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Sample GSM2793863 Query DataSets for GSM2793863
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.

Data table header descriptions
ID_REF
VALUE Quantification
DETECTION P-VALUE

Data table
ID_REF VALUE DETECTION P-VALUE
20500112 8.48931 8.72176e-16
20500113 0.254866 0.675853
20500114 1.08894 0.259288
20500115 10.3883 8.72176e-16
20500116 2.36099 0.0252542
20500117 8.43607 8.72176e-16
20500118 0.964421 0.255309
20500119 8.60292 8.72176e-16
20500120 3.97953 0.000118593
20500121 7.76125 8.72176e-16
20500122 0.880434 0.441369
20500123 5.85556 2.36546e-11
20500124 0.612279 0.177781
20500125 -0.0549484 0.737689
20500126 4.01676 4.15698e-08
20500127 0.309268 0.897886
20500128 7.96674 8.72176e-16
20500129 0.165886 0.899128
20500130 7.88148 8.72176e-16
20500131 3.34145 0.000445144

Total number of rows: 6658

Table truncated, full table size 175 Kbytes.




Supplementary file Size Download File type/resource
GSM2793863_09122017_SKMEL_mirna_TSA1.ga.CEL.gz 783.9 Kb (ftp)(http) CEL
GSM2793863_09122017_SKMEL_mirna_TSA1.ga.rma-dabg.chp.gz 67.4 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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