|
| Status |
Public on Nov 08, 2015 |
| Title |
APC-KRAS Bcl9/9l-WT tumor 13 |
| Sample type |
SRA |
| |
|
| Source name |
colorectal tumor
|
| Organism |
Mus musculus |
| Characteristics |
tumor model: APC-KRAS
genotype/variation: APC-1638N/wt, Vil-KrasG12V/+, Bcl9-loxP/loxP, Bcl9l-loxP/loxP
|
| 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: BAK_13
Loss of Bcl9/9l proteins was assessed in a genetic model (mutated APC and Kras) of murine colon cancer.
|
| 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 |
SAMN03010187 |
| SRA |
SRX688734 |
