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Sample GSM482670 Query DataSets for GSM482670
Status Public on Feb 18, 2010
Title Prostate cell line PC3_Hahn
Sample type genomic
 
Source name PC3_Hahn
Organism Homo sapiens
Characteristics cell type: Prostate cell line
cell line: PC3
Growth protocol Cell lines were grown according to standard conditions.
Extracted molecule genomic DNA
Extraction protocol DNA was obtained from cell line pellets or tumors frozen at the time of surgical dissection and maintained at -80C until use, with the exception of 11 gliomas from which sufficiently high-quality DNA could be obtained from paraffin-embedded samples. The majority of tumors were obtained at primary surgery, with the exceptions of 27 prostate tumors obtained through rapid autopsy programs at the Universities of Washington and Michigan
Label Biotin
Label protocol As per manufacturer (Affymetrix)
 
Hybridization protocol Each sample was genotyped using the Sty I chip of the 500K Human Mapping Array wet (Affymetrix), containing probes to 238,270 SNP loci, according to manufacturer’s instructions. In brief, 250 ng of genomic DNA was digested with the StyI restriction enzyme (New England Biolabs), ligated to an adaptor with T4 ligase (New England Biolabs), and PCR-amplified using a 9700 Thermal Cycler I (Applied Biosystems) and Titanium Taq (Clontech) to achieve fragments ranging from 200-1100 bp. These fragments were pooled, concentrated, processed through a clean-up step, and further fragmented with DNaseI (Affymetrix) before being labeled, denatured, and hybridized to arrays
Scan protocol Arrays were washed and scanned using the GeneChip Scanner 3000 7G (Affymetrix)
Description Hybridized to 250K_Sty
Data processing Probe-level signal intensities were normalized to a common reference array using quantile normalization and combined to form SNP-level signal intensities using the dChip model-based expression (PM/MM) method . Genome-wide copy number estimates were obtained using tangent normalization, in which tumor signal intensities are divided by signal intensities from the linear combination of all normal samples that is most similar to the tumor (as described in Beroukhim et al, In Press; and Getz et al., In Preparation). Cancer samples were normalized against a pool of 1,480 reference samples derived from multiple studies; the code and reference data necessary to replicate this analysis are available for download in GEO. Genotype Call (SNP call) are provided in .CHP.TXT files: AA, AB, BB, NC, and NoCall.
 
Submission date Dec 09, 2009
Last update date Feb 18, 2010
Contact name Craig Mermel
E-mail(s) cmermel@broadinstitute.org
Phone 617-714-7563
Organization name Broad Institute
Department Cancer Program
Lab Matthew Meyerson Lab
Street address 7 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platform ID GPL3720
Series (1)
GSE19399 Affymetrix 250K StyI SNP array data across multiple human cancer types

Data table header descriptions
ID_REF
VALUE copy number via tangent normalization

Data table
ID_REF VALUE
SNP_A-1909444 1.118411
SNP_A-2237149 1.383085
SNP_A-4303947 1.397081
SNP_A-2236359 1.427120
SNP_A-2205441 1.015191
SNP_A-2116190 2.592680
SNP_A-4291020 2.262192
SNP_A-2109914 1.974442
SNP_A-2291997 2.410111
SNP_A-4277872 2.337792
SNP_A-2118217 2.420610
SNP_A-1866065 2.123622
SNP_A-2288244 1.915262
SNP_A-1783407 2.146081
SNP_A-2169457 0.999934
SNP_A-4271011 1.936046
SNP_A-2082515 2.251794
SNP_A-1910751 1.987293
SNP_A-2081399 1.978724
SNP_A-2223642 2.107457

Total number of rows: 238230

Table truncated, full table size 5350 Kbytes.




Supplementary file Size Download File type/resource
GSM482670_HAREM_p_STY35_Redo_Mapping250K_Sty_G01_150974.CEL.gz 28.3 Mb (ftp)(http) CEL
GSM482670_HAREM_p_STY35_Redo_Mapping250K_Sty_G01_150974.CHP.TXT.gz 1.9 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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