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Sample GSM1654346 Query DataSets for GSM1654346
Status Public on Jun 09, 2015
Title 21NT_H3K27me3_ChIPSeq
Sample type SRA
 
Source name Breast cancer cells
Organism Homo sapiens
Characteristics cell line: 21NT
cell type: Luminal cells
chip-antibody: H3K27me3
chip-antibody vendor: CST
chip-antibody cat. #: C36B11
Extracted molecule genomic DNA
Extraction protocol Following cell purification, cells were immediately cross-linked with formaldehyde (final concentration is 0.5%) at room temperature for 10 minutes. Cells were washed, lysed, and the DNA was fragmented with a Covaris S2 (Covaris). The fragmented DNA was incubated with a specific antibody for 8 hours. The immunoprecipitates were sequentially washed, reverse-crosslinked, and purified by AMPureXP Agencourt Bioscience). ChIP-ed DNA was end-repaired by END-It DNA End Repair Kit (Epicentre), and adaptor oligo (Life technologies) was ligated and subjected to PCR amplification (15 cycles) using specific primers provided by the Life technologies. The PCR product was purified with AMPureXP and the emulsion PCR performed according to the manufacturer's instructions and sequenced by SOLiD4 (Life technologies).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model AB SOLiD 4 System
 
Data processing Basecalls performed using the SOLiD4 Pipeline.
ChIP-seq reads were aligned to the hg18 (March, 2006) human genome assembly using bowtie version 0.12.7 with default configuration.
peaks were called using SICER version 1.03 with the following setting: Window size (200bp), Gap size (600bp), Other parameters (default).
Genome_build: hg18
Supplementary_files_format_and_content: Bed files were generated using SICER. Each raw represents each peak detected by SICER. Numbers in the fifth column represent enrichment scores calculated by SICER.
 
Submission date Apr 08, 2015
Last update date May 15, 2019
Contact name Kornelia Polyak
E-mail(s) kornelia_polyak@dfci.harvard.edu
Phone 617-632-2106
Organization name Dana-Farber Cancer Institute
Department Medical Oncology
Lab Polyak
Street address 450 Brookline Ave
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
 
Platform ID GPL13393
Series (2)
GSE38548 Somatic cell fusions reveal extensive heterogeneity in basal-like breast cancer
GSE38789 Somatic cell fusions reveal extensive heterogeneity in basal-like breast cancer [ChIP-Seq 2]
Relations
BioSample SAMN03466594
SRA SRX984106

Supplementary file Size Download File type/resource
GSM1654346_21NT_H3K27me3-W200-G600.probscoreisland.gz 839.3 Kb (ftp)(http) PROBSCOREISLAND
GSM1654346_21NT_H3K27me3.bed.gz 293.7 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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