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Sample GSM960043 Query DataSets for GSM960043
Status Public on Jul 07, 2013
Title Metastatic Bladder Cancer 1602
Sample type genomic
Source name Metastatic Bladder Cancer
Organism Homo sapiens
Characteristics unique_patient_id: 1602
sample_type: tumor
surgery_type: radical cystectomy
summarystage: invasive
tumor stage: 2
visceral_metastasis: y
ecog_ps (eastern cooperative oncology group performance status): 1
adjuvant_chemo: y
recurrence_status: recurrence
days_to_death: 89
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 0.374610974787817
A_18_P10001325 -1.18074181486747
A_18_P10001390 -0.710911132225637
A_18_P10001457 -0.980251291192036
A_18_P10001545 -0.347019791545037
A_16_P15001543 0.0140961731583447
A_16_P15001594 0.170023104261649
A_16_P00000099 -0.166441500409227
A_18_P10001772 -0.275057939113732
A_16_P00000136 -0.0769899847044297
A_16_P15001756 -0.739024659502235
A_16_P00000179 0.184672236746106
A_16_P00000195 0.238355981140224
A_16_P15001886 0.247581778652044
A_16_P00000237 -0.166150600131262
A_16_P15001967 0.0154968899280172
A_16_P00000285 0.0823655625437159
A_16_P00000311 0.21860422310139
A_16_P15002151 -0.104487563368449
A_18_P17422640 0.0415793493337704

Total number of rows: 164629

Table truncated, full table size 5338 Kbytes.

Supplementary file Size Download File type/resource
GSM960043_1602.txt.gz 18.6 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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