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Sample GSM960034 Query DataSets for GSM960034
Status Public on Jul 07, 2013
Title Metastatic Bladder Cancer 1587
Sample type genomic
Source name Metastatic Bladder Cancer
Organism Homo sapiens
Characteristics unique_patient_id: 1587
sample_type: tumor
surgery_type: radical cystectomy
summarystage: invasive
tumor stage: 3
visceral_metastasis: n
ecog_ps (eastern cooperative oncology group performance status): 2
adjuvant_chemo: y
recurrence_status: recurrence
days_to_death: 168
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 0.678968272128625
A_18_P10001325 0.177070800929764
A_18_P10001390 -0.314600488399619
A_18_P10001457 -0.233771123942565
A_18_P10001545 -0.00357905551977089
A_16_P15001543 0.322568203094163
A_16_P15001594 0.80691866224595
A_16_P00000099 0.657917719279721
A_18_P10001772 0.676317940614316
A_16_P00000136 0.395768385706152
A_16_P15001756 -0.0473864212164808
A_16_P00000179 0.591834881522944
A_16_P00000195 0.424781014857717
A_16_P15001886 0.235007084100392
A_16_P00000237 -0.135937175471092
A_16_P15001967 0.667116799390287
A_16_P00000285 0.381874465128887
A_16_P00000311 0.691528785502782
A_16_P15002151 0.479858635682878
A_18_P17422640 0.417290833625858

Total number of rows: 164629

Table truncated, full table size 5332 Kbytes.

Supplementary file Size Download File type/resource
GSM960034_1587.txt.gz 18.7 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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