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Sample GSM960032 Query DataSets for GSM960032
Status Public on Jul 07, 2013
Title Metastatic Bladder Cancer 1583
Sample type genomic
Source name Metastatic Bladder Cancer
Organism Homo sapiens
Characteristics unique_patient_id: 1583
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: 287
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 0.457682075104148
A_18_P10001325 -0.004967650286964
A_18_P10001390 -0.1018381238405
A_18_P10001457 -0.420235833613735
A_18_P10001545 -0.328656638708647
A_16_P15001543 -0.16052042884244
A_16_P15001594 -0.111628287347524
A_16_P00000099 -0.130902048801364
A_18_P10001772 -0.0895723099953849
A_16_P00000136 -0.286635065167714
A_16_P15001756 -0.657661475931855
A_16_P00000179 -0.592668803724124
A_16_P00000195 -0.0459088791386809
A_16_P15001886 0.0648858695864745
A_16_P00000237 -0.548058589596664
A_16_P15001967 -0.175807864132698
A_16_P00000285 0.0336617023680219
A_16_P00000311 -0.306674161399743
A_16_P15002151 -0.107066344652414
A_18_P17422640 0.0298864804569432

Total number of rows: 164629

Table truncated, full table size 5349 Kbytes.

Supplementary file Size Download File type/resource
GSM960032_1583.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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