ChIP and ChIPseq were performed as described previously (20 (link), 21 (link)). Antibodies used were anti-ASCL1 (Abcam) and anti-IgG (Abcam). ChiPSeq data and full associated methods are both available as an associated file at the GEO database https://www.ncbi.nlm.nih.gov/geo/ and assigned the identifier GSE153823. ChIPseq experiments were performed in two separate clones of each of WT and S-A SH-SY5Y tetracycline-inducible stable cell lines induced with 1 μg/ml doxycycline for 24 hours in four biological replicates. Differential binding analysis (Diffbind) was performed as described previously (20 (link)). ChIP-qPCR primer sequences are provided in Supplementary Table S1 .
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ChIP-Seq Profiling of ASCL1 Binding
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Corresponding Organization :
Other organizations : University of Cambridge, Wellcome/MRC Cambridge Stem Cell Institute, Mohammed Bin Rashid University of Medicine and Health Sciences, Cancer Research UK
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Variable analysis
independent variables
- Genotype (WT vs. S-A SH-SY5Y tetracycline-inducible stable cell lines)
- Doxycycline treatment (1 μg/ml for 24 hours)
- ASCL1 binding detected by ChIP-seq
- Cell line (SH-SY5Y)
- Antibodies used (anti-ASCL1 and anti-IgG)
- Positive control: anti-ASCL1 antibody
- Negative control: anti-IgG antibody
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