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Sample GSM1689855 Query DataSets for GSM1689855
Status Public on Dec 31, 2015
Title Multiple Myeloma patient, diagnosis, rep 1 [MM patient #98]
Sample type genomic
Source name CD138+ cell fractions obtained from MM patients' BM
Organism Homo sapiens
Characteristics patient id: MM patient #98
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: VGPR
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 AB 0.004740 AB 1860.896484 1940.450562
SNP_A-1967418 BB 0.007709 BB 260.036713 950.326904
SNP_A-1969580 BB 0.002820 BB 1125.828003 3780.635254
SNP_A-4263484 BB 0.002897 BB 502.084564 1372.007812
SNP_A-1978185 AA 0.004771 AA 1594.628784 396.858032
SNP_A-4264431 AB 0.002065 AB 1575.516968 1169.804688
SNP_A-1980898 AB 0.006721 AB 1040.209106 694.206055
SNP_A-1983139 AA 0.002510 AA 1507.396973 541.337769
SNP_A-4265735 AA 0.002129 AA 1139.965332 395.933258
SNP_A-1995832 AB 0.004301 AB 1471.580933 1019.310486
SNP_A-1995893 AB 0.002853 AB 1703.268799 1924.655884
SNP_A-1997689 BB 0.003878 BB 713.281677 3413.470947
SNP_A-1997709 AA 0.010694 AA 1154.478149 190.084259
SNP_A-1997896 AB 0.002816 AB 1311.809570 1563.164917
SNP_A-1997922 AA 0.004071 AA 1046.494019 278.350342
SNP_A-2000230 AA 0.006233 AA 2206.274414 1328.917114
SNP_A-2000332 AA 0.012432 AA 3051.084229 1244.735718
SNP_A-2000337 AA 0.004851 AA 1561.872437 357.000732
SNP_A-2000342 AA 0.004209 AA 3893.308105 1040.739624
SNP_A-4268173 AA 0.002676 AA 2148.721924 357.000732

Total number of rows: 909622

Table truncated, full table size 46161 Kbytes.

Supplementary file Size Download File type/resource
GSM1689855_20100205_MART_MM_SNP39__GenomeWideSNP_6__2.CEL.gz 27.8 Mb (ftp)(http) CEL
GSM1689855_20100205_MART_MM_SNP39__GenomeWideSNP_6__2.birdseed-v2.chp.gz 13.2 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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