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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 18, 2013 |
| Title |
ER_XENO_REP1 |
| Sample type |
SRA |
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| Source name |
ER_XENO_ChIP
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| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF7
library id: JC546
antibody: ER; sc-534 (santa cruz) Lot-(HC-20)
treatment: MCF7 xenograft tumour in mouse
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| Treatment protocol |
Tamoxifen or ICI 182 drug treatments done at 100nM concentration for the indicated time
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| Growth protocol |
MCF7 cells were grown in DMEM with 10% FBS.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA extracted according to Schmidt D.(Methods,2009)
Library constructed according to Schmidt D.(Methods,2009)
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
Chromatin IP against ER
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| Data processing |
Single end 36-bp ChIP-seq data were generated by the Illumina analysis pipeline version 1.6.1. For samples JC830, JC832, JC888, JC907 and JC945, version 1.7.0 was used.
Reads were aligned to the Human Reference Genome (assembly hg18, NCBI Build 36.6, March 2008 using BWA version 0.5.5; Li and Durbin, 2010). For samples JC830, JC832, JC888, JC907 and JC945, reads were aligned to the Human Reference Genome (assembly hg18, NCBI Build 36.6, March 2008 using BWA version 0.6.1-r104; Li and Durbin, 2010).
Reads were filtered by an alignment quality score removing all reads with a score less than 15. For samples JC830, JC832, JC888, JC907 and JC945, reads were filtered by an mapping quality score removing all reads with a score less than 5.
Peaks were called using MACS, version 1.3.7.1. For samples JC830, JC832, JC888, JC907 and JC945, peaks were called using MACS, version 1.4.1.
Genome_build: hg18
Supplementary_files_format_and_content: MACS peak files in .bed format
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| Submission date |
Oct 12, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Chandra Chilamakuri |
| E-mail(s) |
datasubmissions@cruk.cam.ac.uk
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| Organization name |
Cancer Research UK Cambridge Institute
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| Street address |
Robinson Way
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| City |
Cambridge |
| ZIP/Postal code |
CB2 0RE |
| Country |
United Kingdom |
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| Platform ID |
GPL10999 |
| Series (1) |
| GSE41561 |
A novel proteomic approach reveals GREB1 as an Estrogen Receptor co-factor |
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| Relations |
| SRA |
SRX194575 |
| BioSample |
SAMN01765261 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1019131_SLX-3404.564.s_4_SLX-2574.433.s_2_peaks.bed.gz |
693.5 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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