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Status |
Public on Nov 08, 2015 |
Title |
AOM-DSS Bcl9/9l-KO tumor 3 |
Sample type |
SRA |
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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.
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
Sample name: AOM_KO_3 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).
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|
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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 |
SAMN03010169 |
SRA |
SRX688716 |