High-Resolution Transcriptome

of Human Macrophages

by Beyer & colleagues PLOS one 2012

Presented by Nacho Caballero

CD14+ Monocyte

Monocytes follow two paths of differentiation

M1 Macrophage

IFNG TNF

IRF6

M2 Macrophage

IL4 IL13

CSF1 CSF2

Fluorescence

Each macrophage subtype expresses a unique phenotype

% of max cells

Mean Fluorescence

Units

FCGR1A

isotype m1 m2

m1 m2

Fluorescence

% of max cells

Mean Fluorescence

Units

m1 m2

isotype m1 m2

FCER2

Arrays can discriminate between macrophage phenotypes

m1 m2 M0

Sequencing and microarray data are highly correlated

900 308 595  

Sequencing Array Log2 FC   Log2 FC  

Sequencing Fold Change

Array Fold Change

Canonical macrophage markers

Array Sequencing

(z-scores and heatmaps)

Absolute values Z-scores

Canonical macrophage markers

Array Sequencing

Advantages of sequencing: Detecting alternative splicing

PDLIM7 gene  

m1

m2

m1 m2 m1 m2 m1 m2

Array

mRNA (relative)  

Sequencing

Isoform 1   Isoform 2   Isoform 4  

mRNA (relative)  

Advantages of sequencing: Identifying novel macrophage markers

Array Sequencing

Favor gene lists or line charts over z-score heatmaps

Sequencing improves resolution and can answer additional questions

Arrays may be good enough to assess gene expression