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Series GSE73117 Query DataSets for GSE73117
Status Public on Jul 10, 2017
Title Evaluation of DNA-binding preferences of non-metazoan C2H2 zinc finger proteins by PBM
Platform organism synthetic construct
Sample organisms Physcomitrium patens; Arabidopsis thaliana; Schizosaccharomyces pombe; Histoplasma capsulatum; Neurospora crassa; Puccinia graminis; Schizophyllum commune; Toxoplasma gondii; Dictyostelium discoideum; Batrachochytrium dendrobatidis; Rhizopus delemar
Experiment type Other
Summary The largest and most diverse class of eukaryotic transcription factors contain Cys2-His2 zinc fingers (C2H2-ZFs). Here, we have explored the diversity of sequence preferences of C2H2-ZF proteins in non-metazoan organisms using PBM experiments.
 
Overall design Protein binding microarray (PBM) experiments were performed for a set of 43 full-length non-metazoan C2H2-ZF proteins. 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.
 
Contributor(s) Najafabadi HS, Weirauch MT, Yang A, Albu M, Hughes TR
Citation(s) 28877740
Submission date Sep 17, 2015
Last update date Oct 09, 2017
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 (86)
GSM1887114 Plasmid ID: pTH10217 - Assay ID: 10720 (ME layout)
GSM1887115 Plasmid ID: pTH10217 - Assay ID: 10736 (HK layout)
GSM1887116 Plasmid ID: pTH10219 - Assay ID: 10722 (ME layout)
Relations
BioProject PRJNA296081

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
GSE73117_RAW.tar 109.0 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table
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