|
| Status |
Public on Sep 08, 2023 |
| Title |
Control_MDA_MB231_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Cell line drived from breast cancer tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Cell line drived from breast cancer tissue
cell line: MDA-MB-231
cell type: Cancer cell, adherent
treatment: DMSO 24hrs
|
| Treatment protocol |
24 h
|
| Growth protocol |
Standard (ATCC)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Qiagen RNeasy Micro Kit (50), Cat. No. / ID: 74004
PolyA-enriched, strand-specific RNA libraries were constructed and 100bp paired-end reads were sequenced on an Illumina NovaSeq 6000 platform
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
ET43
|
| Data processing |
Raw data were analyzed using the Hisat aligner with stand-specific settings.
Differential gene expression was analyzed using the DESeq R package (Bioconductor) and the negative binomial model
Criteria for significant differences in gene expression were (1) false discovery rate (FDR) <0.05, (2) expression level >10th percentile, and (3) ≥ 2-fold change.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: htseq output with gene counts for each sample
|
| |
|
| Submission date |
Sep 06, 2023 |
| Last update date |
Sep 08, 2023 |
| Contact name |
Carrie McCracken |
| E-mail(s) |
cmccracken@som.umaryland.edu
|
| Organization name |
Institute of Genome
|
| Department |
Institute for Genome Sciences
|
| Street address |
670 W. Baltimore St
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21201 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE242514 |
Inhibitory effect of VNLG-152R on breast cancer cells MDA-MB-231 |
|
| Relations |
| BioSample |
SAMN37307493 |
| SRA |
SRX21653368 |
