|
| Status |
Public on Jun 16, 2021 |
| Title |
S0.2: Sensitive PH039 source tumor (rrbs) |
| Sample type |
SRA |
| |
|
| Source name |
Sensitive PH039 source tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: HGSOC PDX samples
arm: source tumor arm
|
| 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 |
genomic DNA |
| Extraction protocol |
Nextera XT libraries were prepared from Nextera Index Kit v2 set B or set C barcoding primers were integrated into amplicons to create illumina sequecing libraries (Iluumina, cat #FC-131-2002 or FC-131-2003).
RRBS sequenced on the Illumina MiSeq using Miseq Nano Reagent Kit v2 (Illumina; Cat# MS-102-2002).
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Demultiplexed reads were merged and grouped using AmpliVar genotyping mode (PMID: 25664426).
Processed using a custom script, available on github (https://github.com/okon/MethAmplicons).
Reads with deletions, insertions or substitutions variants in CpG positions were filtered out.
Epialleles below 5% frequency were grouped together for individual epiallele plots.
Genome_build: hg38 and mm9
Supplementary_files_format_and_content: raw counts for epiallele detected (13 CpG sites of interest)
|
| |
|
| Submission date |
Jan 18, 2021 |
| 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 |
GPL15520 |
| Series (2) |
| GSE165051 |
Targeted (amplicon) reduced representation bisulfite sequencing (RRBS) 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 |
SAMN17376287 |
| SRA |
SRX9892281 |
