|
| Status |
Public on Mar 22, 2020 |
| Title |
SK-Mel5 scrambled 2 |
| Sample type |
RNA |
| |
|
| Source name |
SK-Mel5 melanoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SK-Mel5 melanoma cell line
shRNA: scrambled control shRNA
|
| Treatment protocol |
250,000 human melanoma cells were transduced with each harvested lentivirus (500μL) in the presence of 8 μg/mL of polybrene. Subsequently, melanoma cells transduced with pLKO1-based shRNAs were selected in 1.5 μg/mL of puromycin after 48 hour following transduction in their respective culture medium.
|
| Growth protocol |
Melanoma cells were maintained in Dulbecco’s modified Eagle medium. The medium was supplemented with 10% fetal bovine serum (FBS), 1% penicillin-streptomycin (pen-strep), and 1% L-glutamine. The media, pen-strep, and L-glutamine, FBS were purchased from Invitrogen. All cell lines were grown at 37°C in an atmosphere containing 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from melanoma cells transduced with either shp300 or scrambled lentiviruses was purified using the Qiagen RNAeasy Plus Kit.
|
| Label |
biotin
|
| Label protocol |
Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.
|
| |
|
| Hybridization protocol |
The labeled, fragmented DNA was hybridized to the Affymetrix Human Gene 2.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.
|
| Scan protocol |
After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.
|
| Description |
Gene expression data from SK-Mel5 cells treated with scrambled control shRNA.
|
| Data processing |
Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray hugene20sthsentrezgcdf R package (version 17.0.0).
|
| |
|
| Submission date |
Mar 22, 2019 |
| Last update date |
Mar 22, 2020 |
| Contact name |
Boston University Microarray and Sequencing Resource |
| E-mail(s) |
msrdata@bu.edu
|
| Organization name |
Boston University
|
| Department |
Microarray and Sequencing Resource
|
| Street address |
72 East Concord Street, E631
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02118 |
| Country |
USA |
| |
|
| Platform ID |
GPL17930 |
| Series (1) |
| GSE128737 |
MITF Expression Predicts Therapeutic Vulnerability to p300 Inhibition in Human Melanoma |
|
