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Sample GSM1689875 Query DataSets for GSM1689875
Status Public on Dec 31, 2015
Title Multiple Myeloma patient, diagnosis, rep 1 [MM patient #273]
Sample type genomic
Source name CD138+ cell fractions obtained from MM patients' BM
Organism Homo sapiens
Characteristics patient id: MM patient #273
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: 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 0.001873 BB 503.100891 2437.836182
SNP_A-1967418 BB 0.003343 BB 276.001190 618.224426
SNP_A-1969580 BB 0.001735 BB 1126.678223 4261.856445
SNP_A-4263484 AB 0.000226 AB 1473.420898 1089.581055
SNP_A-1978185 AA 0.007447 AA 1178.141113 440.539062
SNP_A-4264431 AA 0.002482 AA 1953.971924 331.178589
SNP_A-1980898 AA 0.003470 AA 1250.584473 287.737976
SNP_A-1983139 AA 0.007777 AA 2260.756348 692.660645
SNP_A-4265735 AB 0.007990 AB 1311.252075 1258.571533
SNP_A-1995832 AB 0.000847 AB 1476.701660 1321.718506
SNP_A-1995893 AB 0.009349 AB 1894.069702 1767.897461
SNP_A-1997689 BB 0.002361 BB 671.164185 2856.764404
SNP_A-1997709 AA 0.004417 AA 1730.723633 309.550934
SNP_A-1997896 AA 0.002875 AA 1406.949219 429.934723
SNP_A-1997922 AB 0.006858 AB 535.197815 503.677277
SNP_A-2000230 AA 0.001583 AA 2590.000000 1101.584595
SNP_A-2000332 AB 0.001998 AB 2681.502930 2909.104980
SNP_A-2000337 AA 0.006251 AA 1162.161743 251.024231
SNP_A-2000342 AA 0.004131 AA 3312.212402 753.287964
SNP_A-4268173 AA 0.004664 AA 2217.974121 301.192963

Total number of rows: 909622

Table truncated, full table size 46145 Kbytes.

Supplementary file Size Download File type/resource
GSM1689875_20110920_MART_MM_SNP117__GenomeWideSNP_6_.CEL.gz 27.9 Mb (ftp)(http) CEL
GSM1689875_20110920_MART_MM_SNP117__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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