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Sample GSM1689865 Query DataSets for GSM1689865
Status Public on Dec 31, 2015
Title Multiple Myeloma patient, diagnosis, rep 1 [MM patient #85]
Sample type genomic
Source name CD138+ cell fractions obtained from MM patients' BM
Organism Homo sapiens
Characteristics patient id: MM patient #85
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 BB 0.002269 BB 462.960510 2304.783691
SNP_A-1967418 BB 0.008633 BB 290.757080 529.324707
SNP_A-1969580 BB 0.003939 BB 1339.691650 3931.784668
SNP_A-4263484 AB 0.007162 AB 1167.903809 970.250916
SNP_A-1978185 AA 0.005416 AA 1251.425903 268.678741
SNP_A-4264431 AA 0.003333 AA 2130.717041 307.291046
SNP_A-1980898 BB 0.002102 BB 318.037964 1112.932495
SNP_A-1983139 AA 0.011199 AA 1774.456543 424.295441
SNP_A-4265735 BB 0.001909 BB 413.284332 1356.462769
SNP_A-1995832 BB 0.000082 BB 585.760132 1964.965454
SNP_A-1995893 BB 0.001374 BB 443.064819 2294.527832
SNP_A-1997689 BB 0.003159 BB 622.263123 2539.518799
SNP_A-1997709 AA 0.002265 AA 1196.834229 286.510803
SNP_A-1997896 AB 0.001982 AB 1033.250244 1519.756592
SNP_A-1997922 AB 0.010594 AB 518.413879 451.835907
SNP_A-2000230 AA 0.000738 AA 2463.028809 1070.177002
SNP_A-2000332 AA 0.002040 AA 3558.605957 808.843689
SNP_A-2000337 AA 0.002347 AA 1489.581787 334.576172
SNP_A-2000342 AA 0.004353 AA 2876.392822 860.398010
SNP_A-4268173 AA 0.013142 AA 1376.117554 302.083801

Total number of rows: 909622

Table truncated, full table size 46151 Kbytes.

Supplementary file Size Download File type/resource
GSM1689865_20110905_MART_MM_SNP107__GenomeWideSNP_6_.CEL.gz 28.0 Mb (ftp)(http) CEL
GSM1689865_20110905_MART_MM_SNP107__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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