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Sample GSM960046 Query DataSets for GSM960046
Status Public on Jul 07, 2013
Title Metastatic Bladder Cancer 1605
Sample type genomic
 
Source name Metastatic Bladder Cancer
Organism Homo sapiens
Characteristics unique_patient_id: 1605
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: 592
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 -0.151102689616551
A_18_P10001325 -0.467587656013437
A_18_P10001390 -0.252682462568316
A_18_P10001457 -0.212802753910618
A_18_P10001545 -0.159199527303286
A_16_P15001543 0.53337161076699
A_16_P15001594 0.266744106401614
A_16_P00000099 0.251159247993963
A_18_P10001772 0.292350160487975
A_16_P00000136 0.0175192840127639
A_16_P15001756 0.0280407925494013
A_16_P00000179 0.66084310254673
A_16_P00000195 0.567264969266716
A_16_P15001886 0.340279175684769
A_16_P00000237 0.181995805048115
A_16_P15001967 0.336631940449411
A_16_P00000285 0.434330958165748
A_16_P00000311 0.491897270647257
A_16_P15002151 0.101138887967785
A_18_P17422640 0.181536692199914

Total number of rows: 164629

Table truncated, full table size 5347 Kbytes.




Supplementary file Size Download File type/resource
GSM960046_1605.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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