 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 30, 2014 |
| Title |
CHG051 |
| Sample type |
SRA |
| |
|
| Source name |
Gastric Primary Sample
|
| Organism |
Homo sapiens |
| Characteristics |
tissuetype: Tumor
chip antibody: H3K27me3
reads length: 36
|
| 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 (~ 5 ml by apparent volume). Tissue pieces were fixed in 1% formaldehyde/TBSE buffer for 10 minutes (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, and transferred into Lysonator cartridges (SG Microlab Devices, Singapore). Tissues were dissociated following the manufacturer’s guidelines (4K Hz for 3 min), and taken directly to the lysis step in the Nano ChIP assay. Dissociated tissues were lysed in 200 ml of lysis buffer and divided into two 1.5 ml tubes for sonication (6 min) using a Bioruptor (Diagenode). 5 CHiPs were performed on individual chromatin preparations using the following antibodies: H3K4me3 (07-473, Millipore); H3K4me1 (ab8895, Abcam); H3K27ac (ab4729, Abcam); H3K36me3 (ab9050, Abcam); H3K27me3 (07-449, Millipore).
Amplified DNA was digested with BpmI (New EngliandBiolabs), ligated to a 2ndBpmI adaptor and digested again to trim the WGA primer regions and semi-random priming ends. 15 ng of amplified DNA was used for each Illumina sequencing library using the ChIPseq kit (Illumina). Each library was sequenced on one lane of HiSeq2000 to obtain either 36- or 101-base single reads.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Sequencing tags were mapped against the human reference genome (hg19) using Burrows-Wheeler Aligner (BWA)
101-base reads were trimmed by the first and last 10-base to increase SNP call performance.
Uniquely mapped tags were used for peak calling by CCAT version 3.0.
Peak regions were filtered by a p-value cut-off of 0.05 for all marks except for H3K27me3 for which 1.5-fold above input was used to filter peak regions. For each histone modification, peak regions from all tissue samples were pooled, and overlapping peak regions were merged to create a total set of peak regions for that modification.
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 |
Oct 28, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Niantao Deng |
| Organization name |
Duke NUS Graduate Medical School
|
| Street address |
Center for Computational Biology, level 6, 8 College Road
|
| City |
Singapore |
| State/province |
Singapore |
| ZIP/Postal code |
169857 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE51776 |
Nanoscale Chromatin Profiling of Gastric Adenocarcinoma |
|
| Relations |
| BioSample |
SAMN02385110 |
| SRA |
SRX369098 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1252301_2000986T_H3K27me3.interval.txt.gz |
246.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
