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Series GSE34791 Query DataSets for GSE34791
Status Public on Dec 31, 2011
Title "Calling Cards" for DNA-binding proteins in mammalian cells
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary The ability to chronicle transcription factor binding events throughout the development of an organism would facilitate mapping of transcriptional networks that control cell fate decisions. We describe a method for permanently recording protein-DNA interactions in mammalian cells. We endow transcription factors with the ability to deposit a transposon into the genome near to where they bind. The transposon becomes a “Calling Card” the transcription factor leaves behind to record its visit to the genome. The locations of the Calling Cards can be determined by massively-parallel DNA sequencing. We show that the transcription factor SP1 fused to the piggyBac transposase directs insertion of the piggyBac transposon near SP1 binding sites. The locations of transposon insertions are highly reproducible, and agree with sites of SP1-binding determined by ChIP-seq. Genes bound by SP1 are more likely to be expressed in the HCT116 cell line we used, and SP1-bound CpG islands show a strong preference to be unmethylated. This method has the potential to trace transcription factor binding throughout cellular and organismal development in a way that has heretofore not been possible.
Overall design These data contain mapped insertion sites from the piggyBac (PB) transposon into HCT116 cell line and sequenced using an Illumina GAII analyzer. The first set contains the insertion sites of transposons mapped from the wild-type PB transposase and the second set contains the insertion sites of transposons mapped with the PB transposase fused to the transcription factor SP1. Other sequencing data present are ChIP-seq data for SP1 in the HCT116 cell line and RNA-seq data.
Contributor(s) Mitra R, Johnston M
Citation(s) 22214611
Submission date Dec 30, 2011
Last update date May 15, 2019
Contact name David Mayhew
Organization name GlaxoSmithKline
Department Target Sciences, Computation Biology, R&D
Street address 1250 South Collegeville Road
City Collegeville
State/province PA
ZIP/Postal code 19426
Country USA
Platforms (1)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
Samples (7)
GSM855444 Wild-type PB insertions Rep #1
GSM855445 Wild-type PB insertions Rep #2
GSM855446 Wild-type PB insertions Rep #3
SRA SRP010064
BioProject PRJNA151051

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

Supplementary file Size Download File type/resource
GSE34791_RAW.tar 1.9 Mb (http)(custom) TAR (of BED, TXT)
GSE34791_readme.txt.gz 377 b (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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