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| Status |
Public on Apr 08, 2013 |
| Title |
FAIRE_Islet |
| Sample type |
SRA |
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| Source name |
Pancreatic islets
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Pancreatic islets
individual/replicate: Sample 3
f-seq parameter: L=600, T=8
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| Growth protocol |
Cord blood-derived CD34+ hematopoietic progenitor cells from two unrelated individuals were differentiated in vitro into either megakaryocytes in the presence of thrombopoietin (TPO) and interleukin-1β (IL-1β), or erythroblasts in the presence of erythropoietin (EPO), interleukin-3 (IL-3) and stem cell factor (SCF). Monocytes were purified from peripheral blood from another two individuals. CHRF-288-11 cells were cultured as previously described (D.S. Paul et al, 2011, PLoS Genet 7(6), e1002139).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
FAIRE DNA was processed following the Illumina paired-end library generation protocol.
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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 |
We retrieved FAIRE sequencing data for the erythroblastoid cell line K562 (GSM864361) and pancreatic islets ('sample 3'; GSM491290), and reanalyzed these data sets using the same methodology as described below.
Raw sequence reads were aligned to the human reference sequence (NCBI build 37, hg19) using the read mapper Stampy.
Reads were realigned around known insertions and deletions, followed by base quality recalibration using the Genome Analysis Toolkit (GATK). Duplicates were flagged using the software Picard and excluded from subsequent analyses.
Regions of enrichment (peaks) were determined using the software F-Seq v1.84. We applied a feature length of L=600 bp and two different standard deviation thresholds of T=6.0 (‘moderate’) and T=8.0 (‘stringent’) over the mean across a local background. For the K562 and pancreatic islets single-end sequencing data sets, we adjusted the mode of the peak width distribution to the mean of the modes across all non-K562 cells/pancreatic islets.
In order to reduce false-positive peak calls, we removed regions of collapsed repeats, applying a threshold of 0.1% (http://eqtl.uchicago.edu/Masking).
For comparison of cell type-specific chromatin profiles, we merged all read fragments into one data set for each cell type and then called peaks as described.
Genome_build: hg19
Supplementary_files_format_and_content: Peak files in bed format, with the following columns: chromosome, peak start, peak end, name, F-Seq score.
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| Submission date |
Oct 26, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Dirk Stefan Paul |
| E-mail(s) |
dp5@sanger.ac.uk
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| Organization name |
Wellcome Trust Sanger Institute
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| Department |
Human Genetics
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| Street address |
Wellcome Trust Genome Campus
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| City |
Hinxton |
| ZIP/Postal code |
CB10 1SA |
| Country |
United Kingdom |
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| Platform ID |
GPL9115 |
| Series (1) |
| GSE37916 |
FAIRE-seq in primary human megakaryocytes, erythroblasts and monocytes |
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| Relations |
| Reanalysis of |
GSM491290 |
| BioSample |
SAMN02051948 |
| SRA |
SRX016328 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1026917_Peaks_Islet_t8_l600.bed.gz |
282.9 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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