GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM637987 Query DataSets for GSM637987
Status Public on Dec 11, 2010
Title KM-H2
Sample type genomic
Source name Hodgkin lymphoma cell line KM-H2
Organism Homo sapiens
Characteristics cell type: Pleural effusion cells
cell line: KM-H2
Extracted molecule genomic DNA
Extraction protocol Qiagen Allprep extraction columns
Label biotin
Label protocol standard Affymetrix protocol
Hybridization protocol DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
Scan protocol GeneChips were scanned using Affymetrix GeneChip Scanner
Description Genome-wide SNP/CN data of Hodgkin lymphoma cell line KM-H2
Data processing The Affymetrix SNP 6.0 data were processed using the R-based aroma.affymetrix package (Bengsston et al, Bioinformatics 2009). Total copy number was estimated according to the CRMA procedure, calibrating for allelic cross talk, nucleotide-position probe sequence effects, robust probe summarization and correction for fragment length effects.
Submission date Dec 10, 2010
Last update date Dec 11, 2010
Contact name Christian Steidl
Phone 1-604-675-8046
Organization name BC Cancer Agency
Department Pathology
Lab Steidl lab
Street address 675 West 10th Avenue
City Vancouver
State/province BC
ZIP/Postal code V5Z 1L3
Country Canada
Platform ID GPL6801
Series (2)
GSE25989 Copy number analysis of Hodgkin lymphoma cell lines KM-H2 and L-428
GSE25990 Hodgkin lymphoma

Data table header descriptions
VALUE CRMA normalized copy number: compared to a reference derived from the HapMap 270 set of arrays downloaded from the Affymetrix website

Data table
CN_473963 2.72185798200013
CN_473964 3.94954372567463
CN_473965 2.52401406100448
CN_477984 1.99760560488277
CN_473981 2.21811555508813
CN_473982 2.76909344988453
CN_497980 1.97378697215518
CN_497981 2.12591707750459
CN_513369 4.0148419137293
CN_513370 2.39936757188956
CN_517762 2.77304117129198
CN_517763 2.83781625409933
CN_502615 3.05855462178667
CN_502613 3.20922136123628
CN_502614 3.7321538571846
CN_502616 3.48674755928764
CN_502842 3.63102992010528
CN_502843 2.29952088805983
CN_466171 2.62017496116009
CN_466172 2.34236178621945

Total number of rows: 1879489

Table truncated, full table size 53491 Kbytes.

Supplementary file Size Download File type/resource
GSM637987_KMH2_GenomeWideSNP_6_.CEL.gz 29.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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