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Sample GSM1689850 Query DataSets for GSM1689850
Status Public on Dec 31, 2015
Title Multiple Myeloma patient, diagnosis, rep 1 [MM patient #9]
Sample type genomic
Source name CD138+ cell fractions obtained from MM patients' BM
Organism Homo sapiens
Characteristics patient id: MM patient #9
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: MR
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 0.002392 BB 675.848450 2409.262451
SNP_A-1967418 BB 0.001283 BB 270.064911 771.034302
SNP_A-1969580 BB 0.006366 BB 1037.188232 3406.218506
SNP_A-4263484 BB 0.004014 BB 425.091125 1279.816650
SNP_A-1978185 AA 0.005459 AA 1053.719238 392.030457
SNP_A-4264431 AB 0.013803 AB 1020.843140 793.640503
SNP_A-1980898 AB 0.002139 AB 834.975037 790.726135
SNP_A-1983139 AA 0.002136 AA 1425.869385 508.637970
SNP_A-4265735 AB 0.006256 AB 558.582397 672.610535
SNP_A-1995832 AA 0.003998 AA 1870.067871 412.425323
SNP_A-1995893 AA 0.006737 AA 1828.610840 935.506775
SNP_A-1997689 BB 0.005291 BB 726.135925 2922.489990
SNP_A-1997709 AA 0.003765 AA 1146.308594 236.658356
SNP_A-1997896 AA 0.005164 AA 1302.170410 526.954163
SNP_A-1997922 AA 0.001908 AA 893.377136 243.954315
SNP_A-2000230 AA 0.004246 AA 1877.491699 1042.249878
SNP_A-2000332 AA 0.008964 AA 2544.975098 722.206482
SNP_A-2000337 AA 0.001033 AA 1456.908325 317.287994
SNP_A-2000342 AA 0.003771 AA 3090.261963 965.955505
SNP_A-4268173 AA 0.054512 AA 1242.181396 302.484955

Total number of rows: 909622

Table truncated, full table size 46156 Kbytes.

Supplementary file Size Download File type/resource
GSM1689850_20090728_MART_MM_SNP32__GenomeWideSNP_6_.CEL.gz 28.7 Mb (ftp)(http) CEL
GSM1689850_20090728_MART_MM_SNP32__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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