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Sample GSM1689890 Query DataSets for GSM1689890
Status Public on Dec 31, 2015
Title Multiple Myeloma patient, diagnosis, rep 1 [MM patient #341]
Sample type genomic
Source name CD138+ cell fractions obtained from MM patients' BM
Organism Homo sapiens
Characteristics patient id: MM patient #341
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 0.002185 BB 472.201813 1972.822632
SNP_A-1967418 BB 0.004517 BB 235.020218 601.888916
SNP_A-1969580 BB 0.004032 BB 1190.555542 3676.315918
SNP_A-4263484 AB 0.007865 AB 1751.750732 1339.070190
SNP_A-1978185 AA 0.002139 AA 1250.339233 311.397278
SNP_A-4264431 AB 0.004562 AB 1080.952759 1009.310669
SNP_A-1980898 AB 0.000828 AB 932.328186 757.031311
SNP_A-1983139 AA 0.005083 AA 1358.134277 531.857483
SNP_A-4265735 AA 0.005401 AA 831.605225 325.580444
SNP_A-1995832 AB 0.002214 AB 1538.733887 1208.579346
SNP_A-1995893 AB 0.001684 AB 1625.427856 1884.949829
SNP_A-1997689 BB 0.001903 BB 612.522156 3089.158936
SNP_A-1997709 AA 0.021508 AA 2157.175537 385.906158
SNP_A-1997896 AA 0.000571 AA 1568.739990 468.752655
SNP_A-1997922 AB 0.001752 AB 722.811707 688.842712
SNP_A-2000230 AA 0.005480 AA 1864.021484 793.933411
SNP_A-2000332 BB 0.002451 BB 1311.336182 3630.972656
SNP_A-2000337 AA 0.008328 AA 1616.640991 229.112198
SNP_A-2000342 AA 0.013403 AA 4212.063477 1209.581787
SNP_A-4268173 AA 0.009174 AA 1499.845947 392.546936

Total number of rows: 909622

Table truncated, full table size 46150 Kbytes.

Supplementary file Size Download File type/resource
GSM1689890_20110920_MART_MM_SNP124_GenomeWideSNP_6_.CEL.gz 29.8 Mb (ftp)(http) CEL
GSM1689890_20110920_MART_MM_SNP124_GenomeWideSNP_6_.birdseed-v2.chp.gz 13.4 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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