|
| 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 |
