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Sample GSM1689891 Query DataSets for GSM1689891
Status Public on Dec 31, 2015
Title Multiple Myeloma patient, diagnosis, rep 1 [MM patient #359]
Sample type genomic
Source name CD138+ cell fractions obtained from MM patients' BM
Organism Homo sapiens
Characteristics patient id: MM patient #359
disease state: Multiple Myeloma
tumor stage: diagnosis
hh cluster: 1
cell type: mononuclear bone marrow cells
cell subtype: CD138+ cell fractions
response to vtd therapy: PR
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 0.004559 BB 590.622620 1763.499146
SNP_A-1967418 BB 0.000543 BB 294.287872 795.182373
SNP_A-1969580 BB 0.003137 BB 1031.871338 3991.306885
SNP_A-4263484 BB 0.010807 BB 525.480835 2087.771484
SNP_A-1978185 AA 0.001030 AA 1330.426880 373.846313
SNP_A-4264431 AA 0.001653 AA 2018.432373 344.584656
SNP_A-1980898 AB 0.002572 AB 981.729614 741.872986
SNP_A-1983139 AA 0.004275 AA 1359.766724 521.802490
SNP_A-4265735 AB 0.010920 AB 606.074158 568.942688
SNP_A-1995832 BB 0.005011 BB 563.540588 1517.777588
SNP_A-1995893 BB 0.005995 BB 406.746063 1935.500610
SNP_A-1997689 BB 0.002714 BB 679.372009 3296.860352
SNP_A-1997709 AA 0.000613 AA 1404.154419 273.636658
SNP_A-1997896 AB 0.001432 AB 1067.042969 1565.595215
SNP_A-1997922 AB 0.009839 AB 895.643982 777.093445
SNP_A-2000230 AA 0.001700 AA 2455.774902 991.474243
SNP_A-2000332 AA 0.003056 AA 3061.015137 737.504944
SNP_A-2000337 AA 0.007587 AA 1614.246094 234.226822
SNP_A-2000342 AA 0.000233 AA 3481.151367 914.767944
SNP_A-4268173 AA 0.010787 AA 1412.916382 319.059357

Total number of rows: 909622

Table truncated, full table size 46162 Kbytes.

Supplementary file Size Download File type/resource
GSM1689891_20110920_MART_MM_SNP125_GenomeWideSNP_6_.CEL.gz 29.3 Mb (ftp)(http) CEL
GSM1689891_20110920_MART_MM_SNP125_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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