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Sample GSM1250009 Query DataSets for GSM1250009
Status Public on Oct 24, 2013
Title 4239166219
Sample type genomic
 
Source name Urinary bladder carcinoma
Organism Homo sapiens
Characteristics gender: M
tissue: bladder
disease state: carcinoma
Treatment protocol N/A
Growth protocol N/A
Extracted molecule genomic DNA
Extraction protocol Extraction of genomic DNA from fresh frozen tissue using the DNAeasy blood and tissue kit (Qiagen)
Label biotin
Label protocol 400ng of genomic DNA was whole-genome amplified, fragmented , precipitated and resuspended in hybridization buffer
 
Hybridization protocol Resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48ºC, single-base extension and allele-specific staining was performed on a Teflow chamber rack system.
Scan protocol After allele-specific staining BeadChip arrays were scanned on a BeadArray Reader
Description Genomic DNA extracted from bladder tumors was genotyped using Infinium Human 1M Genotyping BeadChips (Illumina).
Data processing Data processing was carried out with BeadStudio software v3.1.0 provided by Illumina
 
Submission date Oct 24, 2013
Last update date Oct 24, 2013
Contact name Enrique Carrillo de Santa Pau
E-mail(s) [email protected]
Organization name Spanish National Cancer Research Centre (CNIO)
Department Cancer Cell Biology Programme
Lab Epithelial Carcinogenesis group
Street address C/ Melchor Fernández Almagro, 3
City Madrid
ZIP/Postal code 28029
Country Spain
 
Platform ID GPL6983
Series (2)
GSE51640 Recurrent inactivation of STAG2 in bladder cancer is not associated with aneuploidy [GPL6983]
GSE51641 Recurrent inactivation of STAG2 in bladder cancer is not associated with aneuploidy

Data table header descriptions
ID_REF
VALUE Genotype: AA,AB,BB,or NC (no call)
GC_SCORE
Theta
R
B_Allele_Freq
Log_R_Ratio

Data table
ID_REF VALUE GC_SCORE Theta R B_Allele_Freq Log_R_Ratio
cnv10000p1-126_T_R_IFB1185517302:0 NC 0 0.0169667 0.1540417 0 -0.7551554
cnv10003p1-126_T_R_IFB1185533989:0 NC 0 0.9786105 0.7272391 0.9894456 -0.22272
cnv10003p5-126_T_F_IFB1185542215:0 NC 0 0.009974496 1.090339 0 -0.05579429
cnv10004p1-126_T_F_IFB1185358920:0 NC 0 0.9913996 1.278369 0.9970746 0.03803867
cnv10005PP1-126_T_R_IFB1185518190:0 NC 0 0.05765762 0.8364199 0 -0.4303261
cnv10005PP2-126_B_R_IFB1185523987:0 NC 0 0.02910091 0.4250301 0.008901917 -0.2803964
cnv10008PP2-126_T_F_IFB1185297901:0 NC 0 1 0.4655371 1 0.1387327
cnv10012p1-126_B_R_IFB1187734862:0 NC 0 0.9296494 1.261593 1 0.0581333
cnv10017p1-126_T_F_IFB1185495854:0 NC 0 0.0400812 2.005164 0 0.03578058
cnv10019PP2-126_T_R_IFB1187637367:0 NC 0 0.1204215 4.788199 0.5066903 0.110201
cnv10021p1-126_T_F_IFB1185294366:0 NC 0 0.04773975 1.348045 0 0.332383
cnv10021p2-126_B_F_IFB1185322031:0 NC 0 0.04904002 0.4362492 0 -0.1057454
cnv10023p7-126_T_R_IFB1185379801:0 NC 0 0.2778322 1.781971 0 0.08754588
cnv10025p4-126_T_F_IFB1185504366:0 NC 0 0.009523734 1.279709 0 0.1925556
cnv10026p1-126_T_F_IFB1185372940:0 NC 0 0.9178504 2.081581 0.7865469 0.1105394
cnv10026PP3-126_B_F_IFB1185534682:0 NC 0 0.05685762 1.561191 0 0.1754468
cnv10027p2-126_B_F_IFB1185490394:0 NC 0 0.04530491 1.955769 0 0.5411757
cnv10027p3-126_T_F_IFB1185537004:0 NC 0 0.9761724 1.582953 0.9920791 0.03735944
cnv10028p1-126_B_F_IFB1185521899:0 NC 0 0.984821 1.855014 0.9867302 0.1709451
cnv10028p3-126_T_F_IFB1185532891:0 NC 0 0.990343 1.632977 0.9973655 -0.006497582

Total number of rows: 1072820

Table truncated, full table size 89388 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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