|
| Status |
Public on Jun 16, 2021 |
| Title |
P2A1: Sensitive PH039 third passage source tumor |
| Sample type |
SRA |
| |
|
| Source name |
Sensitive PH039 third passage source tumor
|
| Organism |
Homo sapiens |
| Characteristics |
disease: high-grade serous ovarian cancer (HGSOC)
tissue: PDX tumor
|
| Treatment protocol |
HGSOC PH039 PDXs were passed and treated with cycles of 100 mg/kg niraparib for 21 days for four treatment cycles. Following niraparib, mice were monitored by transabdominal ultrasound monitored for regrowth of tumors. RNA sequencing was done on matched baseline tumors and niraparib treated tumors in cycles #1, 2 and 3 in triplicates.
|
| Growth protocol |
HGSOC PH039 PDXs were established intraperitoneally utilizing previously described methods.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was column-extracted using Rneasy Mini kit (qiagen)
RNA-seq libraries were prepared from 100-200 ng high-quality RNA using TruSeq RNA Library Prep Kit v2 (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Fastq files of pair-end RNA-Seq reads were aligned with Tophat 2.0.14 to the reference genome UCSC hg38 or UCSC MM10 using Bowtie2 2.2.6 with default parameters.
Reads that aligned to the mouse genome were then removed and the unaligned reads were mapped to the human genome.
Gene level counts were obtained using featureCounts 1.4.6 from the subRead package with gene models from corresponding UCSC annotation packages.
Genome_build: hg38
Supplementary_files_format_and_content: raw counts in tab-delimited text file
|
| |
|
| Submission date |
Dec 24, 2020 |
| Last update date |
Jun 16, 2021 |
| Contact name |
Hu Li |
| E-mail(s) |
li.hu@mayo.edu
|
| Organization name |
Mayo Clinic
|
| Department |
Molecular Pharmacology & Experimental Therapeutics
|
| Lab |
Systems Biology and Pharmacology
|
| Street address |
200 First Street, Gonda Building G19-408
|
| City |
Rochester |
| State/province |
MN |
| ZIP/Postal code |
55904 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE163854 |
RNAseq data for HGSOC PH039 PDXs at baseline and treated with cycles of 100 mg/kg niraparib for 21 days for four treatment rounds |
| GSE165052 |
Characterization of a RAD51C-Silenced High Grade Serous Ovarian Cancer Model During PARP Inhibitor Resistance Development |
|
| Relations |
| BioSample |
SAMN17153400 |
| SRA |
SRX9734355 |
