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Sample GSM960004 Query DataSets for GSM960004
Status Public on Jul 07, 2013
Title Metastatic Bladder Cancer 1529
Sample type genomic
Source name Metastatic Bladder Cancer
Organism Homo sapiens
Characteristics unique_patient_id: 1529
sample_type: tumor
surgery_type: radical cystectomy
summarystage: invasive
tumor stage: 3
visceral_metastasis: y
ecog_ps (eastern cooperative oncology group performance status): 0
adjuvant_chemo: y
recurrence_status: recurrence
days_to_death: 356
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 0.286611408495344
A_18_P10001325 -0.0374207878700785
A_18_P10001390 0.179704560186687
A_18_P10001457 -0.0468320000866234
A_18_P10001545 0.0704507877533498
A_16_P15001543 0.0386196011655588
A_16_P15001594 0.275388950650248
A_16_P00000099 0.0226967840540329
A_18_P10001772 0.337283955367729
A_16_P00000136 0.242284530955126
A_16_P15001756 -0.134053436981699
A_16_P00000179 0.124626232340144
A_16_P00000195 0.150756763274505
A_16_P15001886 0.0101756504494963
A_16_P00000237 -0.0911489656159155
A_16_P15001967 -0.160035907527718
A_16_P00000285 0.0219459404063946
A_16_P00000311 0.238565825555161
A_16_P15002151 -0.181339288057358
A_18_P17422640 0.171688024590301

Total number of rows: 164629

Table truncated, full table size 5349 Kbytes.

Supplementary file Size Download File type/resource
GSM960004_1529.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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