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Sample GSM1431247 Query DataSets for GSM1431247
Status Public on Oct 07, 2014
Title Whole bone marrow_MD27
Sample type genomic
 
Source name Whole bone marrow from MDS_5q-
Organism Homo sapiens
Characteristics tissue: Whole bone marrow from MDS 5q-
disease state: Myelodysplastic syndrome
Treatment protocol None
Growth protocol None
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 As per manufacturer (Affymetrix)
 
Hybridization protocol DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
Scan protocol The Arrays were then washed using Affymetrix fluidics stations, and scanned according to the manufacturer's instructions.
Description Hybridized to 6.0 Array
Data processing CEL files, generated by AGCC Viewer. CNCHP and LOHCHP, generated by Genotyping Console (all provided by Affymetrix)
CNCHP (from 6.0 arrays) provide data for copy number and LOH analysis.
 
Submission date Jul 09, 2014
Last update date Oct 07, 2014
Contact name Vera Adema
E-mail(s) vera.adema@gmail.com
Organization name Josep Carreras Leukaemia Research Institute
Department MDS Group
Street address Carretera de Can Ruti, Cami de les Escoles s/n
City Badalona
ZIP/Postal code 08916
Country Spain
 
Platform ID GPL6801
Series (1)
GSE59244 Affymetrix SNP array data for 5q- myelodysplastic syndromes

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 0.411431 2.220752 nan nan
CN_473964 2.000000 1 51659 0.335605 2.220463 nan nan
CN_473965 2.000000 1 51674 0.350526 2.220403 nan nan
CN_473981 2.000000 1 52771 0.467313 2.216058 nan nan
CN_473982 2.000000 1 52788 0.539744 2.215991 nan nan
CN_497981 2.000000 1 62627 -0.005639 2.177641 nan nan
CN_502615 2.000000 1 75787 -0.906062 2.128335 nan nan
CN_502613 2.000000 1 75849 -0.322747 2.128109 nan nan
CN_502614 2.000000 1 76175 -0.151032 2.126920 nan nan
CN_502616 2.000000 1 76192 -0.255979 2.126858 nan nan
CN_502843 2.000000 1 88453 0.286506 2.083406 nan nan
CN_466171 2.000000 1 218557 0.643180 2.738058 nan nan
CN_468414 2.000000 1 218926 -0.101928 2.738040 nan nan
CN_468412 2.000000 1 219009 0.355991 2.738035 nan nan
CN_468413 2.000000 1 219024 0.207217 2.738035 nan nan
CN_470565 2.000000 1 219470 0.163812 2.738012 nan nan
CN_468424 2.000000 1 225521 0.431350 2.737708 nan nan
CN_468425 2.000000 1 225579 0.063339 2.737705 nan nan
CN_460512 2.000000 1 346294 -0.528407 2.117494 nan nan
CN_460513 2.000000 1 346393 0.619960 2.117497 nan nan

Total number of rows: 1813441

Table truncated, full table size 114305 Kbytes.




Supplementary file Size Download File type/resource
GSM1431247_Patient_2_N_GenomeWideSNP_6_.CEL.gz 28.6 Mb (ftp)(http) CEL
GSM1431247_Patient_2_T_GenomeWideSNP_6_.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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