Mountain View
biomedical and healthCAre Data Discovery Index Ecosystem
help Advanced Search
Title: Identification of in vivo binding sites of human C2H2-ZF proteins      
keywords:
Epigenomics
ID:
PRJNA252040
description:
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.
accesstypes:
download
landingpage: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA252040
authentication:
none
authorization:
none
ID:
pmid:25690854
name:
synthetic construct
ncbiID:
ncbitax:32630
abbreviation:
NCBI
homePage: http://www.ncbi.nlm.nih.gov
ID:
SCR:006472
name:
National Center for Biotechnology Information
homePage: http://www.ncbi.nlm.nih.gov/bioproject
ID:
SCR:004801
name:
NCBI BioProject
  • MOP-111007/Canadian Institutes of Health Research/Canada

  • MOP-272138/Canadian Institutes of Health Research/Canada

  • MOP-77721/Canadian Institutes of Health Research/Canada

Feedback?

If you are having problems using our tools, or if you would just like to send us some feedback, please post your questions on GitHub.