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Sample GSM1249987 Query DataSets for GSM1249987
Status Public on Oct 24, 2013
Title 4235966118
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 0.03014021 0.1789444 0.07957506 -0.5389653
cnv10003p1-126_T_R_IFB1185533989:0 NC 0 0.9919126 0.7283163 1 -0.2205846
cnv10003p5-126_T_F_IFB1185542215:0 NC 0 0.01656784 1.10282 0.003674768 -0.03937439
cnv10004p1-126_T_F_IFB1185358920:0 NC 0 0.9901211 1.236442 0.9953786 -0.01007138
cnv10005PP1-126_T_R_IFB1185518190:0 NC 0 0.08377602 0.9682986 0.2086148 -0.2191014
cnv10005PP2-126_B_R_IFB1185523987:0 NC 0 0.03393102 0.4039359 0.01431369 -0.3538347
cnv10008PP2-126_T_F_IFB1185297901:0 NC 0 0.9963159 0.5019203 1 0.2472948
cnv10012p1-126_B_R_IFB1187734862:0 NC 0 0.8845606 1.503103 0.973235 0.3108305
cnv10017p1-126_T_F_IFB1185495854:0 NC 0 0.05188591 1.750536 0.005253226 -0.1601429
cnv10019PP2-126_T_R_IFB1187637367:0 NC 0 0.1190689 4.904199 0.5058407 0.1447352
cnv10021p1-126_T_F_IFB1185294366:0 NC 0 0.06297712 1.273494 0.1116165 0.2503071
cnv10021p2-126_B_F_IFB1185322031:0 NC 0 0.1267921 0.5077499 0 0.1132199
cnv10023p7-126_T_R_IFB1185379801:0 NC 0 0.2953023 1.784979 0 0.0899796
cnv10025p4-126_T_F_IFB1185504366:0 NC 0 0.01045613 1.363104 0.001343787 0.2836354
cnv10026p1-126_T_F_IFB1185372940:0 NC 0 0.9104047 2.042912 0.7036758 0.0834868
cnv10026PP3-126_B_F_IFB1185534682:0 NC 0 0.06157688 1.683378 0 0.2841583
cnv10027p2-126_B_F_IFB1185490394:0 NC 0 0.06050451 1.450196 0.002100331 0.109688
cnv10027p3-126_T_F_IFB1185537004:0 NC 0 0.9773971 1.633194 0.9935226 0.08243722
cnv10028p1-126_B_F_IFB1185521899:0 NC 0 0.9910237 1.611956 1 -0.03167264
cnv10028p3-126_T_F_IFB1185532891:0 NC 0 0.9897631 1.769966 0.9966947 0.1097196

Total number of rows: 1072820

Table truncated, full table size 89533 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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