GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM959977 Query DataSets for GSM959977
Status Public on Jul 07, 2013
Title Metastatic Bladder Cancer 1350
Sample type genomic
Source name Metastatic Bladder Cancer
Organism Homo sapiens
Characteristics unique_patient_id: 1350
sample_type: tumor
surgery_type: radical cystectomy
summarystage: superficial
tumor stage: 1
visceral_metastasis: y
ecog_ps (eastern cooperative oncology group performance status): 0
adjuvant_chemo: y
recurrence_status: recurrence
days_to_death: 342
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
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 -0.528803894140065
A_18_P10001325 -0.284944554341704
A_18_P10001390 -0.0682830700693633
A_18_P10001457 -0.283761492409893
A_18_P10001545 -0.0879120994341502
A_16_P15001543 0.0605802831521605
A_16_P15001594 0.15816509452371
A_16_P00000099 0.338770847829448
A_18_P10001772 0.0950930625848632
A_16_P00000136 0.472020120148463
A_16_P15001756 -0.0894643812444315
A_16_P00000179 0.376864014507164
A_16_P00000195 0.374686965722493
A_16_P15001886 0.0632634562137074
A_16_P00000237 -0.0148741965155319
A_16_P15001967 0.328346816131128
A_16_P00000285 0.157605768195738
A_16_P00000311 0.297494765604289
A_16_P15002151 0.0657005399939841
A_18_P17422640 -0.0662196719223271

Total number of rows: 164629

Table truncated, full table size 5348 Kbytes.

Supplementary file Size Download File type/resource
GSM959977_1350.txt.gz 18.4 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap