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| 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
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| 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.
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| 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).
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| Contributor(s) |
Stefanski J, Symul L |
| Citation(s) |
25007071 |
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| Submission date |
Feb 11, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Laura Symul |
| E-mail(s) |
laurasymul@gmail.com
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| Organization name |
EPFL
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| Department |
SV-IBI
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| Lab |
Naef Lab
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| Street address |
EPFL SV IBI UPNAE, AAB 039
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| City |
Lausanne |
| State/province |
Station 15 |
| ZIP/Postal code |
CH-1015 |
| Country |
Switzerland |
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| Platforms (1) |
| GPL10999 |
Illumina Genome Analyzer IIx (Homo sapiens) |
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| Samples (3) |
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| Relations |
| BioProject |
PRJNA189335 |
| SRA |
SRP018565 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE44236_RAW.tar |
456.6 Mb |
(http)(custom) |
TAR (of BEDGRAPH) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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