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Sample GSM1689828 Query DataSets for GSM1689828
Status Public on May 31, 2016
Title Multiple Myeloma patient, diagnosis, rep 1 [MM patient #429]
Sample type genomic
 
Source name CD138+ cell fractions obtained from MM patients' BM
Organism Homo sapiens
Characteristics patient id: MM patient #429
disease state: Multiple Myeloma
tumor stage: diagnosis
hh cluster: 1
cell type: mononuclear bone marrow cells
cell subtype: CD138+ cell fractions
Treatment protocol Pre-treatment plasma cells (PC) were purified from mononuclear bone marrow cells obtained by Ficoll-Hypaque density gradient centrifugation using anti-CD138 micro beads on an AutoMacs Magnetic Cell Separator (MACS system, Miltenyi Biotec, Auburn, CA). CD138+ cell fractions were than stored at -80°C in guanidium thiocyanate, until use.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from CD138+ plasma cells obtained from bone marrow at diagnosis using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.
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 GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 7G.
Data processing The array image was acquired using Affymetrix Command Console, version 4.0. Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using Affymetrix Genotyping Console, version 4.0, software. Nexus, version 7.5 (BioDiscovery) was employed to perform CNAs comparisons; inferred copy number states were derived from segmentation algorithm implemented in Nexus.
 
Submission date May 18, 2015
Last update date May 31, 2016
Contact name Carolina Terragna
E-mail(s) carolina.terragna@unibo.it
Organization name Institute of Hematology "L.A.Seràgnoli"
Department Department of Experimental, Diagnostic and Specialty Medicine - DIMES
Street address Via Massarenti, 9
City Bologna
ZIP/Postal code 40138
Country Italy
 
Platform ID GPL6801
Series (2)
GSE68999 Affymetrix SNP array data from BM-CD138+, obtained from newly diagnosed Multiple Myeloma patients
GSE69000 Hedgehog pathway analysis in both CD138+ and B-cells obtained from newly diagnosed Multiple Myeloma patients

Data table header descriptions
ID_REF PROBE SET NAME
VALUE Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal
CONFIDENCE
FORCED CALL
SIGNAL A
SIGNAL B

Data table
ID_REF VALUE CONFIDENCE FORCED CALL SIGNAL A SIGNAL B
SNP_A-2131660 BB 0.009849 BB 628.116943 1536.791382
SNP_A-1967418 BB 0.004128 BB 250.438995 836.411255
SNP_A-1969580 BB 0.034791 BB 2039.194580 5447.726562
SNP_A-4263484 BB 0.010873 BB 494.430969 1076.156860
SNP_A-1978185 AA 0.004328 AA 1295.405762 280.321259
SNP_A-4264431 AA 0.006479 AA 2777.226318 400.778778
SNP_A-1980898 AB 0.008035 AB 1027.613037 973.818909
SNP_A-1983139 AA 0.001858 AA 1625.729492 560.462463
SNP_A-4265735 AB 0.003319 AB 990.476868 1086.003784
SNP_A-1995832 BB 0.010062 BB 532.453857 2467.231689
SNP_A-1995893 BB 0.002423 BB 453.281342 2174.502197
SNP_A-1997689 BB 0.013278 BB 483.804169 1672.403076
SNP_A-1997709 AA 0.007384 AA 943.439636 219.446030
SNP_A-1997896 BB 0.005874 BB 880.691895 2760.094971
SNP_A-1997922 AA 0.002924 AA 789.144714 230.560928
SNP_A-2000230 AA 0.005104 AA 2175.311768 781.254150
SNP_A-2000332 AA 0.001788 AA 3632.854248 862.907715
SNP_A-2000337 AA 0.011879 AA 961.445923 269.602661
SNP_A-2000342 AA 0.004104 AA 2962.553955 784.606506
SNP_A-4268173 AA 0.013982 AA 2828.583008 648.350159

Total number of rows: 909622

Table truncated, full table size 46161 Kbytes.




Supplementary file Size Download File type/resource
GSM1689828_20090121_MM02_SNP6.0__GenomeWideSNP_6_.CEL.gz 28.0 Mb (ftp)(http) CEL
GSM1689828_20090121_MM02_SNP6.0__GenomeWideSNP_6_.birdseed-v2.chp.gz 13.3 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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