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Series GSE61775 Query DataSets for GSE61775
Status Public on Dec 31, 2016
Title Context-specific regulation of BMAL1 target genes during the circadian cycle in mammals
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Third-party reanalysis
Expression profiling by high throughput sequencing
Summary While the circadian rhythm is a highly conserved phenomenon, it has highly specific functions, which differ from one cell type to another. Hence, although the master regulators BMAL1-CLOCK are conserved, the input and output conveying the tissue specificity vary. Through comparative analyses of ChIP-seq data in mouse liver and NIH3T3 fibroblasts, we reveal that only a fraction of BMAL1 binding sites are shared between different cell types and that many sites are bound, active and accessible in a cell-type-specific way. While we found a large fraction of the overall active liver transcriptome to be rhythmically expressed, rhythmic genes among BMAL1 targets are more enriched compared to the overall cyclic transcriptome in NIH3T3 than in liver. Thus, BMAL1 may launch and reinforce oscillations of a number of genes that propagate timing information rather than globally drive rhythmic gene expression.
Overall design We conducted a comparative functional genomics study based on ChIP Seq and RNA Seq time courses in dexamethasone synchronized NIH3T3 cells and mouse liver. We assessed rhythmic gene expression in NIH3T3 cells through RNA Seq time courses that contained RNA samples taken for 48 every 4 hours starting at 16h after Dex.
The raw data of BMAL1 ChIP-seq in mouse liver is deposited under GSE26602 (Rey et al., 2011). The reprocessed data file for the liver BMAL1_ZT06_ChIP-Seq Samples (GSM654882, GSM654883), BMAL1_ZT06_Liver_Stringent_peaks_all_withannotation.bed, is linked below as a supplementary file.
Contributor(s) Cajan J, Gobet C, Rey G, Sobel J, Naef F
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Submission date Sep 25, 2014
Last update date May 15, 2019
Contact name Jonathan Aryeh Sobel
Organization name EPFL
Department School of Life Sciences
Lab Felix Naef Lab
Street address EPFL SV IBI-SV UPNAE AAB 0 36 (Batiment AAB) Station 15
City Lausanne
State/province Vaud
ZIP/Postal code CH-1015
Country Switzerland
Platforms (2)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (58)
GSM1513743 RNA_PolII_ChIPSeq_NIH3T3_12h
GSM1513744 RNA_PolII_ChIPSeq_NIH3T3_20h
GSM1513745 BMAL1_ChIPSeq_NIH3T3_12h
Reanalysis of GSM654882
Reanalysis of GSM654883
BioProject PRJNA262091
SRA SRP047497

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
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Supplementary file Size Download File type/resource
GSE61775_BMAL1_20h_NIH3T3_Stringent_peaks_all_withannotation.bed.gz 7.1 Kb (ftp)(http) BED
GSE61775_BMAL1_ZT06_Liver_Stringent_peaks_all_withannotation.bed.gz 19.4 Kb (ftp)(http) BED
GSE61775_CLOCK_Liver_sites.bed.gz 3.9 Kb (ftp)(http) BED
GSE61775_CLOCK_NIH3T3_filtered_withannot.bed.gz 13.0 Kb (ftp)(http) BED
GSE61775_PolII_12h_vs_Input.wig.gz 221.9 Mb (ftp)(http) WIG
GSE61775_PolII_20h_vs_Input.wig.gz 268.2 Mb (ftp)(http) WIG
GSE61775_RAW.tar 17.7 Gb (http)(custom) TAR (of BW)
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Raw data are available in SRA
Processed data are available on Series record

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