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Sample GSM2210451 Query DataSets for GSM2210451
Status Public on Dec 21, 2017
Title SKMEL103 shCUGBP1 rep2
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 2
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

Data table header descriptions
ID_REF
VALUE RMA signal intensity

Data table
ID_REF VALUE
1 10.17191
2 12.58046
3 12.93308
4 13.46911
5 12.17256
6 10.321
7 9.154617
8 12.08011
9 11.86399
10 11.36108
11 11.38638
12 8.941715
13 11.17372
14 12.21229
15 10.52866
16 10.86379
17 9.659941
18 10.24122
19 12.03288
20 11.23717

Total number of rows: 573410

Table truncated, full table size 8788 Kbytes.




Supplementary file Size Download File type/resource
GSM2210451_SKMEL103_shCUGBP1_rep2.CEL.gz 24.6 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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