|
| Status |
Public on May 22, 2024 |
| Title |
kura_T40 |
| Sample type |
SRA |
| |
|
| Source name |
Cell line
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Cell line
cell line: Kuramochi
cell type: Epithelial
genotype: BRCA2-mutant
treatment: untreated and treated cells with 10uM or 320uM of olaparib
|
| Treatment protocol |
Kuramochi cells were treated in dose escalation from 1uM to 320uM of olaparib, generating populations resistant to a range of doses plus untreated control (C). The cells resistant to 10 uM (T10), 40 uM (T40) and 320 uM (T320) plus untreated control (C) were collected for whole exome sequencing.
|
| Growth protocol |
Cells were cultured in RPMI-1640 (ThermoFisher) with 10% Fetal Bovine Serum (FBS), 1% MEM Non-Essential Amino Acids, 1% L-Glutamine 200 mM, 1% Antibiotic-Antimycotic solution 100X and 0.25 U/mL insulin solution (Sigma-Aldrich)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were trypsinized and single-cell suspensions were counted. Genomic DNA extraction for whole exome sequencing was performed using Qiagen Blood and Cell DNA kit (Catalog no: 13323).
The extracted DNA from representative samples (C, T10, T40 and T320) was sent to the Broad Institute facility and processed according to the in-house pipeline. Briefly, 125ng in 50μL was prepared for sequencing using the KAPA Hyper Prep Kit. Hybridization and capture were performed using the relevant components of IDT’s XGen hybridization and wash kit and following the manufacturer’s suggested protocol. Sequencing was performed using Illumina Novaseq.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
tables containing detected copy number alterations and single nucleotide variants. Annotations are relative to a reference sample in the second column (Ex: REFERENCE:SUBJECT) refers to a reference sample
|
| Data processing |
Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software. The FASTQ files were processed using the Seq-N-Slide pipeline (https://doi.org/10.5281/zenodo.5550459). Adapter sequences were trimmed with Trimmomatic and then aligned to the human reference genome (build hg38/GRCh38) using the Burrows-Wheeler Aligner with the BWA-MEM algorithm.
Low confidence mappings (mapping quality < 10) and duplicate reads were removed using Sambamba. Further local indel realignment and base-quality score recalibration were performed using the Genome Analysis Toolkit (GATK). Copy number profiles were calculated using Control-FREEC with untreated samples as the matched controls. ANNOVAR was used to annotate variants with genomic context such as functional consequence on genes and identify presence in public variant databases gnomAD and COSMIC.
Assembly: hg38/GRCh38
Supplementary files format and content: Kuramochi_WES_CNVs.tsv, tsv, list of copy number alterations relative to a specified reference sample (Ex column 2: REFERENCE:SUBJECT)
Supplementary files format and content: Kuramochi_WES_SNVs.tsv, tsv, list of single nucleotide variants relative to a specified reference sample.
Library strategy: WES (whole exome sequencing)
|
| |
|
| Submission date |
Nov 14, 2023 |
| Last update date |
May 22, 2024 |
| Contact name |
Itai Yanai |
| Organization name |
NYU Langone Health
|
| Street address |
435 East. 30th St.
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE247687 |
Cellular adaptation to cancer therapy along a resistance continuum [Whole Exome: Kuramochi] |
| GSE247691 |
Cellular adaptation to cancer therapy along a resistance continuum |
|
| Relations |
| BioSample |
SAMN38247434 |
| SRA |
SRX22519757 |
