|
Status |
Public on Aug 20, 2019 |
Title |
48h_CKI_1/20_M231_3 |
Sample type |
SRA |
|
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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.
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|
|
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
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|
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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 |