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Sample GSM1249990 Query DataSets for GSM1249990
Status Public on Oct 24, 2013
Title 4235966189
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 0.09522694 0 -1.449035
cnv10003p1-126_T_R_IFB1185533989:0 NC 0 1 0.6539475 1 -0.375975
cnv10003p5-126_T_F_IFB1185542215:0 NC 0 0.005912128 0.9451744 0 -0.2619189
cnv10004p1-126_T_F_IFB1185358920:0 NC 0 0.9962363 1.233747 1 -0.01321937
cnv10005PP1-126_T_R_IFB1185518190:0 NC 0 0.1094306 0.7648578 0.5009796 -0.5593618
cnv10005PP2-126_B_R_IFB1185523987:0 NC 0 0 0.2775978 0 -0.8949653
cnv10008PP2-126_T_F_IFB1185297901:0 NC 0 1 0.3295265 1 -0.3597692
cnv10012p1-126_B_R_IFB1187734862:0 NC 0 0.9034622 1.236038 0.996479 0.02860993
cnv10017p1-126_T_F_IFB1185495854:0 NC 0 0.03785209 1.692334 0 -0.208925
cnv10019PP2-126_T_R_IFB1187637367:0 NC 0 0.1378434 3.583925 0.5176338 -0.3077414
cnv10021p1-126_T_F_IFB1185294366:0 NC 0 0.05773938 1.06027 0.05004599 -0.01405403
cnv10021p2-126_B_F_IFB1185322031:0 NC 0 0.08620121 0.4436086 0 -0.08161059
cnv10023p7-126_T_R_IFB1185379801:0 NC 0 0.3198096 1.487613 0.05090878 -0.1729284
cnv10025p4-126_T_F_IFB1185504366:0 NC 0 0.009896481 1.047996 0.0002256614 -0.09562676
cnv10026p1-126_T_F_IFB1185372940:0 NC 0 0.9286302 1.997208 0.9065263 0.05084456
cnv10026PP3-126_B_F_IFB1185534682:0 NC 0 0.06711997 1.235595 0.001356581 -0.1619942
cnv10027p2-126_B_F_IFB1185490394:0 NC 0 0.05737391 1.223101 0 -0.1360161
cnv10027p3-126_T_F_IFB1185537004:0 NC 0 0.9766834 1.420265 0.9926814 -0.1190994
cnv10028p1-126_B_F_IFB1185521899:0 NC 0 0.988152 1.617952 1 -0.02631612
cnv10028p3-126_T_F_IFB1185532891:0 NC 0 0.9905694 1.623123 0.9976274 -0.01522954

Total number of rows: 1072820

Table truncated, full table size 87688 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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