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| Status |
Public on Nov 13, 2019 |
| Title |
Sleep-wake driven and circadian contributions to daily rhythms in gene expression and chromatin accessibility in the murine cortex |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
We monitored gene expression and chromatin accessibility in the cerebral cortex of 10-12 week-old male C57BL/6J mice for 24 hours before and until 48 hours after the end of a single total sleep deprivation (SD) episode. The aim was to characterise the response to SD and recovery thereafter.
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| Overall design |
Mice were sleep deprived for 6 hours starting at light onset (ZT0-ZT6; Time 24-30) of the light-dark cycle. Control mice (NSD, Non Sleep Deprived) were sacrificed at ZT0, ZT3, ZT6, ZT12, ZT18 of the first day of experimentation (named samples T0-T24 and corresponding to the 24 hours before SD), serving as a baseline day (Day 0). On Day 1, SD mice were sacrificed at the same time of day as on Day 0 (samples T27-42, with T27 and T30 samples being taken after 3h and 6h SD, respectively), on Day 2 at ZT0, ZT6, ZT12, ZT18 (samples T48-66), as well as ZT0 and ZT6 on Day 3 (samples T72-78). Two groups of mice were allowed to recover for 7 days after SD, before being sacrificed at ZT0 and ZT6 (Day 8, samples T192-198). We collected 3-4 replicates per time point and condition, and 8 replicates of ZT0 controls from two different animal batches. RNAseq and ATAC-seq libraries originate each time from the same animal, i.e. the data sets are paired. Sequencing failed for 2 ATAC-seq libraries at T66, resulting in only one biological replicate at this time point (corresponding RNAseq was not affected and thus comprises 3 biological replicates)..
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| Contributor(s) |
Hor CN, Yeung J, Jan M, Emmenegger Y, Hubbard J, Xenarios I, Naef F, Franken P |
| Citation(s) |
31776259 |
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| Submission date |
Nov 13, 2019 |
| Last update date |
Mar 25, 2024 |
| Contact name |
Maxime Jan |
| E-mail(s) |
[email protected]
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| Organization name |
University of Lausanne
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| Department |
CIG
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| Street address |
University of Lausanne
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| City |
Lausanne |
| State/province |
Suisse |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
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| Platforms (1) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (123)
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| Relations |
| BioProject |
PRJNA589315 |
| SRA |
SRP229742 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE140345_ATAC_PeaksLocation.gtf.gz |
1.5 Mb |
(ftp)(http) |
GTF |
| GSE140345_ATAC_level_all_peaks.txt.gz |
42.8 Mb |
(ftp)(http) |
TXT |
| GSE140345_RNA_level_all_genes.txt.gz |
6.5 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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