|
| Status |
Public on Feb 14, 2018 |
| Title |
C021 scrambled 2 |
| Sample type |
RNA |
| |
|
| Source name |
C021 melanoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: C021
cell type: melanoma
shRNA: scrambled control
|
| Treatment protocol |
C021 melanoma cells treated with shRNA against DOT1L or scrambled control were exposed to UVB (100J/m2), and 3 hours later RNA was extracted from the cells.
|
| Growth protocol |
Cells were grown in Medium 254 (Thermo Fisher M-254-500) with the addition of Human Melanocyte Growth Supplement (HMGS).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the QIAgen RNeasy Mini Kit according to the manufacturer's protocol.
|
| 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 C021 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 hugene20sthsentrezg R package (version 17.0.0).
|
| |
|
| Submission date |
Aug 24, 2017 |
| Last update date |
Jun 25, 2019 |
| 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 (2) |
| GSE103080 |
Profiling of expression data in melanoma cells following DOT1L shRNA knockdown |
| GSE103081 |
Profiling of expression data in melanoma cells with mutant DOT1L, DOT1L inhibitor or shRNA knockdown |
|
