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Sample GSM1689867 Query DataSets for GSM1689867
Status Public on Dec 31, 2015
Title Multiple Myeloma patient, diagnosis, rep 1 [MM patient #116]
Sample type genomic
Source name CD138+ cell fractions obtained from MM patients' BM
Organism Homo sapiens
Characteristics patient id: MM patient #116
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: SD
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 0.005288 AB 1228.069580 1288.877319
SNP_A-1967418 BB 0.004539 BB 239.964813 592.317688
SNP_A-1969580 BB 0.002726 BB 1392.463013 4257.126465
SNP_A-4263484 AB 0.001629 AB 1539.971802 1173.116943
SNP_A-1978185 AA 0.016692 AA 1949.001099 333.233521
SNP_A-4264431 AA 0.009033 AA 1901.113647 441.410034
SNP_A-1980898 AB 0.005016 AB 1057.353760 770.830688
SNP_A-1983139 AA 0.006050 AA 1627.449951 427.773651
SNP_A-4265735 AA 0.000957 AA 1504.430054 415.953217
SNP_A-1995832 BB 0.006991 BB 653.033691 2568.432861
SNP_A-1995893 BB 0.003356 BB 459.792358 2109.806396
SNP_A-1997689 BB 0.004212 BB 523.766357 2261.748535
SNP_A-1997709 AA 0.000813 AA 1388.019287 269.228851
SNP_A-1997896 AA 0.006571 AA 1420.854614 621.133606
SNP_A-1997922 BB 0.007969 BB 254.269028 770.830688
SNP_A-2000230 AA 0.001047 AA 2197.303711 1056.635498
SNP_A-2000332 AB 0.003314 AB 2864.334961 2942.548828
SNP_A-2000337 AA 0.002959 AA 1504.614502 262.299866
SNP_A-2000342 AA 0.005386 AA 2785.220703 842.241150
SNP_A-4268173 AA 0.011679 AA 1350.758301 257.793243

Total number of rows: 909622

Table truncated, full table size 46140 Kbytes.

Supplementary file Size Download File type/resource
GSM1689867_20110905_MART_MM_SNP109__GenomeWideSNP_6_.CEL.gz 28.2 Mb (ftp)(http) CEL
GSM1689867_20110905_MART_MM_SNP109__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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