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Sample GSM2877320 Query DataSets for GSM2877320
Status Public on Dec 07, 2017
Title 575A RXRA WT Pio 1
Sample type SRA
 
Source name urinary bladder carcinoma cells
Organism Homo sapiens
Characteristics tissue: bladder
cell line: 575A
passages: 8
drug treatment: 1 uM pioglitazone
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 SAMN08138372
SRA SRX3450348

Supplementary file Size Download File type/resource
GSM2877320_575a_rxra_wt_pio_1_gene_counts.txt.gz 3.5 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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