|
Status |
Public on Sep 08, 2023 |
Title |
Control_MDA_MB231_rep2 |
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 |
ET44
|
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 |
SAMN37307492 |
SRA |
SRX21653369 |