|
| Status |
Public on Jan 09, 2017 |
| Title |
KPCS 530 Hx |
| Sample type |
SRA |
| |
|
| Source name |
pancreatic ductal adenocarcinoma
|
| Organism |
Mus musculus |
| Characteristics |
strain: KrasG12D; p53R172H, Sf3b1 fl/f, Ptf1aCre
tissue: Pancreas
age: post natal 13 weeks
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Organoids were collected in RA1 buffer + TCEP, RNA was harvested using MN kit. Illumina TruSeq SR cluster kit v4-cBot-HS was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
data_norm.txt
DEA_hits.txt
|
| Data processing |
Starting from the raw .fastq files (1x81bp) the reads were mapped against the mouse reference genome and simultaneously soft‐clipped using the STAR aligner (version 2.4.2a).
Standard quality control (Picard, RSeQC, QoRTs was run to assess the quality of the resulting alignments. Subsequently, strand‐specific (reversely stranded) read counting was performed using featureCount (subread, version 1.5.0).
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files
|
| |
|
| Submission date |
Jan 06, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Cédric Cortijo |
| E-mail(s) |
cedric.cortijo@biol.ethz.ch
|
| Organization name |
ETHZ
|
| Department |
HPL
|
| Street address |
Otto-Stern-Weg 7
|
| City |
zurich |
| ZIP/Postal code |
8093 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE93279 |
RNA sequencing of organoids isolated from pancreatic cancer mouse model KRASG12D; p53R172H; Ptf1a-Cre. |
|
| Relations |
| BioSample |
SAMN06210696 |
| SRA |
SRX2470294 |
