|
| Status |
Public on Sep 27, 2017 |
| Title |
SK-MEL-3 TSA Replicate1 [miRNA] |
| Sample type |
RNA |
| |
|
| Source name |
SK-MEL-3 TSA
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SK-MEL-3
treatment: Trichostatin A
|
| Treatment protocol |
Trichostatin A was prepared in DMSO ( 2 mg/ml), then diluted in HBSS and added to cell culture media to a final working concentration of 1uM (sublethal concentration). Grape Seed extract [Vitis Vinifera ] was prepared in absolute ethanol ( 50mg/ml ) then diluted in HBSS and added to cell culture media to a final working concentration of 120 ug/ml. Both conditions were evaluted vs control in SK-MEL-3 cells.
|
| Growth protocol |
SK-MEL-3, [ATCC HTB-69] cells were cultured in 175 cm2 flasks containing ATCCs-formulated McCoy's 5a Medium Modified , [ATCC Catalog No. 30-2007] supplemented with fetal bovine serum [ 10%,] and [100 U/ml penicillin G sodium/100 μg/ml streptomycin sulfate]. Cells were grown at 37°C with 95% air and 5% CO2 and sub-cultured every three to five days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After treatment, cells were washed three times in HBSS, rapidly frozen and stored at -80 C. miRNA was isolated using the quiazol reagent and miRNeasy Mini Kit (Qiagen, Germantown, MD), quality was assessed and concentration was equalized to 50ng/ul in nuclease free water.
|
| Label |
Biotin
|
| Label protocol |
Briefly, after RNA purification, samples were labeled with a POLY A tail, and ligated using a flash tag ligation mix from the FlashTag™ Biotin HSR RNA kit (Affymetrix). Subsequently, biotin labeled RNA was detected using streptavidin – EP and hybridized on to a Genechip miRNA 4.1 human array, prior to fluidics and imaging by the Gene Atlas.
|
| |
|
| Hybridization protocol |
Hybrization was conducted according to manufacturer's instructions as per the Genechip miRNA 4.1 human array / FlashTag™ Biotin HSR RNA kit (Affymetrix, ThermoFisher Scientific).
|
| Scan protocol |
Arrays were scanned with GeneAtlas Imaging station scanner (Affymetrix, ThermoFisher Scientific)
|
| Description |
Malignant melanoma (P13) hypotetraploid to hypertetraploid with abnormalities including dicentrics, pulverizations, secondary constrictions and minutes
miRNA expression data from SK-MEL-3 cells grown under variable experimental treatment
|
| Data processing |
The data was processed using Affymetrix expression console and evaluated by Affymetrix transcription console software (Affymetrix, ThermoFisher Scientific). RMA algorithm.
|
| |
|
| Submission date |
Sep 26, 2017 |
| Last update date |
Jan 23, 2018 |
| Contact name |
Elizabeth A Mazzio |
| Organization name |
Florida Agricultural & Mechanical University
|
| Department |
College of Pharmacy & Pharmaceutical Science
|
| Lab |
Molecular Genetics Core Facility :241 Fred Humphries Science Research Building
|
| Street address |
1515 MLK Blvd
|
| City |
Tallahassee |
| State/province |
Florida |
| ZIP/Postal code |
32307 |
| Country |
USA |
| |
|
| Platform ID |
GPL21572 |
| Series (2) |
| GSE104266 |
Whole miRNA transcriptome profiling of Trichostatin A and Grape Seed Extract treated SK-MEL-3 human melanoma cells. |
| GSE104268 |
Whole Transcriptomic Analysis of Trichostatin A or Grape Seed Extract treated SK-MEL-3 melanoma cells. |
|
