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Sample GSM959998 Query DataSets for GSM959998
Status Public on Jul 07, 2013
Title Metastatic Bladder Cancer 1522
Sample type genomic
Source name Metastatic Bladder Cancer
Organism Homo sapiens
Characteristics unique_patient_id: 1522
sample_type: tumor
surgery_type: radical cystectomy
summarystage: superficial
tumor stage: 0
visceral_metastasis: n
ecog_ps (eastern cooperative oncology group performance status): 0
adjuvant_chemo: y
recurrence_status: recurrence
days_to_death: 630
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 -0.0375284083288745
A_18_P10001325 -1.04787868156914
A_18_P10001390 -0.485667406615881
A_18_P10001457 -0.490828056025385
A_18_P10001545 0.0223261110797792
A_16_P15001543 0.0511518830609785
A_16_P15001594 0.0353982044793855
A_16_P00000099 -0.0388513608604066
A_18_P10001772 -0.102338663351677
A_16_P00000136 0.339627670127471
A_16_P15001756 -0.410879737674042
A_16_P00000179 0.0914122938152684
A_16_P00000195 0.396899032086216
A_16_P15001886 -0.0728456205513177
A_16_P00000237 0.172327677010102
A_16_P15001967 -0.0895720211011712
A_16_P00000285 -0.0735033945620984
A_16_P00000311 0.202778919871545
A_16_P15002151 -0.0154805114462144
A_18_P17422640 -0.12793682771801

Total number of rows: 164629

Table truncated, full table size 5342 Kbytes.

Supplementary file Size Download File type/resource
GSM959998_1522.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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