|
| Status |
Public on Feb 27, 2023 |
| Title |
Rat hippocampus - sdG5_fst_20_m |
| Sample type |
SRA |
| |
|
| Source name |
hippocampus
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: hippocampus
strain: Sprague Dawley
batch: Batch 2
treatment: forced swimming test - 20 min after
|
| Treatment protocol |
FST 20 m group were decapitated 20 minutes after FST presentation. FST 24 h group were decapitated 24 hours after FST presentation. Control group did not undergo FST.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA isolation was conducted using a Direct-Zol RNA Mini-Prep Kit (ZymoResearch) according to the manufacturer's recommendations. The concentration of total RNA isolated was measured using a Quant-iT RNA BR Assay Kit and a Qubit fluorimeter (Invitrogen). RNA quality was monitored using an Experion automated electrophoresis system (Bio-Rad Laboratories). The RNA quality index was higher than 8.5 in all samples.
Poly-a fraction of RNA was extracted from total RNA for RNA-seq. Sequencing libraries were prepared using NEBNext® mRNA Library Perp Reagent Set (NEB, USA). Sequencing was performed using HiSeq1500 (Illumina, USA), obtaining no less then 15 mln. reads of 50 length per library.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
Trimming was perfromed using Adapter Removal v2, using defaul parameters
Alignment on Rnor6.0 genome assembly was performed using STAR and RSEM
SVA batch correction was applied to different batches to compensate for batch effects. Repeated sequences of sdG10_fst_20_m, sdG21_fst_control and sdG27_fst_control were combined due to lower number of reads obtained.
differential expression was obtained using limma voom protocol, using TMM and CPM normalizations
Genome_build: Rnor6.0
Supplementary_files_format_and_content: Processed count files were obtained using RSEM.
|
| |
|
| Submission date |
Dec 02, 2020 |
| Last update date |
Feb 27, 2023 |
| Contact name |
Ivan Nikolaevitch Vlasov |
| E-mail(s) |
invlasov@mail.ru
|
| Organization name |
National Research Center «Kurchatov Institute»
|
| Lab |
Laboratory of Molecular Genetics of Hereditary Disease
|
| Street address |
Akademika Kurchatova square, 2
|
| City |
Moscow |
| ZIP/Postal code |
123182 |
| Country |
Russia |
| |
|
| Platform ID |
GPL18404 |
| Series (1) |
| GSE162524 |
Differential expression of Dusp1 and immediate early response genes in hippocampus of rats, subjected to forced swimming test |
|
| Relations |
| BioSample |
SAMN16981801 |
| SRA |
SRX9620543 |
