NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2598087 Query DataSets for GSM2598087
Status Public on Aug 15, 2018
Title mRNA sequencing of MCF-7 cells treated with 100nM TCDD, replicate 3
Sample type SRA
 
Source name MCF-7 breast cancer cells
Organism Homo sapiens
Characteristics treatment: TCDD
concentration: 100nM
cell line: MCF-7
Treatment protocol 6hrs treatment withTCDD
Growth protocol 250,000 MCF-7 cells were seeded in 35 mm plates in DMEM supplemented with 10 % FBS for 24 hr, followed by overnight serum-starvation in phenol red-free DMEM
Extracted molecule total RNA
Extraction protocol Total RNA purification kits from Qiagen (Valencia, CA) were used according to manufacturers instructions
Libraries were prepared from 1 µg of total RNA using a TruSeq RNA Prep Kit (Illumina Inc., San Diego, CA)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Data processing Alignment to hg19 using TopHat 2.0.7 with BowTie 0.12.9 and SamTools 0.1.18
Counts by gene calculated using R/Bioconductor packages GenomicFeatures and GenomicRanges, with Ensembl gene annotations
Normalized counts calculated using DESeq
Differential Gene expression calculated using DESeq (version 1) with treatment as the single variable
Genome_build: hg19
Supplementary_files_format_and_content: raw_counts_100nM_TCDD.txt is a tab-delimited text file containing raw read counts per gene. Samples DMSO-1, DMSO-2, DMSO-3, and DMSO-4 refer to GSM2028919, GSM2028920, GSM202821, and GSM2028922, respectively.
Supplementary_files_format_and_content: normalized_counts_100nM_TCDD.txt is a tab-delimited text file containing counts per gene after normalization by the estimateSizeFactors function in the Bioconductor package DESeq. Samples DMSO-1, DMSO-2, DMSO-3, and DMSO-4 refer to GSM2028919, GSM2028920, GSM202821, and GSM2028922, respectively.
 
Submission date May 03, 2017
Last update date May 15, 2019
Contact name James Denvir
E-mail(s) denvir@marshall.edu
Organization name Marshall University School of Medicine
Department Biochemistry and Microbiology
Lab Genomics and Bioinformatics Core Facility
Street address One John Marshall Drive
City Huntington
State/province WV
ZIP/Postal code 25755
Country USA
 
Platform ID GPL18460
Series (2)
GSE98514 Expression profiling of four replicates of MCF-7 cells treated with 100nM TCDD
GSE98515 Expression profiling of MCF-7 cells with treatment of TCDD
Relations
BioSample SAMN06887160
SRA SRX2781387

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap