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Sample GSM1689837 Query DataSets for GSM1689837
Status Public on Dec 31, 2015
Title Multiple Myeloma patient, diagnosis, rep 1 [MM patient #402]
Sample type genomic
Source name CD138+ cell fractions obtained from MM patients' BM
Organism Homo sapiens
Characteristics patient id: MM patient #402
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 0.000755 BB 568.389709 2429.489746
SNP_A-1967418 NC 0.823573 BB 492.417206 764.855652
SNP_A-1969580 BB 0.007606 BB 1578.820435 5082.335938
SNP_A-4263484 AB 0.000461 AB 1449.783447 1062.002075
SNP_A-1978185 AA 0.007927 AA 1482.706787 259.989807
SNP_A-4264431 AA 0.007793 AA 2513.818604 475.851044
SNP_A-1980898 AA 0.003511 AA 1458.299805 351.824219
SNP_A-1983139 AA 0.002413 AA 1581.419312 462.068817
SNP_A-4265735 AA 0.002005 AA 1612.685669 421.529968
SNP_A-1995832 AA 0.002420 AA 2052.411621 336.050201
SNP_A-1995893 AA 0.008978 AA 2873.486816 1211.980957
SNP_A-1997689 BB 0.001117 BB 610.815552 2700.250000
SNP_A-1997709 AA 0.006597 AA 1449.783447 345.352692
SNP_A-1997896 AA 0.001910 AA 1691.397461 553.530640
SNP_A-1997922 AA 0.002889 AA 771.381775 240.300171
SNP_A-2000230 AA 0.003296 AA 2557.186523 950.393799
SNP_A-2000332 AB 0.001600 AB 2489.265869 2509.274170
SNP_A-2000337 AA 0.003719 AA 1595.624023 269.861877
SNP_A-2000342 AA 0.002622 AA 3786.725586 900.940857
SNP_A-4268173 AA 0.017578 AA 2910.835205 574.169861

Total number of rows: 909622

Table truncated, full table size 46156 Kbytes.

Supplementary file Size Download File type/resource
GSM1689837_20090604_MM19_SNP6.0__GenomeWideSNP_6_.CEL.gz 27.5 Mb (ftp)(http) CEL
GSM1689837_20090604_MM19_SNP6.0__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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