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| Status |
Public on Apr 08, 2013 |
| Title |
FAIRE_CHRF_1_2 |
| Sample type |
SRA |
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| Source name |
Cell culture
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| Organism |
Homo sapiens |
| Characteristics |
cell type: CHRF-288-11
individual/replicate: Repl-1 + Repl-2
f-seq parameter: L=600, T=6 and 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 HiSeq 2000 |
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| Description |
This sample includes bed files from two different standard deviation thresholds (T=6.0 and T=8.0) from two biological replicates and a bed file from the replicates combined.
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| Data processing |
We obtained the raw sequence files from two independent FAIRE experiments in K562 erythroblastoid cells from the ENCODE Project (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/) and remapped the data as described below. For the K562 single-end sequencing data set, we adjusted the mode of the peak width distribution to the mean of the modes across all non-K562 cell types.
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.
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 the 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 |
May 10, 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 |
GPL11154 |
| Series (1) |
| GSE37916 |
FAIRE-seq in primary human megakaryocytes, erythroblasts and monocytes |
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| Relations |
| SRA |
SRX147735 |
| SRA |
SRX147736 |
| BioSample |
SAMN00993278 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM929901_Peaks_CHRF_1_2_t6_l600.bed.gz |
3.3 Mb |
(ftp)(http) |
BED |
| GSM929901_Peaks_CHRF_1_2_t8_l600.bed.gz |
1.7 Mb |
(ftp)(http) |
BED |
| GSM929901_Peaks_CHRF_1_t6_l600.bed.gz |
1.9 Mb |
(ftp)(http) |
BED |
| GSM929901_Peaks_CHRF_1_t8_l600.bed.gz |
948.1 Kb |
(ftp)(http) |
BED |
| GSM929901_Peaks_CHRF_2_t6_l600.bed.gz |
1.9 Mb |
(ftp)(http) |
BED |
| GSM929901_Peaks_CHRF_2_t8_l600.bed.gz |
988.7 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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