GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM637988 Query DataSets for GSM637988
Status Public on Dec 11, 2010
Title L-428
Sample type genomic
Source name Hodgkin lymphoma cell line L-428
Organism Homo sapiens
Characteristics cell type: Pleural effusion cells
cell line: L-428
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 L-428
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 2.29948668474528
CN_473964 2.21185793758836
CN_473965 1.80978839227243
CN_477984 1.90804006873809
CN_473981 1.47401057454418
CN_473982 1.88426168965260
CN_497980 1.67085464818468
CN_497981 2.25048752048328
CN_513369 1.37023563066654
CN_513370 2.15180470263772
CN_517762 1.42060848357212
CN_517763 2.42437514985775
CN_502615 0.973530900830836
CN_502613 2.01782346702845
CN_502614 1.50996464732517
CN_502616 0.91237985043949
CN_502842 2.49601837540875
CN_502843 2.13200235517778
CN_466171 2.56674591862627
CN_466172 2.72271231956802

Total number of rows: 1879489

Table truncated, full table size 53489 Kbytes.

Supplementary file Size Download File type/resource
GSM637988_L428_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