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Sample GSM1892622 Query DataSets for GSM1892622
Status Public on Apr 25, 2016
Title CM5 - FFPE RNAseq
Sample type SRA
 
Source name Primary colorectal cancer
Organism Homo sapiens
Characteristics tissue: FFPE
Treatment protocol 5 sections of 10 μm thickness were scraped into plastic tubes and RNA was isolated with trizol
Extracted molecule total RNA
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 RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description H3K4me2 bw file in colonic mucosa from patient 5 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
E-mail(s) ramesh_shivdasani@dfci.harvard.edu
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
Relations
BioSample SAMN04110980
SRA SRX1286289

Supplementary file Size Download File type/resource
GSM1892622_CM_5.genes.fpkm_tracking.gz 672.1 Kb (ftp)(http) FPKM_TRACKING
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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