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Sample GSM1689845 Query DataSets for GSM1689845
Status Public on Dec 31, 2015
Title Multiple Myeloma patient, diagnosis, rep 1 [MM patient #185]
Sample type genomic
Source name CD138+ cell fractions obtained from MM patients' BM
Organism Homo sapiens
Characteristics patient id: MM patient #185
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 0.008854 AB 1982.900513 2297.788818
SNP_A-1967418 BB 0.002184 BB 329.804260 771.117798
SNP_A-1969580 BB 0.004981 BB 1217.674072 3625.250000
SNP_A-4263484 AB 0.001302 AB 1567.349243 1133.120483
SNP_A-1978185 AA 0.003319 AA 1560.948975 355.450470
SNP_A-4264431 AA 0.012365 AA 2335.786865 503.579193
SNP_A-1980898 BB 0.001270 BB 280.768982 1183.723999
SNP_A-1983139 AA 0.010281 AA 843.811768 379.470764
SNP_A-4265735 AB 0.003370 AB 1211.503052 1090.380615
SNP_A-1995832 AB 0.004355 AB 1326.143066 939.893250
SNP_A-1995893 BB 0.002474 BB 394.128143 2267.596680
SNP_A-1997689 BB 0.007666 BB 793.468262 3339.299805
SNP_A-1997709 AA 0.002677 AA 1282.689819 305.037903
SNP_A-1997896 BB 0.000867 BB 675.414185 2563.776367
SNP_A-1997922 AA 0.005044 AA 1076.231079 282.574036
SNP_A-2000230 AA 0.008537 AA 3093.287598 1400.387085
SNP_A-2000332 AB 0.018096 AB 1864.428833 1836.547241
SNP_A-2000337 AA 0.008314 AA 1748.338135 357.143250
SNP_A-2000342 AA 0.004085 AA 3971.300781 943.352234
SNP_A-4268173 AA 0.003630 AA 2296.224365 519.666687

Total number of rows: 909622

Table truncated, full table size 46154 Kbytes.

Supplementary file Size Download File type/resource
GSM1689845_20090728_MART_MM_SNP27__GenomeWideSNP_6_.CEL.gz 28.1 Mb (ftp)(http) CEL
GSM1689845_20090728_MART_MM_SNP27__GenomeWideSNP_6_.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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