ChIP assay was performed as described previously (Esvald et al., 2020) using 10 min fixation with 1% formaldehyde. 5 µg of CREB antibody (catalog #06–863, lot 2446851, Merck Millipore, Burlington, MA) or TCF4 antibody (CeMines, Golden, CO) was used per immunoprecipitation (IP). DNA enrichment was measured using qPCR. All qPCR reactions were performed in 10 µl volume in triplicates with 1× LightCycler 480 SYBR Green I Master kit (Roche, Basel, Switzerland) and primers listed in Supplementary file 1 on LightCycler 480 PCR instrument II (Roche, Basel, Switzerland). Primer efficiencies were determined by serial dilutions of input samples and were used for analyzing the results. Percentage of input enrichments was calculated for each region and IP, and data were log-transformed before statistical analysis.

ENCODE data of different ChIP-seq experiments were visualized using UCSC Genome Browser track ‘Transcription Factor ChIP-seq Peaks (340 factors in 129 cell types) from ENCODE 3 Data version: ENCODE 3 Nov 2018’. Data of previously published ChIP-seq experiments were obtained from Gene Expression Omnibus with accession numbers GSM530173, GSM530174, GSM530182, GSM530183 (Kim et al., 2010), GSM1467429, GSM1467434 (Malik et al., 2014), GSM1820990 (Moen et al., 2017), GSM1647867 (Sun et al., 2019), GSM1649148 (Bayam et al., 2015), and visualized using Integrative Genomics Viewer version 2.8.0 (Robinson et al., 2011).

Note: The content above has been extracted from a research article, so it may not display correctly.



Q&A
Please log in to submit your questions online.
Your question will be posted on the Bio-101 website. We will send your questions to the authors of this protocol and Bio-protocol community members who are experienced with this method. you will be informed using the email address associated with your Bio-protocol account.



We use cookies on this site to enhance your user experience. By using our website, you are agreeing to allow the storage of cookies on your computer.