|
| Status |
Public on Jul 22, 2020 |
| Title |
E1_Control cells replica 1 |
| Sample type |
SRA |
| |
|
| Source name |
MDA-MB-468 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-468
tissue: Triple negative breast tumor
drug incubation time: 72 h
drug concentration: -
|
| Treatment protocol |
Cells were seeded on a T25 culture flask (1 million cells per flask) overnight and then treated with PBS (control), the drugs alone (salinomycin or dasatinib), or the drug combination (Sal + Das) for 24 or 72 h.
|
| Growth protocol |
MDA-MB-468 cells were cultured in RPMI 1640 medium supplemented with 10% (v/v) fetal bovine serum (FBS), penicillin (50,000 units/L), and streptomycin (50 mg/mL), and then maintained in 5% of CO2 at 37˚C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA was extracted and purified using the Rneasy Mini Kit (Qiagen), according to the manufacturer's instructions. The final RNAs were quality controlledusing Agilent 2100 Bioanalyzer and quantified by absorbance using NanoDrop, prior RNA-seq analysis.
Library was constructed on the purified RNAs obtained from the PBS- or drug-treated MDA-MB-468 cells (4 biological replicates per condition), using Illumina TruSeq RNA preparation kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
E1
|
| Data processing |
The samples were sequenced using HiSeq4000 sequencer with single-end 50 bps reads. The raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing.
The RNA reads were aligned and mapped to the GRCh37 human reference genome by STAR (Version2.5.2).
The transcriptome reconstruction was performed by Cufflinks (Version 2.1.1). The abundance of transcripts was measured with Cufflinks in Fragments Per Kilobase of exon model per Million mapped reads (FPKM).
Gene expression profiles were constructed using the DESeq2 package.
The resulting corrected p-values were calculated based on the Benjamin-Hochberg’s method to adjust multiple testing and control the false discovery rate.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text file include raw read counts at gene level for each samples. Excel file includes output from DESeq2.
|
| |
|
| Submission date |
Aug 07, 2019 |
| Last update date |
Jul 22, 2020 |
| Contact name |
Genomics-core-facility WCM |
| E-mail(s) |
yit2001@med.cornell.edu
|
| Organization name |
Weill Cornell Medicine
|
| Street address |
1300 York Ave
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE135514 |
Transcriptomic insight into salinomycin mechanisms in breast cancer cell lines: synergistic effects with dasatinib and induction of estrogen receptor beta |
|
| Relations |
| BioSample |
SAMN12525576 |
| SRA |
SRX6666579 |
