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Sample GSM1689885 Query DataSets for GSM1689885
Status Public on Dec 31, 2015
Title Multiple Myeloma patient, diagnosis, rep 1 [MM patient #277]
Sample type genomic
Source name CD138+ cell fractions obtained from MM patients' BM
Organism Homo sapiens
Characteristics patient id: MM patient #277
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: 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 0.006757 BB 447.440826 2791.630371
SNP_A-1967418 BB 0.003296 BB 257.929779 620.156006
SNP_A-1969580 BB 0.004085 BB 988.318909 3906.106445
SNP_A-4263484 AB 0.004265 AB 1671.709595 1247.908691
SNP_A-1978185 AA 0.008209 AA 1689.755981 305.852600
SNP_A-4264431 AA 0.002758 AA 1913.240967 356.447174
SNP_A-1980898 BB 0.005278 BB 262.198303 968.118713
SNP_A-1983139 AA 0.006339 AA 2002.057373 682.785645
SNP_A-4265735 BB 0.003888 BB 689.347473 1695.855835
SNP_A-1995832 AB 0.007420 AB 1721.079590 1629.343750
SNP_A-1995893 AB 0.000451 AB 1492.195557 1806.565430
SNP_A-1997689 BB 0.007113 BB 630.437317 2308.807617
SNP_A-1997709 AA 0.015293 AA 2129.437012 340.800995
SNP_A-1997896 AA 0.000765 AA 1557.742554 510.690308
SNP_A-1997922 AB 0.003181 AB 599.459900 612.224487
SNP_A-2000230 AA 0.005443 AA 1887.468750 787.968567
SNP_A-2000332 AB 0.007120 AB 3123.433350 3006.456299
SNP_A-2000337 AA 0.001404 AA 1434.788208 323.301239
SNP_A-2000342 AA 0.002973 AA 3516.566895 1026.590332
SNP_A-4268173 AA 0.019026 AA 1412.011475 378.349548

Total number of rows: 909622

Table truncated, full table size 46144 Kbytes.

Supplementary file Size Download File type/resource
GSM1689885_20110920_MART_MM_SNP118_GenomeWideSNP_6_.CEL.gz 29.6 Mb (ftp)(http) CEL
GSM1689885_20110920_MART_MM_SNP118_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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