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Series GSE20012 Query DataSets for GSE20012
Status Public on Jun 24, 2010
Title Deciphering the cis-regulatory architecture of mammalian photoreceptors
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary In order to define the genomic targets of Crx, we carried out Crx chromatin-immunoprecipitation followed by massively parallel sequencing (ChIP-seq) of eight-week-old mouse retinas using the Solexa platform. Sequence reads were mapped to the genome and 'peaks' were identified. These data were subjected to extensive bioinformatic analysis. In addition, selected peaks were experimentally tested for cis-regulatory activity by electroporation as promoter-reporter fusions into living mouse retinas. Over 5,000 Crx-bound regions (CBRs) were identified throughout the mouse genome. Many of these clusters of CBRs occur specifically around photoreceptor genes. In fact, Crx directly regulates the majority of known photoreceptor transcription factors as well as most known photoreceptor disease genes. Cis-regulatory analysis revealed that individual CBRs contribute in a combinatorial fashion to the overall activity of the gene they control. In addition, multiple Crx-binding sites within CBRs cooperatively interact via precise spacing rules to generate optimal levels of transcription.
 
Overall design Crx ChIP-Seq analysis of C57BL/6 and Nrl-/- retinas. IgG ChIP-Seq was performed as a control. 1-2 replicates each.
 
Contributor(s) Langmann T, Corbo JC
Citation(s) 20693478
Submission date Jan 22, 2010
Last update date May 15, 2019
Contact name Thomas Langmann
E-mail(s) thomas.langmann@klinik.uni-regensburg.de
Phone +49-941-944-5423
Fax +49-941-944-5402
Organization name Institute of Human Genetics
Department University of Regensburg
Street address Franz-Josef-Strauss-Allee 11
City Regensburg
ZIP/Postal code 93042
Country Germany
 
Platforms (1)
GPL9185 Illumina Genome Analyzer (Mus musculus)
Samples (7)
GSM499736 Crx-ChIP-Seq, wt, 1
GSM499737 Crx-ChIP-Seq, wt, 2
GSM499738 IgG-ChIP-Seq, wt, 1
Relations
SRA SRP002186
BioProject PRJNA124083

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
GSE20012_RAW.tar 957.7 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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