|
| Status |
Public on Mar 20, 2023 |
| Title |
B6 or rep2_AZA |
| Sample type |
SRA |
| |
|
| Source name |
organoid
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: APC min
tissue: organoid
age: 15-19 weeks
treatment: 5-aza-cytidine
|
| 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 NextSeq 500 |
| |
|
| Description |
B6_or_2_AZA
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 |
GPL19057 |
| 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 |
SAMN14567097 |
| SRA |
SRX8089786 |
