|
| Status |
Public on May 26, 2016 |
| Title |
MCF-7 cells treated with 10nM TCDD, replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
MCF-7 breast cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: TCDD
concentration: 10nM
|
| Treatment protocol |
6hrs treatment with either vehicle (DMSO) or TCDD
|
| 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: counts_10nM_TCDD.txt is a tab-delimited text file containing raw read counts per gene
Supplementary_files_format_and_content: normalized_counts_10nM_TCDD.txt is a tab-delimited text file containing counts per gene after normalization by the estimateSizeFactors function in the Bioconductor package DESeq
|
| |
|
| Submission date |
Jan 06, 2016 |
| 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) |
| GSE76608 |
Expression profiling of MCF-7 cells with 10nM treatment of TCDD |
| GSE98515 |
Expression profiling of MCF-7 cells with treatment of TCDD |
|
| Relations |
| BioSample |
SAMN04386886 |
| SRA |
SRX1520602 |
