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Sample GSM959974 Query DataSets for GSM959974
Status Public on Jul 07, 2013
Title Metastatic Bladder Cancer 1340
Sample type genomic
 
Source name Metastatic Bladder Cancer
Organism Homo sapiens
Characteristics unique_patient_id: 1340
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: 80
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 0.451953381354048
A_18_P10001325 -0.543873319280749
A_18_P10001390 -0.602949576958555
A_18_P10001457 -0.702315079595133
A_18_P10001545 -0.525962152531754
A_16_P15001543 0.261924017939188
A_16_P15001594 0.195747107570401
A_16_P00000099 0.136375866055582
A_18_P10001772 0.0965836481794424
A_16_P00000136 0.11144396991707
A_16_P15001756 -0.553852599182846
A_16_P00000179 -0.101709857805622
A_16_P00000195 0.0655602815345058
A_16_P15001886 0.0789933159870888
A_16_P00000237 0.107110373787895
A_16_P15001967 0.353312668607396
A_16_P00000285 0.10987133443295
A_16_P00000311 0.279549781956209
A_16_P15002151 0.268705375617205
A_18_P17422640 0.112790072026946

Total number of rows: 164629

Table truncated, full table size 5339 Kbytes.




Supplementary file Size Download File type/resource
GSM959974_1340.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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