 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 08, 2018 |
| Title |
RNA sequencing of whole, ventral and dorsal hippocampus after different stress conditions |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Purpose: The goal of this study was to characterize molecular stress responses on transcriptional level in dorsal and ventral hippocampus separately.
Methods: mRNA profiles of whole, dorsal and ventral hippocampus of mice 45min after first exposure to different acute stressors. The stressors were novelty (6min novel environment), restraint (30min immobilization), or cold swim (6min in 18 degree Celcius water). 5 mice were used per condition, using Illumina HiSeq4000. The sequence reads that passed quality filters were mapped with STAR, counted with RSEM and differential gene expression was calculated using the bioconducter package edgeR.
Results: With our workflow, we identified 13902 genes per sample. Approximately 20% of the genes were differentially expressed between dorsal and ventral hippocampus at baseline, with a log2 fold change >±0.3 and p value <0.005. Approximately 100 genes are differentially expressed upon stress treatment in the whole hippocampus. If ventral and dorsal hippocampus were analyzed separately, numbers increased to 150 and 250 respectively. Stress-responsive genes vary between dorsal and ventral hippocampus, and also vary between different stressors. Further analysis identified a functional epigenetic gene cluster specific for the stress response in the ventral hippocampus.
Conclusions: Our study represents the first RNA-seq analysis of dorsal and ventral hippocampus after different acute stress exposures.
|
| |
|
| Overall design |
mRNA profiles of whole, dorsal and ventral hippocampus of mice 45min after different stress treatments, 5 mice per condition, using Illumina HiSeq4000.
|
| |
|
| Contributor(s) |
Floriou-Servou A, von Ziegler L, Stalder L, Sturman O, Privitera M, Bohacek J |
| Citation(s) |
29605177 |
| Submission date |
Jun 20, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Johannes Bohacek |
| E-mail(s) |
johannes.bohacek@hest.ethz.ch
|
| Organization name |
University of Zurich/ ETH Zurich
|
| Street address |
Winterthurerstrasse 190
|
| City |
Zurich |
| ZIP/Postal code |
8057 |
| Country |
Switzerland |
| |
|
| Platforms (1) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
|
| Samples (60)
|
|
| Relations |
| BioProject |
PRJNA391140 |
| SRA |
SRP109804 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE100236_dorsalH_Homecage_vs_Handling.csv.gz |
918.3 Kb |
(ftp)(http) |
CSV |
| GSE100236_dorsalH_Homecage_vs_Restraint.csv.gz |
994.2 Kb |
(ftp)(http) |
CSV |
| GSE100236_dorsalH_Homecage_vs_Swim.csv.gz |
1011.3 Kb |
(ftp)(http) |
CSV |
| GSE100236_dorsalH_Homecage_vs_ventralH_Homecage.csv.gz |
1.0 Mb |
(ftp)(http) |
CSV |
| GSE100236_ventralH_Homecage_vs_Handling.csv.gz |
995.2 Kb |
(ftp)(http) |
CSV |
| GSE100236_ventralH_Homecage_vs_Restraint.csv.gz |
1018.9 Kb |
(ftp)(http) |
CSV |
| GSE100236_ventralH_Homecage_vs_Swim.csv.gz |
1.0 Mb |
(ftp)(http) |
CSV |
| GSE100236_wholeH_Homecage_vs_Handling.csv.gz |
928.2 Kb |
(ftp)(http) |
CSV |
| GSE100236_wholeH_Homecage_vs_Restraint.csv.gz |
925.8 Kb |
(ftp)(http) |
CSV |
| GSE100236_wholeH_Homecage_vs_Swim.csv.gz |
980.3 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...