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Sample GSM959979 Query DataSets for GSM959979
Status Public on Jul 07, 2013
Title Metastatic Bladder Cancer 1355
Sample type genomic
 
Source name Metastatic Bladder Cancer
Organism Homo sapiens
Characteristics unique_patient_id: 1355
sample_type: tumor
surgery_type: radical cystectomy
summarystage: invasive
tumor stage: 3
visceral_metastasis: n
ecog_ps (eastern cooperative oncology group performance status): 0
adjuvant_chemo: y
recurrence_status: recurrence
days_to_death: 703
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
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 0.0977411475228234
A_18_P10001325 -0.215041785443456
A_18_P10001390 -0.42309334556549
A_18_P10001457 -1.36546602047142
A_18_P10001545 -0.0430992476656182
A_16_P15001543 -0.0983617230346836
A_16_P15001594 0.190452029029415
A_16_P00000099 -0.120103453156879
A_18_P10001772 0.0864723076447093
A_16_P00000136 0.255145647614097
A_16_P15001756 -0.611024849263624
A_16_P00000179 0.00986892691290531
A_16_P00000195 0.0503386714519158
A_16_P15001886 0.278769791611583
A_16_P00000237 -0.520051945244263
A_16_P15001967 -0.0490420876436213
A_16_P00000285 0.00023957567037125
A_16_P00000311 -0.00189806927217773
A_16_P15002151 -0.104758890015727
A_18_P17422640 0.0693495766193712

Total number of rows: 164629

Table truncated, full table size 5344 Kbytes.




Supplementary file Size Download File type/resource
GSM959979_1355.txt.gz 18.5 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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