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Series GSE76494 Query DataSets for GSE76494
Status Public on Oct 25, 2016
Title Identification of in vivo binding sites of human GFP-tagged C2H2-ZF proteins
Organism Homo sapiens
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 2000. 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) Schmitges FW, Najafabadi HS, Radovani E, Greenblatt J, Hughes TR
Citation(s) 27852650
Submission date Jan 04, 2016
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)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (160)
GSM2026739 ChIP-seq of GFP-tagged FEZF1 in HEK293 cells [FEZF1_rep1]
GSM2026740 ChIP-seq of GFP-tagged ZNF320 in HEK293 cells [ZNF320_rep1]
GSM2026741 ChIP-seq of GFP-tagged ZNF320 in HEK293 cells [ZNF320_rep2]
This SubSeries is part of SuperSeries:
GSE76496 Multiparameter functional diversity of human C2H2 zinc finger proteins
Relations
BioProject PRJNA307573
SRA SRP068022

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
GSE76494_RAW.tar 117.8 Mb (http)(custom) TAR (of TXT)
GSE76494_combined_summits.motif_hits.per_protein.hg19.tar.gz 19.0 Mb (ftp)(http) TAR
GSE76494_combined_summits.per_protein.hg19.tar.gz 86.0 Mb (ftp)(http) TAR
GSE76494_motifs.pfm.txt.gz 29.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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