GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM960020 Query DataSets for GSM960020
Status Public on Jul 07, 2013
Title Metastatic Bladder Cancer 1567
Sample type genomic
Source name Metastatic Bladder Cancer
Organism Homo sapiens
Characteristics unique_patient_id: 1567
sample_type: tumor
surgery_type: radical cystectomy
summarystage: invasive
tumor stage: 3
visceral_metastasis: y
ecog_ps (eastern cooperative oncology group performance status): 0
adjuvant_chemo: y
recurrence_status: recurrence
days_to_death: 484
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 0.339055597571367
A_18_P10001325 -0.133322106811582
A_18_P10001390 -0.102875656238387
A_18_P10001457 -0.197025038585649
A_18_P10001545 -0.0758991757728099
A_16_P15001543 0.242848883999398
A_16_P15001594 0.15145935496346
A_16_P00000099 -0.162166829181735
A_18_P10001772 0.227896672677786
A_16_P00000136 -0.236397865121282
A_16_P15001756 -0.420701585116969
A_16_P00000179 0.119107005950693
A_16_P00000195 0.0187874511422077
A_16_P15001886 -0.0859281422025353
A_16_P00000237 -0.0492255149170432
A_16_P15001967 0.0268114625867814
A_16_P00000285 0.0280414088804676
A_16_P00000311 0.137422412317315
A_16_P15002151 0.193413616785818
A_18_P17422640 0.201681348371828

Total number of rows: 164629

Table truncated, full table size 5346 Kbytes.

Supplementary file Size Download File type/resource
GSM960020_1567.txt.gz 18.4 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap