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Sample GSM1689886 Query DataSets for GSM1689886
Status Public on Dec 31, 2015
Title Multiple Myeloma patient, diagnosis, rep 1 [MM patient #315]
Sample type genomic
Source name CD138+ cell fractions obtained from MM patients' BM
Organism Homo sapiens
Characteristics patient id: MM patient #315
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 0.005691 BB 530.626343 2913.839111
SNP_A-1967418 BB 0.002499 BB 257.621124 793.187134
SNP_A-1969580 BB 0.005882 BB 1481.453247 4170.964355
SNP_A-4263484 BB 0.007258 BB 653.153015 1729.861938
SNP_A-1978185 AA 0.006209 AA 1660.930542 327.566772
SNP_A-4264431 AB 0.000794 AB 1339.449219 1069.922363
SNP_A-1980898 AB 0.001938 AB 832.901550 707.019958
SNP_A-1983139 AA 0.006298 AA 2164.193359 677.239624
SNP_A-4265735 BB 0.011889 BB 529.946777 1822.613770
SNP_A-1995832 AB 0.003959 AB 1614.441772 1508.364502
SNP_A-1995893 AB 0.004879 AB 1794.436401 2006.569580
SNP_A-1997689 BB 0.004681 BB 741.471375 3157.414062
SNP_A-1997709 AA 0.030271 AA 2065.702881 425.744019
SNP_A-1997896 AA 0.006366 AA 1462.944458 629.301270
SNP_A-1997922 AB 0.005287 AB 559.258789 575.615112
SNP_A-2000230 AA 0.004913 AA 2112.829834 784.895142
SNP_A-2000332 AB 0.001328 AB 2684.712158 2652.212646
SNP_A-2000337 AA 0.004319 AA 1244.786865 255.678055
SNP_A-2000342 AA 0.003376 AA 3449.603271 1032.110352
SNP_A-4268173 AA 0.004874 AA 1547.830200 358.004181

Total number of rows: 909622

Table truncated, full table size 46145 Kbytes.

Supplementary file Size Download File type/resource
GSM1689886_20110920_MART_MM_SNP119_GenomeWideSNP_6_.CEL.gz 28.9 Mb (ftp)(http) CEL
GSM1689886_20110920_MART_MM_SNP119_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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