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Sample GSM608157 Query DataSets for GSM608157
Status Public on Nov 15, 2010
Title TR4_GM_ChIP-seq_rep1
Sample type SRA
 
Source name lymphoblastoid cell line
Organism Homo sapiens
Characteristics cell line: GM12878
harvest date: 2008-10-22
chip antibody: rabbit anti TR4 (JD Engel lab)
Biomaterial provider Coriell; http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM12878
Growth protocol All cells were grown according to ENCODE standards (http://genomewiki.ucsc.edu/EncodeDCC/index.php/Cell_lines)
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3 to 5 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer
 
Description Chromatin IP against TR4
Data processing Alignment: Sequence reads were obtained and mapped to the human genome assembly hg18 (March, 2006) or hg19 (February, 2009) using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows.
Peaks were called with Sole-Search (http://chipseq.genomecenter.ucdavis.edu/cgi-bin/chipseq.cgi)
 
Submission date Oct 13, 2010
Last update date May 15, 2019
Contact name Philip Cayting
E-mail(s) pcayting@stanford.edu
Organization name Stanford University
Department Genetics
Lab Snyder
Street address 1501 S California Ave
City Palo Alto
State/province CA
ZIP/Postal code 94304
Country USA
 
Platform ID GPL9052
Series (1)
GSE24685 Genome-wide binding of the orphan nuclear receptor TR4 suggests its general role in fundamental biological processes
Relations
SRA SRX028640
BioSample SAMN00115802

Supplementary file Size Download File type/resource
GSM608157_wgEncodeYaleChIPseqAlignmentsRep1Gm12878Tr4.TAGALIGN.gz 311.6 Mb (ftp)(http) TAGALIGN
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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