[methods in molecular biology™] leukemia volume 538 || genome-wide determination of dna...

Chapter 20

Genome-Wide Determination of DNA Methylation by Hpa II Tiny Fragment Enrichment by Ligation-Mediated PCR (HELP) for the Study of Acute Leukemias

Maria E. Figueroa , Ari Melnick , and John M. Greally

Summary

Aberrant distribution of cytosine methylation in cancer has been linked to deregulation of gene expres-sion and genomic instability. DNA methylation changes in cancer include both hyper and hypomethyla-tion, and the precise localization of these changes is directly related to the impact they have on gene regulation. To determine both the localization and extent of DNA methylation status under different conditions, we have developed the Hpa II tiny fragment enrichment by ligation-mediated PCR (HELP) assay, a microarray-based technique that allows the simultaneous interrogation of the methylation status of hundreds of thousands of CpG dinucleotides. The HELP assay allows methylation levels throughout the genome to be accurately determined so that the epigenetic state of leukemia cells can be identified, compared, and contrasted.

Key words: Cytosine methylation, CpG dinucleotide , Microarray , Epigenetic , Epigenome , Acute leukemia

Epigenetic deregulation is now recognized as a hallmark of cancer (1) . Abnormal cytosine methylation in cancer has been linked to aberrant gene expression as well as genomic instability (2) . Specific changes in DNA cytosine methylation of gene pro-moters that alter their regulatory status have been described for a number of genes involved in differentiation and cell cycle regula-tion, such as p15 CDKN2B (3, 4) , homeobox protein A5 ( HOXA5 ) (5) , CCAAT/enhancer binding protein delta (C/EBP delta) (6) , and the tumor suppressor deleted in bladder cancer 1 ( DBC1 ) (7) .

1. Introduction

C.W.E. So (ed.), Leukemia, Methods in Molecular Biology, vol. 538© Humana Press, a part of Springer Science + Business Media, LLC 2009DOI: 10.1007/978-1-59745-418-6_20

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396 Figueroa, Melnick, and Greally

Furthermore, the methylation status of p15 CDKN2B and the estro-gen receptor α ( ER α ) has recently been shown to predict relapse risk in patients with acute myeloid leukemia (AML) (8) . The development of methods to study epigenetic marks on a genome-wide basis is therefore crucial for furthering our understanding of epigenetic mechanisms in leukemogenesis. The HELP ( Hpa II tiny fragment enrichment by ligation-mediated PCR) assay is a microarray-based technique, which allows the determination of DNA methylation status at hundreds of thousands of Hpa II sites simultaneously across the genome (9) .

The assay is based on the differential digestion of genomic DNA by the two isoschizomers Hpa II and Msp I. These enzymes both recognize the same restriction site (5 ¢ -CCGG-3 ¢ ). The second cyto-sine is part of a CpG dinucleotide, a target for cytosine methylation in vertebrate genomes. Although Msp I will always cut between the first and second cytosines, whether the CpG is methylated or not, Hpa II will only cut when both cytosines are unmethylated. Because

Fig. 1. Schematic representation of the HELP assay. Genomic DNA is digested by either Msp I or its methylation-sensitive isoschizomer Hpa II. Specific adapters are ligated onto the fragments generated by both digestions, and then amplified by ligation-mediated PCR. Each fraction is then labeled with a specific dye and co-hybridized onto a microarray designed to cover Hpa II amplifiable fragments across the genome. The proportional intensity of each signal will reflect the methyla-tion status of the Hpa II sites interrogated by each fragment. ( a ) When both flanking sites are unmethylated a signal will be obtained with both enzymes. ( b and c ) When either one or both flanking sites are methylated, then a signal will be detected only on the Msp I channel. ( d ) partial methylation will be reflected by an increase in the Hpa II signal proportional to the amount of hypomethylation present in the samples. ( e ) Fragments greater than 2,000 bp will not be successfully amplified during the PCR and will therefore give no signal on either channel of the microarray .

Genome-Wide Determination of DNA Methylation by Hpa II Tiny Fragment Enrichment 397

of the presence of methylated CpG dinucleotides in the genome, Hpa II will therefore generate fewer and longer fragments than Msp I. DNA adapters of known sequence are then ligated to the sticky ends of the DNA generated by the enzymes, and a primer complimentary to these linkers is subsequently used in a PCR reac-tion for the amplification of the Hpa II and Msp I representations, in a ligation-mediated PCR reaction. PCR conditions have been optimized to amplify fragments between 200 and 2,000 bp, thus ensuring the preferential amplification of CpG dinucleotide-dense regions that may be contained within CpG islands and other regu-latory sequences. Any given fragment will be present in both the Msp I and Hpa II fractions only when both of its flanking Hpa II sites are unmethylated. If, however, one or both of the flanking Hpa II restriction sites are methylated, then Hpa II will not be able to cut at that site and the fragment will therefore only appear in the Msp I representation of the genome. By determining the relative abundance of any given fragment in both representations we can estimate the proportional cytosine methylation at that region of the genome ( Fig. 1 ).

1. 1× PBS: 137 mM NaCl, 2.7 mM KCl, 4.3 mM Na 2 HPO 4 ·7H 2 O, 1.4 mM KH s PO 4 . 2. 1 M Tris–HCl, pH 8.0: Dissolve 121.14 g Tris-base into about

800 ml of de-ionized ultra-filtered (DIUF) water and adjust pH to 8.0 with HCl. Fill up the solution to 1 L and autoclave.

3. 1 M EDTA: Dissolve 186.12 g EDTA into DIUF water; make up to 1 L and autoclave.

4. 20% SDS: Dissolve 20 g of SDS in autoclaved DIUF water. Bring the solution to a final volume of 100 ml.

5. RNAse A (Sigma, St Louis, MO): Resuspend in water to a final concentration of 10 mg/ml. Aliquot and store at −20°C.

6. Extraction buffer: 10 mM Tris–HCl, pH 8.0, 0.1 M EDTA, pH 8.0, 0.5% SDS, 20 μ g/ml RNAse A. Make up fresh each time.

7. Phenol–Chloroform–Isoamyl alcohol (PCI): 25 volumes of phenol: 24 volumes of chloroform: 1 volume of isoamyl alco-hol. Make up fresh each time.

8. 3 M Sodium acetate, pH 5.2: Dissolve 123.04 g of sodium acetate in distilled water and fill it up to 500 ml. Use glacial acetic acid to adjust pH to 5.2.

2. Materials

2.1. Genomic DNA Extraction


9. 100% Ethanol. 10. 70% Ethanol. 11. Glass Pasteur pipette.

1. Hpa II (New England Biolabs, Ipswich, MA). 2. Msp I (New England Biolabs). 3. Phenol–chloroform mix: 1 volume of TE-saturated phenol:1

volume of chloroform. Make up fresh each time. 4. Primer JHpaII12 (HPLC purified): 5 ¢ -CGGCTGTTCATG-3 ¢

– Resuspended to a concentration of 6 OD/ml 5. Primer JHpaII24 (HPLC purified): 5¢-CGACGTCGAC-

TATCCATGAACAGC-3 ¢ – Resuspended to a concentration of 12 OD/ml

6. Pre-annealing of linkers: Mix equal volumes of the 12-mer and 24-mer linkers (6 OD/ml and 12 OD/ml, respectively) in a screw-top Eppendorf tube. Boil for 5 min and then allow the reaction to cool down to room temperature. The annealed linkers can then be stored at −20°C.

7. 1 M Tris–HCl, pH 8.9: Dissolve 121.14 g Tris-base into about 800 ml of DIUF water and adjust pH to 8.9 with HCl. Fill up the solution to 1 L and autoclave.

8. 1 M Ammonium sulfate: Dissolve 13.21 g of ammonium sulfate in distilled water, make up to 100 ml and autoclave.

9. TE buffer pH 8.0: 10 mM Tris–HCl pH 8.0, 1 mM EDTA pH 8.0

10. 5× RDA buffer: 335 mM Tris–HCl pH 8.9, 20 mM MgCl 2 , 80 mM (NH 4 ) 2 SO 4 , 50 mM of β -mercaptoethanol and 0.5 mg/ml of BSA in a final volume of 50 ml with autoclaved DIUF water. Filter-sterilize and aliquot into 1.5-ml tubes and store at 4°C. The buffer is stable for 2 months at 4°C.

11. 4 mM dNTP mix: Dilute from 10 mM stock. Make 200 ml aliquots and store at −20°C.

12. Native Taq polymerase (Invitrogen, Carlsbad, CA).

Identification of hypomethylated regions by the HELP assay depends on the differential digestion and amplification of genomic DNA based on its 5-methylcytosine content. For this difference to become evident, the assay relies on the selective digestion of the DNA at the 5 ¢ -CCGG-3 ¢ restriction site recognized by Hpa II and

2.2. Amplification of HpaII Tiny Fragments from Genomic DNA

3. Methods


Msp I. For this purpose, intact high molecular weight genomic DNA must be used and the restriction digestion reaction must be carried out in such a fashion that digestion to completion is ensured. The protocol as described here has been optimized for such purposes and it is highly recommended that the reader adhere to it in order to ensure the effectiveness and reproducibility of the assay.

High molecular weight genomic DNA is required for the HELP assay. As the assay is based on selective cutting of the DNA at specific cytosines, genomic DNA used in this assay must appear intact, without any signs of shearing. Although any method for genomic DNA extraction that produces DNA of this quality can be used, we recommend using a standard phenol–chloroform extraction followed by ethanol precipitation and spooling of the DNA with a glass rod as follows ( see Note 1 ): 1. Pellet down 2–3 million cells ( see Note 2 ) at room tempera-

ture for 5 min at 300 × g . Remove supernatant, resuspend the cell pellet in 1 ml of 1× PBS and wash once by spinning 5 min at 300 × g . Discard the supernatant.

2. Resuspend the cell pellet in 50 μ l of 1× PBS. Pipet up and down until no cell clumps are visible. Add 500 μ l of extraction buffer and incubate at 37°C for 1 h in a water bath.

3. Add 2.75 μ l of proteinase K (20 μ g/ μ l) to a final concentration of 100 μ g/ml and incubate overnight at 50°C in a water bath.

4. Add 1 volume (550 μ l) of TE-saturated phenol and mix well by inversion (10 min on the rocker is best); centrifuge for 5 min at room temperature at top speed in micro centrifuge (16,000 × g ). Do not mix by vortexing, as this may shear the DNA.

5. Transfer the supernatant into a new tube, leaving behind any impurities and being careful not to disturb the interface. Add an equal volume of PCI (25:24:1) and mix well by rocking for 10 min at room temperature; then centrifuge for 5 min at room temperature at 16,000 × g .

6. Transfer the supernatant into a new tube, measure the volume. If the supernatant is not totally clear, then repeat step 5 until the supernatant becomes completely clear.

7. Add 1 μ l of glycogen (20 mg/ μ l stock), 1/10 volume of 3 M sodium acetate (pH 5.2), and 2.5 volumes 100% ethanol. Mix gently by inversion. A visible DNA fiber will form. Remove it with the tip of a pipette or with a glass hook (made from heating and twisting the tip of a glass Pasteur pipette). Rinse thoroughly by submerging in 70% ethanol and then transfer into a 2-ml Eppendorf tube ( see Note 3 ) containing 200 μ l of 10 mM Tris–HCl pH 8.0 ( see Note 4 ). • If a DNA fiber does not become clearly visible after adding

the 100% ethanol, then proceed to step 8 .

3.1. Genomic DNA Extraction


8. Spin at 4°C for 1 h at 16,000 × g and then carefully remove the supernatant without disturbing the DNA pellet. Add 700 μ l of 70% ethanol and spin for 30 min at 4°C at 16,000 × g . Carefully remove the supernatant without loosening the pel-let. Do not air dry the pellet as this may significantly reduce its solubility. Dissolve the pellet in 200 μ l of 10 mM Tris–HCl pH 8.0. Place on the rocker at room temperature and allow it to dissolve completely over 24 h.

9. On the following day, quantify the DNA using a spectropho-tometer and run 1 μ l on a 1% agarose gel ( Fig. 2a ). If the DNA is still very sticky, then increase the volume of 10 mM Tris–HCl pH 8.0 and leave another 24 h on the rocker to dissolve.)

10. Do not proceed with digestion or amplification if the DNA does not appears to be intact.

1. Set up a restriction digestion of 1 μ g genomic DNA with 2 μ l of either Hpa II or Msp I in separate 200 μ l reactions, using NEB buffer #1 for Hpa II and buffer #2 for Msp I as recommended by the manufacturer. Incubate overnight at 37°C ( see Note 5 ).

3.2. Amplification of HpaII Tiny Fragments by Ligation-Mediated PCR

Fig. 2. Genomic DNA electrophoresis. ( a ) High molecular weight genomic DNA from an Acute Myeloid Leukemia (AML) sample. ( b ) Uncut AML high molecular weight genomic DNA ( left lane ) and after digestion with Hpa II ( center lane ) and Msp I ( right lane ). ( c ) HELP PCR amplification products. A smear spanning from 2,000 to 200 bp can be clearly seen when 10 μ L of PCR products are run on a 1.5% agarose gel .


2. Run 15 μ l of the digested DNA on a 1% agarose gel. The two digests should appear different: for the Hpa II digest, most of the DNA will remain high molecular weight, whereas with Msp I there should appear an almost even smear with no rem-nant of high molecular weight DNA ( see Note 6 ) ( Fig 2b ).

3. Add 200 μ l of TE buffer pH 8.0 to the digested DNA and 400 μ l of saturated phenol:chloroform mix (1:1) and vortex briefly. Centrifuge at 16,000 × g for 10 min at room temperature.

4. Remove top (aqueous) phase (about 400 μ l) from last step and transfer into a clean tube. Add 1 μ l of glycogen (20 μ g/ μ l) and 40 μ l of 3 M NaOAc pH 5.2 and mix well. Then add 1,000 μ l of 100% ethanol, vortex and spin at 16,000 × g for 45 min at 4°C.

5. Remove the supernatant and wash the pellet with 70% ethanol. Once you have carefully removed all of the ethanol, resuspend the pellet in 15.5 μ l of 10 mM Tris–HCl pH 8.0. Set up the linker ligation on the same day, as the digested DNA will have sticky, single-stranded overhangs that may re-anneal or degrade.

6. Set up ligation reaction in a PCR tube as follows:

Msp I Hpa II

Diluted ligated DNA from last step ( μ l) 40 80

JHpaII 24 (12 OD/ml) ( μ l) 8 8

5× RDA buffer ( μ l) 80 80

4 mM dNTP mix ( μ l) 32 32

Native Taq (Invitrogen) ( μ l) 3 3

Water ( μ l) 237 197

Total ( μ l) 400 400

5× T4 DNA ligase buffer 6 μ l

DNA from last step 15.5 μ l

Pre-annealed JHpaII linkers 7.5 μ l

T4 DNA ligase 1 μ l

Incubate overnight at 16°C in a PCR thermocycler with a heated lid ( see Note 7 ). 7. On the following day, remove the reactions from the ther-

mocycler and transfer to a clean Eppendorf tube. Dilute each reaction with 970 μ l of 10 mM Tris–HCl pH 8.0. The linker-ligated DNA can be stored indefinitely at −20°C.

Set up the PCR reaction as follows in a 1.5-ml tube:


Divide the reaction mix in four PCR tubes and incubate in a thermocycler as follows: 1. 72°C for 10 min 2. 20 cycles of: 30 s at 95°C 3 min at 72°C 3. 10 min at 72°C 4. Hold at 4°C.

8. Run 10 μ l of PCR product on a 1.5% agarose gel. A smear of DNA from 200–2,000 bp should be clearly visible ( Fig 2c ).

9. Clean the product using a QIAquick PCR purification kit from Qiagen (Qiagen, Valencia, CA) ( see Note 8 ), eluting in 50 μ l of elution buffer. Quantify the PCR products using a spectro-photometer and run 1 μ l on a 1.5% gel to verify that the frag-ment size range was not altered during the clean-up process.

To determine the proportion of Hpa II (unmethylated) to Msp I (methylated + unmethylated) representations, HELP PCR prod-ucts must then be labeled and both fractions co-hybridized onto a microarray. The array must be specifically designed to cover genomic regions contained between two consecutive Hpa II restriction sites. These sites occur at different intervals across the genome, but since PCR conditions have been optimized to amplify fragments between 200 and 2,000 bp, only genomic regions contained between Hpa II sites located within this distance should be included in the design of the array. These fragments are referred to as “ Hpa II amplifiable fragments” and 1,016,980 of them can be found in the March 2006 assembly of the human genome (HG18), of which the majority is expected to be unique. The choice of which Hpa II amplifiable frag-ments should be included in the array design is highly dependent on the biological question of interest to the researcher. Both whole genome and focused arrays have been successfully used for DNA methylation studies using HELP by our group and others (10, 11) . Similarly, the choice of microarray platform is also something that can be adapted to the needs and resources of each investigator. Any of the currently available technologies that allow the researcher to customize the platform can be used, and the extent of the coverage of each fragment can be adjusted according to the number of frag-ments to be included and the density of oligonucleotides allowed by the technology of choice.

Our group has chosen to use custom-designed oligonucle-otide microarrays from Roche NimbleGen for our studies. The standard microarray has been designed to cover between 1 and 3 Hpa II amplifiable fragments per promoter region, using between 10 and 15 probes per Hpa II amplifiable fragment. Such designs have been used not only for human studies (12, 13) , but also for other species, such as mouse (9) , and rat (14) . However, cur-rent ongoing studies are also using microarrays that have been

3.3. Product Labeling and Microarray Hybridization


specifically designed to cover the needs of particular research groups (i.e., covering every single Hpa II amplifiable fragment on specific chromosomes or selectively covering promoters known to be regulated by a specific transcription factor)

Roche NimbleGen uses Cy-labeled random primers (9mers) for the labeling of the Hpa II and Msp I fractions for hybridization. The Cy5-labeled Hpa II and Cy3-labeled Msp I representations are then co-hybridized onto the corresponding microarray platform and scanned using a GenePix 4000B scanner (Axon Instruments) (15) . Specific labeling, hybridization, and scanning protocols will vary according to the microarray platform of choice, and we therefore recommend that the reader refer to the manufacturer’s protocols for these steps, as this will help to ensure the highest level of performance in each case.

After hybridization and image acquisition, two raw data files are generated for each sample: one for Hpa II and one for Msp I. The actual steps involved in the analysis will be highly dependent on the microarray platform and assay design chosen by the researcher. However, some general concepts will be common to all designs. As discussed above, proportional methylation at the different Hpa II sites can be determined by the relative abundance of the fragment contained between them in the two fractions. Three steps must be followed in order to arrive to that point: 1. Data summarization: If more than one oligonucleotide was

used to represent each Hpa II amplifiable fragment, then the information (i.e., intensity) from all of these oligonucleotides must be summarized as one value per fragment.

2. Identification of failed fragments: As Msp I represents the total population of possible fragments and therefore the internal control of the method, any fragments that are not generating signal in the Msp I representation must be excluded from the analysis. A fragment may be absent in the Msp I fraction both for technical and biological reasons. Technical reasons include lack of amplification of the fragment during the PCR step, as well as failure during the labeling or hybridization reactions. Biologically, a given fragment can be absent due to the pres-ence of a genomic deletion, a frequent event in cancer, or the presence of a polymorphism at the restriction site, which pre-vents it from being recognized by the restriction enzymes.

3. Computation of HpaII to MspI ratios for each fragment: In a final step, the relative proportion of Hpa II to Msp I signal must be determined for each fragment. When the distribution of the population of these proportions is studied, a bimodal distribution becomes readily apparent, showing the presence of a methylated fraction of the genome (lacking a Hpa II signal) and a hypomethylated fraction, with increasing amounts of Hpa II signal ( Fig. 3 ).

3.4. Data Analysis and Interpretation


Fig. 3. Frequency histogram of the log Hpa II to Msp I ratios. In a typical analysis a bimodal distribution will reflect the presence of a methylated fraction of the genome -with no or minimal Hpa II signal- ( left peak ), and a hypomethylated fraction -with increasing amounts of Hpa II signal- ( right peak ) .

Fig. 4. Correlation between methylation profiles from leukemia patients. Correlation matrix showing scatter plots ( upper panel ) and Pearson correlation value ( lower panel ) for ( a ) three technical replicates from an Acute Lymphoblastic Leukemia (ALL) case, showing high degree of technical reproducibility, and ( b ) an ALL vs. AML comparison, where the lower correla-tions and broader scatter plots reflect the underlying differences in DNA methylation profiles between the two cases .


When the protocol is followed as described above, we find that technical reproducibility is very high, with Pearson correlation coefficients between replicates greater than 0.96 ( Fig. 4 ).

Once the data has been processed as described above, com-parisons between different biological samples may be carried out. To identify the methylation differences that naturally sepa-rate the samples into different groups, unsupervised clustering analysis may be carried out. A number of different algorithms may be used for this type of analysis, including hierarchical clus-tering, k-means clustering, principal component analysis, and correspondence analysis. In all these cases the algorithms look for variability in methylation profiles across the different samples, and then segregate them according to their dissimilarities. Unsu-pervised analysis therefore, permits the unbiased identification of subgroups based on the similarities and differences in their DNA methylation profiles.

If, on the other hand, one wishes to compare the DNA meth-ylation profiles of two previously known groups of samples (e.g., normal hematopoietic progenitors vs. leukemia blasts), then a supervised analysis has to be carried out, in which one group is compared to the other. Several statistical tools have been devel-oped specifically for the supervised analysis of microarray data. Many algorithms have been published that deal with the specific problems and limitations of analysis of complex microarray data, and an extensive review of these exceeds the scope of this chap-ter. We would like however, to briefly mention the permutation-based method SAM (significance analysis of microarrays) (16) , which is widely used and well accepted for the supervised analysis of microarray data. This algorithm, like most of these tools, was initially developed for gene expression microarrays, yet it is like-wise useful for the analysis of HELP microarrays.

All of these biological comparisons of HELP data will lead to the identification of differentially methylated Hpa II fragments, which are linked to specific genomic regions. Depending on the microarray design chosen by the researcher, these regions may cor-respond to gene promoters, intergenic regulatory regions and/or even intragenic regions. The known genes as well as the genomic sequences themselves that align with the Hpa II amplifiable frag-ments identified as differentially methylated can then be easily extracted from the microarray design file and used for more com-plex bioinformatic studies. Currently there are many bioinformatic tools available, such as DAVID (17) , GeneMerge, (18) TRANS-FAC (19) , and SOMBRERO (20) , among others. These tools can be used for pathway analysis (DAVID), gene ontology analysis (DAVID and GeneMerge), for the identification of common tran-scription factor binding sites (TRANSFAC) or for the discovery of new sequence motifs (SOMBRERO) that are enriched in the differentially methylated regions identified with HELP.


1. If however, a limited number of cells are available (less than 1 million cells), we then recommend the use of Qiagen’s Gentra PureGene kit (Qiagen) according to manufacturer’s instructions. This kit has proven useful in recovering sufficient DNA of good quality under these conditions. We strongly advise against the use of column-based DNA extraction kits, since these produce DNA that is sheared and difficult to cut with restriction enzymes.

2. This number is adequate when working with frozen samples. If using fresh cell lines, then we recommend using between 1 and 2 million since the yield of DNA is typically higher.

3. A 2-ml tube is recommended since the glass hook may not fit adequately in a smaller tube.

4. The volume of Tris–HCl buffer will depend on starting cell numbers and usual yields for each cell type. Usually volumes between 100 and 1,000 μ l are required.

5. Since the success of the assay relies on the comparison of the Msp I representation to the Hpa II representation, incomplete digestion of the DNA can significantly affect results. For this reason, we strongly recommend adhering to the overnight digestion of DNA by the two isoschizomers, rather than attempting shorter incubations, which may cause incomplete digestion of the genomic DNA.

6. Samples with extreme genome-wide hypomethylation will show only very little high molecular weight remnant with Hpa II.

7. To ensure the ligation of the linkers to the vast majority of the genomic DNA fragments, a standard overnight ligation with T4 DNA ligase is recommended instead of a fast ligation reac-tion. Using a fast ligation might result in only a fraction of the fragments being ligated to the linkers, with the subsequent loss of the remaining fragments during the PCR amplification step.

8. Qiagen recently changed the binding buffer from the previous PB buffer to a version including a pH indicator (PBI buffer). This pH indicator may interfere with subsequent labeling of the PCR products for microarray hybridization, so it is Qiagen’s recom-mendation that for this purpose the old PB buffer be used. The company supplies this buffer at no extra cost when requested.

4. Notes

References

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21. Genome-Wide Determination of DNA Meth-ylation by Hpa II Tiny Fragment Enrichment

22. Genome-Wide Determination of DNA Meth-ylation by Hpa II Tiny Fragment Enrichment

[methods in molecular biology™] leukemia volume 538 || genome-wide determination of dna...

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