High-resolution transcriptome of human macrophages
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Transcript of High-resolution transcriptome of human macrophages
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High-Resolution Transcriptome
of Human Macrophages
by Beyer & colleagues PLOS one 2012
Presented by Nacho Caballero
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CD14+ Monocyte
Monocytes follow two paths of differentiation
M1 Macrophage
IFNG TNF
IRF6
M2 Macrophage
IL4 IL13
CSF1 CSF2
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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
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Arrays can discriminate between macrophage phenotypes
m1 m2 M0
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Sequencing and microarray data are highly correlated
900 308 595
Sequencing Array Log2 FC Log2 FC
Sequencing Fold Change
Array Fold Change
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Canonical macrophage markers
Array Sequencing
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(z-scores and heatmaps)
Absolute values Z-scores
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Canonical macrophage markers
Array Sequencing
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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)
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Advantages of sequencing: Identifying novel macrophage markers
Array Sequencing
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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