|
| Status |
Public on Sep 26, 2017 |
| Title |
KP rep1 |
| Sample type |
SRA |
| |
|
| Source name |
lung adenocarcinoma cells
|
| Organism |
Mus musculus |
| Characteristics |
mouse genotype: LSL-KrasG12D; p53 fl/fl
replicate: 1
|
| Growth protocol |
Primary murine lung adenocarcinoma cells were obtained from p53 fl/fl; LSL-Kras-G12D (KP) or KP; cJun fl/fl (JKP) mice. Briefly, lung tumors were isolated macroscopically from mice 12 weeks post infection with AdV-CMV-Cre, subjected to collagen digest and then cultured on standard tissue culture plates in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with Pen/Strep and 10% fetal calf serum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the RNeasy Mini Kit (QIAGEN) according to the manufacturer's instructions
mRNA-seq libraries were prepared using TruSeq RNA Library Preparation Kit v2 (Illumina) according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were mapped and quantified to mm10 whole genome and refseq transcript RSEM v 1.2.11 (including bowtie v2.1.0) with parameters --bowtie2-sensitivity-level very_sensitive --estimate-rspd
Genome_build: mm10
Supplementary_files_format_and_content: Quantified reads were normalised by DESeq2 v1.10.1 in R v3.2, and saved in R-readable rds format.
|
| |
|
| Submission date |
Sep 27, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Gavin Kelly |
| Organization name |
Francis Crick institute
|
| Lab |
Bioinformatics
|
| Street address |
1 Midland Road
|
| City |
London |
| State/province |
London |
| ZIP/Postal code |
NW1 1AT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE87387 |
RNA-seq of primary murine lung adenocarcinoma cells from KP and JKP mice |
|
| Relations |
| BioSample |
SAMN05829393 |
| SRA |
SRX2193277 |
