Journal club presentation

1. High-Resolution
Transcriptome
of Human
Macrophages
by Beyer & colleagues
PLOS one 2012
Presented by
Nacho Caballero

2. CD14+ Monocyte
Monocytes follow two
paths of differentiation
M1
Macrophage
IFNG
TNF
IRF6
M2
Macrophage
IL4
IL13
CSF1
CSF2

3. 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

4. Arrays can discriminate
between macrophage phenotypes
m1
m2
M0

5. Sequencing and microarray
data are highly correlated
900
308
595
Sequencing
Array
Log2 FC
Log2 FC
Sequencing
Fold Change
Array Fold Change

6. Canonical
macrophage markers
Array
Sequencing

7. (z-scores and
heatmaps)
Absolute values
Z-scores

8. Canonical
macrophage markers
Array
Sequencing

9. 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)

10. Advantages of sequencing:
Identifying novel macrophage markers
Array
Sequencing

11. 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