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Sample GSM959981 Query DataSets for GSM959981
Status Public on Jul 07, 2013
Title Metastatic Bladder Cancer 1357
Sample type genomic
Source name Metastatic Bladder Cancer
Organism Homo sapiens
Characteristics unique_patient_id: 1357
sample_type: tumor
surgery_type: radical cystectomy
summarystage: invasive
tumor stage: 2
visceral_metastasis: n
ecog_ps (eastern cooperative oncology group performance status): 0
adjuvant_chemo: y
recurrence_status: recurrence
days_to_death: 764
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
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 0.501430196192854
A_18_P10001325 -0.294408925656963
A_18_P10001390 -0.0544396838810752
A_18_P10001457 -0.17594732186209
A_18_P10001545 0.152407237798075
A_16_P15001543 0.497521738335183
A_16_P15001594 0.790696029906147
A_16_P00000099 0.673349213367512
A_18_P10001772 0.723890789055391
A_16_P00000136 0.0773446733608709
A_16_P15001756 0.240116642262163
A_16_P00000179 0.710882455769728
A_16_P00000195 0.416089746086524
A_16_P15001886 0.145578507142901
A_16_P00000237 0.372083389299049
A_16_P15001967 0.442776040995342
A_16_P00000285 0.994616436946994
A_16_P00000311 0.703283309487358
A_16_P15002151 0.488010793005598
A_18_P17422640 0.592864761886056

Total number of rows: 164629

Table truncated, full table size 5334 Kbytes.

Supplementary file Size Download File type/resource
GSM959981_1357.txt.gz 18.2 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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