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Sample GSM959961 Query DataSets for GSM959961
Status Public on Jul 07, 2013
Title Metastatic Bladder Cancer 1280
Sample type genomic
 
Source name Metastatic Bladder Cancer
Organism Homo sapiens
Characteristics unique_patient_id: 1280
sample_type: tumor
surgery_type: radical cystectomy
summarystage: superficial
tumor stage: 1
visceral_metastasis: n
ecog_ps (eastern cooperative oncology group performance status): 1
adjuvant_chemo: y
recurrence_status: recurrence
days_to_death: 796
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
E-mail(s) markus@jimmy.harvard.edu
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
ID_REF
VALUE CopyNumber

Data table
ID_REF VALUE
A_16_P15000916 0.339739508136684
A_18_P10001325 -0.0238413305665783
A_18_P10001390 -0.224847007906648
A_18_P10001457 -0.514370507712477
A_18_P10001545 0.0326234075864389
A_16_P15001543 0.351710784468219
A_16_P15001594 0.691999311630997
A_16_P00000099 0.218840300305524
A_18_P10001772 0.241291693483996
A_16_P00000136 0.390535001401686
A_16_P15001756 0.0623220743590107
A_16_P00000179 0.135830074042756
A_16_P00000195 0.49664679731663
A_16_P15001886 0.321123006033813
A_16_P00000237 0.193612506629496
A_16_P15001967 0.0823538301187026
A_16_P00000285 0.42833642240717
A_16_P00000311 0.301548223867148
A_16_P15002151 0.377145539064186
A_18_P17422640 0.0666106081620454

Total number of rows: 164629

Table truncated, full table size 5342 Kbytes.




Supplementary file Size Download File type/resource
GSM959961_1280.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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