RNA-seq example: Analysis of RNA-seq counts
Louie Van De Lagemaat (louie.vandelagemaat@abdn.ac.uk)
2026-04-24
Overview
This pipeline output recapitulates a portion of the analysis described in
D Mukherjee, et al. 2021. Egr2 induction in spiny projection neurons
of the ventrolateral striatum contributes to cocaine place preference in mice.
eLife 10:e65228 (PMID: 33724178)
RNA-sequencing analysis was performed on group in R. Analysis was
carried out on the following contrasts: Acute_DS_1h-Acute_DS_0h,
Acute_NAc_1h-Acute_NAc_0h, Acute_DS_0h-Acute_NAc_0h,
Acute_DS_1h-Acute_NAc_1h,
Acute_DSvNAc_1v0h=(Acute_DS_1h-Acute_DS_0h)-(Acute_NAc_1h-Acute_NAc_0h).
In
all aspects of the study, false discovery rate (FDR) of 0.05 was
considered significant, and in gene expression tests, absolute log2 fold
change was required to be greater than 0.
The analysis proceeded
in several stages outlined below. These included quality control of the
data, multi-dimensional scaling analysis, and differential gene
expression, which was performed using the edgeR package.
Quality control
37558 of 55367 genes were filtered out by requiring >1 CPM in at least 3 samples, leaving 17809 genes. Then 0 of 29 samples were filtered out based on total counts mapped to genes > 10000, leaving 29 samples.
MDS plots
MDS analysis was performed on all samples in up to 30000 genes with respect to group.
MDS by group
