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Sample GSM960006 Query DataSets for GSM960006
Status Public on Jul 07, 2013
Title Metastatic Bladder Cancer 1531
Sample type genomic
Source name Metastatic Bladder Cancer
Organism Homo sapiens
Characteristics unique_patient_id: 1531
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: 251
vital_status: deceased
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 0.375541936619961
A_18_P10001325 0.0466019801573219
A_18_P10001390 -0.409347040327677
A_18_P10001457 0.266168403468335
A_18_P10001545 -0.0575464685845146
A_16_P15001543 0.074598389399533
A_16_P15001594 0.454241975559687
A_16_P00000099 0.113614507234619
A_18_P10001772 0.201956162571085
A_16_P00000136 0.395843239487617
A_16_P15001756 0.0926197148553549
A_16_P00000179 0.979896626135655
A_16_P00000195 0.497261300434555
A_16_P15001886 -0.0257449367867979
A_16_P00000237 0.404753811374281
A_16_P15001967 0.174005582233399
A_16_P00000285 0.551532286901259
A_16_P00000311 0.418528562537327
A_16_P15002151 0.115520800397281
A_18_P17422640 0.133091252334456

Total number of rows: 164629

Table truncated, full table size 5340 Kbytes.

Supplementary file Size Download File type/resource
GSM960006_1531.txt.gz 18.4 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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