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Sample GSM1689896 Query DataSets for GSM1689896
Status Public on Dec 31, 2015
Title Multiple Myeloma patient, diagnosis, rep 1 [MM patient #155]
Sample type genomic
Source name CD138+ cell fractions obtained from MM patients' BM
Organism Homo sapiens
Characteristics patient id: MM patient #155
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: CR
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 0.007800 BB 528.568970 1444.968750
SNP_A-1967418 BB 0.003695 BB 280.077393 610.561340
SNP_A-1969580 BB 0.002010 BB 1240.130737 3953.389648
SNP_A-4263484 BB 0.014293 BB 604.875183 2204.616699
SNP_A-1978185 AA 0.010764 AA 1790.422119 419.077850
SNP_A-4264431 AA 0.001856 AA 1990.601440 348.292786
SNP_A-1980898 AB 0.004148 AB 1016.913086 889.203186
SNP_A-1983139 AA 0.010959 AA 770.363586 290.291016
SNP_A-4265735 AA 0.010028 AA 619.719299 280.783386
SNP_A-1995832 AB 0.002387 AB 1424.439575 1069.897705
SNP_A-1995893 AB 0.002827 AB 1285.442261 1677.033447
SNP_A-1997689 BB 0.005480 BB 760.775757 3433.711670
SNP_A-1997709 AA 0.001766 AA 1463.006226 265.166504
SNP_A-1997896 AB 0.004234 AB 1337.016846 1717.850220
SNP_A-1997922 AA 0.005202 AA 1091.621216 313.500214
SNP_A-2000230 AA 0.002126 AA 2168.116699 1135.885742
SNP_A-2000332 AA 0.009162 AA 2619.237061 909.167664
SNP_A-2000337 AA 0.000793 AA 1489.054077 305.495087
SNP_A-2000342 AA 0.001127 AA 3273.270752 914.708313
SNP_A-4268173 AA 0.023410 AA 1360.397339 345.467712

Total number of rows: 909622

Table truncated, full table size 46164 Kbytes.

Supplementary file Size Download File type/resource
GSM1689896_20110920_MART_MM_SNP131_GenomeWideSNP_6_.CEL.gz 29.4 Mb (ftp)(http) CEL
GSM1689896_20110920_MART_MM_SNP131_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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