|
| Status |
Public on Feb 26, 2020 |
| Title |
p53-R158G cell treated with belinostat (0.1uM) + 10uM Cisplatin |
| Sample type |
SRA |
| |
|
| Source name |
Cell Line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Calu-1
genotype/variation: p53 R158G mutant
treatment: belinostat (0.1µM) + 10µM Cisplatin
|
| Treatment protocol |
Cell lines were cultured in petri dishes and treated with either 0.01% DMSO or 0.1uM belinostat with 10uM cisplatin for 48 hours
|
| Growth protocol |
Cell lines were obtained directly from the American Type Culture Collection (ATCC), and were maintained in a humidified 37°C incubator, in culture medium (RPMI for Calu-1 and H2170; EMEM for MRC-5) supplemented with 10% fetal bovine serum, 2mM L-glutamine, 100 μg/mL streptomycin and 100 U/mL penicillin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were treated with the indicated treatment for 48hours, and RNA was extracted using Qiagen RNAeasy kit.
For Ion AmpliSeq Transcriptome Human Gene Expression (Thermo Fisher), 10 ng RNA was used for barcoded cDNA library preparation using PCR-based targeted-amplicon amplification according to manufacturer’s protocol. Pooled libraries were amplified emulsion PCR on Ion Torrent OneTouch2 instruments (OT2) and sequenced on Ion Torrent Proton sequencing system.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
Calu-1 lung cancer cell line with p53-R158G mutant treated with Belinostat and Cisplatin
IonXpress_014
|
| Data processing |
For AmpliSeq, fastq files was analyzed with the ampliSeqRNA plugin available for Ion Torrent sequencing platforms that used the Torrent Mapping Alignment Program (TMAP). TMAP first identify a list of Candidate Mapping Locations (CMLs) and aligned with Smith Waterman algorithm for specific and sensitive mapping.
Genome_build: hg19
Supplementary_files_format_and_content: RPM normalization values for each samples
|
| |
|
| Submission date |
Mar 29, 2019 |
| Last update date |
Feb 26, 2020 |
| Contact name |
Tuan Zea Tan |
| E-mail(s) |
csittz@nus.edu.sg
|
| Organization name |
National University of Singapore
|
| Department |
Cancer Science Institute Singapore
|
| Street address |
14 Medical Drive, #11-01, Singapore
|
| City |
Singapore |
| ZIP/Postal code |
117599 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL17303 |
| Series (2) |
| GSE129026 |
Targeting codon 158 p53-mutant cancers via the induction of p53 acetylation [RNA-seq] |
| GSE129027 |
Targeting codon 158 p53-mutant cancers via the induction of p53 acetylation |
|
| Relations |
| BioSample |
SAMN11284857 |
| SRA |
SRX5599461 |
