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Sample GSM960016 Query DataSets for GSM960016
Status Public on Jul 07, 2013
Title Metastatic Bladder Cancer 1541
Sample type genomic
Source name Metastatic Bladder Cancer
Organism Homo sapiens
Characteristics unique_patient_id: 1541
sample_type: tumor
surgery_type: radical cystectomy
summarystage: invasive
tumor stage: 2
visceral_metastasis: n
ecog_ps (eastern cooperative oncology group performance status): 1
adjuvant_chemo: y
recurrence_status: recurrence
days_to_death: 770
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 0.453719891070316
A_18_P10001325 -0.668996478360478
A_18_P10001390 -0.538388378911281
A_18_P10001457 -0.429174020686985
A_18_P10001545 -0.366199996311667
A_16_P15001543 -0.0716036283000852
A_16_P15001594 0.495558254749174
A_16_P00000099 0.200251894972265
A_18_P10001772 0.662587217185658
A_16_P00000136 0.416653379228012
A_16_P15001756 -0.105902202941133
A_16_P00000179 0.592577634863377
A_16_P00000195 0.474931796219706
A_16_P15001886 0.311373441394863
A_16_P00000237 0.0101675172155302
A_16_P15001967 0.407800112601908
A_16_P00000285 0.587896250822677
A_16_P00000311 0.681752938965078
A_16_P15002151 0.283235205890221
A_18_P17422640 0.321451695141065

Total number of rows: 164629

Table truncated, full table size 5337 Kbytes.

Supplementary file Size Download File type/resource
GSM960016_1541.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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