|
| Status |
Public on Sep 04, 2022 |
| Title |
Integrative multi-omics landscape of fluoxetine action across 27 brain regions [bulk RNA-seq] |
| Organism |
Rattus norvegicus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
We constructed a comprehensive multi-omics map of the molecular effects of fluoxetine (an SSRI antidepressant), in 27 rat brain regions. We profiled gene expression (bulk RNA-seq, 210 datasets) and chromatin state (bulk chromatin immunoprecipitation sequencing (ChIP-seq) for the histone marker H3K27ac, 100 datasets) in a broad, unbiased panel of 27 brain regions across the entire rodent brain, in naive and fluoxetine-treated animals. We complemented this approach with single-cell RNA-seq (scRNA-seq) analysis of two brain regions. Using diverse integrative data analysis techniques we characterized the complex and multifaceted effects of fluoxetine on region-specific and cell-type-specific gene regulatory networks and pathways. Remarkably, we observed profound molecular changes across the brain (>4,000 differentially expressed genes and differentially acetylated ChIP-seq peaks each) that were highly region-dependent. We leveraged this atlas to identify fluoxetine-moduated genes and gene-regulatory loci, predict enriched motifs that suggest potential upstream regulators, and validate global mechanisms of fluoxetine action.
|
| |
|
| Overall design |
To complement our multi-regional epigenome map, we used bulk RNA-seq to profile genome-wide fluoxetine-induced transcriptome changes in 27 brain regions. Here we deposit these RNA-seq profiles (27 regions,2 treatment groups - Sham and Fluoxetine, 4 replicates; 27*8= 216 profiles, postQC- 210 RNAseq datasets). To reduce the effects of inter-animal biological variation each RNA-seq sample was pooled from 10 animals (40 in Sham, 40 in FT; 80 animals in total).
Some samples lack raw data due to file corruption.
|
| |
|
| Contributor(s) |
Arul Rayan N, Kumar V, Prabhakar S, Meaney M |
| Citation(s) |
36056172 |
| Submission date |
Jan 24, 2022 |
| Last update date |
Oct 05, 2022 |
| Contact name |
Nirmala Arul Rayan |
| E-mail(s) |
arulrayan@gis.a-star.edu.sg
|
| Organization name |
Genome Institute of Singapore
|
| Street address |
60 Biopolis Street
|
| City |
Singapore |
| ZIP/Postal code |
138672 |
| Country |
Singapore |
| |
|
| Platforms (1) |
| GPL18694 |
Illumina HiSeq 2500 (Rattus norvegicus) |
|
| Samples (212)
|
|
| Relations |
| BioProject |
PRJNA800072 |
| SRA |
SRP356493 |
Less...
More...