|
| Status |
Public on Jun 17, 2020 |
| Title |
MCF7-WT_Deoxycholic acid_rep3_P-5_D07 |
| Sample type |
SRA |
| |
|
| Source name |
MCF-7 cells
|
| Organism |
Homo sapiens |
| Characteristics |
chemical: Deoxycholic acid
dose (um): 100
|
| Treatment protocol |
Chemicals, purchased from Sigma-Aldrich, were ≥ 95% pure. All chemical stock solutions were made in DMSO. After a 48 hour incubation, MCF-7 cells were exposed for 6 hours to DMSO (0.05%) or one of the six test chemicals in DMSO (final concentration 0.05%) at a concentration of 1-100 uM. Media was removed and cells were lysed in 0.5 mL Trizol.
|
| Growth protocol |
MCF-7 cells were cultured in DMEM media (GIBCO) supplemented with 10% FBS (Omega Scientific, Australia) and 1x penicillin/streptomycin/glutamine. Cells were plated at 15 x10^5 cells per well in 12-well plates and cultured for 48 hours and then exposed to test chemicals for 6 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After cells were lysed in 0.5 mL Trizol, total RNA was extracted from each lysate and prepared for gene expression analysis using the human 1500+ Tempo-Seq platform (BioSpyder, Inc, Carlsbad, CA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
TempO-Seq data are analyzed using the Tempo-SeqR software package which uses the statistical computing language R. The input data analyzed was taken from the FASTQ files. Each file was aligned to a pseudo-transcriptome input using the Bowtie algorithm. The data analysis output is a table of counts with each column representing a sample and each row representing a gene.
Supplementary_files_format_and_content: counts
|
| |
|
| Submission date |
Jun 17, 2020 |
| Last update date |
Jun 18, 2020 |
| Contact name |
Christopher Corton |
| E-mail(s) |
[email protected]
|
| Organization name |
US-EPA
|
| Lab |
MD B105-01
|
| Street address |
109 TW Alexander Dr.
|
| City |
Research Triangle Park |
| State/province |
NC |
| ZIP/Postal code |
27711 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE152703 |
Transcript profiling of putative MTF-1 activating chemicals in wild-type and MTF-1-null MCF-7 cells |
|
| Relations |
| BioSample |
SAMN15300281 |
| SRA |
SRX8567985 |
