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Sample GSM872977 Query DataSets for GSM872977
Status Public on Jul 01, 2013
Title Bone marrow 4_34543
Sample type genomic
 
Source name Bone marrow
Organism Homo sapiens
Characteristics cell type: Bone marrow
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 2.000000 1 51586 0.232342 2.060172 nan nan
CN_473964 2.000000 1 51659 -0.049373 2.060109 nan nan
CN_473965 2.000000 1 51674 0.173111 2.060096 nan nan
CN_473981 2.000000 1 52771 -0.360546 2.059151 nan nan
CN_473982 2.000000 1 52788 0.430076 2.059137 nan nan
CN_497981 2.000000 1 62627 0.461130 2.050936 nan nan
CN_502615 2.000000 1 75787 -0.669342 2.040865 nan nan
CN_502613 2.000000 1 75849 0.278525 2.040821 nan nan
CN_502614 2.000000 1 76175 -0.092522 2.040586 nan nan
CN_502616 2.000000 1 76192 -0.659314 2.040574 nan nan
CN_502843 2.000000 1 88453 0.502372 2.032348 nan nan
CN_466171 2.000000 1 218557 0.473151 3.561453 nan nan
CN_468414 2.000000 1 218926 0.901444 3.560960 nan nan
CN_468412 2.000000 1 219009 0.813109 3.560849 nan nan
CN_468413 2.000000 1 219024 0.876333 3.560829 nan nan
CN_470565 2.000000 1 219470 0.011589 3.560234 nan nan
CN_468424 2.000000 1 225521 0.355639 3.552137 nan nan
CN_468425 2.000000 1 225579 -0.199923 3.552059 nan nan
CN_460512 2.000000 1 346294 -0.465562 2.270468 nan nan
CN_460513 2.000000 1 346393 0.668982 2.270471 nan nan

Total number of rows: 1813441

Table truncated, full table size 114253 Kbytes.




Supplementary file Size Download File type/resource
GSM872977_4_34543_GenomeWideSNP_6_2.CEL.gz 29.9 Mb (ftp)(http) CEL
GSM872977_4_34543_GenomeWideSNP_6_2.CN5.CNCHP.gz 34.9 Mb (ftp)(http) CNCHP
Processed data included within Sample table
Processed data provided as supplementary file

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