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Sample GSM7764788 Query DataSets for GSM7764788
Status Public on Sep 08, 2023
Title Control_MDA_MB231_rep3
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 ET45
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 SAMN37307491
SRA SRX21653370

Supplementary file Size Download File type/resource
GSM7764788_ET45.accepted_hits.sorted_by_name.exon.counts.gz 211.6 Kb (ftp)(http) COUNTS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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