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Sample GSM3690894 Query DataSets for GSM3690894
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
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
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
BioSample SAMN11284857
SRA SRX5599461

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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