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Sample GSM1689860 Query DataSets for GSM1689860
Status Public on Dec 31, 2015
Title Multiple Myeloma patient, diagnosis, rep 1 [MM patient #396]
Sample type genomic
Source name CD138+ cell fractions obtained from MM patients' BM
Organism Homo sapiens
Characteristics patient id: MM patient #396
disease state: Multiple Myeloma
tumor stage: diagnosis
hh cluster: 2
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 0.004998 BB 383.518188 1759.757080
SNP_A-1967418 BB 0.003289 BB 279.006134 621.488281
SNP_A-1969580 BB 0.003586 BB 1361.682861 4025.612305
SNP_A-4263484 AB 0.009925 AB 1279.507202 1250.851196
SNP_A-1978185 AA 0.004807 AA 1051.167480 378.669067
SNP_A-4264431 AA 0.011570 AA 1598.875366 402.279114
SNP_A-1980898 BB 0.006376 BB 261.131866 932.653992
SNP_A-1983139 AA 0.002811 AA 1358.955444 497.254089
SNP_A-4265735 AB 0.011655 AB 934.652283 648.624390
SNP_A-1995832 AA 0.080817 AA 2163.133545 1284.258545
SNP_A-1995893 AB 0.011574 AB 1737.099121 1525.569580
SNP_A-1997689 BB 0.006788 BB 472.541901 2698.866943
SNP_A-1997709 AA 0.006701 AA 1706.964111 255.469315
SNP_A-1997896 AB 0.017163 AB 1035.264160 997.260132
SNP_A-1997922 AA 0.008182 AA 652.032471 250.974564
SNP_A-2000230 AA 0.004885 AA 1846.497925 842.539551
SNP_A-2000332 AB 0.048641 AB 1912.567139 2904.180420
SNP_A-2000337 AA 0.003460 AA 1546.197266 343.425171
SNP_A-2000342 AA 0.004029 AA 2910.453125 871.083008
SNP_A-4268173 AA 0.016301 AA 1418.387085 369.998779

Total number of rows: 909622

Table truncated, full table size 46145 Kbytes.

Supplementary file Size Download File type/resource
GSM1689860_20110714_MART_MM_SNP100__GenomeWideSNP_6_.CEL.gz 29.0 Mb (ftp)(http) CEL
GSM1689860_20110714_MART_MM_SNP100__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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