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Series GSE114845 Query DataSets for GSE114845
Status Public on Jun 26, 2018
Title Systems genetics of sleep regulation
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary We used a systems genetics approach in the BXD genetic reference population of mice and assembled a comprehensive experimental knowledge base comprising a deep ‘sleep-wake’ phenome, central and peripheral transcriptomes, and plasma metabolome data, collected under undisturbed baseline conditions and after sleep deprivation.
Overall design We subjected mice from 33 BXD/RwwJ lines, 4 BXD/TyJ, the two parental strains (B6 and D2), as well as F1 individuals from reciprocal crosses between the parental lines, to a deep behavioral and molecular phenotyping with steady-state RNA levels in brain and liver under control and sleep deprivation.
Sleep deprivation was performed during 6h (ZT0-6), animals were sleep deprived in their home cage by “gentle handling” . Half of the animals were sleep deprived (SD), the other half was left undisturbed in another room (i.e., control or Ctr). Both SD and Ctr mice were sacrificed at ZT6, i.e., immediately after the end of the SD, for sampling of liver and cerebral cortex tissue.
The mice initially sacrificed for tissue collection yielded to 277 cortex and 277 liver samples of good quality. Equal amounts of RNA from biological replicates (same strain/line and experimental condition) were pooled.
In addition, to assess the stability of outcome variables over time, parental lines were sampled twice; i.e., at the start (labelled B61 and DB1) and end (labelled B62 and DB2) of the breeding and data-collecting phase which spanned 2 years (March 2012- December 2013).
In summary we generated 172 RNA-seq data sets.
Contributor(s) Diessler S, Jan M, Emmenegger Y, Xenarios I, Franken P
Citation(s) 30091978
Submission date May 23, 2018
Last update date Mar 21, 2019
Contact name Maxime Jan
Organization name University of Lausanne
Department CIG
Street address University of Lausanne
City Lausanne
State/province Suisse
ZIP/Postal code 1015
Country Switzerland
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (172)
GSM3151467 05nsd_Cortex_Control
GSM3151468 05sd_Cortex_SleepDeprived
GSM3151469 100nsd_Cortex_Control
BioProject PRJNA472805
SRA SRP148818

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE114845_htseq-count_summary.Cortex.txt.NSD.log2CPM.txt.gz 4.8 Mb (ftp)(http) TXT
GSE114845_htseq-count_summary.Cortex.txt.SD.log2CPM.txt.gz 4.8 Mb (ftp)(http) TXT
GSE114845_htseq-count_summary.Liver.txt.NSD.log2CPM.txt.gz 4.4 Mb (ftp)(http) TXT
GSE114845_htseq-count_summary.Liver.txt.SD.log2CPM.txt.gz 4.4 Mb (ftp)(http) TXT
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