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Series GSE72082 Query DataSets for GSE72082
Status Public on Aug 31, 2015
Title CETCh-Seq of Mammalian Transcription Factors
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Chromatin immunoprecipitation followed by next-generation DNA sequencing (ChIP-seq) is a widely used technique for identifying transcription factor (TF) binding events throughout an entire genome. However, ChIP-seq is limited by the availability of suitable ChIP-seq grade antibodies, and the vast majority of commercially available antibodies fail to generate usable datasets. To ameliorate these technical obstacles, we present a robust methodological approach for performing ChIP-seq through epitope tagging of endogenous TFs. We used Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9-based genome editing technology to develop CRISPR Epitope Tagging ChIP-seq (CETCh-seq) of DNA-binding proteins. We assessed the feasibility of CETCh-seq by tagging several TFs spanning a wide range of endogenous expression levels in the hepatocellular carcinoma cell line HepG2. Our data exhibit strong correlations between both replicate types as well as with standard ChIP-seq approaches that use TF antibodies. Notably, we also observed minimal changes to the cellular transcriptome and to the expression of the tagged TF. To examine the robustness of our technique, we further performed CETCh-seq in the breast adenocarcinoma cell line MCF7 as well as mouse embryonic stem cells and observed similarly high correlations. Collectively, these data highlight the applicability of CETCh-seq to accurately define the genome-wide binding profiles of DNA-binding proteins, allowing for a straightforward methodology to potentially assay the complete repertoire of TFs, including the large fraction for which ChIPquality antibodies are not available.
 
Overall design CRISPR/Cas9 mediated epitope tagging of transcription factors in human cell types
 
Contributor(s) Mendenhall EM, Myers RM
Citation(s) 26355004
Submission date Aug 14, 2015
Last update date May 15, 2019
Contact name Eric Mendenhall
E-mail(s) eric.mendenhall@uah.edu
Phone 6127605454
Organization name University of Alabama Huntsville
Department Biological Sceinces
Lab Mendenhall Lab
Street address 301 Sparkman Dr
City Huntsville
State/province Alabama
ZIP/Postal code 35899
Country USA
 
Platforms (2)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (29)
GSM1861919 Rad21 ChIP-Seq Rep 1 in HepG2 cells
GSM1861920 Rad21 ChIP-Seq Rep 2 in HepG2 cells
GSM1861921 RAD21 ChIP-Seq in Modified HepG2 cells
Relations
BioProject PRJNA293987
SRA SRP062873

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE72082_RAW.tar 662.9 Mb (http)(custom) TAR (of BEDGRAPH, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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