16919158 ENST00000361475 // TGM2 // transglutaminase 2 (C polypeptide, protein-‐glutamine-‐gamma-‐gTGM2 ENST00000361475ENST00000361475 // ENSEMBL // cdna:known chromosome:GRCh37:20:36756863:36793774:-‐1 gene0.00303308 0.00303308 0.268395 -‐3.72586 41.1628 5.40117 0.524859 129971 16921724 ENST00000400546 // NCAM2 // neural cell adhesion molecule 2 // 21q21.1 // 4685 /// NM_0NCAM2 ENST00000400546ENST00000400546 // ENSEMBL // cdna:known chromosome:GRCh37:21:22370633:22915650:1 gene:0.00038051 0.00038051 0.264977 -‐3.77391 122.246 5.50693 0.180192 143680 17063254 NM_002825 // PTN // pleiotrophin // 7q33 // 5764 /// BC005916 // PTN // pleiotrophin //PTN NM_002825 NM_002825 // RefSeq // Homo sapiens pleiotrophin (PTN), mRNA. // chr7 // 100 // 75 // 10.0149284 0.0149284 0.261618 -‐3.82237 16.7593 5.61325 1.33974 145493 17080251 NM_198123 // CSMD3 // CUB and Sushi multiple domains 3 // 8q23.3 // 114788 /// ENST0000CSMD3 NM_198123 NM_198123 // RefSeq // Homo sapiens CUB and Sushi multiple domains 3 (CSMD3), transcrip0.00089932 0.00089932 0.252881 -‐3.95442 78.3574 5.90122 0.301246 17245 16695853 NM_006917 // RXRG // retinoid X receptor, gamma // 1q22-‐q23 // 6258 /// NM_001256570 //RXRG NM_006917 NM_006917 // RefSeq // Homo sapiens retinoid X receptor, gamma (RXRG), transcript varia0.0014098 0.0014098 0.238136 -‐4.19927 61.9172 6.42822 0.415278 152142 17123600 -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ 0.0002893 0.0002893 0.186858 -‐5.35165 140.687 8.78448 0.24976 13961 16661155 NM_024674 // LIN28A // lin-‐28 homolog A (C. elegans) // 1p36.11 // 79727 /// ENST000003LIN28A NM_024674 NM_024674 // RefSeq // Homo sapiens lin-‐28 homolog A (C. elegans) (LIN28A), mRNA. // ch0.00098702 0.00098702 0.166805 -‐5.99503 74.6451 10.0138 0.536607 112029 16743721 NM_002421 // MMP1 // matrix metallopeptidase 1 (interstitial collagenase) // 11q22.3 //MMP1 NM_002421 NM_002421 // RefSeq // Homo sapiens matrix metallopeptidase 1 (interstitial collagenase0.00364353 0.00364353 0.135242 -‐7.39418 37.2682 12.4969 1.34129 112643 16750154 NM_001843 // CNTN1 // contactin 1 // 12q11-‐q12 // 1272 /// ENST00000551295 // CNTN1 // CNTN1 NM_001843 NM_001843 // RefSeq // Homo sapiens contactin 1 (CNTN1), transcript variant 1, mRNA. //2.60E-‐05 2.60E-‐05 0.105606 -‐9.46918 476.856 15.7779 0.132349 1


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Genes in dataset Prediction (based on expression direction) Fold Change Findings

TOP2A Decreased -1.542 Increases (2) CENPF Decreased -1.519 Increases (1) MMP1 Decreased -7.394 Increases (3) FOS Decreased -2.373 Increases (22) FOSB Decreased -1.927 Increases (2) PAX9 Decreased -1.699 Increases (4) MAGI2 Decreased 1.583 Decreases (1) SMPD1 Decreased 1.565 Decreases (1) EPGN Decreased -2.505 Increases (1) TNFAIP6 Decreased -1.965 Increases (4) EYA1 Decreased -1.652 Increases (2) SEMA6A Decreased -1.859 Increases (2) ALOX5AP Decreased -1.515 Increases (2) TACR1 Decreased -1.727 Increases (2) PYGM Decreased -1.624 Increases (1) KIF11 Decreased -1.513 Increases (1) AGTR1 Decreased -3.103 Increases (8) TAC1 Decreased -2.636 Increases (24) TTK Decreased -1.552 Increases (1) BCL2 Decreased -2.124 Increases (53) TGM2 Decreased -3.726 Increases (6) TPX2 Decreased -1.573 Increases (5) ANGPT1 Decreased -2.080 Increases (4) SIX1 Decreased -1.727 Increases (13) POU5F1 Decreased -2.169 Increases (7) NPY1R Decreased -2.083 Increases (2) CD34 Decreased -2.379 Increases (1) PTN Decreased -3.822 Increases (19) mir-221 Decreased -1.801 Increases (26) TBX2 Decreased -1.598 Increases (3) SPP1 Decreased -3.416 Increases (45) MMP9 Decreased -1.919 Increases (19) DLX2 Decreased -1.709 Increases (1) ZIC2 Decreased -1.612 Increases (2) NRCAM Decreased -1.697 Increases (1) MYBL1 Decreased -1.828 Increases (5) AVPR1A Decreased -3.280 Increases (2) COL6A3 Decreased -2.190 Increases (1) DLGAP5 Decreased -1.586 Increases (6) A2M Decreased -1.593 Increases (9) RRAD Decreased 1.512 Decreases (7) SOX2 Decreased -1.840 Increases (14) IGF1 Decreased -2.292 Increases (389) MCM10 Decreased -1.738 Increases (1) LIN28B Decreased -1.837 Increases (6)

Supplementary Table 2: Predicted activation states of differentially

expressed cell proliferation transcripts in OTX2 hEN vs. hEN cells. All

transcripts are significantly and differentially expressed. P<0.05 is considered

significant.


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NANOG Decreased -1.551 Increases (12) PODN Decreased 2.238 Decreases (1) FEZF1 Decreased -1.831 Increases (10) UNC5C Increased -2.897 Decreases (2) IL6 Increased 1.571 Increases (268) ADAMTS5 Increased -1.654 Decreases (1) PTPRZ1 Increased -3.232 Decreases (4) ADCY1 Increased -2.215 Decreases (1) SNAI2 Increased -1.606 Decreases (6) TEK Increased -1.660 Decreases (6) HTRA1 Increased -1.743 Decreases (1) C3 Increased 1.756 Increases (9) H19 Increased -1.658 Decreases (4) IGFBP3 Increased -1.822 Decreases (42) PIM1 Increased 2.018 Increases (43) GNAO1 Increased -2.445 Decreases (1) FABP4 Increased 2.893 Increases (4) TIMP4 Increased -1.954 Decreases (2) CNTN1 Increased -9.469 Decreases (3) STC1 Increased -2.977 Decreases (1) RXFP2 Increased -1.502 Decreases (1) CYP2S1 Increased -1.899 Decreases (1) HTR2B Increased 3.014 Increases (16) LIN28A Increased -5.995 Decreases (1) LECT1 Increased -1.620 Decreases (1) TNMD Affected -1.672 Affects (2) CSMD3 Affected -3.954 Affects (1) KIF15 Affected -1.794 Affects (1) LXN Affected 1.737 Affects (1) CLDN6 Affected -1.862 Affects (2) SCG2 Affected -1.586 Affects (2) EFEMP1 Affected 2.833 Affects (2) IL32 Affected 1.538 Affects (2) DLK1 Affected -2.598 Affects (3) GDF5 Affected 1.564 Affects (2) DNMT3B Affected -1.782 Affects (7)

** 48 of 81 genes have expression direction consistent with decreases in cell

proliferation


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Genes in dataset Prediction (based on expression direction) Fold Change Findings PLCL1 Decreased -1.759 Increases (1) MMP1 Decreased -7.394 Increases (5) MAGI2 Decreased 1.583 Decreases (1) SMPD1 Decreased 1.565 Decreases (2) SNAI2 Decreased -1.606 Increases (16) GDF5 Decreased 1.564 Decreases (1) TEK Decreased -1.660 Increases (8) ALOX5AP Decreased -1.515 Increases (3) TACR1 Decreased -1.727 Increases (4) TAC1 Decreased -2.636 Increases (16) IL32 Decreased 1.538 Decreases (1) BCL2 Decreased -2.124 Increases (3) TGM2 Decreased -3.726 Increases (26) GNAO1 Decreased -2.445 Increases (2) ANGPT1 Decreased -2.080 Increases (13) SCG2 Decreased -1.586 Increases (10) CNTN1 Decreased -9.469 Increases (1) PTN Decreased -3.822 Increases (39) SPP1 Decreased -3.416 Increases (79) MMP9 Decreased -1.919 Increases (37) DLX2 Decreased -1.709 Increases (4) DLX1 Decreased -1.526 Increases (3) IGF1 Decreased -2.292 Increases (73) LIN28B Decreased -1.837 Increases (2) PODN Decreased 2.238 Decreases (1) IL6 Increased 1.571 Increases (37) PTPRZ1 Increased -3.232 Decreases (10) C3 Increased 1.756 Increases (23) PIM1 Increased 2.018 Increases (1) FABP4 Increased 2.893 Increases (3) POU5F1 Increased -2.169 Decreases (1) mir-221 Increased -1.801 Decreases (3) ACAN Increased -1.832 Decreases (2) STC1 Increased -2.977 Decreases (4) A2M Increased -1.593 Decreases (1) CYP2S1 Increased -1.899 Decreases (1) FEZF1 Affected -1.831 Affects (2) ROBO2 Affected -1.547 Affects (1) HTR2B Affected 3.014 Affects (1) CD34 Affected -2.379 Affects (1) SIX1 Affected -1.727 Affects (1) IGFBP3 Affected -1.822 Affects (4) SEMA6A Affected -1.859 Affects (2) FAP Affected -1.506 Affects (1) UNC5C Affected -2.897 Affects (1)

Supplementary Table 3: Predicted activation states of differentially expressed cell migration transcripts in OTX2 hEN vs. hEN cells. All

transcripts are significantly and differentially expressed. P<0.05 is considered

significant.

** 25 of 45 genes have expression direction consistent with decreases in cell

migration.


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Column # Transcript ID category seqname start stop strand gene_assignmentGene SymbolRefSeq mrna_assignmentp-‐value(Type)p-‐value(trans-‐hEN OTX2 KD vs. trans-‐hEN)Fold-‐Change(trans-‐hEN OTX2 KD vs. trans-‐hEN)F(Type) SS(Type) SS(Error) F(Error)21289 16835635 normgene-‐>exon-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // pos_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0442442 0.0442442 3.77791 21.1132 3.67715 0.348327 12803 16655831 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0032117 0.0032117 3.48599 309.862 3.24565 0.020949 15604 16678332 normgene-‐>exon-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // pos_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0285916 0.0285916 2.65533 33.4826 1.98497 0.118567 1555 16651139 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.00245284 0.00245284 2.64994 406.191 1.97672 0.00973293 1

42990 17056105 main chr7 27139721 27142430 -‐ ENST00000222718 // HOXA2 // homeobox A2 // 7p15.2 // 3199 /// NM_006735 // HOXA2 // homHOXA2 ENST00000222718ENST00000222718 // ENSEMBL // cdna:known chromosome:GRCh37:7:27139721:27142430:-‐1 gene:0.00011153 0.00011153 2.39703 8964.91 1.59075 0.00035488 19106 16713391 main chr10 42383279 42391866 -‐ -‐-‐-‐ -‐-‐-‐ TCONS_00017955-‐XLOC_008785 // Rinn lincRNA // linc-‐ZNF25-‐1 chr10:-‐:42383278-‐42391866 //0.0143869 0.0143869 2.37711 68.0114 1.56052 0.04589 18505 16707534 main chr10 94821021 94828454 + NM_183374 // CYP26C1 // cytochrome P450, family 26, subfamily C, polypeptide 1 // 10q23CYP26C1 NM_183374 NM_183374 // RefSeq // Homo sapiens cytochrome P450, family 26, subfamily C, polypeptid0.0165887 0.0165887 2.32867 58.7862 1.48719 0.0505967 1345 16650695 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.00329892 0.00329892 2.2727 301.631 1.40283 0.00930161 1844 16651737 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0438086 0.0438086 2.2526 21.3378 1.37263 0.128657 11160 16652415 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0117845 0.0117845 2.20771 83.36 1.30542 0.0313199 149731 17118180 main chr6 132269313 132269801 + -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ 0.0351103 0.0351103 2.18353 26.9906 1.26936 0.0940595 13313 16656871 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.00496667 0.00496667 2.18309 199.843 1.26871 0.0126971 1936 16651935 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0106171 0.0106171 2.1781 92.69 1.26128 0.0272151 11247 16652599 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0106171 0.0106171 2.1781 92.69 1.26128 0.0272151 131988 16942958 main chr3 89156674 89531284 + NM_005233 // EPHA3 // EPH receptor A3 // 3p11.2 // 2042 /// ENST00000336596 // EPHA3 //EPHA3 NM_005233 NM_005233 // RefSeq // Homo sapiens EPH receptor A3 (EPHA3), transcript variant 1, mRNA0.0134928 0.0134928 2.03597 72.6168 1.05209 0.0289766 1106 16650199 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0118823 0.0118823 2.02705 82.6619 1.03914 0.0251419 12892 16656009 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0305686 0.0305686 2.01168 31.221 1.01687 0.06514 117985 16801173 main chr15 52176753 52176850 + -‐-‐-‐ -‐-‐-‐ ENST00000384753 // ENSEMBL // ncrna:misc_RNA chromosome:GRCh37:15:52176753:52176850:1 g0.00273505 0.00273505 1.91427 364.124 0.877585 0.00482025 145845 17084130 main chr9 27109139 27230173 + NM_000459 // TEK // TEK tyrosine kinase, endothelial // 9p21 // 7010 /// ENST0000038003TEK NM_000459 NM_000459 // RefSeq // Homo sapiens TEK tyrosine kinase, endothelial (TEK), mRNA. // ch0.00994382 0.00994382 1.90978 99.0675 0.871243 0.0175889 1256 16650511 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0004854 0.0004854 1.90726 2058.64 0.867688 0.00084297 19431 16716587 main chr10 94819420 94820183 -‐ -‐-‐-‐ -‐-‐-‐ TCONS_00018025-‐XLOC_008907 // Rinn lincRNA // linc-‐IDE-‐1 chr10:-‐:94819419-‐94820183 // c0.0236604 0.0236604 1.89818 40.7707 0.854911 0.0419375 139464 17016221 main chr6 24804513 25042238 -‐ NM_014722 // FAM65B // family with sequence similarity 65, member B // 6p22.3-‐p21.32 //FAM65B NM_014722 NM_014722 // RefSeq // Homo sapiens family with sequence similarity 65, member B (FAM650.0276947 0.0276947 1.89485 34.615 0.850245 0.0491259 131602 16938407 main chr3 25215823 25639423 + ENST00000330688 // RARB // retinoic acid receptor, beta // 3p24.2 // 5915 /// NM_000965RARB ENST00000330688ENST00000330688 // ENSEMBL // cdna:known chromosome:GRCh37:3:25469802:25639423:1 gene:E0.00726133 0.00726133 1.89043 136.218 0.84403 0.0123924 137763 17000235 main chr5 136310987 136934068 -‐ NM_004598 // SPOCK1 // sparc/osteonectin, cwcv and kazal-‐like domains proteoglycan (tesSPOCK1 NM_004598 NM_004598 // RefSeq // Homo sapiens sparc/osteonectin, cwcv and kazal-‐like domains prot0.00277005 0.00277005 1.87875 359.505 0.827694 0.00460463 13323 16656891 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0116072 0.0116072 1.87324 84.6563 0.819992 0.0193723 12861 16655947 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.037228 0.037228 1.87162 25.371 0.817742 0.0644627 147463 17099703 main chr9 137742416 137742487 -‐ NR_039695 // MIR3689E // microRNA 3689e // -‐-‐-‐ // 100616460MIR3689E NR_039695 NR_039695 // RefSeq // Homo sapiens microRNA 3689e (MIR3689E), microRNA. // chr9 // 1000.00304376 0.00304376 1.86487 327.042 0.80833 0.00494329 12855 16655935 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0283397 0.0283397 1.86184 33.7934 0.804118 0.0475903 146110 17086386 main chr9 87283466 87638505 + NM_006180 // NTRK2 // neurotrophic tyrosine kinase, receptor, type 2 // 9q22.1 // 4915 NTRK2 NM_006180 NM_006180 // RefSeq // Homo sapiens neurotrophic tyrosine kinase, receptor, type 2 (NTR0.0103262 0.0103262 1.84877 95.3441 0.785994 0.0164875 133835 16963687 main chr4 403598 403704 + -‐-‐-‐ -‐-‐-‐ ENST00000390148 // ENSEMBL // ncrna:miRNA chromosome:GRCh37:4:403598:403704:1 gene:ENSG0.0306111 0.0306111 1.82989 31.1757 0.759965 0.0487537 146049 17085901 main chr9 75766673 75785309 + ENST00000376911 // ANXA1 // annexin A1 // 9q21.13 // 301 /// ENST00000257497 // ANXA1 /ANXA1 ENST00000376911ENST00000376911 // ENSEMBL // cdna:known chromosome:GRCh37:9:75772570:75785309:1 gene:E0.0178976 0.0178976 1.7993 54.3781 0.718143 0.026413 142289 17048450 main chr7 93551011 93555831 + NM_004126 // GNG11 // guanine nucleotide binding protein (G protein), gamma 11 // 7q21 GNG11 NM_004126 NM_004126 // RefSeq // Homo sapiens guanine nucleotide binding protein (G protein), gam0.00769995 0.00769995 1.78746 128.373 0.702091 0.0109383 116394 16786587 main chr14 75745477 75748937 + NM_005252 // FOS // FBJ murine osteosarcoma viral oncogene homolog // 14q24.3 // 2353 /FOS NM_005252 NM_005252 // RefSeq // Homo sapiens FBJ murine osteosarcoma viral oncogene homolog (FOS0.002189 0.002189 1.78711 455.33 0.701618 0.0030818 115630 16779667 main chr13 66876966 67804468 -‐ NM_203487 // PCDH9 // protocadherin 9 // 13q21.32 // 5101 /// ENST00000544246 // PCDH9 PCDH9 NM_203487 NM_203487 // RefSeq // Homo sapiens protocadherin 9 (PCDH9), transcript variant 1, mRNA0.0289903 0.0289903 1.78436 33.0017 0.6979 0.0422948 133186 16956532 main chr3 86987119 87040269 -‐ NM_016206 // VGLL3 // vestigial like 3 (Drosophila) // 3p12.1 // 389136 /// ENST0000039VGLL3 NM_016206 NM_016206 // RefSeq // Homo sapiens vestigial like 3 (Drosophila) (VGLL3), mRNA. // chr0.0114391 0.0114391 1.7784 85.9226 0.689861 0.0160577 148107 17105183 main chrX 85403455 86087607 + NM_001139514 // DACH2 // dachshund homolog 2 (Drosophila) // Xq21.3 // 117154 /// ENST0DACH2 NM_001139514NM_001139514 // RefSeq // Homo sapiens dachshund homolog 2 (Drosophila) (DACH2), transc0.00860017 0.00860017 1.76608 114.779 0.673308 0.0117323 17048 16693533 normgene-‐>exon-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // pos_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0156686 0.0156686 1.74564 62.3259 0.646019 0.0207303 120293 16825866 main chr16 30712658 30712756 -‐ -‐-‐-‐ -‐-‐-‐ ENST00000410355 // ENSEMBL // ncrna:snRNA chromosome:GRCh37:16:30712658:30712756:-‐1 gen0.0206497 0.0206497 1.74475 46.9321 0.644848 0.0274801 138988 17011825 main chr6 114026059 114026126 + -‐-‐-‐ -‐-‐-‐ ENST00000408632 // ENSEMBL // ncrna:miRNA chromosome:GRCh37:6:114026059:114026126:1 gen0.0154517 0.0154517 1.73322 63.2216 0.629568 0.0199162 123351 16855545 main chr18 56148479 56296189 -‐ NM_052947 // ALPK2 // alpha-‐kinase 2 // 18q21.31 // 115701 /// ENST00000361673 // ALPK2ALPK2 NM_052947 NM_052947 // RefSeq // Homo sapiens alpha-‐kinase 2 (ALPK2), mRNA. // chr18 // 100 // 100.040776 0.040776 1.7231 23.0346 0.616231 0.0535047 135917 16983026 main chr5 7396321 7830194 + NM_020546 // ADCY2 // adenylate cyclase 2 (brain) // 5p15.3 // 108 /// ENST00000338316 ADCY2 NM_020546 NM_020546 // RefSeq // Homo sapiens adenylate cyclase 2 (brain) (ADCY2), mRNA. // chr5 0.024151 0.024151 1.72194 39.9122 0.61471 0.0308031 13381 16657013 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0223861 0.0223861 1.71036 43.1762 0.599542 0.0277719 114710 16771559 normgene-‐>exon-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // pos_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0499018 0.0499018 1.69346 18.5521 0.577555 0.0622629 18768 16710342 main chr10 126454765 126454866 + -‐-‐-‐ -‐-‐-‐ ENST00000362596 // ENSEMBL // ncrna:misc_RNA chromosome:GRCh37:10:126454765:126454866:10.0498823 0.0498823 1.68859 18.56 0.571263 0.0615587 115980 16782040 main chr14 22965872 22965937 + ENST00000390495 // TRAJ42 // T cell receptor alpha joining 42 // -‐-‐-‐ // -‐-‐-‐TRAJ42 ENST00000390495ENST00000390495 // ENSEMBL // cdna:known chromosome:GRCh37:14:22965872:22965937:1 gene:0.0132782 0.0132782 1.67319 73.8146 0.551456 0.0149417 1158 16650309 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0194753 0.0194753 1.66096 49.8521 0.535845 0.0214974 1

39044 17012245 main chr6 124125069 125146803 + NM_001040214 // NKAIN2 // Na+/K+ transporting ATPase interacting 2 // 6q21 // 154215 //NKAIN2 NM_001040214NM_001040214 // RefSeq // Homo sapiens Na+/K+ transporting ATPase interacting 2 (NKAIN20.00248801 0.00248801 1.65793 400.428 0.532 0.00265715 137233 16995719 main chr5 40911169 40911230 -‐ -‐-‐-‐ -‐-‐-‐ ENST00000517289 // ENSEMBL // ncrna:snRNA chromosome:GRCh37:5:40911169:40911230:-‐1 gene0.012103 0.012103 1.64592 81.1272 0.516808 0.0127407 140189 17023646 main chr6 132269316 132272518 -‐ ENST00000367976 // CTGF // connective tissue growth factor // 6q23.1 // 1490 /// NM_001CTGF ENST00000367976ENST00000367976 // ENSEMBL // cdna:known chromosome:GRCh37:6:132269316:132272513:-‐1 gen0.0113248 0.0113248 1.64354 86.805 0.51381 0.0118383 115860 16781440 main chr14 20248401 20249516 + ENST00000315957 // OR4M1 // olfactory receptor, family 4, subfamily M, member 1 // 14q1OR4M1 ENST00000315957ENST00000315957 // ENSEMBL // cdna:known chromosome:GRCh37:14:20248401:20249516:1 gene:0.0134055 0.0134055 1.6385 73.0997 0.507483 0.0138847 140232 17024161 main chr6 137813336 137815531 -‐ NM_175747 // OLIG3 // oligodendrocyte transcription factor 3 // 6q23.3 // 167826 /// ENOLIG3 NM_175747 NM_175747 // RefSeq // Homo sapiens oligodendrocyte transcription factor 3 (OLIG3), mRN0.0016029 0.0016029 1.63673 622.369 0.505261 0.00162367 123779 16859800 main chr19 18497372 18497444 + NR_036156 // MIR3189 // microRNA 3189 // -‐-‐-‐ // 100422943MIR3189 NR_036156 NR_036156 // RefSeq // Homo sapiens microRNA 3189 (MIR3189), microRNA. // chr19 // 100 0.0249784 0.0249784 1.63314 38.541 0.50077 0.0259864 133064 16955117 main chr3 53564349 53564428 -‐ -‐-‐-‐ -‐-‐-‐ ENST00000516178 // ENSEMBL // ncrna:snoRNA chromosome:GRCh37:3:53564349:53564428:-‐1 gen0.0390285 0.0390285 1.62841 24.1323 0.494863 0.0410125 1

Supplementary Table 4: Differentially expressed transcripts in trans-hEN OTX2 KD vs. trans-hEN cells. All transcripts are significantly and differentially

expressed. P<0.05 is considered significant.


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35330 16977833 main chr4 88394487 88452213 -‐ NM_001128310 // SPARCL1 // SPARC-‐like 1 (hevin) // 4q22.1 // 8404 /// ENST00000418378 /SPARCL1 NM_001128310NM_001128310 // RefSeq // Homo sapiens SPARC-‐like 1 (hevin) (SPARCL1), transcript varia0.0134194 0.0134194 1.62708 73.0224 0.493203 0.0135083 115594 16779486 main chr13 53418109 53422775 -‐ NM_002590 // PCDH8 // protocadherin 8 // 13q21.1 // 5100 /// ENST00000377942 // PCDH8 /PCDH8 NM_002590 NM_002590 // RefSeq // Homo sapiens protocadherin 8 (PCDH8), transcript variant 1, mRNA0.0419429 0.0419429 1.62249 22.3527 0.487492 0.0436182 132022 16943233 main chr3 98706231 98706293 + -‐-‐-‐ -‐-‐-‐ ENST00000517102 // ENSEMBL // ncrna:snRNA chromosome:GRCh37:3:98706231:98706293:1 gene:0.0173293 0.0173293 1.62247 56.2102 0.487468 0.0173445 132404 16947357 main chr3 157154578 157161417 + NM_002852 // PTX3 // pentraxin 3, long // 3q25 // 5806 /// ENST00000295927 // PTX3 // pPTX3 NM_002852 NM_002852 // RefSeq // Homo sapiens pentraxin 3, long (PTX3), mRNA. // chr3 // 100 // 10.0478901 0.0478901 1.60452 19.3934 0.465312 0.0479866 12816 16655857 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0198876 0.0198876 1.60409 48.7877 0.464789 0.0190535 19247 16714776 main chr10 64571756 64679660 -‐ NM_000399 // EGR2 // early growth response 2 // 10q21.1 // 1959 /// ENST00000242480 // EGR2 NM_000399 NM_000399 // RefSeq // Homo sapiens early growth response 2 (EGR2), transcript variant 0.0324164 0.0324164 1.6001 29.3569 0.4599 0.0313317 122721 16850412 main chrU 164643 164725 -‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ 0.0114584 0.0114584 1.59889 85.7751 0.458426 0.010689 115355 16777209 main chr13 21007917 21007985 -‐ NR_039721 // MIR4499 // microRNA 4499 // -‐-‐-‐ // 100616304MIR4499 NR_039721 NR_039721 // RefSeq // Homo sapiens microRNA 4499 (MIR4499), microRNA. // chr13 // 100 0.021903 0.021903 1.59888 44.1614 0.458417 0.020761 137125 16994703 main chr5 19473060 20575982 -‐ ENST00000542864 // CDH18 // cadherin 18, type 2 // 5p14.3 // 1016 /// NM_004934 // CDH1CDH18 ENST00000542864ENST00000542864 // ENSEMBL // cdna:known chromosome:GRCh37:5:19473157:20575982:-‐1 gene:0.00506756 0.00506756 1.59487 195.835 0.453521 0.00463166 11222 16652547 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0234598 0.0234598 1.59454 41.132 0.453113 0.0220322 114290 16768468 main chr12 92751373 92757553 -‐ -‐-‐-‐ -‐-‐-‐ TCONS_00020870-‐XLOC_010152 // Rinn lincRNA // linc-‐BTG1-‐2 chr12:-‐:92751372-‐92757553 // 0.0419547 0.0419547 1.59134 22.346 0.44922 0.0402059 146683 17092526 main chr9 14719722 14722715 -‐ NM_005454 // CER1 // cerberus 1, cysteine knot superfamily, homolog (Xenopus laevis) //CER1 NM_005454 NM_005454 // RefSeq // Homo sapiens cerberus 1, cysteine knot superfamily, homolog (Xen0.0113593 0.0113593 1.59004 86.5368 0.447644 0.0103458 12371 16654937 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0131829 0.0131829 1.5898 74.3593 0.447356 0.0120323 134294 16968047 main chr4 77558776 77565521 + -‐-‐-‐ -‐-‐-‐ ENST00000425645 // ENSEMBL // havana:sense_intronic chromosome:GRCh37:4:77558776:7756550.0315578 0.0315578 1.58962 30.1959 0.447133 0.0296155 16476 16687875 main chr1 59246463 59249785 -‐ ENST00000371222 // JUN // jun proto-‐oncogene // 1p32-‐p31 // 3725 /// NM_002228 // JUN /JUN ENST00000371222ENST00000371222 // ENSEMBL // cdna:known chromosome:GRCh37:1:59246465:59249785:-‐1 gene:0.0098091 0.0098091 1.58814 100.449 0.445339 0.008867 138257 17005223 main chr6 19837601 19842431 + NM_001546 // ID4 // inhibitor of DNA binding 4, dominant negative helix-‐loop-‐helix protID4 NM_001546 NM_001546 // RefSeq // Homo sapiens inhibitor of DNA binding 4, dominant negative helix0.0497977 0.0497977 1.57239 18.594 0.426351 0.045859 136323 16987287 main chr5 92919043 92930321 + ENST00000327111 // NR2F1 // nuclear receptor subfamily 2, group F, member 1 // 5q14 // NR2F1 ENST00000327111ENST00000327111 // ENSEMBL // cdna:known chromosome:GRCh37:5:92919043:92930321:1 gene:E0.0188891 0.0188891 1.57145 51.4453 0.425235 0.0165315 11990 16654141 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0426709 0.0426709 1.57063 21.9461 0.424247 0.0386627 1464 16650945 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0402582 0.0402582 1.57057 23.3499 0.424176 0.0363321 1

34422 16969553 main chr4 108356275 108356377 + -‐-‐-‐ -‐-‐-‐ ENST00000516661 // ENSEMBL // ncrna:snRNA chromosome:GRCh37:4:108356275:108356377:1 gen0.00176761 0.00176761 1.56631 564.238 0.419088 0.0014855 128679 16909551 main chr2 232786530 232791113 -‐ ENST00000409852 // NPPC // natriuretic peptide C // 2q24-‐qter // 4880 /// NM_024409 // NPPC ENST00000409852ENST00000409852 // ENSEMBL // cdna:known chromosome:GRCh37:2:232786530:232791113:-‐1 gen0.0429934 0.0429934 1.56155 21.7704 0.413423 0.0379803 139923 17020715 main chr6 72053204 72130522 -‐ NR_026807 // LINC00472 // long intergenic non-‐protein coding RNA 472 // 6q13 // 79940LINC00472 NR_026807 NR_026807 // RefSeq // Homo sapiens long intergenic non-‐protein coding RNA 472 (LINC0040.015191 0.015191 1.56051 64.3322 0.412192 0.0128145 19424 16716520 main chr10 93666345 93669258 -‐ NM_152429 // FGFBP3 // fibroblast growth factor binding protein 3 // 10q23.32 // 143282FGFBP3 NM_152429 NM_152429 // RefSeq // Homo sapiens fibroblast growth factor binding protein 3 (FGFBP3)0.0143034 0.0143034 1.55787 68.4171 0.409057 0.0119577 127550 16897859 main chr2 56190326 56274461 -‐ -‐-‐-‐ -‐-‐-‐ ENST00000446139 // ENSEMBL // havana:lincRNA chromosome:GRCh37:2:56190326:56274461:-‐1 g0.0131609 0.0131609 1.54833 74.4857 0.397797 0.0106812 127941 16901068 main chr2 100163715 100759201 -‐ NM_002285 // AFF3 // AF4/FMR2 family, member 3 // 2q11.2-‐q12 // 3899 /// NM_001025108 /AFF3 NM_002285 NM_002285 // RefSeq // Homo sapiens AF4/FMR2 family, member 3 (AFF3), transcript varian0.00694396 0.00694396 1.54757 142.512 0.396911 0.00557021 128382 16906140 main chr2 183004763 183387919 -‐ NM_005019 // PDE1A // phosphodiesterase 1A, calmodulin-‐dependent // 2q32.1 // 5136 /// PDE1A NM_005019 NM_005019 // RefSeq // Homo sapiens phosphodiesterase 1A, calmodulin-‐dependent (PDE1A),0.0249729 0.0249729 1.54706 38.5497 0.396303 0.0205606 114273 16768270 main chr12 88885885 88974628 -‐ NM_000899 // KITLG // KIT ligand // 12q22 // 4254 /// NM_003994 // KITLG // KIT ligand KITLG NM_000899 NM_000899 // RefSeq // Homo sapiens KIT ligand (KITLG), transcript variant b, mRNA. // 7.33E-‐05 7.33E-‐05 1.54669 13635.4 0.395869 5.81E-‐05 110196 16724715 main chr11 55029658 55038595 + NM_024114 // TRIM48 // tripartite motif containing 48 // 11q11 // 79097 /// ENST0000041TRIM48 NM_024114 NM_024114 // RefSeq // Homo sapiens tripartite motif containing 48 (TRIM48), mRNA. // c0.0215829 0.0215829 1.5436 44.8384 0.392252 0.0174962 116298 16785127 main chr14 63670832 63760230 + NM_020663 // RHOJ // ras homolog family member J // 14q23.2 // 57381 /// ENST0000031675RHOJ NM_020663 NM_020663 // RefSeq // Homo sapiens ras homolog family member J (RHOJ), mRNA. // chr14 0.0390118 0.0390118 1.54248 24.1432 0.390941 0.0323852 1924 16651911 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0251119 0.0251119 1.54245 38.3281 0.390904 0.0203978 1

39003 17011949 main chr6 116832808 116845955 + ENST00000368599 // FAM26E // family with sequence similarity 26, member E // 6q22.1 // FAM26E ENST00000368599ENST00000368599 // ENSEMBL // cdna:known chromosome:GRCh37:6:116832809:116845955:1 gene0.0122091 0.0122091 1.54159 80.4089 0.389895 0.00969779 11558 16653253 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.025077 0.025077 1.5408 38.3835 0.388975 0.0202678 149818 17118411 main chr9 66699495 66708473 -‐ -‐-‐-‐ -‐-‐-‐ TCONS_l2_00029962-‐XLOC_l2_015202 // Broad TUCP // linc-‐FAM75A7-‐18 chr9:-‐:66688087-‐666990.036988 0.036988 1.54063 25.5452 0.388783 0.0304388 149820 17118415 main chr9 69882492 69891468 -‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ 0.036988 0.036988 1.54063 25.5452 0.388783 0.0304388 12842 16655909 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.039715 0.039715 1.53968 23.6895 0.387673 0.0327295 133619 16961449 main chr3 170177342 170303863 -‐ NM_020949 // SLC7A14 // solute carrier family 7 (orphan transporter), member 14 // 3q26SLC7A14 NM_020949 NM_020949 // RefSeq // Homo sapiens solute carrier family 7 (orphan transporter), membe0.025762 0.025762 1.53937 37.3233 0.387302 0.0207539 1664 16651365 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0249986 0.0249986 1.53631 38.5085 0.383748 0.0199305 1

15305 16776616 main chr13 112721913 112726020 + NM_005986 // SOX1 // SRY (sex determining region Y)-‐box 1 // 13q34 // 6656 /// ENST0000SOX1 NM_005986 NM_005986 // RefSeq // Homo sapiens SRY (sex determining region Y)-‐box 1 (SOX1), mRNA. 0.0188501 0.0188501 1.53021 51.5549 0.376666 0.0146122 134618 16971272 main chr4 148402069 148466106 + NM_001957 // EDNRA // endothelin receptor type A // 4q31.22 // 1909 /// ENST00000324300EDNRA NM_001957 NM_001957 // RefSeq // Homo sapiens endothelin receptor type A (EDNRA), transcript vari0.013601 0.013601 1.52972 72.0275 0.376097 0.0104431 113431 16758998 main chr12 126910536 126918554 + -‐-‐-‐ -‐-‐-‐ ENST00000544419 // ENSEMBL // havana:lincRNA chromosome:GRCh37:12:126910536:126918554:10.0420212 0.0420212 1.52904 22.3082 0.375309 0.0336476 127565 16897938 main chr2 60614497 60614580 -‐ NR_039631 // MIR4432 // microRNA 4432 // -‐-‐-‐ // 100616473MIR4432 NR_039631 NR_039631 // RefSeq // Homo sapiens microRNA 4432 (MIR4432), microRNA. // chr2 // 100 /0.0211687 0.0211687 1.52744 45.745 0.373463 0.016328 122925 16852296 main chr18 47088427 47119278 + NM_006033 // LIPG // lipase, endothelial // 18q21.1 // 9388 /// ENST00000261292 // LIPGLIPG NM_006033 NM_006033 // RefSeq // Homo sapiens lipase, endothelial (LIPG), mRNA. // chr18 // 100 /0.00985735 0.00985735 1.52725 99.9496 0.373242 0.00746861 12365 16654925 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0373388 0.0373388 1.52697 25.2913 0.372918 0.0294898 133503 16960304 main chr3 148880197 148939842 -‐ NM_000096 // CP // ceruloplasmin (ferroxidase) // 3q23-‐q25 // 1356 /// ENST00000264613 CP NM_000096 NM_000096 // RefSeq // Homo sapiens ceruloplasmin (ferroxidase) (CP), transcript varian0.0163371 0.0163371 1.52213 59.7145 0.367348 0.0123035 122882 16851852 main chr18 31158541 31327399 + NM_030632 // ASXL3 // additional sex combs like 3 (Drosophila) // 18q11 // 80816 /// ENASXL3 NM_030632 NM_030632 // RefSeq // Homo sapiens additional sex combs like 3 (Drosophila) (ASXL3), m0.0247317 0.0247317 1.51966 38.9402 0.364517 0.0187219 17989 16702798 main chr10 17445507 17445619 + -‐-‐-‐ -‐-‐-‐ ENST00000515994 // ENSEMBL // ncrna:misc_RNA chromosome:GRCh37:10:17445507:17445619:1 g0.019363 0.019363 1.51582 50.1497 0.360115 0.0143616 115813 16781101 main chr13 112760409 112761196 -‐ -‐-‐-‐ -‐-‐-‐ TCONS_00021697-‐XLOC_010727 // Rinn lincRNA // linc-‐ANKRD10-‐2 chr13:-‐:112760408-‐112761190.0114624 0.0114624 1.51423 85.7449 0.3583 0.00835735 11547 16653229 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.00436074 0.00436074 1.51393 227.82 0.357962 0.0031425 128299 16904827 main chr2 169983619 170219195 -‐ NM_004525 // LRP2 // low density lipoprotein receptor-‐related protein 2 // 2q24-‐q31 // LRP2 NM_004525 NM_004525 // RefSeq // Homo sapiens low density lipoprotein receptor-‐related protein 2 0.0478976 0.0478976 1.50573 19.3901 0.348644 0.035961 14422 16665755 main chr1 66037232 66037335 + -‐-‐-‐ -‐-‐-‐ ENST00000459362 // ENSEMBL // ncrna:snoRNA chromosome:GRCh37:1:66037232:66037335:1 gene0.0436112 0.0436112 1.50169 21.441 0.344084 0.0320959 125914 16880667 main chr2 64567893 64567973 + NR_039632 // MIR4433 // microRNA 4433 // -‐-‐-‐ // 100616265MIR4433 NR_039632 NR_039632 // RefSeq // Homo sapiens microRNA 4433 (MIR4433), microRNA. // chr2 // 100 /0.022302 0.022302 1.50128 43.3446 0.343618 0.0158552 146069 17086048 main chr9 79034752 79122332 + NM_001490 // GCNT1 // glucosaminyl (N-‐acetyl) transferase 1, core 2 // 9q13 // 2650 ///GCNT1 NM_001490 NM_001490 // RefSeq // Homo sapiens glucosaminyl (N-‐acetyl) transferase 1, core 2 (GCNT0.0268871 0.0268871 -‐1.50121 35.6994 0.343547 0.0192467 134741 16972293 main chr4 169926400 169926495 + ENST00000364948 // RNY4P17 // RNA, Ro-‐associated Y4 pseudogene 17 // -‐-‐-‐ // -‐-‐-‐RNY4P17 ENST00000364948ENST00000364948 // ENSEMBL // ncrna:misc_RNA chromosome:GRCh37:4:169926400:169926495:1 0.0488254 0.0488254 -‐1.50933 18.9937 0.352728 0.0371416 130855 16930166 main chr22 39410088 39414931 + NM_014508 // APOBEC3C // apolipoprotein B mRNA editing enzyme, catalytic polypeptide-‐liAPOBEC3C NM_014508 NM_014508 // RefSeq // Homo sapiens apolipoprotein B mRNA editing enzyme, catalytic pol0.00154783 0.00154783 -‐1.51316 644.566 0.357086 0.00110799 1101 16650189 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0163064 0.0163064 -‐1.51437 59.8298 0.35846 0.0119826 18576 16708293 main chr10 102495360 102589698 + NM_003987 // PAX2 // paired box 2 // 10q24 // 5076 /// NM_003988 // PAX2 // paired box PAX2 NM_003987 NM_003987 // RefSeq // Homo sapiens paired box 2 (PAX2), transcript variant a, mRNA. //0.00506231 0.00506231 -‐1.51664 196.04 0.361056 0.0036835 11721 16653587 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0362295 0.0362295 -‐1.51823 26.111 0.362879 0.0277951 146493 17090512 main chr9 134083774 134086760 + -‐-‐-‐ -‐-‐-‐ AL110169 // GenBank // Homo sapiens mRNA; cDNA DKFZp586N2224 (from clone DKFZp586N2224)0.0451992 0.0451992 -‐1.52135 20.6358 0.366452 0.0355161 130548 16926998 main chr22 18927009 18935205 + -‐-‐-‐ -‐-‐-‐ AK075337 // GenBank // Homo sapiens cDNA PSEC0015 fis, clone NT2RM1001028. // chr22 // 0.0386622 0.0386622 -‐1.52302 24.3749 0.368372 0.0302255 13412 16657077 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0120973 0.0120973 -‐1.5244 81.1658 0.369954 0.009116 129956 16921652 main chr21 18091317 18091476 + -‐-‐-‐ -‐-‐-‐ ENST00000458992 // ENSEMBL // ncrna:snRNA chromosome:GRCh37:21:18091317:18091476:1 gene0.021322 0.021322 -‐1.52503 45.4054 0.370688 0.0163279 1


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36730 16991345 main chr5 153570290 153800544 + NM_198321 // GALNT10 // UDP-‐N-‐acetyl-‐alpha-‐D-‐galactosamine:polypeptide N-‐acetylgalactosGALNT10 NM_198321 NM_198321 // RefSeq // Homo sapiens UDP-‐N-‐acetyl-‐alpha-‐D-‐galactosamine:polypeptide N-‐ac0.032075 0.032075 -‐1.52723 29.6851 0.373216 0.0251451 13516 16657293 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.00778691 0.00778691 -‐1.53591 126.923 0.383273 0.00603948 111928 16742738 main chr11 78635501 78732838 -‐ ENST00000529798 // ODZ4 // odz, odd Oz/ten-‐m homolog 4 (Drosophila) // 11q14.1 // 26011ODZ4 ENST00000529798ENST00000529798 // ENSEMBL // cdna:putative chromosome:GRCh37:11:78635501:78732838:-‐1 g0.0366798 0.0366798 -‐1.53639 25.7723 0.383835 0.0297867 115993 16782066 main chr14 22982921 22982980 + ENST00000390508 // TRAJ29 // T cell receptor alpha joining 29 // -‐-‐-‐ // -‐-‐-‐TRAJ29 ENST00000390508ENST00000390508 // ENSEMBL // cdna:known chromosome:GRCh37:14:22982921:22982980:1 gene:0.0478973 0.0478973 -‐1.53998 19.3903 0.388024 0.0400225 13460 16657173 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0315069 0.0315069 -‐1.53999 30.2471 0.388026 0.0256571 138504 17007252 main chr6 32358287 32361468 + -‐-‐-‐ -‐-‐-‐ TCONS_00012469-‐XLOC_005254 // Rinn lincRNA // linc-‐C6orf10-‐AS chr6:+:32360319-‐32361247 0.0333224 0.0333224 -‐1.54415 28.5183 0.392893 0.0275538 133268 16957356 main chr3 112065553 112085485 -‐ XR_108464 // LOC100506591 // uncharacterized LOC100506591 // -‐-‐-‐ // 100506591 /// XR_10LOC100506591XR_108464 XR_108464 // RefSeq // PREDICTED: Homo sapiens hypothetical LOC100506591, transcript va0.00743587 0.00743587 -‐1.54761 132.985 0.396949 0.00596983 13027 16656283 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0401288 0.0401288 -‐1.55619 23.43 0.407062 0.0347471 111413 16737344 main chr11 35453370 35551848 -‐ ENST00000378880 // PAMR1 // peptidase domain containing associated with muscle regeneraPAMR1 ENST00000378880ENST00000378880 // ENSEMBL // cdna:known chromosome:GRCh37:11:35453370:35547579:-‐1 gene0.0155593 0.0155593 -‐1.56072 62.7742 0.412436 0.0131403 113884 16763968 main chr12 49061240 49061376 -‐ NR_002951 // SNORA2B // small nucleolar RNA, H/ACA box 2B // 12q13.11 // 677794SNORA2B NR_002951 NR_002951 // RefSeq // Homo sapiens small nucleolar RNA, H/ACA box 2B (SNORA2B), small 0.0443483 0.0443483 -‐1.56162 21.0601 0.413503 0.0392687 113676 16761615 main chr12 12442161 12442263 -‐ -‐-‐-‐ -‐-‐-‐ ENST00000384283 // ENSEMBL // ncrna:snRNA chromosome:GRCh37:12:12442161:12442263:-‐1 gen0.0325179 0.0325179 -‐1.56742 29.2605 0.420407 0.0287355 111195 16735366 main chr11 8245851 8290263 -‐ NR_073006 // LMO1 // LIM domain only 1 (rhombotin 1) // 11p15 // 4004 /// NM_002315 // LMO1 NR_073006 NR_073006 // RefSeq // Homo sapiens LIM domain only 1 (rhombotin 1) (LMO1), transcript 0.0405041 0.0405041 -‐1.57425 23.1992 0.428588 0.0369485 148258 17106673 main chrX 120181462 120183796 + NM_012084 // GLUD2 // glutamate dehydrogenase 2 // Xq24-‐q25 // 2747 /// ENST00000328078GLUD2 NM_012084 NM_012084 // RefSeq // Homo sapiens glutamate dehydrogenase 2 (GLUD2), nuclear gene enc0.0148684 0.0148684 -‐1.57505 65.7606 0.429541 0.0130638 12988 16656205 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0175772 0.0175772 -‐1.57866 55.3962 0.433886 0.0156648 120991 16832717 main chr17 28210024 28210127 + -‐-‐-‐ -‐-‐-‐ ENST00000459235 // ENSEMBL // ncrna:snoRNA chromosome:GRCh37:17:28210024:28210127:1 gen0.0244429 0.0244429 -‐1.58096 39.4178 0.436654 0.0221551 1835 16651719 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0145367 0.0145367 -‐1.58114 67.2952 0.436872 0.0129837 14258 16664332 main chr1 46921495 46948147 + -‐-‐-‐ -‐-‐-‐ TCONS_00000191-‐XLOC_000170 // Rinn lincRNA // linc-‐DMBX1 chr1:+:46921494-‐46948147 // ch0.0136086 0.0136086 -‐1.58673 71.9866 0.443634 0.0123255 13897 16660620 main chr1 23046010 23046091 + NR_039832 // MIR4684 // microRNA 4684 // -‐-‐-‐ // 100616391MIR4684 NR_039832 NR_039832 // RefSeq // Homo sapiens microRNA 4684 (MIR4684), microRNA. // chr1 // 100 /0.00584448 0.00584448 -‐1.59048 169.603 0.448182 0.00528507 136493 16988915 main chr5 129450102 129450203 + ENST00000362585 // RN5S191 // RNA, 5S ribosomal 191 // -‐-‐-‐ // -‐-‐-‐RN5S191 ENST00000362585ENST00000362585 // ENSEMBL // ncrna:rRNA chromosome:GRCh37:5:129450102:129450203:1 gene0.035452 0.035452 -‐1.59239 26.7162 0.4505 0.0337249 17252 16695934 main chr1 166123980 166124035 -‐ NR_030626 // MIR921 // microRNA 921 // 1q24.1 // 100126349MIR921 NR_030626 NR_030626 // RefSeq // Homo sapiens microRNA 921 (MIR921), microRNA. // chr1 // 100 // 0.0477637 0.0477637 -‐1.59865 19.4486 0.458128 0.0471115 19453 16716956 main chr10 98124363 98273683 -‐ NM_012465 // TLL2 // tolloid-‐like 2 // 10q23-‐q24 // 7093 /// ENST00000357947 // TLL2 //TLL2 NM_012465 NM_012465 // RefSeq // Homo sapiens tolloid-‐like 2 (TLL2), mRNA. // chr10 // 100 // 88 9.19E-‐05 9.19E-‐05 -‐1.62017 10880.9 0.484615 8.91E-‐05 1

51 16650087 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.00397617 0.00397617 -‐1.62236 249.999 0.487332 0.00389867 138432 17006312 normgene-‐>exon-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // pos_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0452477 0.0452477 -‐1.62327 20.6121 0.488463 0.0473957 117108 16793329 main chr14 57267425 57277197 -‐ NM_021728 // OTX2 // orthodenticle homeobox 2 // 14q22.3 // 5015 /// ENST00000339475 //OTX2 NM_021728 NM_021728 // RefSeq // Homo sapiens orthodenticle homeobox 2 (OTX2), transcript variant0.0227334 0.0227334 -‐1.63007 42.4939 0.496937 0.0233886 126993 16891816 main chr2 230470954 230471015 + ENST00000459349 // RNU7-‐9P // RNA, U7 small nuclear 9 pseudogene // -‐-‐-‐ // -‐-‐-‐RNU7-‐9P ENST00000459349ENST00000459349 // ENSEMBL // ncrna:snRNA chromosome:GRCh37:2:230470954:230471015:1 gen0.0174155 0.0174155 -‐1.64247 55.9246 0.512465 0.018327 18981 16712277 main chr10 17360382 17496386 -‐ ENST00000377602 // ST8SIA6 // ST8 alpha-‐N-‐acetyl-‐neuraminide alpha-‐2,8-‐sialyltransferasST8SIA6 ENST00000377602ENST00000377602 // ENSEMBL // cdna:known chromosome:GRCh37:10:17361873:17496329:-‐1 gene0.0430752 0.0430752 -‐1.64802 21.7262 0.519458 0.0478185 131990 16942983 main chr3 90233784 90233883 + -‐-‐-‐ -‐-‐-‐ ENST00000410558 // ENSEMBL // ncrna:snRNA chromosome:GRCh37:3:90233784:90233883:1 gene:0.0373139 0.0373139 -‐1.65204 25.3092 0.524536 0.0414503 145118 17076965 main chr8 49220487 49220590 -‐ -‐-‐-‐ -‐-‐-‐ ENST00000516901 // ENSEMBL // ncrna:snRNA chromosome:GRCh37:8:49220487:49220590:-‐1 gene0.0441158 0.0441158 -‐1.6535 21.1789 0.526378 0.0497079 13212 16656663 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0125171 0.0125171 -‐1.65523 78.394 0.528572 0.013485 118778 16810061 main chr15 60365867 60410519 -‐ -‐-‐-‐ -‐-‐-‐ ENST00000560503 // ENSEMBL // havana:lincRNA chromosome:GRCh37:15:60365867:60410519:-‐1 0.0155203 0.0155203 -‐1.66505 62.9358 0.541054 0.0171939 111206 16735557 main chr11 9041047 9159661 -‐ NM_020974 // SCUBE2 // signal peptide, CUB domain, EGF-‐like 2 // 11p15.3 // 57758 /// ESCUBE2 NM_020974 NM_020974 // RefSeq // Homo sapiens signal peptide, CUB domain, EGF-‐like 2 (SCUBE2), tr0.00827932 0.00827932 -‐1.6688 119.285 0.545839 0.00915185 114650 16771480 normgene-‐>exon-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // pos_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0453194 0.0453194 -‐1.68601 20.5772 0.567937 0.0552006 13015 16656259 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0288043 0.0288043 -‐1.68691 33.2243 0.569094 0.0342577 11418 16652965 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0127706 0.0127706 -‐1.69573 76.8079 0.580495 0.0151155 15397 16676405 main chr1 205012325 205047627 + NM_005076 // CNTN2 // contactin 2 (axonal) // 1q32.1 // 6900 /// ENST00000331830 // CNTCNTN2 NM_005076 NM_005076 // RefSeq // Homo sapiens contactin 2 (axonal) (CNTN2), mRNA. // chr1 // 100 0.0388017 0.0388017 -‐1.69847 24.282 0.584054 0.048106 15146 16673507 main chr1 168545711 168551315 + NM_002995 // XCL1 // chemokine (C motif) ligand 1 // 1q23 // 6375 /// ENST00000367818 /XCL1 NM_002995 NM_002995 // RefSeq // Homo sapiens chemokine (C motif) ligand 1 (XCL1), mRNA. // chr1 0.0156616 0.0156616 -‐1.69869 62.3543 0.584339 0.0187425 114528 16770606 main chr12 113899838 113910085 -‐ ENST00000261731 // LHX5 // LIM homeobox 5 // 12q24 // 64211 /// NM_022363 // LHX5 // LILHX5 ENST00000261731ENST00000261731 // ENSEMBL // cdna:known chromosome:GRCh37:12:113899838:113909877:-‐1 ge0.0242071 0.0242071 -‐1.70894 39.8164 0.597683 0.030022 11401 16652925 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0443804 0.0443804 -‐1.72495 21.0438 0.618663 0.0587976 13136 16656503 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.042484 0.042484 -‐1.72723 22.0491 0.621665 0.0563891 110943 16733038 main chr11 125147448 125147553 + -‐-‐-‐ -‐-‐-‐ ENST00000410912 // ENSEMBL // ncrna:snRNA chromosome:GRCh37:11:125147448:125147553:1 ge0.0365184 0.0365184 -‐1.76217 25.8928 0.668072 0.051603 134671 16971526 main chr4 153857504 153900848 + ENST00000511601 // FHDC1 // FH2 domain containing 1 // 4q31.3 // 85462 /// NM_033393 //FHDC1 ENST00000511601ENST00000511601 // ENSEMBL // cdna:known chromosome:GRCh37:4:153857504:153900838:1 gene0.0321552 0.0321552 -‐1.77581 29.6074 0.68638 0.0463655 141933 17044956 main chr7 31726329 31748069 + ENST00000342032 // PPP1R17 // protein phosphatase 1, regulatory subunit 17 // 7p15 // 1PPP1R17 ENST00000342032ENST00000342032 // ENSEMBL // cdna:known chromosome:GRCh37:7:31726329:31748069:1 gene:E0.00877581 0.00877581 -‐1.7822 112.452 0.694992 0.0123607 135149 16976029 main chr4 55944426 55991762 -‐ NM_002253 // KDR // kinase insert domain receptor (a type III receptor tyrosine kinase)KDR NM_002253 NM_002253 // RefSeq // Homo sapiens kinase insert domain receptor (a type III receptor 0.016188 0.016188 -‐1.78787 60.2781 0.702651 0.0233136 114647 16771477 normgene-‐>exon-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // pos_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0140157 0.0140157 -‐1.81947 69.8519 0.74567 0.02135 19810 16721053 main chr11 3802625 3802686 + ENST00000459175 // RNU7-‐50P // RNA, U7 small nuclear 50 pseudogene // -‐-‐-‐ // -‐-‐-‐RNU7-‐50P ENST00000459175ENST00000459175 // ENSEMBL // ncrna:snRNA chromosome:GRCh37:11:3802625:3802686:1 gene:E0.0142837 0.0142837 -‐1.82206 68.5137 0.74921 0.0218704 148209 17106297 main chrX 111326253 111700473 + NM_001004308 // ZCCHC16 // zinc finger, CCHC domain containing 16 // Xq23 // 340595 ///ZCCHC16 NM_001004308NM_001004308 // RefSeq // Homo sapiens zinc finger, CCHC domain containing 16 (ZCCHC16)0.00198391 0.00198391 -‐1.83101 502.555 0.7615 0.00303052 114427 16769730 normgene-‐>exon-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // pos_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0070319 0.0070319 -‐1.83441 140.711 0.766184 0.0108902 113280 16757505 main chr12 113909808 113918286 + ENST00000551357 // LOC100506452 // uncharacterized LOC100506452 // -‐-‐-‐ // 100506452LOC100506452ENST00000551357ENST00000551357 // ENSEMBL // cdna:known chromosome:GRCh37:12:113909808:113918286:1 gen0.00379903 0.00379903 -‐1.84073 261.726 0.774888 0.00592137 14259 16664335 main chr1 46972668 46979898 + NM_172225 // DMBX1 // diencephalon/mesencephalon homeobox 1 // 1p33 // 127343 /// NM_14DMBX1 NM_172225 NM_172225 // RefSeq // Homo sapiens diencephalon/mesencephalon homeobox 1 (DMBX1), tran0.0206376 0.0206376 -‐1.84796 46.9606 0.78488 0.0334272 111205 16735545 main chr11 9002123 9025596 -‐ NM_020645 // NRIP3 // nuclear receptor interacting protein 3 // 11p15.3 // 56675 /// ENNRIP3 NM_020645 NM_020645 // RefSeq // Homo sapiens nuclear receptor interacting protein 3 (NRIP3), mRN0.00869211 0.00869211 -‐1.90646 113.549 0.866573 0.0152634 18223 16705011 main chr10 54074041 54077802 + NM_012242 // DKK1 // dickkopf 1 homolog (Xenopus laevis) // 10q11.2 // 22943 /// ENST00DKK1 NM_012242 NM_012242 // RefSeq // Homo sapiens dickkopf 1 homolog (Xenopus laevis) (DKK1), mRNA. /0.0136031 0.0136031 -‐1.97876 72.0163 0.969425 0.0269224 1443 16650901 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0410861 0.0410861 -‐2.02983 22.8496 1.04317 0.0913076 1

38236 17005072 main chr6 15315151 15315257 + -‐-‐-‐ -‐-‐-‐ ENST00000364497 // ENSEMBL // ncrna:snRNA chromosome:GRCh37:6:15315151:15315257:1 gene:0.0422319 0.0422319 -‐2.03263 22.1896 1.04724 0.0943905 113689 16761707 main chr12 13714144 14133053 -‐ NM_000834 // GRIN2B // glutamate receptor, ionotropic, N-‐methyl D-‐aspartate 2B // 12p12GRIN2B NM_000834 NM_000834 // RefSeq // Homo sapiens glutamate receptor, ionotropic, N-‐methyl D-‐aspartat0.0279436 0.0279436 -‐2.0371 34.2934 1.05374 0.0614542 11050 16652177 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0393977 0.0393977 -‐2.08958 23.8922 1.13042 0.0946262 11124 16652339 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.011022 0.011022 -‐2.45768 89.2302 1.68297 0.0377221 12318 16654827 normgene-‐>intron-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // neg_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0295375 0.0295375 -‐2.88049 32.3627 2.32964 0.143971 139926 17020729 main chr6 72248587 72248679 -‐ -‐-‐-‐ -‐-‐-‐ ENST00000390810 // ENSEMBL // ncrna:miRNA chromosome:GRCh37:6:72248587:72248679:-‐1 gene0.0189218 0.0189218 -‐3.05616 51.3539 2.59764 0.101166 139585 17017174 normgene-‐>exon-‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ -‐-‐-‐ // -‐-‐-‐ // pos_control // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐ // -‐-‐-‐0.0142376 0.0142376 -‐4.26267 68.7401 4.37545 0.127304 1


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Gene Symbol p-value Fold Change (OTX2 KD trans-hEN vs. trans-hEN) LIN28A 0.00136836 -1.0455 ZIC3 0.257253 1.05817 OCT4 0.381855 -1.33657 SOX2 0.689611 -1.01432 LIN28B 0.0372652 1.11452 ALPL 0.27077 -1.05844 NANOG 0.483128 -1.25043

*** Transcripts differentially expressed at least 1.5-fold (up- or down-regulated) in Otx2

KD trans-hEN vs. trans-hEN AND with a p<0.05 were considered significant.

Supplementary Table 5: Expression of hESC and differentiation/development transcripts following knockdown of OTX2 in trans-hENs. hESC genes were not differentially expressed (A); however, a

series of transcripts associated with differentiation and development were

differentially expressed at least 1.5-fold (up- or down-regulated) in OTX2 KD

trans-hEN vs. trans-hEN AND with a p<0.05 (B).

Supplementary Table 5A: Expression levels of hESC transcripts are not significantly different following knockdown of OTX2 in trans-hENs


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Supplementary Table 5B: Development and differentiation transcripts significantly and differentially expressed in OTX2 KD trans-hEN vs. trans-hEN

Diseases or Functions Annotation p-Value Molecules development of melanocytes 2.58E-04 ECE1,KITLG development of connective tissue cells 3.65E-04 DKK1,FOS,HOXA2,JUN,KITLG

differentiation of connective tissue cells 9.64E-04 ADAMTS7,BAG6,CTGF,DKK1,EGR2,FOS, JUN,KITLG,NPPC,NR3C1

myelination of neurons 1.39E-03 EGR2,NTRK2 lymphopoiesis of B lymphocytes 1.96E-03 FOS,KITLG

differentiation of cells 2.24E-03

ADAMTS7,BAG6,CD6,CNTN2,CTGF, DKK1,EGR2,FOS,HOXA2,HSP90B1,IFRD1, JUN,KITLG,LMO1,NPPC,NR3C1,NTRK2, OLIG3,OTX2,PAX2,SPARCL1,TENM4

proliferation of liver cells 2.75E-03 CTGF,FOS,JUN,KITLG,NPPC axonogenesis 3.01E-03 CNTN2,FOS,NTRK2,PAX2,TENM4 proliferation of chondrocytes 4.95E-03 CTGF,FOS,NPPC arborization of pyramidal neurons 5.14E-03 NTRK2 colony formation of leukemic blasts 5.14E-03 EIF4EBP1 commitment of photoreceptors 5.14E-03 OTX2 development of enteric neurons 5.14E-03 ECE1 development of serotonergic neurons 5.14E-03 OTX2 development of trigeminal motor neurons 5.14E-03 EGR2 differentiation of cell membrane leading edge 5.14E-03 JUN differentiation of salivary mucous cells 5.14E-03 DKK1 neurogenesis of dopaminergic neurons 5.14E-03 OTX2 proliferation of peritoneal mast cells 5.14E-03 KITLG sprouting of mechanosensory neurons 5.14E-03 NTRK2 transdifferentiation of sebaceous gland tumor 5.14E-03 FOS transdifferentiation of squamous cell tumor 5.14E-03 FOS differentiation of stem cells 5.28E-03 ADAMTS7,DKK1,HSP90B1,JUN,KITLG commitment of cells 5.56E-03 HOXA2,IFRD1,OTX2,PAX2

differentiation of tumor cell lines 5.93E-03 CTGF,FOS,JUN,KITLG,NTRK2,OTX2,SPARCL1

differentiation of neuroglia 7.79E-03 EGR2,NTRK2,PAX2,TENM4 fate determination of cells 7.83E-03 HOXA2,PAX2 branching of neurons 9.05E-03 JUN,NTRK2 arrest in growth of hepatoma cell lines 1.03E-02 NR3C1 commitment of myoblasts 1.03E-02 IFRD1 conversion of mesenchymal cells 1.03E-02 FOS development of burst-forming erythroid cells 1.03E-02 KITLG development of chromaffin cells 1.03E-02 NR3C1 development of colony forming multilineage cells 1.03E-02 KITLG development of granulocyte-macrophage progenitor cells 1.03E-02 KITLG differentiation of blood-derived mast cells 1.03E-02 KITLG differentiation of melanoblasts 1.03E-02 KITLG proliferation of cd56+ natural killer cells 1.03E-02 KITLG proliferation of type A spermatogonia 1.03E-02 KITLG sprouting of basal dendrites 1.03E-02 NTRK2 transdifferentiation of retinal pigment epithelium 1.03E-02 PAX2


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Gene Forward Sequence (for ChIP-qPCR) Reverse Sequence (for ChIP-qPCR) LIN28A 5’-TGT GTG TGT GTG TGT GTG T -3’ 5’-GGA ATT TGA GAT CCT GCA CTT TG -3’

NANOG 5’-GGA CAT AGT AGG TGC TCA GTA AAT -3’ 5’-CCG GGC TAA GAA AGA AGA GAG -3’

OCT4 5’-AGC CCC ACT AAA CAA AGC AC-3’ 5’-GCA ATC CCC TCA AAG ACT GA-3’

SOX2 5’-GGA CTG AGA GAA AGA AGA GGA GAG-3’ 5’-CGC CGC CGA TGA TTG TTA TTA-3’

Gene Forward Sequence Reverse Sequence LIN28A 5’-GAG CCA AGC CAC TAC ATT CTG-3’ 5’-ATC CCA AAA GTG GGT ATG AGG-3’

NANOG 5’-CGA AGA ATA GCA ATG GTG TGA CG-3’

5’-TTC CAA GGC AGC CTC CAA GTC-3’

OCT4 5’-CTG AAG CAG AAG AGG ATC AC-3’ 5’-GAC CAC ATC CTT CTC GAG CC-3’

OTX2 5’-GAG GTG GCA CTG AAA ATC AAC-3’ 5’-TCT TCT TTT TGG CAG GTC TCA-3’

SOX2 5’-CAG CTC GCA GAC CTA CAT GA-3’ 5’-GGG AGG AAG AGG TAA CCA CAG-3’

MMP1 5’-CCT AGT CTA TTC ATA GCT AAT CAA GAG GAT GT-3’

5’-AGT GGA GGA AAG CTG TGC ATA C-3’

TIMP4 5’-GCT AGT GGA TCC CTG CAG CTG CGC CCC GGC G-3’

5’-CGG CTT CTA GAA GGG CTG AAC GAT GTC AAC-3’

CNTN1 5’-GAT GGT CAG AAG CAC TGA AGC-3’ 5’-TCA CAG AGA AGC ACC ATT CCT-3’

UNC5C 5’-GCA AAT TGC TGG CTA AAT ATC AGG AA-3’

5’-GCT CCA CTG TGT TCA GGC TAA ATC TT-3’

FOS 5’-CTG GCG TTG TGA AGA CCA TGA-3’ 5’-CCC TTC GGA TTC TCC TTT TCT C-3’

FOSB 5’-ACC CCA CGG ACT ACT CTC CTA-3’ 5’-CTG AGG CAA AAT GGG TTG TTA-3’

IGF1 5’-TGG AGA GGG TCT TAT CGT CCT-3’ 5’-GGG ATG GGA GAG CAA TTT TAG-3’

Supplementary Table 6: Primer sequences utilized for ChIP-qPCR and qPCR reactions


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supplementary figures and tables · 10/1/2015 · supplementary figures and tables ... otx2

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