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| Status |
Public on Feb 02, 2018 |
| Title |
FOXA1 ChIP-seq Female_1 |
| Sample type |
SRA |
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| Source name |
Human breast tumor
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| Organism |
Homo sapiens |
| Characteristics |
antibody: FOXA1
patient id: Female_1
tissue: Human breast tumor
Sex: female
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tissue was defrosted and crosslinked in solution A (50 mM Hepes, 100 mM NaCl, 1mM EDTA, 0.5 mM EGTA, pH= 7.4) containing 2 mM DSG, incubated for 25 minutes at room temperature while rotating. After 25 minutes formaldehyde was added to 1% final and incubated another 20 minutes at room temperature with rotation. Samples were quenched by adding a surplus of 0.2M glycine, pelleted by centrifugation (5'@4000rcf 4°C), washed with cold PBS and mechanically disrupted in cold PBS using a pellet pestle (Sigma). The PicoBioruptor (Diagenode) was used for sonication. For ChIP, antibodies were used to detect ERα (sc-543, Santa Cruz), AR (sc-816, Santa Cruz), FOXA1 (sc-6554, Santa Cruz), PR (sc-7208, Santa Cruz), GR (12041S lot 3, Cell Signaling Technology) and H3K4me1 (ab8895, AbCam). Immunoprecipitated DNA was prepared for Illumina multiplex-sequencing with 10 samples per lane at 65bp single end. For steroid hormone receptor ChIPs, 5µg of antibody and 50µl dynabeads (Invitrogen) were used, for FOXA1 and H3K4me1, 4µg of antibody and 40µl magnetic beads were used.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Sequences were generated by the Illumina Hiseq 2000 genome analyser (using 50bp reads) and were processed by the Illumina pipeline.
Reads were aligned to the Human Reference Genome (hg19) using BWA version 0.5.9. Reads with a BWA alignment quality score less than 20 were removed.
Peaks were called using DFilter (Kumar V et al. Nat Biotechnol 2013;31(7):615-22) and MACS peak caller version 1.4 (Zhang Y et al. Genome Biol 2008;9(9):R137). Only peaks called by both algorithms were used for the analysis. MACS was run with the default parameters, except p=10-7 for ChIP-seq data. DFilter was run with bs=100, ks=50 for FAIRE data and bs=50, ks=30, refine, nonzero for ChIP data.
Genome_build: hg19
Supplementary_files_format_and_content: peak.intersect files contain peaks called by both peak calling algorithms in bed format
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| Submission date |
Sep 28, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Wilbert Zwart |
| E-mail(s) |
w.zwart@nki.nl
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| Organization name |
The Netherlands Cancer Institute
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| Street address |
Plesmanlaan 121
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| City |
Amsterdam |
| ZIP/Postal code |
1066 CX |
| Country |
Netherlands |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE104399 |
Characterizing steroid hormone receptor chromatin binding landscapes in male and female breast cancer |
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| Relations |
| BioSample |
SAMN07716689 |
| SRA |
SRX3229123 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2797077_wz1975.peak.intersect.bed.gz |
275.8 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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