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Sample GSM959971 Query DataSets for GSM959971
Status Public on Jul 07, 2013
Title Metastatic Bladder Cancer 1301
Sample type genomic
 
Source name Metastatic Bladder Cancer
Organism Homo sapiens
Characteristics unique_patient_id: 1301
sample_type: tumor
surgery_type: radical cystectomy
summarystage: invasive
tumor stage: 3
visceral_metastasis: y
ecog_ps (eastern cooperative oncology group performance status): 1
adjuvant_chemo: y
recurrence_status: recurrence
days_to_death: 439
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 0.566331321671033
A_18_P10001325 0.435272034676863
A_18_P10001390 0.336358767306992
A_18_P10001457 0.251369522894274
A_18_P10001545 -0.131406386840168
A_16_P15001543 -0.0913999016944929
A_16_P15001594 0.155355669135395
A_16_P00000099 0.0672550009874713
A_18_P10001772 0.0443808812400484
A_16_P00000136 -0.054426738005992
A_16_P15001756 -0.106767014290746
A_16_P00000179 -0.108207763636974
A_16_P00000195 0.136831914159001
A_16_P15001886 0.142170615975595
A_16_P00000237 -0.55818107578955
A_16_P15001967 -0.397555642004156
A_16_P00000285 -0.428600678601369
A_16_P00000311 -0.498648888056503
A_16_P15002151 -0.0421311140265219
A_18_P17422640 0.341274835336609

Total number of rows: 164629

Table truncated, full table size 5339 Kbytes.




Supplementary file Size Download File type/resource
GSM959971_1301.txt.gz 18.6 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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