NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM872978 Query DataSets for GSM872978
Status Public on Jul 01, 2013
Title CD3 lymphocytes from 4_34543
Sample type genomic
 
Source name CD3 lymphocytes isolated from peripheral blood
Organism Homo sapiens
Characteristics cell type: CD3 lymphocytes isolated from peripheral blood
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from whole bone marrow, whole peripheral blood or CD3 lymphocytes isolated from peripheral blood prior to treatment with lenalidomide, at the individual centers participating in the study. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.
Label biotin
Label protocol DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
 
Hybridization protocol The Arrays were then washed using Affymetrix fluidics stations, and scanned according to the manufacturer's instructions.
Scan protocol CEL files, generated by AGCC Viewer. CNCHP and LOHCHP, generated by Genotyping Console (all provided by Affymetrix)
Description Hybridized to 6.0 Array
Data processing CNCHP (from 6.0 arrays) provide data for copy number and LOH analysis.
Genotyping Console; algorithm-name = CN5
 
Submission date Feb 09, 2012
Last update date Jul 01, 2013
Contact name Mar Mallo
Organization name Josep Carreras Leukaemia Research Institute
Street address Ctra de Can Ruti, s/n, camí de les escoles. Edifici IMPPC
City Badalona
ZIP/Postal code 08916
Country Spain
 
Platform ID GPL6801
Series (1)
GSE35656 Affymetrix SNP array data for myelodysplastic syndrome with 5q deletion treated with lenalidomide

Data table header descriptions
ID_REF
VALUE CN STATE
CHROMOSOME
POSITION
LOG2 RATIO
SMOOTH SIGNAL
LOH
ALLELE DIFFERENCE

Data table
ID_REF VALUE CHROMOSOME POSITION LOG2 RATIO SMOOTH SIGNAL LOH ALLELE DIFFERENCE
CN_473963 3.000000 1 51586 0.175684 2.469331 nan nan
CN_473964 3.000000 1 51659 0.448660 2.469079 nan nan
CN_473965 3.000000 1 51674 0.363333 2.469027 nan nan
CN_473981 3.000000 1 52771 0.406635 2.465233 nan nan
CN_473982 3.000000 1 52788 0.770855 2.465174 nan nan
CN_497981 3.000000 1 62627 0.095899 2.431581 nan nan
CN_502615 3.000000 1 75787 -0.311374 2.388092 nan nan
CN_502613 3.000000 1 75849 -0.091213 2.387892 nan nan
CN_502614 3.000000 1 76175 -0.265055 2.386838 nan nan
CN_502616 3.000000 1 76192 -0.180606 2.386784 nan nan
CN_502843 3.000000 1 88453 0.306438 2.348150 nan nan
CN_466171 3.000000 1 218557 1.222880 4.057393 nan nan
CN_468414 3.000000 1 218926 0.304888 4.057255 nan nan
CN_468412 3.000000 1 219009 0.035065 4.057224 nan nan
CN_468413 3.000000 1 219024 0.640068 4.057218 nan nan
CN_470565 3.000000 1 219470 0.802091 4.057051 nan nan
CN_468424 3.000000 1 225521 0.885659 4.054777 nan nan
CN_468425 3.000000 1 225579 0.078346 4.054756 nan nan
CN_460512 3.000000 1 346294 -0.986917 2.226778 nan nan
CN_460513 3.000000 1 346393 1.159176 2.226784 nan nan

Total number of rows: 1813441

Table truncated, full table size 114234 Kbytes.




Supplementary file Size Download File type/resource
GSM872978_38482_GenomeWideSNP_6_.CEL.gz 29.1 Mb (ftp)(http) CEL
GSM872978_38482_GenomeWideSNP_6_.CN5.CNCHP.gz 35.0 Mb (ftp)(http) CNCHP
Processed data included within Sample table
Processed data provided as supplementary file

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