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| Status |
Public on Nov 08, 2013 |
| Title |
VAS050_H3K27ac |
| Sample type |
SRA |
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| Source name |
pancreatic islets, H3K27ac ChIP
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| 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)
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| 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.
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| 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).
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| 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.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
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| 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.
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| Submission date |
Nov 08, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Francis S Collins |
| E-mail(s) |
collinsf@mail.nih.gov
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| Organization name |
NHGRI
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| Department |
Genome Technology Branch
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| Lab |
Molecular Genetics Section
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| Street address |
1 Center Drive, Rm 126
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN02400892 |
| SRA |
SRX375323 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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