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Series GSE44236 Query DataSets for GSE44236
Status Public on Feb 11, 2016
Title ChIP-seq of three core components of the circadian clock (BMAL1, CLOCK and CRY1) in unsynchronized human U2OS cells
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The human osteosarcoma cell line U2OS contains a functional circadian clock but expresses only a few rhythmic genes. We identified by ChIP-seq analysis 3040 binding sites of the circadian transcription factors BMAL1, CLOCK, and CRY1 in the genome of U2OS cells, comparable to the number found in highly rhythmic tissues like liver.
Overall design ChIP was performed as described previously (Rey et al, 2011; doi:10.1371/journal.pbio.1000595) using confluent desynchronized U2OS cells and BMAL1, CLOCK, and CRY1-antibodies. Immunoprecipitated chromatin (10 ng DNA of 8 independent BMAL1 ChIPs with enrichment levels > 80-fold, 9 ng DNA of a CRY1 ChIP with 10-fold enrichment, and 8 ng DNA of a CLOCK ChIP with 40-fold enrichment) was used for library preparation. Three lanes of the BMAL1 library, and one lane each of the CRY1 and CLOCK library were sequenced on the Illumina Genome Analyzer IIx using Single-Read Cluster Generation Kit and 36 Cycle Sequencing Kit v2 (Lausanne Genomics Technologies Facility).
Contributor(s) Stefanski J, Symul L
Citation(s) 25007071
Submission date Feb 11, 2013
Last update date May 15, 2019
Contact name Laura Symul
Organization name EPFL
Department SV-IBI
Lab Naef Lab
Street address EPFL SV IBI UPNAE, AAB 039
City Lausanne
State/province Station 15
ZIP/Postal code CH-1015
Country Switzerland
Platforms (1)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
Samples (3)
GSM1081127 BMAL1 ChIP-seq
GSM1081128 CLOCK ChIP-seq
GSM1081129 CRY1 ChIP-seq
BioProject PRJNA189335
SRA SRP018565

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Supplementary file Size Download File type/resource
GSE44236_RAW.tar 456.6 Mb (http)(custom) TAR (of BEDGRAPH)
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Raw data are available in SRA
Processed data provided as supplementary file

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