|
| Status |
Public on Jul 01, 2014 |
| Title |
Inf-VidD-C |
| Sample type |
RNA |
| |
|
| Source name |
THP-1 cells, 24 hr, Mtb-infected, Vit D-treated
|
| Organism |
Homo sapiens |
| Characteristics |
time: 24 hr
infection: M. tuberculosis H37Rv
treatment: 100 nM of 1α,25-dihydroxyvitamin D3
cell line: THP-1
|
| Treatment protocol |
Cells were treated with VITD 4 hours after infection. THP-1 cells were washed with PBS at 24h and collected for analysis
|
| Growth protocol |
Cells cultured in 24-well flat bottom plates 5 X 105 cells per well were pre-treated with 20ng/ml PMA for 24 h, and incubated with M. tuberculosis H37Rv.After 4 hours of infection, the medium was removed, cells were washed to remove extracellular bacteria, and fresh medium was added
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
The Ambion WT Expression Kit with accompanying protocol was used to label the samples
|
| |
|
| Hybridization protocol |
The Affymetrix Genechip WT Terminal Labeling and Hybridization protocol was used
|
| Scan protocol |
Chips were scanned using the Affymetrix 7G Plus scanner and Command Console Software
|
| Description |
THP-1 cells were cultured in 24-well flat bottom plates, pre-treated with 20ng/ml PMA for 24 h
|
| Data processing |
Probeset expression was summarized with the RMA method using APT 1.15.0 software. Command options included -a rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish.expon=true and --qc-probesets.
|
| |
|
| Submission date |
Apr 23, 2014 |
| Last update date |
Jul 05, 2014 |
| Contact name |
Hugh Salamon |
| E-mail(s) |
hugh@knowledgesynthesis.com
|
| Organization name |
Knowledge Synthesis Inc.
|
| Street address |
725 Folger Avenue
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94710 |
| Country |
USA |
| |
|
| Platform ID |
GPL16686 |
| Series (1) |
| GSE57028 |
Transcriptomics of vitamin D treatment effects in Mycobacterium tuberculosis-infected THP-1 cells |
|
