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Sample GSM3736801 Query DataSets for GSM3736801
Status Public on Aug 20, 2019
Title 48h_CKI_1/20_M231_3
Sample type SRA
 
Source name total RNAs, cell line
Organism Homo sapiens
Characteristics agent: CKI_1/20
cell line: MDA-MB-231
tumor type: adenocarcinoma
Treatment protocol Drug treatments were designed as follows: CKI (1.0 mg/mL), doxorubicin (1 ng/ml and 5 mg/ml) and 5-Fu (10 ug/ml )
Growth protocol Human epidermoid carcinoma cell line A431 and huaman adenocarcinoma cell line were purchased from ATCC (CRL-1555™ for A431 and HTB-26™ for MDA-MB-231, VA, USA) and were cultured in DMEM medium (Thermo Fisher Scientifc, MA, USA) supplemented with 10% fetal bovine serum (Thermo Fisher Scientifc, MA, USA) at 37°C with 5% CO2.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using PureLink™ RNA Mini Kit (Thermo Fisher Scientific) according to the manufacturer’s protocol.
RNA libraries were prepared using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, Massachusetts, USA) according to the manufacturer's protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Description unstranded paired-end RNA-seq
M231_C1_20_3
Data processing Illumina Casava1.7 software used for basecalling.
Trim_galore (v0.3.7, Babraham Bioinformatics) was used to trim adaptors and low-quality sequences in raw reads with parameters:  --stringency 5 --paired. Then trimmed reads were aligned to reference genome (hg19, UCSC) using STAR (v2.5.3a) with parameters: --outSAMstrandField intronMotif --outSAMattributes All --outFilterMismatchNmax 10 --seedSearchStartLmax 30
Differential expression analysis was performed with edgeR and DE genes were selected with a False Discovery Rate (FDR) < 0.05.
Genome_build: hg19, UCSC
Supplementary_files_format_and_content: Tab delimited matrix showing raw counts of refGenes
 
Submission date Apr 26, 2019
Last update date Aug 20, 2019
Contact name David L. Adelson
E-mail(s) [email protected]
Organization name University of Adelaide
Department Molecular and biomedical science
Street address University of Adelaide
City Adelaide
State/province South Australia
ZIP/Postal code 5005
Country Australia
 
Platform ID GPL20795
Series (1)
GSE130359 A new strategy for identifying mechanisms of drug-drug interaction using transcriptome analysis: Compound Kushen injection as a proof of principle
Relations
BioSample SAMN11514583
SRA SRX5741631

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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