|
| Status |
Public on Mar 01, 2017 |
| Title |
RT4 GSK343 rep 2_7days |
| Sample type |
SRA |
| |
|
| Source name |
RT4 GSK343
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Urothelial Bladder Carcinoma Cell line
genotype: wildtype
|
| Treatment protocol |
Urothelial bladder carcinoma cel lnese were treated with GSK343 (1 uM) for 14 days prior RNA extraction
|
| Growth protocol |
Urothelial bladder carcinoma cell lines were maintained under 10% FBS contained culture medium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) 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 2000 |
| |
|
| Description |
D7-RT4-T2_TAGCTT
|
| Data processing |
Illumina Casava1.9 software was used for basecalling
Sequenced reads were trimmed for adaptor sequence,, then mapped to hg19 whole genome using STAR-2.3.0e with parameters --outSAMstrandField intronMotif
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks-2.1.1 with parameters -b -u --max-bundle-frags 100000000
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each Sample
|
| |
|
| Submission date |
Dec 21, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiaoran Chai |
| E-mail(s) |
chaix@gis.a-star.edu.sg
|
| Organization name |
Genome Institute of Singapore
|
| Street address |
60 Biopolis Street, Genome, #02-01
|
| City |
Singapore |
| State/province |
Singapore |
| ZIP/Postal code |
138672 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE92723 |
Transcriptome analysis for KDM6A mutated urothelial bladder carcinoma and EZH2 inhibitor treated KDM6A mutated urothelial bladder carcinoma |
|
| Relations |
| BioSample |
SAMN06173527 |
| SRA |
SRX2439448 |
