|
| Status |
Public on Dec 07, 2017 |
| Title |
575A S427F DMSO 3 |
| Sample type |
SRA |
| |
|
| Source name |
urinary bladder carcinoma cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: bladder
cell line: 575A
passages: 8
drug treatment: 0.1% DMSO
|
| Treatment protocol |
Cells were cultured in 0.1% DMSO or 1 uM pioglitazone for 16-17 hours prior to RNA extraction
|
| Growth protocol |
Cells were seeded in biological triplicate in 6-well tissue culture plates at 300,000 cells (JMSU-1) or 125,000 (575A) cells per well. 48 hours later, 0.1% DMSO or 1 µM pioglitazone was added to cells. RNA was isolated 16-17 hours after addition of drugs. Cells were cultured in recommended medium supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin, and 1x GlutaMAX Supplement. Cells were grown at 37°C in 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy Mini Kit (Qiagen) was used to isolate RNA from cell pellets
Ribosomal RNA was removed by poly-A selection using Oligo-dT beads. mRNA was then fragmented and reverse transcribed to yield double stranded cDNA using random hexamers. cDNA was blunt ended, had an A base added to the 3’ ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12 cycles using primers incorporating unique index tags.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Basecalling with Illumina RTA 1.18.64 for the HiSeq 2500 samples and Illumina RTA 2.7.3 for the HiSeq 3000 samples
Demultiplexing with custom demultipler written in python
Technical replicate fastq files were combined and aligned with STAR 2.0.4b
Gene counts dervied with Subread:featureCount 1.45 and annotated with Ensembl Biomart
Genome_build: Ensembl GRCh38.76
Supplementary_files_format_and_content: Gene counts in tab-delimitted text table
|
| |
|
| Submission date |
Dec 05, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Vivek K Arora |
| E-mail(s) |
arorav@wustl.edu
|
| Organization name |
Washington University School of Medicine
|
| Street address |
660 S Euclid Ave
|
| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (2) |
| GSE107735 |
Bladder-cancer-associated mutations in RXRA activate peroxisome proliferator-activated receptors to drive urothelial proliferation |
| GSE107783 |
Bladder cancer associated mutations in RXRA activate peroxisome proliferator-activated receptors |
|
| Relations |
| BioSample |
SAMN08138367 |
| SRA |
SRX3450353 |
