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Sample GSM1489676 Query DataSets for GSM1489676
Status Public on Nov 08, 2015
Title AOM-DSS Bcl9/9l-KO tumor 5
Sample type SRA
 
Source name colorectal tumor
Organism Mus musculus
Characteristics tumor model: AOM-DSS
genotype/variation: Bcl9-loxP/loxP, Bcl9l-loxP/loxP, Vil-Cre
Extracted molecule total RNA
Extraction protocol Sample extraction: Macrodissected colon tumor sample, fresh frozen
Fresh frozen samples were homogenized manually with an RNAse free pestle. Total RNA was extracted using the NucleoSpin RNA kit (Macherey-Nagel, 740955.250) according to the manufacturer’s instructions.All samples were ethanol precipitated. RNA integrity of each sample was assessed using a Fragment Analyzer (Advanced Analytical).
Sequencing libraries were prepared with the TruSeq Stranded mRNA kit (Illumina, RS-122-2101) according to the manufacturer’s instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description Sample name: AOM_KO_5
Loss of Bcl9/9l proteins was assessed in chemically induced AOM-DSS murine colon tumors.
Data processing Basecalls performed using Illumina HiSeq Control Software 2.0.12.0, default parameters.
Demultiplexing-software: configureBclToFastq.pl from Casava 1.82 allowing 1 mismatch on index sequence.
Demultiplexed read files were mapped to a mouse reference transcriptome (GRCm38/mm10, Ensembl) with CLC genomics workbench 7.0.3 (CLC bio).
Counts of unique genes as defined by default settings of CLC software were exported (see respective processed files).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text matrix, unique gene counts (gene symbols obtained from mm10 assembly) as defined by default alignment settings using CLC genomics workbench 7.0.3 (CLC bio).
 
Submission date Aug 27, 2014
Last update date May 15, 2019
Contact name Andreas Moor
E-mail(s) andreas.moor@bsse.ethz.ch
Organization name ETH Zurich
Department Department of Biosystems Science and Engineering
Street address Mattenstrasse 26
City Basel
ZIP/Postal code 4058
Country Switzerland
 
Platform ID GPL17021
Series (1)
GSE60837 BCL9/9L-β-catenin Signaling is Associated With Poor Outcome in Colorectal Cancer
Relations
BioSample SAMN03010171
SRA SRX688718

Supplementary file Size Download File type/resource
GSM1489676_AOM_KO_5.txt.gz 189.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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