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Sample GSM1689835 Query DataSets for GSM1689835
Status Public on Dec 31, 2015
Title Multiple Myeloma patient, diagnosis, rep 1 [MM patient #204]
Sample type genomic
Source name CD138+ cell fractions obtained from MM patients' BM
Organism Homo sapiens
Characteristics patient id: MM patient #204
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 0.001152 BB 614.692505 2260.576172
SNP_A-1967418 BB 0.006884 BB 383.237854 914.373596
SNP_A-1969580 BB 0.021775 BB 1850.405029 5659.351074
SNP_A-4263484 AB 0.004218 AB 1372.594116 891.234070
SNP_A-1978185 AA 0.011331 AA 1779.506226 302.957092
SNP_A-4264431 AA 0.009354 AA 2749.151611 333.415833
SNP_A-1980898 AB 0.015100 AB 1010.053589 1063.241211
SNP_A-1983139 AA 0.012080 AA 1984.460938 481.183441
SNP_A-4265735 AA 0.001764 AA 1130.223511 363.940674
SNP_A-1995832 AB 0.002270 AB 1337.312988 1062.726685
SNP_A-1995893 AB 0.003988 AB 1659.725952 2028.279785
SNP_A-1997689 BB 0.005363 BB 641.237915 3452.125000
SNP_A-1997709 AA 0.002042 AA 1361.957642 253.160278
SNP_A-1997896 AB 0.004913 AB 1356.667969 1736.087036
SNP_A-1997922 AA 0.002319 AA 890.139099 236.566895
SNP_A-2000230 AA 0.002611 AA 2260.912842 1205.840942
SNP_A-2000332 AB 0.001100 AB 2569.740479 2576.443359
SNP_A-2000337 AA 0.002187 AA 1535.320801 326.707520
SNP_A-2000342 AA 0.004673 AA 3686.199219 793.052124
SNP_A-4268173 AB 0.001538 AB 1242.266479 1203.643188

Total number of rows: 909622

Table truncated, full table size 46159 Kbytes.

Supplementary file Size Download File type/resource
GSM1689835_20090604_MM17_SNP6.0__GenomeWideSNP_6_.CEL.gz 27.6 Mb (ftp)(http) CEL
GSM1689835_20090604_MM17_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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