|
| Status |
Public on May 16, 2022 |
| Title |
6289_10_10_ACTTGAA_S73 |
| Sample type |
SRA |
| |
|
| Source name |
A2780
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A2780 WT
cell type: ovarian cancer cells
treatment: -SG carbo
|
| Treatment protocol |
For experiments under serine/glycine deprivation conditions, cells were fed homemade medium (homemade RPMI with the same formulation as commercial RPMI from Gibco, supplemented with 10% dialyzed FBS (Gibco) and standard concentrations of penicillin-streptomycin and glutamine) with or without serine and/or glycine (Sigma Aldrich). Isogenic resistant A2780cis were obtained by chronically exposing parental cells to cisplatin.
|
| Growth protocol |
A2780 wt and its cisplatin resistant analogue A2780 cis cells were obtained from the ECACC (Sigma Aldrich ECACC 93112519 and Sigma Aldrich ECACC 93112517, respectively) and were maintained in RPMI medium containing 10% FBS (Gibco), 2 mM glutamine (L-Glutamine, Gibco), 100 IU penicillin and 100 μg/mL streptomycin (PenStrep, Gibco).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
5x10^6 cells per condition per replicate were lysed using RLT buffer (Qiagen) and stored at -80°C. For the generation of total RNA libraries, total RNA was extracted using TRI Reagent (SIGMA), and mRNA was purified using Dynabeads mRNA DIRECT Purification Kit (Invitrogen), according to the manufacturers’ protocol.
Total RNA libraries were constructed using SENSE Total RNA-Seq Library Prep Kit for Illumina (LEXOGEN).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
A2780 WT -SG carbo
A2780 wild type cell line without serine/glycine + 6 M carboplatin
Total RNAseq
RNAseq_readscounts.txt
|
| Data processing |
RNA-seq: Data, as FASTQ file, were aligned with STAR to the human genome GRCh37.p13. HTSEQ with gencode.v19 annotation was used to count reads at exons of genes. Normalization of read counts was done using DEseq and DEseq2.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: RNAseq_readscounts.txt: Tab-delimited text file containing raw read counts (HTSeq).
|
| |
|
| Submission date |
Jun 05, 2021 |
| Last update date |
May 16, 2022 |
| Contact name |
Pierre-Rene Körner |
| Organization name |
Netherlands Cancer Institute (NKI)
|
| Department |
Oncogenomics
|
| Street address |
Plesmanlaan 121
|
| City |
Amsterdam |
| ZIP/Postal code |
1066CX |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE176218 |
Decreased serine biosynthesis identifies a subgroup of platinum resistant ovarian cancers and novel actionable metabolic vulnerabilities |
|
| Relations |
| BioSample |
SAMN19580513 |
| SRA |
SRX11075082 |
