|
Status |
Public on Jul 31, 2017 |
Title |
T23/emp RNA-Seq |
Sample type |
SRA |
|
|
Source name |
T23/emp organoid
|
Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 cell type: Mouse PDA primary tumor organoid (T23) peturbation: Transduced with MSCV/emp retrovirus
|
Treatment protocol |
For cDNA overepxression, cDNAs were retrovirally introduced and selected with G418. For shRNA expression, shRNAs were retrovirally introduced and selected with puromycin. For sgRNA expression, sgRNAs were lentivirally introduced and GFP-sorted with FACS.
|
Growth protocol |
Mouse/human PDA organoids or cell lines were cultured in conditions as described in this study.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNAs were extracted using Trizol reagent Libraries were made following the instructions of Illumina TruSeq RNA sample prep kit v2
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Data processing |
Raw reads were mapped to the reference mouse (mm9) or human (hg19) genome assembly with Tophat, and rpkm values were calucated with Cufflink Genome_build: mm9 and hg19
|
|
|
Submission date |
May 25, 2017 |
Last update date |
May 15, 2019 |
Contact name |
Jae Seok Roe |
E-mail(s) |
jroe@yonsei.ac.kr
|
Organization name |
Yonsei University
|
Street address |
Yonsei-ro, 50
|
City |
Seoul |
ZIP/Postal code |
03722 |
Country |
South Korea |
|
|
Platform ID |
GPL19057 |
Series (2) |
GSE99310 |
Enhancer reprogramming promotes pancreatic cancer progression and metastasis [RNA-seq] |
GSE99311 |
Enhancer reprogramming promotes pancreatic cancer progression and metastasis |
|
Relations |
BioSample |
SAMN07168841 |
SRA |
SRX2858122 |