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Sample GSM1689887 Query DataSets for GSM1689887
Status Public on Dec 31, 2015
Title Multiple Myeloma patient, diagnosis, rep 1 [MM patient #48]
Sample type genomic
Source name CD138+ cell fractions obtained from MM patients' BM
Organism Homo sapiens
Characteristics patient id: MM patient #48
disease state: Multiple Myeloma
tumor stage: diagnosis
hh cluster: 1
cell type: mononuclear bone marrow cells
cell subtype: CD138+ cell fractions
response to vtd therapy: PR
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 Dec 31, 2015
Contact name Carolina Terragna
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 (4)
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
GSE69028 Affymetrix SNP array data from BM-CD138+, obtained from newly diagnosed Multiple Myeloma patients [response to VTD therapy]

Data table header descriptions
VALUE Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

Data table
SNP_A-2131660 BB 0.003348 BB 478.912659 2559.056396
SNP_A-1967418 BB 0.001479 BB 295.444336 698.887634
SNP_A-1969580 BB 0.004831 BB 1375.013794 3936.221436
SNP_A-4263484 BB 0.005623 BB 624.395081 1818.540405
SNP_A-1978185 AA 0.002090 AA 1451.214478 329.914276
SNP_A-4264431 AB 0.006473 AB 1343.307617 904.009155
SNP_A-1980898 AB 0.001204 AB 886.344849 806.058533
SNP_A-1983139 AA 0.006699 AA 2209.312988 661.437622
SNP_A-4265735 AA 0.003761 AA 1382.029053 485.456787
SNP_A-1995832 AB 0.002284 AB 1581.245117 1367.761475
SNP_A-1995893 AB 0.005459 AB 1215.440308 1784.102783
SNP_A-1997689 BB 0.004049 BB 495.035431 2470.473145
SNP_A-1997709 AA 0.017412 AA 2177.916260 309.309875
SNP_A-1997896 AB 0.006086 AB 1043.277588 1251.104004
SNP_A-1997922 AA 0.015043 AA 612.848572 266.700775
SNP_A-2000230 AA 0.004084 AA 2048.042480 1176.614868
SNP_A-2000332 AA 0.005944 AA 3965.900146 830.419739
SNP_A-2000337 AA 0.000432 AA 1414.627563 306.697906
SNP_A-2000342 AA 0.001906 AA 3138.478760 864.359558
SNP_A-4268173 AB 0.003670 AB 935.854492 1058.691284

Total number of rows: 909622

Table truncated, full table size 46142 Kbytes.

Supplementary file Size Download File type/resource
GSM1689887_20110920_MART_MM_SNP120_GenomeWideSNP_6_.CEL.gz 29.2 Mb (ftp)(http) CEL
GSM1689887_20110920_MART_MM_SNP120_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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