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Sample GSM959982 Query DataSets for GSM959982
Status Public on Jul 07, 2013
Title Metastatic Bladder Cancer 1500
Sample type genomic
Source name Metastatic Bladder Cancer
Organism Homo sapiens
Characteristics unique_patient_id: 1500
sample_type: tumor
surgery_type: radical cystectomy
summarystage: superficial
tumor stage: 0
visceral_metastasis: n
ecog_ps (eastern cooperative oncology group performance status): 1
adjuvant_chemo: y
recurrence_status: recurrence
days_to_death: 796
vital_status: living
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from tumors using the QIAamp DNA FFPE Tissue Kit (Qiagen, Valencia, CA)
Label ULS-Cy5
Label protocol The Genomic DNA ULS labeling kit for FFPE Samples (Agilent Technologies, Inc., Palo Alto, CA) was used to chemically label 500ng of DNA with either ULS-Cy5 (tumor) or ULS-Cy3 dye (normal/reference DNA) following the manufacturer's protocol
Hybridization protocol Genomic DNA samples were hybridized to the array using an Agilent microarray hybridization chamber for 40 hours in a Robbins Scientific oven with rotation at 20 rpm at 65°C
Scan protocol Post-hybridization, the slides were washed and scanned using an Agilent DNA microarray scanner
Description Genomic DNA isolated from metastatic bladder cancer
Data processing CGH Analytics software (version 3.4, Agilent Technologies, CA) was used to analyze the aCGH data
Copy numbers were segmented using the GLAD algorithm. The 'spanishaCGH.glad.txt' are the segmented data (like the Level 3 data in TCGA), calculated with the GLAD algorithm: Sample ID, Chromosome, Start, End, Number of Probes in the segment, log2 copy number ratio of the segment (available on a Series records).
Submission date Jul 11, 2012
Last update date Jul 07, 2013
Contact name Markus Riester
Organization name Dana-Farber Cancer Institute
Department Biostatistics & Computational Biology
Lab Michor
Street address 3 Blackfan Circle
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
Platform ID GPL10150
Series (2)
GSE39281 DNA copy number gain at 1q23.3 is associated with poor survival in metastatic bladder cancer [Agilent]
GSE39282 DNA copy number gain at 1q23.3 is associated with poor survival in metastatic bladder cancer

Data table header descriptions
VALUE CopyNumber

Data table
A_16_P15000916 -1.45175211142712
A_18_P10001325 -1.29603085821791
A_18_P10001390 -0.852891464073893
A_18_P10001457 -1.03159515123989
A_18_P10001545 -0.396536422992873
A_16_P15001543 0.0160832680508305
A_16_P15001594 0.528191884963452
A_16_P00000099 -0.196990603039649
A_18_P10001772 0.342754341988676
A_16_P00000136 -0.134191682359118
A_16_P15001756 -0.263506519308414
A_16_P00000179 0.226658012851677
A_16_P00000195 0.318075424351943
A_16_P15001886 0.0261733244404265
A_16_P00000237 -0.0981546032939051
A_16_P15001967 0.360641874859081
A_16_P00000285 -0.155627579995345
A_16_P00000311 0.973086485727729
A_16_P15002151 -0.31213084973863
A_18_P17422640 -0.093399205297735

Total number of rows: 164629

Table truncated, full table size 5336 Kbytes.

Supplementary file Size Download File type/resource
GSM959982_1500.txt.gz 18.5 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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