1
Abstract
2
Time-tracking
3
Methods
3.1
Individual reprocessing of published experiments
3.1.1
Microarrays
3.1.2
RNA-Seq
3.2
Integration plots
3.3
R session environment
4
Results
4.1
Microarray datasets
4.1.1
GSE84185
4.1.1.1
Stressed VS Unstressed
4.1.1.1.1
Default settings
4.1.1.1.2
Force normalization
4.1.1.2
Stressed VS Unstressed in Dentate Gyrus
4.1.1.2.1
Default settings
4.1.1.2.2
Force normalization
4.1.1.3
Fluoxetine VS Control For Stressed in Dentate Gyrus
4.1.1.3.1
Default settings
4.1.1.4
Fluoxetine VS Control for No Stressed in Dentate Gyrus
4.1.1.4.1
Default settings
4.1.1.5
Fluoxetine VS Control for Stressed Responder in Dentate Gyrus
4.1.1.5.1
Default settings
4.1.1.6
Fluoxetine VS Control for Stressed NonResponder in Dentate Gyrus
4.1.1.6.1
Default settings
4.1.2
GSE43261
4.1.2.1
Stressed VS Unstressed
4.1.2.1.1
Default settings
4.1.2.2
Fluoxetine Responder VS Control for Stressed mice
4.1.2.2.1
Default settings
4.1.3
GSE56028
4.1.3.1
Stressed VS Unstressed
4.1.3.1.1
Default settings
4.1.3.2
Fluoxetine VS Untreated for stressed rats
4.1.3.2.1
Default settings
4.1.4
GSE118669
4.1.4.1
Fluoxetine VS Vehicle
4.1.4.1.1
Default settings
4.1.5
GSE54307
4.1.5.1
Fluoxetine VS Other
4.1.5.1.1
Default settings
4.1.5.2
Fluoxetine VS Vehicle
4.1.5.2.1
Default settings
4.1.6
GSE6476
4.1.6.1
Stressed VS Unstressed
4.1.6.1.1
Default settings
4.1.7
GSE42940
4.1.7.1
Fluoxetine VS Control
4.1.7.1.1
Default settings
4.1.8
Surget 2009
4.1.8.1
Stressed VS Unstressed
4.1.8.1.1
Default settings
4.1.8.2
Fluoxetine VS Saline for stressed in Dentate Gyrus
4.1.8.2.1
Default settings
4.2
RNA-Seq datasets
4.2.1
SRP056481
4.2.1.1
DEA
4.2.1.1.1
Fluoxetine VS Methylcellulose
4.2.1.1.1.1
Apeglm shrinkage
4.2.1.1.1.2
Ashr shrinkage
4.2.1.1.1.3
Normal shrinkage
4.2.1.1.1.4
Normal shrinkage with lower FC Threshold
4.2.1.2
Isoform quantification
4.2.1.3
DTU
4.2.1.3.1
Fluoxetine VS Methylcellulose
4.2.2
SRP057486
4.2.2.1
PCA
4.2.2.2
UMAP
4.2.2.3
DEA
4.2.2.3.1
Fluoxetine VS Vehicle with Tissue and Treatment as covariates
4.2.2.3.1.1
Apgelm shrinkage
4.2.2.3.1.2
Normal shrinkage
4.2.2.3.2
Fluoxetine VS Vehicle for Brain CA1 subset with Treatment as covariate
4.2.2.3.2.1
Apeglm shrinkage
4.2.2.3.2.2
Normal shrinkage
4.2.2.3.3
Fluoxetine VS Vehicle for Brain CA1 and Stressed subset
4.2.2.3.3.1
Apeglm shrinkage
4.2.2.3.3.2
Normal shrinkage
4.2.2.3.4
Fluoxetine VS Vehicle for Brain CA1 and non-shocked
4.2.2.3.4.1
Apeglm shrinkage
4.2.2.3.4.2
Normal shrinkage
4.2.2.4
Isoform quantification
4.2.2.5
DTU
4.2.2.5.1
Fluoxetine VS Vehicle
4.2.2.5.2
Fluoxetine VS Vehicle for Brain CA1 subset with Treatment as covariate
4.2.2.5.3
Fluoxetine VS Vehicle for Brain CA1 shocked subset
4.2.2.5.4
Fluoxetine VS Vehicle for Brain CA1 NonShocked subset
4.2.3
SRP084288
4.2.3.1
PCA
4.2.3.2
DEA
4.2.3.2.1
Fluoxetine VS Control with Tissue as covariate
4.2.3.2.1.1
Apeglm shrinkage
4.2.3.2.1.2
Normal shrinkage
4.2.3.2.2
Fluoxetine VS Control in Hippocampus
4.2.3.2.3
Fluoxetine VS ModelOfDepression with Tissue as covariate
4.2.3.2.3.1
Apeglm shrinkage
4.2.3.2.3.2
Normal shrinkage
4.2.3.2.4
Fluoxetine VS ModelOfDepression in Hippocampus
4.2.3.3
Isoform quantification
4.2.3.4
DTU
4.2.3.4.1
Fluoxetine VS Control
4.2.3.4.2
Fluoxetine VS ModelOfDepression
4.2.3.5
Check Sex
4.2.4
SRP131063
4.2.4.1
DEA
4.2.4.1.1
Fluoxetine VS Saline for Stressed
4.2.4.1.1.1
Apeglm
4.2.4.1.1.2
Normal
4.2.4.2
Isoform quantification
4.2.4.3
DTU
4.2.4.3.1
Fluoxetine VS Methylcellulose
4.2.4.4
Check Sex
4.2.5
Check Sex Control (GSE195833)
4.3
Integration
4.3.1
To closest human ortholog
4.3.1.1
Mouse Fluoxetine VS Control for Stressed in Dentate Gyrus
4.3.1.2
Rat Stress Alone VS Stress Fluoxetine in Dentate Gyrus
4.3.1.3
Rat+Mouse Fluoxetine VS Control for Stressed in Dentate Gyrus
4.3.1.4
Mouse Fluoxetine VS Control for NoStressed in Dentate Gyrus
4.3.1.5
Rat Fluoxetine VS Control for NoStressed in Dentate Gyrus
4.3.1.6
Rat+Mouse Fluoxetine VS Control for NoStressed in Dentate Gyrus
4.3.1.7
Rat+Mouse Fluoxetine VS Control for Stressed and no stressed in Dentate Gyrus
4.3.2
Using original specie Gene.name
4.3.2.1
Mouse Fluoxetine VS Control for Stressed in Dentate Gyrus
4.3.2.2
Rat Stress Alone VS Stress Fluoxetine in Dentate Gyrus
4.3.2.3
Rat+Mouse Fluoxetine VS Control for Stressed in Dentate Gyrus
4.3.2.4
Mouse Fluoxetine VS Control for NoStressed in Dentate Gyrus
4.3.2.5
Rat Fluoxetine VS Control for NoStressed in Dentate Gyrus
4.3.2.6
Rat+Mouse Fluoxetine VS Control for NoStressed in Dentate Gyrus
4.3.2.7
Rat+Mouse Fluoxetine VS Control for Stressed and no stressed in Dentate Gyrus
ANTARES
4.2.3.5
Check Sex
Before doing the analysis on this dataset, we want to check the sex of these samples.
