|
| Status |
Public on Jul 01, 2018 |
| Title |
BM1107_mouse_10_allograft_DAC |
| Sample type |
SRA |
| |
|
| Source name |
subcutaneous allograft
|
| Organism |
Mus musculus |
| Characteristics |
model: KPC derived tumor cells allografted in syngeneic host mice
genotype: KrasG12D/+;Trp53R172H/+;Pdx-1-Cre
treatment: 1uM DAC, 3 consecutive days before SC injection
rin: 8.9
tissue: subcutaneous allograft
|
| Treatment protocol |
1uM, 5 uM or 10uM DAC during 3 consecutive days or 3 times every 48h
|
| Growth protocol |
For paradigm I and II, KPC cells were cultured in DMEM media, 10% FBS, 1% penicillin/streptomycin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using Trizol reagent (Invitrogen, MA, USA)
Poly-A pull-down was used to enrich for mRNAs, and libraries were prepared using the Illumina TruSeq RNA kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
1 month allograft tumors from pre-treated cultured KPC tumor cells, paradigm II
|
| Data processing |
Base calling using (RTA, Illumina, San Diego, CA, USA)
conversion of BCL to FASTQ format (bcl2fastq version 1.8.4)
adaptor trimming
alignment using Tophat version 2.0.4
Genome_build: USCS/mm9
Supplementary_files_format_and_content: FPKM matrix with gene ID, TSS ID and locus coordinates
|
| |
|
| Submission date |
Jul 12, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Tamas Gonda |
| E-mail(s) |
tg2214@columbia.edu
|
| Organization name |
Columbia University
|
| Department |
Department of Medicine, Division of Digestive and Liver Diseases
|
| Street address |
630 West 168th Street
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE101336 |
RNA-seq in KPC mice treated with a hypomethylating drug (decitabine) and in untreated KPC mice |
|
| Relations |
| BioSample |
SAMN07346900 |
| SRA |
SRX2998709 |
