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Series GSE31332 Query DataSets for GSE31332
Status Public on Sep 29, 2011
Title Genomic maps of lincRNA occupancy reveal principles of RNA-chromatin interactions.
Organisms Drosophila melanogaster; Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Long intergenic noncoding RNAs (lincRNAs) are key regulators of chromatin state, yet the nature and sites of RNA-chromatin interaction are mostly unknown. Here we introduce Chromatin Isolation by RNA Purification (ChIRP), where tiling oligonucleotides retrieve specific lincRNAs and bound protein and DNA sequences, which are enumerated by deep sequencing. ChIRP-seq of two lincRNAs reveal that RNA binding sites in the genome are focal, sequence-specific, and numerous. Human telomerase RNA TERC occupies telomeres and Wnt pathway genes. HOTAIR lincRNA preferentially binds a GA-rich homopurine DNA motif to nucleate broad domains of Polycomb occupancy and histone H3 lysine 27 trimethylation. HOTAIR occupancy occurs independently of EZH2, defining the order of RNA guidance of Polycomb occupancy. ChIRP-seq is readily applicable to numerous RNAs in different cell types and biological states, thus enabling the study of RNA regulation of chromatin and gene expression at a genomic scale.
 
Overall design Examination of 3 lincRNAs in 5 cell types
 
Contributor(s) Chu C, Qu K, Chang H
Citation(s) 21963238
Submission date Aug 11, 2011
Last update date May 15, 2019
Contact name Kun Qu
E-mail(s) kqu@stanford.edu
Organization name Stanford University
Department Dermatology
Lab Howard Chang
Street address 269 Campus Dr. CCSR 2150
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platforms (2)
GPL9061 Illumina Genome Analyzer II (Drosophila melanogaster)
GPL9115 Illumina Genome Analyzer II (Homo sapiens)
Samples (14)
GSM820427 S2_roX2_even
GSM820428 S2_roX2_odd
GSM820429 S2_roX2_input
Relations
SRA SRP007863
BioProject PRJNA146003

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
GSE31332_RAW.tar.gz 328.7 Mb (ftp)(http) TAR
GSE31332_hela_merge.sam.gz 103.5 Mb (ftp)(http) SAM
GSE31332_hela_merge.txt.gz 4.8 Mb (ftp)(http) TXT
GSE31332_hela_peaks.bed.gz 24.8 Kb (ftp)(http) BED
GSE31332_hotair_oe_merge_MDA231.sam.gz 17.4 Mb (ftp)(http) SAM
GSE31332_hotair_oe_merge_MDA231.txt.gz 2.6 Mb (ftp)(http) TXT
GSE31332_hotair_oe_peaks.bed.gz 7.7 Kb (ftp)(http) BED
GSE31332_hotair_oe_shezh2_merge_MDA231.wig.gz 12.3 Mb (ftp)(http) WIG
GSE31332_lacz_MDA231.bedgraph.gz 82.3 Mb (ftp)(http) BEDGRAPH
GSE31332_rox2_merge_s2.sam.gz 47.6 Mb (ftp)(http) SAM
GSE31332_rox2_merge_s2.txt.gz 60.7 Mb (ftp)(http) TXT
GSE31332_rox2_peaks.bed.gz 2.4 Kb (ftp)(http) BED
GSE31332_terc_merge_supert.sam.gz 103.5 Mb (ftp)(http) SAM
GSE31332_terc_merge_supert.txt.gz 3.4 Mb (ftp)(http) TXT
GSE31332_terc_peaks.bed.gz 19.8 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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