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Series GSE58341 Query DataSets for GSE58341
Status Public on Feb 17, 2015
Title Identification of in vivo binding sites of human C2H2-ZF proteins
Organism synthetic construct
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The largest and most diverse class of eukaryotic transcription factors contain Cys2-His2 zinc fingers (C2H2-ZFs), each of which typically binds a DNA nucleotide triplet within a larger binding site. Frequent recombination and diversification of their DNA-contacting residues suggests that these zinc fingers play a prevalent role in adaptive evolution. Very little is known about the function and evolution of the vast majority of C2H2-ZFs, including whether they even bind DNA. We determined in vivo binding sites of 39 human C2H2-ZF proteins, and correlated them with potential functions for these proteins.
Overall design We expressed GFP-tagged C2H2-ZF proteins in stable transgenic HEK293 cells. Chromatin immunoprecipitation was performed as described before (Schmidt et al., Methods, 2009), and ChIP samples along with several control samples from different experimental batches were sequenced on Illumina HiSeq 2500. Reads were mapped to hg19 (GRCh37) assembly, and peaks were identified by MACS using an experiment-specific background that controls for various biases, such as the Sono-Seq effect as well as potential co-purification of targets of other (interacting) proteins.
Contributor(s) Najafabadi HS, Schmitges FW, Radovani E, Greenblatt J, Hughes TR
Citation(s) 25690854
Submission date Jun 10, 2014
Last update date May 15, 2019
Contact name Hamed S Najafabadi
Organization name McGill University
Department Human Genetics
Lab Computational and Statistical Genomics Lab
Street address 740 Dr. Penfield Avenue, Room 7202
City Montreal
State/province QC
ZIP/Postal code H3A 0G1
Country Canada
Platforms (1)
GPL15228 Illumina HiSeq 2000 (synthetic construct)
Samples (39)
GSM1407624 ChIP-seq of GFP-tagged ZNF675 in HEK293 cells
GSM1407625 ChIP-seq of GFP-tagged YY1 in HEK293 cells
GSM1407626 ChIP-seq of GFP-tagged ZFP3 in HEK293 cells
This SubSeries is part of SuperSeries:
GSE52523 Large-scale characterization of DNA binding landscape of eukaryotic C2H2 zinc fingers
BioProject PRJNA252040
SRA SRP043061

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

Supplementary file Size Download File type/resource
GSE58341_RAW.tar 8.9 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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