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Sample GSM1689857 Query DataSets for GSM1689857
Status Public on Dec 31, 2015
Title Multiple Myeloma patient, diagnosis, rep 1 [MM patient #422]
Sample type genomic
Source name CD138+ cell fractions obtained from MM patients' BM
Organism Homo sapiens
Characteristics patient id: MM patient #422
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: NR
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 0.000236 BB 564.488403 2334.673584
SNP_A-1967418 BB 0.002086 BB 293.311432 859.168213
SNP_A-1969580 BB 0.004563 BB 1459.145264 4908.357910
SNP_A-4263484 AB 0.004213 AB 1264.996582 1028.909058
SNP_A-1978185 AA 0.003375 AA 1128.159790 309.668640
SNP_A-4264431 AB 0.005865 AB 1778.195190 1241.031494
SNP_A-1980898 BB 0.007548 BB 265.265442 1440.491821
SNP_A-1983139 AA 0.001898 AA 1472.090820 519.784729
SNP_A-4265735 AA 0.007498 AA 791.371704 349.733368
SNP_A-1995832 AB 0.003190 AB 1277.504761 1038.683960
SNP_A-1995893 AB 0.014542 AB 1220.243774 2057.831299
SNP_A-1997689 BB 0.008010 BB 510.757446 3053.135010
SNP_A-1997709 AA 0.006679 AA 967.238464 223.486664
SNP_A-1997896 AA 0.003359 AA 1522.932739 384.464355
SNP_A-1997922 AB 0.007293 AB 856.289673 617.147278
SNP_A-2000230 AA 0.003442 AA 1973.595581 884.218262
SNP_A-2000332 AB 0.001893 AB 2460.376709 2481.642090
SNP_A-2000337 AA 0.003618 AA 1478.889160 252.401749
SNP_A-2000342 AA 0.000466 AA 3477.615234 931.584656
SNP_A-4268173 AA 0.001017 AA 1789.332642 284.343658

Total number of rows: 909622

Table truncated, full table size 46163 Kbytes.

Supplementary file Size Download File type/resource
GSM1689857_20100331_MART_MM_SNP62__GenomeWideSNP_6_.CEL.gz 28.7 Mb (ftp)(http) CEL
GSM1689857_20100331_MART_MM_SNP62__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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