|
| Status |
Public on Jul 01, 2024 |
| Title |
RNA_T12_NSD_T12N4 (re-analysis) |
| Sample type |
SRA |
| |
|
| Source name |
Cortex
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Cortex
ztime: 12
time: 12
condition: NSD
batch: 1
|
| Treatment protocol |
Mice for tissue collection were divided into two experimental cohorts, sleep deprived (SD) and non-sleep deprived (controls, Ctr). After a one-week habituation to the experimental setting, at the age of 11-12 weeks, the SD mice were sleep-deprived by gentle handling for 6 hours starting at light onset (zeitgeber time ZT0-ZT6), and allowed to recover according to the tissue collection schedule.
|
| Growth protocol |
Mice were housed under standard conditions according to the Swiss Animal Protection Act, under a 12h:12h light/dark cycle, with food accessible ad libitum at all times.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mice were anesthetized with isoflurane prior to decapitation. Liver was rapidly dissected and flash frozen in liquid nitrogen. Frozen Liver of each individual was ground in liquid nitrogen and stored at -140°C until further use.
Total RNA was extracted using the miRNeasy kit (Qiagen; Hilden, Germany) following the manufacturer's instructions. RNA-seq libraries were prepared using 10 ng/μl of total RNA and the Illumina TruSeq Stranded mRNA reagents (Illumina; San Diego, CA, USA). Libraries were sequenced on the Illumina HiSeq 4000 sequencer, producing >24 million mappable single-end reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
re-analysis of GSM4159605
|
| Data processing |
Gene quantification was performed as follow for liver samples: Illumina reads were filtered using fastp to keep high quality reads and remove adapter sequences. Reads were aligned on the mouse reference genome mm10 (GRCm38) using STAR v2.7.0e with default parameters. Read counts was done by STAR using “--quantMode GeneCounts”, taking only reverse strand mapped reads. Genes with low counts (mean counts overall samples < 10) were filtered and normalization was performed with edgeR. Batch effects were corrected by ComBat.
Assembly: mm10
Supplementary files format and content: Gene expression [log2 CPM]
|
| |
|
| Submission date |
Mar 25, 2024 |
| Last update date |
Jul 01, 2024 |
| Contact name |
Maxime Jan |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Lausanne
|
| Department |
CIG
|
| Street address |
University of Lausanne
|
| City |
Lausanne |
| State/province |
Suisse |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE262410 |
Model integration of circadian and sleep-wake driven contributions to rhythmic gene expression reveals novel regulatory principles |
|
| Relations |
| Reanalysis of |
GSM4159605 |
| BioSample |
SAMN13280389 |
| SRA |
SRX7135581 |
