|
| Status |
Public on Jun 20, 2014 |
| Title |
AHR knockdown replicate 5 |
| Sample type |
SRA |
| |
|
| Source name |
Breast cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF-7
treatment: Short interfering RNA against the AHR
|
| Treatment protocol |
200,000 MCF-7 cells seeded in 35 mm plates were transfected with 50 nM of cRNAi or AHR-siRNA #2 in phenol red-free DMEM supplemented with 10% charcoal treated FBS and 2 µL of Dharmafect transfection reagent (#1) for 36 hr
|
| Growth protocol |
Human MCF-7 breast cancer cells (ATCC (Manassas, VA)) were maintained in DMEM, 10% FBS, .01 µg/mL bovine insulin (Cell Applications, Inc.) and 1% penicillin/streptomycin (P/S).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using RNA purification columns (Qiagen) and DNase treated (Qiagen)
RNA libraries were prepared for sequencing using Illumina TruSeq RNA preparation protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Description |
AHR_14
|
| Data processing |
CASAVA 1.8.2 was used for base calling
Reads were aligned to hg19 using TopHat 2.0.6 with BowTie 0.12.8.
Gene-level counts for genes in the ensembl database were generated using Rsamtools using script makeCounts.Rscript (supplemental file)
Normalization was performed using DESeq
Samples were clustered using the top 30 expressing genes and outliers eliminated
The bottom 40% of genes by total expression over all samples were removed from analysis
Differentially expressed genes were identified using DESeq with a false discovery rate of 10%
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited file containing counts for each gene for each sample
|
| |
|
| Submission date |
Nov 04, 2013 |
| 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 |
GPL15433 |
| Series (1) |
| GSE52036 |
RNA-seq analysis reveals endogenous aryl hydrocarbon receptor regulation is highly associated with eicosanoid synthesis and tumor necrosis factor activity in MCF-7 cancer cells |
|
| Relations |
| BioSample |
SAMN02391006 |
| SRA |
SRX372838 |
