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Sample GSM959995 Query DataSets for GSM959995
Status Public on Jul 07, 2013
Title Metastatic Bladder Cancer 1518
Sample type genomic
Source name Metastatic Bladder Cancer
Organism Homo sapiens
Characteristics unique_patient_id: 1518
sample_type: tumor
surgery_type: radical cystectomy
summarystage: superficial
tumor stage: 1
visceral_metastasis: y
ecog_ps (eastern cooperative oncology group performance status): 1
adjuvant_chemo: y
recurrence_status: recurrence
days_to_death: 99
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 -0.0784567395834888
A_18_P10001325 -0.973926900759507
A_18_P10001390 -0.568223677786066
A_18_P10001457 -0.331779497127979
A_18_P10001545 0.0215931944604506
A_16_P15001543 0.0502854599710274
A_16_P15001594 -0.00638888094062318
A_16_P00000099 -0.116273527956611
A_18_P10001772 -0.00558840318215625
A_16_P00000136 0.26171393822991
A_16_P15001756 -0.22346123978445
A_16_P00000179 0.282460514189498
A_16_P00000195 0.493610202589682
A_16_P15001886 0.23460464198499
A_16_P00000237 -0.243288077390542
A_16_P15001967 0.113369394725547
A_16_P00000285 -0.0261124999442077
A_16_P00000311 0.406149506753899
A_16_P15002151 0.229709271607817
A_18_P17422640 0.0353656912970655

Total number of rows: 164629

Table truncated, full table size 5340 Kbytes.

Supplementary file Size Download File type/resource
GSM959995_1518.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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