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Status |
Public on Mar 22, 2020 |
Title |
WM983B scrambled 2 |
Sample type |
RNA |
|
|
Source name |
WM983B melanoma cell line
|
Organism |
Homo sapiens |
Characteristics |
cell line: WM983B 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.
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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.
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|
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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.
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Description |
Gene expression data from WM983B 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).
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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 |
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