|
| Status |
Public on Jun 26, 2024 |
| Title |
1650_2 |
| Sample type |
SRA |
| |
|
| Source name |
HT1376
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HT1376
treatment: PF-06821497
|
| Treatment protocol |
Mice were randomized and drug treatments were started 11-15 days after inoculation when tumors reached an average of 139-160 mm3; animals were distributed so that each treatment arm had a similar starting tumor size (3-21 animals per arm, depending on experiment and sampling schedule). Mice were treated with 75 mg/kg of each compound in a PO QD dosing schedule. The tumor were harvested 1hr post dosing at day 15.
|
| Growth protocol |
The HT1376 bladder cancer cell lines was expanded in vitro under routine subculturing procedures in the medium recommended by the supplier, harvested while in the exponential growth phase, and counted for tumor inoculation. Female CB17 SCID mice at 6-8 weeks of age were used for study initiation. Each mouse was inoculated subcutaneously in the right flank with tumor cells in 0.2 ml PBS mixed with Matrigel (BD Biosciences); 5x106 cells per injection were used for HT1376 cells.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were collected at indicated interim timepoints on treatment or at study endpoint for analysis at 1 hr post-dosing for pharmacokinetic (PK) and pharmacodynamic studies (PD), unless indicated otherwise. Tumors were split into two pieces (for PK and PD), snap-frozen in liquid nitrogen, then transferred to -80°C before analysis. Total RNA was extracted with Trizol, in accordance with the manufacturer’s protocol.
Sequencing libraries were constructed using the Illumina TruSeq RNA Sample Preparation Kit (v2). The resulting libraries were sequenced on an Illumina HiSeq 4000, with 9 samples multiplexed per lane. 2x150 base pair paired-end reads using the Illumina TruSeq strand specific protocol, for an expected 40 million reads per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Sequencing reads were mapped to the genome using STAR v2.7.3a with default settings
The transcript and gene read count quantification were performed using RSEM v1.3.1 with default settings
Genome_build: hg38
Supplementary_files_format_and_content: txt file: raw counts
|
| |
|
| Submission date |
Jun 09, 2021 |
| Last update date |
Jun 26, 2024 |
| Contact name |
Patrick Trojer |
| E-mail(s) |
patricktroj@gmail.com
|
| Organization name |
Constellation Pharmaceuticals
|
| Street address |
215 First Street, Suite 200
|
| City |
Cambridge |
| State/province |
Massachusetts |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE176485 |
Xenograft of bladder cancer cell line HT1376 were treated with or without EZH2 inhibitors before subject to RNA-seq |
| GSE176493 |
Comprehensive target engagement by EZH2 inhibitor CPI-0209 allows for preferential targeting of ARID1A mutant urothelial carcinoma |
|
| Relations |
| BioSample |
SAMN19643926 |
| SRA |
SRX11101561 |
