|
| Status |
Public on Aug 21, 2018 |
| Title |
CAF_58 |
| Sample type |
SRA |
| |
|
| Source name |
cancer fibroblast
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
borrman classification: type 4
cell line: CAF
tissue: stomach
|
| Growth protocol |
NFs or CAFs cells were cultured in RPMI 1640 containing 10% fetal bovine serum.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA were extracted from NFs or CAFs cells using an miRNeasy Mini Kit (Qiagen).
Two micrograms of total RNA was used to create libraries with illumina TruSeq RNA Sample Prep Kit v2 (illumina, San Diego, California, USA) according to manufacturer’s instructions. Samples successfully meeting the size and concentration criteria were pooled at equimolar concentrations. Two samples with unique index-tag adapter sequences were combined for multiplex NGS in each lane on the illumina HiSeq 2000 (Illumina, San Diego, California, USA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Sequencing reads were mapped against human genome reference hg19 using Tophat2.
Transcript abundances were estimated by cufflinks-2.2.0 suite and the expression was reported in Fragments per Kilo base of exon per Million fragments mapped (FPKM)
Genome_build: hg19
|
| |
|
| Submission date |
Jun 28, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Tannistha Nandi |
| E-mail(s) |
nandit@gis.a-star.edu.sg
|
| Phone |
68088125
|
| Organization name |
Genome Institute of Singapore
|
| Department |
Cancer Therapeutics & Stratified Oncology
|
| Street address |
60 Biopolis Street, Genome, #02-01
|
| City |
Singapore |
| ZIP/Postal code |
138672 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE83834 |
RHBDF2 in Stromal Fibroblasts Mediates TGF-b Signal and Enhances Cancer Cell Invasion via Intercellular Cross-Talk |
|
| Relations |
| BioSample |
SAMN05323745 |
| SRA |
SRX1884198 |
