|
Status |
Public on Mar 20, 2023 |
Title |
C5 wt rep2 |
Sample type |
SRA |
|
|
Source name |
normal intestinal mucosa
|
Organism |
Mus musculus |
Characteristics |
strain: CSS C57BL/6 chr5 PWD genotype: wild type tissue: normal intestinal mucosa age: 15-19 weeks
|
Extracted molecule |
total RNA |
Extraction protocol |
Intestinal tissue as indicated was processed using the Qiagen Allprep RNA/DANN Kit according to manufacturer's instructions. For RNA sequencing, 4 µg of total RNA were depleted for ribosomal RNA using the RiboMinus Eukaryote Kit for RNA-seq (Invitrogen) following the manufacturer’s instructions. The RiboMinus depleted RNA was then used for the generation of single-end RNA-seq libraries. cDNA libraries were size selected on a 2% agarose gel, fragments of 150-200 nt were excised (corresponding to insert sizes of 80-130 nt) and purified using the QiaQuick Gel extraction kit (Qiagen). Sequencing was performed on an Illumina Genome Analyser IIx.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina Genome Analyzer IIx |
|
|
Description |
C5_wt_2 processed data file: modifiers_rnaseq_counts.csv
|
Data processing |
Alignment of RNA-seq reads to the PWD(assembly)/B6(mm10) mixed reference using bwa. PWD reads are mapped to their corresponding position in the mm10 reference genome. Quantification of reads per gene with htseq-count Genome_build: mm10/PWD assembly version 2b Supplementary_files_format_and_content: modifiers_rnaseq_counts.csv: Comma-separated text file with RNA-seq read counts per gene.
|
|
|
Submission date |
Apr 09, 2020 |
Last update date |
Mar 20, 2023 |
Contact name |
Markus Morkel |
E-mail(s) |
markus.morkel@charite.de
|
Organization name |
Max Planck Institute for molecular Genetics
|
Street address |
Ihnestraße 63-73
|
City |
Berlin |
ZIP/Postal code |
14195 |
Country |
Germany |
|
|
Platform ID |
GPL11002 |
Series (2) |
GSE148365 |
Intestinal cancer modifier RNA-Seq |
GSE148370 |
PWD/Ph-encoded genetic variants suppress ApcMin-triggered intestinal tumor formation by modulating the cellular Wnt/beta-Catenin response |
|
Relations |
BioSample |
SAMN14567055 |
SRA |
SRX8089807 |