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Sample GSM959984 Query DataSets for GSM959984
Status Public on Jul 07, 2013
Title Metastatic Bladder Cancer 1504
Sample type genomic
 
Source name Metastatic Bladder Cancer
Organism Homo sapiens
Characteristics unique_patient_id: 1504
sample_type: tumor
surgery_type: radical cystectomy
summarystage: invasive
tumor stage: 2
visceral_metastasis: y
ecog_ps (eastern cooperative oncology group performance status): 1
adjuvant_chemo: y
recurrence_status: recurrence
days_to_death: 341
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 -0.850738623988491
A_18_P10001325 -0.532871844391136
A_18_P10001390 0.147553460377492
A_18_P10001457 0.0335182925083259
A_18_P10001545 -0.702502809038807
A_16_P15001543 -0.0814582478877628
A_16_P15001594 0.0790434290590891
A_16_P00000099 0.107612079152136
A_18_P10001772 0.178946475118803
A_16_P00000136 -0.298540806924996
A_16_P15001756 -0.514332232263538
A_16_P00000179 -0.0484041169444978
A_16_P00000195 0.511082840417529
A_16_P15001886 0.174211241733989
A_16_P00000237 -0.56516885727727
A_16_P15001967 0.404644355024201
A_16_P00000285 0.184307781597587
A_16_P00000311 0.0989863618283526
A_16_P15002151 0.00677672823526621
A_18_P17422640 0.167304876402769

Total number of rows: 164629

Table truncated, full table size 5344 Kbytes.




Supplementary file Size Download File type/resource
GSM959984_1504.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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