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Sample GSM1892611 Query DataSets for GSM1892611
Status Public on Apr 25, 2016
Title CM11 - FF H3K4ME2-ChIPseq
Sample type SRA
Source name Primary colonic mucosa
Organism Homo sapiens
Characteristics tissue: Snap-frozen tissue
antibody: H3K4me2 (Millipore, 07-030)
Treatment protocol sections of 10 μm thickness were scraped into plastic tubes and treated with 0.2 U micrococcal nuclease (Sigma Aldrich) for 8 min at 37oC, followed by ChIP with 10 µg H3K4me2 Ab. DNA libraries were prepared using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a HiSeq2000 instrument (Illumina)
Extracted molecule genomic DNA
Extraction protocol
For ChIPseq:ThruPLEX-FD kits (Rubicon Genomics) was used and 75 bp single-end reads were sequenced on a NextSeq 500 instrument (Illumina). For RNAseq: TruSeq RNA Sample Preparation Kit (Illumina) was used according to the manufacturer's instructions and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
Description H3K4me2 in H3K4me2 bw file in colonic mucosa from patient 11 CRC
Data processing Alignment: For ChIPseq experiments we used Bowtie2 (2.1.0) with settings (--no-unal). For RNAseq we used Tophat, version 2.0.9, default options.
For big wiggle generation we used MACS analysis.
RNAseq analyses: normalized and differential expression: Cufflinks, version 2.2.1; settings: -b, -u, and default; Cuffmerge was used with reference gtf and default settings; Cuffquant was used with default settings; Cuffnorm was used with default settings; Cuffdiff was used with -b, -u and default settings.
Supplementary_files_format_and_content: RNAseq: Individual samples have an FPKM gene tracking file from Cufflinks, estimating transcript abundance for that sample, along with confidence intervals. There are two processed data matrices that apply to all the samples.
Genome_build: Hg19
Supplementary_files_format_and_content: Bigwiggle files
Submission date Sep 24, 2015
Last update date May 15, 2019
Contact name Ramesh Shivdasani
Organization name Dana Farber Cancer Institute
Department Medical Oncology
Lab Shivdasani
Street address 450 Brookline Ave. Dana 720D
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
Platform ID GPL18573
Series (1)
GSE73398 Fixed tissue ChIP-Seq (FiT-Seq) of archived clinical samples reveals chromatin dynamics and tumor-specific enhancer profiles
BioSample SAMN04110969
SRA SRX1286278

Supplementary file Size Download File type/resource 291.9 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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