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Status |
Public on Sep 28, 2016 |
Title |
CHG284 |
Sample type |
SRA |
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Source name |
Gastric Primary Sample
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Organism |
Homo sapiens |
Characteristics |
tissue: Gastric Primary Sample primary sample type (t=tumor, n=normal): N chip antibody: H3K27Ac
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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 µl 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.
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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 |
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) ‘aln’ 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"
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Submission date |
Dec 10, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Aditi Qamra |
E-mail(s) |
qamraa99@gis.a-star.edu.sg
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Organization name |
GIS
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Street address |
60 Biopolis Street, Genome, #02-01
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City |
Singapore |
ZIP/Postal code |
138672 |
Country |
Singapore |
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Platform ID |
GPL11154 |
Series (1) |
GSE75898 |
Somatic Promoter Landscape of Primary Gastric Adenocarcinoma Delineated by Epigenomic Profiling |
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Relations |
Reanalyzed by |
GSM1975108 |
BioSample |
SAMN04330379 |
SRA |
SRX1474442 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1969553_CHG284.interval.txt.gz |
389.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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