|
| Status |
Public on Dec 21, 2017 |
| Title |
SKMEL103 shCUGBP1 rep1 |
| Sample type |
RNA |
| |
|
| Source name |
shRNA mediated CUGBP1 depleted SK-Mel-103
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SK-Mel-103
cell type: melanoma
time point: Day 4 after infection
knockdown target: CUGBP1
|
| Treatment protocol |
Cells were plated at 70% confluence and infected with lentivirus either scramble control or shCUGBP1-1. Cell were selected at day 2 after infection with puromycin (1ug/ml). Two days after, day 4 of infection, pellets were collected.
|
| Growth protocol |
SK-mel-103 and UACC-62 human melanoma cell lines were grown in DMEM medium supplemented with 10% fetal bovine serum, 1% penicillin and streptomycin (Gibco), and maintained at 37°C in humidified 5% CO2 atmosphere.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated by Qiagen RNeasy Kit following manufacturer instructions.
|
| Label |
Biotin
|
| Label protocol |
Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)
|
| |
|
| Hybridization protocol |
Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001
|
| Scan protocol |
Affymetrix Gene ChIP Scanner 3000 7G
|
| Description |
SK-Mel-103 shCUGBP1 infection replicate 1
|
| Data processing |
Data were normalized using Expression Console from Affymetrix (RMA analyses). Probeset-level RMA values are available in the sample tables. Gene-level RMA values are available on the series record.
probe group file: HJAY_r2.pgf
meta-probeset file: HJAY_r2.full.mps
|
| |
|
| Submission date |
Jun 21, 2016 |
| Last update date |
Dec 21, 2017 |
| Contact name |
Pierre de la Grange |
| E-mail(s) |
pierre.delagrange@genosplice.com
|
| Organization name |
GenoSplice technology
|
| Department |
Paris Biotech Santé
|
| Street address |
29, rue du Faubourg Saint-Jacques
|
| City |
Paris |
| ZIP/Postal code |
75014 |
| Country |
France |
| |
|
| Platform ID |
GPL15106 |
| Series (1) |
| GSE83590 |
CUGBP1 dependent whole genome gene expression and alternative splicing in melanoma cell lines |
|
