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Sample GSM1164233 Query DataSets for GSM1164233
Status Public on Oct 01, 2013
Title H3K27me3 ChIP-seq for GM18505
Sample type SRA
 
Source name lymphoblastoid cell line
Organism Homo sapiens
Characteristics cell line: GM18505
cell type: lymphoblastoid cell line
population: YRI
ethnicity: Yoruba
country of origin: Nigeria
chip antibody: H3K27me3 (Millipore 07-449)
chip antibody manufacturer: Millipore
chip antibody catalog #: 07-449
Biomaterial provider Coriell; http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM18505
Growth protocol Ten lymphoblastoid cell lines from unrelated Yoruba individuals were obtained from the Coriell Institute. Cells were grown in RPMI media with 15% FBS, supplemented with 2mM L-glutamate, 100 I.U./mL penicillin, and 100 ug/mL streptomycin.
Extracted molecule genomic DNA
Extraction protocol Chromatin was extracted using protocol described in Cain et al. 2011, except that for some samples chromatin was sheared with a Covaris S2 (settings: 40 min duty cycle 20%, intensity 8, 200 cycles/burst, 500 uL at a time in 12 x 24 mm tubes).
Prepared Illumina sequencing libraries as described by the ENCODE Project Consortium (2011), starting with 20 uL of ChIP output or 4 ng of pooled input sample.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
 
Data processing Basecalls by Illumina CASAVA 1.7.0
Mapped reads to hg18 using BWA 0.6.1, allowing up to 2 mismatches per read (-n 2), and excluding gapped alignments (-o 0)
Discarded reads that did not uniquely map, taking into account SNPs in YRI 1000 genomes samples as described in Degner 2012.
Discarded reads overlapping multiple SNPs and reads overlapping indels
Discarded duplicate reads mapping to same location and strand randomly (rather than retaining highest scoring)
Extracted reads in 2kb surrounding each segregating SNP and counted reads that could be assigned to each haplotype
Genome_build: hg18
Supplementary_files_format_and_content: Tab-delimited files containing all information used for tests of genetic association. Each row represents 2kb region flanking a test-SNP and gives total number of reads for one individual as well as number of allele-specific reads that can be assigned to each haplotype.
 
Submission date Jun 15, 2013
Last update date May 15, 2019
Contact name Graham McVicker
E-mail(s) gmcvicker@salk.edu
Organization name Salk Institute
Lab McVicker
Street address 10010 N Torrey Pines Rd
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platform ID GPL10999
Series (1)
GSE47991 Identification of genetic variants that affect histone modifications in human cells
Relations
SRA SRX306563
BioSample SAMN02204442

Supplementary file Size Download File type/resource
GSM1164233_H3K27me3_18505_read_counts.txt.gz 225.6 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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