Dataset features

Specifications


Application: ChIP-seq analysis
Number of samples: 9
Release date: Nov 30 2015
Last update date: Oct 18 2018
Access: Public
Computational protocol: TopHat, HTSeq, DESeq2, GENCODE, UCSC Genome Browser
Dataset link Combinatorial Regulation Mediated by Biochemically Distinct Forms of SWI/SNF [ChIP-Seq]

Experimental Protocol


We performed ChIP for 4 subunits of SWI/SNF (Arid1a, Arid1b, Arid2, Snf5) and 2 replicates of each, as well as Input. HepG2 cells were fixed in 0.3% formaldehyde for 30 minutes at 4 degrees C, then washed and cell pellets were stored at -80 until immunoprecipitation. Nuclei were released using Dounce homogenizer and layered over a sucrose cushion. Chromatin was then prepared by digesting with micrococcal nuclease for 15 minutes at 37 degrees. Chromatin equivalent to 2x10^7 cells was used in each IP with the antibodies listed. All scripts used in the data analysis are available at: http://github.com/jraab/raab_swisnf_2015/

Repositories


GEO

GSE69566

ENA

SRP059067

BioProject

PRJNA285873

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Contact


Jesse Raab

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