Chromatin immunoprecipitation-sequencing was conducted as described in (5 (link)), by incubating Beta-TC6 cells (ATCC; CRL-11506) cultured in DMEM supplemented with 15% FBS, 1% L-glutamine, and 1% penicillin/streptomycin with DEC1 (Novus Biologicals; NB100–1800) and DEC2-V5 (GeneCopoeia, Inc. # EX-A4343-LX304) antibodies. Sequencing reads were mapped using STAR (46 (link)) with default parameters. Regions enriched for uniquely-mapped reads relative to input sample were called as binding peaks using MACS (47 (link)) with default parameters and “--pvalue=1e-9 --keep-dup=1”, followed by filtering against overlap with problematic regions of the genome (48 (link)). Peaks from BMAL1, CLOCK, and PDX1 ChIP-sequencing in Beta-TC6 cells (10 (link)) were called in the same manner and concatenated and merged with DEC1 and DEC2 peaks using BEDTools (49 (link)) to obtain a unified peak catalog.
Protocol detail
ChIP-seq analysis of DEC1 and DEC2 in Beta-TC6 cells
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Corresponding Organization : California Institute for Regenerative Medicine
Other organizations : Brigham and Women's Hospital, Northeastern University, Massachusetts Eye and Ear Infirmary
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Variable analysis
independent variables
- DEC1 (Novus Biologicals; NB100–1800) and DEC2-V5 (GeneCopoeia, Inc. # EX-A4343-LX304) antibodies
- Regions enriched for uniquely-mapped reads relative to input sample
- Beta-TC6 cells (ATCC; CRL-11506) cultured in DMEM supplemented with 15% FBS, 1% L-glutamine, and 1% penicillin/streptomycin
- Input sample
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