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Series GSE67963 Query DataSets for GSE67963
Status Public on Jan 01, 2016
Title Widespread RNA Binding by Chromatin Associated Proteins
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Summary Recent evidence suggests that RNA interaction can regulate the activity and localization of DNA binding proteins, particularly chromatin-associated proteins. However, it is unknown if these observations are specialized instances for a few key RNAs and chromatin factors in specific contexts, or a general mechanism underlying the establishment of chromatin state and regulation of gene expression. Here, we introduce formaldehyde RNA ImmunoPrecipitation (fRIP-Seq), a sensitive method for cataloging RNA-protein interactions, to survey the RNA associated with a panel of 24 chromatin-associated and traditional RNA binding proteins. For each protein that reproducibly bound measurable quantities of bulk RNA (90% of the panel), we detected enrichment for hundreds to thousands of both noncoding and mRNA transcripts. We found that the enriched sets of RNA share biochemical, functional, and epigenetic properties. Thus, these data provide strong evidence that non-random RNA association is a common feature across diverse classes of chromatin modifying complexes.
Overall design RNA associated with 24 different proteins using fRIP was compared to total RNA-seq
Contributor(s) Hendrickson DG, Kelley DR
Citation(s) 26883116
Submission date Apr 16, 2015
Last update date May 15, 2019
Contact name David R Kelley
Phone 732-859-4305
Organization name Harvard University
Department Stem Cell and Regenerative Biology
Lab John Rinn
Street address 7 Divinity Ave.
City Cambridge
State/province MA
ZIP/Postal code 02138
Country USA
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (79)
GSM1659705 adar_rep1_fRIP-seq
GSM1659706 adar_rep2_fRIP-seq
GSM1659707 adar_rep3_fRIP-seq
BioProject PRJNA281382
SRA SRP057268

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
GSE67963_fpkm_table_genes.txt.gz 8.5 Mb (ftp)(http) TXT
GSE67963_fpkm_table_isoforms.txt.gz 40.0 Mb (ftp)(http) TXT
GSE67963_significance_calls_genes.txt.gz 41.8 Mb (ftp)(http) TXT
GSE67963_significance_calls_isoforms.txt.gz 165.0 Mb (ftp)(http) TXT
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Processed data are available on Series record

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