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Sample GSM1126512 Query DataSets for GSM1126512
Status Public on Apr 22, 2013
Title T21_H2AZ_ChIP-Seq
Sample type SRA
Source name T21, 2nd pair, 1st individual
Organism Homo sapiens
Characteristics cell type: CD14 cells
individual identifier: T21
monozygotic twin relationship: MZ twin of T22
chip antibody: anti-H2A.Z (Active Motif, Cat no: 39113)
Extracted molecule genomic DNA
Extraction protocol The chromatin immunoprecipitation (ChIP) assay was performed on 5 x 105 CD14+ cells according to previously published protocols. Chromatin was sonicated to get fragments of 100-500 bp and immunoprecipitated with 10 ul of anti-H2A.Z antibody (Active Motif, Cat no: 39113). ChIP-seq libraries were prepared following the Illumina protocol and ligated to standard PE adaptors and sequenced on an Illumina GAIIx instrument.

Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
Description PE76
Data processing ChIP-seq reads were aligned to the reference sequence using bwa-0.6.6 then sorted and indexed using samtools
Read pairs with quality scores >=10 were extracted and the number of read pairs overlapping each probe on the Illumina HumanMethylation450K array were counted.
RNA-seq was aligned with TopHat 1.3.1 and FPKM values were generated using CuffLinks 1.0.3
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Fragment coverage across Illumina HumanMethylation450K probes (GEO Platform GPL13534) for ChIP data.
Supplementary_files_format_and_content: Transcript FPKM numbers for nearest TSS for RNA-seq data.
Submission date Apr 19, 2013
Last update date May 15, 2019
Contact name Thomas A Down
Organization name University of Cambridge
Department WT/CRUK Gurdon Institute
Street address Tennis Court Road
City Cambridge
ZIP/Postal code CB2 1QN
Country United Kingdom
Platform ID GPL10999
Series (2)
GSE46217 Inactive or moderately active human promoters are enriched for inter-individual epialleles [Seq]
GSE46220 Inactive or moderately active human promoters are enriched for inter-individual epialleles
BioSample SAMN02053614
SRA SRX268692

Supplementary file Size Download File type/resource
GSM1126512_T21_H2AZ_counts.txt.gz 1.8 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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