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Sample GSM1689856 Query DataSets for GSM1689856
Status Public on Dec 31, 2015
Title Multiple Myeloma patient, diagnosis, rep 1 [MM patient #14]
Sample type genomic
Source name CD138+ cell fractions obtained from MM patients' BM
Organism Homo sapiens
Characteristics patient id: MM patient #14
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: 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 0.013322 BB 580.725769 3434.624756
SNP_A-1967418 BB 0.006247 BB 306.978333 986.195496
SNP_A-1969580 BB 0.014814 BB 1781.954468 4966.271973
SNP_A-4263484 AB 0.002410 AB 1389.932983 959.164124
SNP_A-1978185 AA 0.006441 AA 1362.433716 261.413483
SNP_A-4264431 AA 0.004498 AA 2501.476074 440.501068
SNP_A-1980898 AB 0.011503 AB 1172.218628 930.167297
SNP_A-1983139 AA 0.005057 AA 1843.422485 646.931641
SNP_A-4265735 AA 0.002329 AA 1199.511353 332.534698
SNP_A-1995832 BB 0.001078 BB 571.973267 2046.849731
SNP_A-1995893 BB 0.003773 BB 614.052917 2789.331543
SNP_A-1997689 BB 0.007226 BB 591.410034 3392.628418
SNP_A-1997709 AA 0.001057 AA 1271.957886 281.157288
SNP_A-1997896 AB 0.006814 AB 1168.848877 1877.435669
SNP_A-1997922 AB 0.007217 AB 871.407166 719.746155
SNP_A-2000230 AA 0.005237 AA 2509.506348 851.472351
SNP_A-2000332 AA 0.003579 AA 3233.568359 680.155518
SNP_A-2000337 AA 0.003116 AA 1623.224976 314.470490
SNP_A-2000342 AA 0.001310 AA 3590.822266 965.921082
SNP_A-4268173 AB 0.004562 AB 1357.743774 1439.378296

Total number of rows: 909622

Table truncated, full table size 46154 Kbytes.

Supplementary file Size Download File type/resource
GSM1689856_20100331_MART_MM_SNP59__GenomeWideSNP_6_.CEL.gz 29.3 Mb (ftp)(http) CEL
GSM1689856_20100331_MART_MM_SNP59__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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