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Journal club presentation
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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