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Sample GSM1078887 Query DataSets for GSM1078887
Status Public on Dec 31, 2013
Title DLD1-siRNA mock treated replicate1
Sample type RNA
 
Source name colorectal cancer cell line
Organism Homo sapiens
Characteristics cell line: DLD1
treatment: siRNA beta-galactosidase
Treatment protocol DLD1 and SW480 cells were harvested 48h after siRNA transfection
Growth protocol The colon carcinoma cell lines DLD1 and SW480 were obtained from ATCC (Manassas, VA, USA) and were cultured in DMEM medium supplemented with 10% calf serum (PAA, Pasching, Austria). Short interfering RNAs targeting β-catenin (cat. no. D-003482-04) and β-Galactosidase (cat. no. D-012539-01) were purchased from Dharmacon (Lafayette, CO, USA) as siGenome siRNAs. Cells were transfected with these siRNAs using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA).
Extracted molecule total RNA
Extraction protocol Trizol method
Label biotin
Label protocol Affymentrix kits for 3'IVT cDNAsynthesis, amplification and labeling
 
Hybridization protocol Fluidics station FS450
Scan protocol Affymetrix GeneChip Scanner 3000
Description colorectal cancer cell line, mock-siRNA treated
Data processing The software package R (version 2.14.1) was used for the statistical analysis of the microarray data. Microarray data were preprocessed using the rma function from the R package “affy”. Two sets with different cell lines(DLD1 and SW480) were normalized separately. The function nsFilter from the package 'genefilter' was used to exclude all probeset that were not associated with a gene name.
 
Submission date Feb 05, 2013
Last update date Dec 31, 2013
Contact name Stefan Krebs
E-mail(s) [email protected]
Phone 0049-89-2180 76715
Organization name Ludwig-Maximilian University
Department Gene Center
Lab Lafuga Genomics
Street address Feodor-Lynen-Str. 25
City Munich
ZIP/Postal code 81377
Country Germany
 
Platform ID GPL570
Series (1)
GSE44097 β-catenin target genes in colorectal carcinoma cell lines with deregulated Wnt/β-catenin signaling

Data table header descriptions
ID_REF
VALUE log2 RMA transformed intensities

Data table
ID_REF VALUE
1007_s_at 10.22254994
1053_at 9.014487451
117_at 4.877132195
121_at 7.587241423
1255_g_at 2.957351803
1294_at 5.297871124
1316_at 5.27062173
1320_at 4.976110144
1405_i_at 4.39597881
1431_at 2.794259227
1438_at 7.140983773
1487_at 8.707731601
1494_f_at 5.816290547
1552256_a_at 9.334263573
1552257_a_at 10.34776655
1552258_at 5.286163801
1552261_at 4.270767175
1552263_at 7.006223414
1552264_a_at 8.449090845
1552266_at 3.365363761

Total number of rows: 41656

Table truncated, full table size 925 Kbytes.




Supplementary file Size Download File type/resource
GSM1078887_DLD1_bgII.CEL.gz 4.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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