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Sample GSM960008 Query DataSets for GSM960008
Status Public on Jul 07, 2013
Title Metastatic Bladder Cancer 1533
Sample type genomic
 
Source name Metastatic Bladder Cancer
Organism Homo sapiens
Characteristics unique_patient_id: 1533
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: 342
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
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 -0.865657923151144
A_18_P10001325 -0.336157272905605
A_18_P10001390 -0.207905247578979
A_18_P10001457 -0.642885479049388
A_18_P10001545 -0.501428648438184
A_16_P15001543 -0.192230073292061
A_16_P15001594 0.563053946075415
A_16_P00000099 0.132378525974976
A_18_P10001772 0.523783915688761
A_16_P00000136 0.283407853354367
A_16_P15001756 -0.364513990373615
A_16_P00000179 0.260471570218819
A_16_P00000195 0.0625550764711034
A_16_P15001886 0.248276470961666
A_16_P00000237 0.158747317765091
A_16_P15001967 0.272413698615908
A_16_P00000285 0.151242740529428
A_16_P00000311 0.184658604066646
A_16_P15002151 0.191953187318418
A_18_P17422640 0.0476222062485159

Total number of rows: 164629

Table truncated, full table size 5338 Kbytes.




Supplementary file Size Download File type/resource
GSM960008_1533.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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