Approximately 50 million NCI-H520 (American Type Culture Collection, HTB-182) cells were fixed with 1% PFA and then subjected to ChIP with an anti-SOX2 antibody (Cell Signaling, catalog no. 5024) using the Cell Signaling SimpleChIP enzymatic ChIP kit (Cell Signaling, catalog no. 9003) as per the manufacturer’s instructions. Input and SOX2-immunoprecipitated chromatin samples were sequenced at the Duke University Genome Sequencing and Analysis Core. Approximately 31 million input and 26 million SOX2-immunoprecipitated 36-base-pair reads were acquired. Reads were mapped to human genome assembly GRCh37/hg19 using Bowtie via the Galaxy online analysis toolkit (http://galaxyproject.org ) (Goecks et al. 2010 (link)). SOX2-binding sites were then predicted using Model-Based Analysis of ChIP-Seq (MACS) version 1.4.1 (Zhang et al. 2008 (link)).
Protocol detail
SOX2 ChIP-seq in NCI-H520 cells
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Anti antibody
Base pair
Binding sites
Cells
Chip
Chip seq
Chromatin
Enzymatic
Genome
Human
Human genome
Sox2
Corresponding Organization :
Other organizations : Tsinghua University
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Variable analysis
independent variables
- ChIP with an anti-SOX2 antibody
- SOX2-binding sites
- Approximately 50 million NCI-H520 (American Type Culture Collection, HTB-182) cells
- 1% PFA fixation
- Cell Signaling SimpleChIP enzymatic ChIP kit
- Mapping reads to human genome assembly GRCh37/hg19 using Bowtie
- SOX2-binding sites predicted using Model-Based Analysis of ChIP-Seq (MACS) version 1.4.1
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