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Sample GSM1261674 Query DataSets for GSM1261674
Status Public on Nov 08, 2013
Title VAS050_H3K27ac
Sample type SRA
 
Source name pancreatic islets, H3K27ac ChIP
Organism Homo sapiens
Characteristics tissue: pancreatic islets
Sex: F
age: 47
purity: 85
viability: 90
chip antibody: rabbit anti-H3K27ac (Abcam ab4729, lots 961080, GR45851-1)
Treatment protocol 12,000-16,000 islet equivalents (12-16 million cells) from each sample were crosslinked in 1% formaldehyde for 20 minutes at room temperature, flash frozen in liquid nitrogen, and stored at -80 C.
Growth protocol Fresh human pancreatic islets were obtained from the Islet Cell Resource (ICR) and National Disease Research Interchange (NDRI). Upon receipt, islets were warmed to 37 C in CMRL shipping medium for 1-2 hours. After equilibration, islets were washed with calcium- and magnesium-free Dulbecco's phosphate-buffered saline (Invitrogen, Carlsbad, CA).
Extracted molecule genomic DNA
Extraction protocol Crosslinked chromatin was prepared and immunoprecipitated as described in Stitzel ML, et al. (Cell Metab, 2010).
Libraries were prepared and sequenced using standard Illumina protocols for GAII.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
 
Data processing Base calling was performed by CASAVA version 1.8.
Reads that fail Illumina chastity filter were removed.
Reads were mapped to hg19 using BWA version 0.5.8c with default parameters.
Duplicate reads were removed using samtools rmdup.
Reads from all islets were combined for each epitope prior to running ChromHMM analysis.
Chromatin states were learned jointly by applying the ChromHMM (version 1.02) hidden Markov model (HMM) algorithm at 200 bp resolution to seven data tracks (Input, CTCF, K27ac, K27me3, K36me3, K4me1, K4me3) from each of the ten cell types, as previously described in Ernst J et al. (Nature, 2011).
We ran ChromHMM with a range of possible states, and settled on a 12 state model as it accurately captured information from higher state models and provided sufficient resolution to identify biologically meaningful patterns in a reproducible way.
Genome_build: GRCh37
Supplementary_files_format_and_content: Integrated chromHMM BED file.
 
Submission date Nov 08, 2013
Last update date May 15, 2019
Contact name Francis S Collins
E-mail(s) collinsf@mail.nih.gov
Organization name NHGRI
Department Genome Technology Branch
Lab Molecular Genetics Section
Street address 1 Center Drive, Rm 126
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL9115
Series (2)
GSE51311 Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants (ChIP-seq)
GSE51312 Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants
Relations
BioSample SAMN02400892
SRA SRX375323

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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