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Sample GSM1975202 Query DataSets for GSM1975202
Status Public on Sep 28, 2016
Title GCC082_mem
Sample type SRA
 
Source name Gastric Primary Sample
Organism Homo sapiens
Characteristics primary sample type (t=tumor, n=normal): N
tissue: Gastric Primary Sample
chip antibody: H3K4Me3
Extracted molecule genomic DNA
Extraction protocol Fresh-frozen cancer and normal tissues were dissected using a razor blade in liquid nitrogen to obtain ~5mg sized pieces for each ChIP. Tissue pieces were fixed in 1% formaldehyde/PBS buffer for 10 min at room temperature. Fixation was stopped by addition of glycine to a final concentration of 125 mM. Tissue pieces were washed 3 times with TBSE buffer. For cell lines, 1 million fresh harvested cells were fixed in 1% formaldehyde/medium buffer for 10 minutes (min) at room temperature. Fixation was stopped by addition of glycine to a final concentration of 125 mM. Fixed cells were washed 3 times with TBSE buffer, and centrifuged (5,000 r.p.m., 5 min). Pelleted cells and pulverized tissues were lysed in 100 ┬Ál 1% SDS lysis buffer and sonicated to 300-500bp using a Bioruptor (Diagenode). ChIP was performed using the following antibodies: H3K4me3 (07-473, Millipore); H3K4me1 (ab8895, Abcam); H3K27ac (ab4729, Abcam).
library construction protocol: 30ng of amplified DNA was used for each sequencing library preparation (New England Biolabs). 8 libraries were multiplexed (New England Biolabs) and sequenced on 2 lanes of a Hiseq2500 sequencer (Illumina) to an average depth of 20-30 million reads per library.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Data processing Sequencing reads were trimmed (10bp from front and back) and mapped against human genome reference hg19 using the Burrows-Wheeler Aligner (BWA) (version 0.6.2) 'mem' algorithm.
We filtered reads based on their mapping quality (MAPQ) and used uniquely mapped reads to perform peak calling using CCAT v3.0 [local FDR < 0.05]
Genome_build: hg19
Supplementary_files_format_and_content: interval format for ucsc genome browser, including 8 columns: "chromosome" "position of the peak" "start of region" "end of region" "read counts in ChIP library" "read counts in control library" "fold-change score" "local FDR"
 
Submission date Dec 18, 2015
Last update date May 15, 2019
Contact name Aditi Qamra
E-mail(s) qamraa99@gis.a-star.edu.sg
Organization name GIS
Street address 60 Biopolis Street, Genome, #02-01
City Singapore
ZIP/Postal code 138672
Country Singapore
 
Platform ID GPL11154
Series (2)
GSE76153 Epigenomic Profiling of Primary Gastric Adenocarcinoma Reveals Super-enhancer Heterogeneity [ChIP-seq]
GSE85467 Epigenomic Profiling of Primary Gastric Adenocarcinoma Reveals Super-enhancer Heterogeneity
Relations
Reanalysis of GSM1969647
BioSample SAMN04350732
SRA SRX1491604

Supplementary file Size Download File type/resource
GSM1975202_GCC082.interval.txt.gz 150.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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