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Series GSE52520 Query DataSets for GSE52520
Status Public on Feb 17, 2015
Title Evaluation of DNA-binding preferences of C2H2 zinc finger domains by PBM
Organism synthetic construct
Experiment type Other
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. Using the bacterial 1-hybrid (B1H) system, we determined DNA-binding motifs for thousands of individual natural C2H2-ZFs, and correlated them with C2H2-ZF specificity residues. The data reported here includes results of protein-binding microarray (PBM) assays for 146 of these natural C2H2-ZFs, performed in order to validate B1H assays and to explore the DNA-binding specificity of C2H2-ZFs.
 
Overall design Protein binding microarray (PBM) experiments were performed for a set of 185 variants of mouse Egr1 in which the third zinc finger was replaced by different C2H2-ZFs from different organisms. Briefly, the PBMs involved binding GST-tagged DNA-binding proteins to two double-stranded 44K Agilent microarrays, each containing a different DeBruijn sequence design, in order to determine their sequence preferences. Details of the PBM protocol are described in Berger et al., Nature Biotechnology 2006. Among the 185 variants examined, 146 variants yielded motifs in PBMs, which are included here.
 
Contributor(s) Najafabadi HS, Mnaimneh S, Yang A, Albu M, Hughes TR
Citation(s) 25690854
Submission date Nov 19, 2013
Last update date Mar 05, 2015
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)
GPL11260 Agilent custom ME and HK design array [8mer]
Samples (292)
GSM1407663 OLS ID: 10510 - Assay ID: 10278 [ME layout]
GSM1407664 OLS ID: 10510 - Assay ID: 10294 [HK layout]
GSM1407665 OLS ID: 10605 - Assay ID: 9161 [ME layout]
This SubSeries is part of SuperSeries:
GSE52523 Large-scale characterization of DNA binding landscape of eukaryotic C2H2 zinc fingers
Relations
BioProject PRJNA229160

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
GSE52520_RAW.tar 376.5 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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