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Sample GSM1689840 Query DataSets for GSM1689840
Status Public on Dec 31, 2015
Title Multiple Myeloma patient, diagnosis, rep 1 [MM patient #407]
Sample type genomic
 
Source name CD138+ cell fractions obtained from MM patients' BM
Organism Homo sapiens
Characteristics patient id: MM patient #407
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: 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
E-mail(s) carolina.terragna@unibo.it
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
ID_REF PROBE SET NAME
VALUE Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal
CONFIDENCE
FORCED CALL
SIGNAL A
SIGNAL B

Data table
ID_REF VALUE CONFIDENCE FORCED CALL SIGNAL A SIGNAL B
SNP_A-2131660 BB 0.005235 BB 762.678894 2470.483643
SNP_A-1967418 BB 0.003347 BB 329.515594 708.200012
SNP_A-1969580 BB 0.004252 BB 1129.619995 3613.489258
SNP_A-4263484 BB 0.003773 BB 544.354431 1845.870605
SNP_A-1978185 AA 0.004728 AA 1117.166260 288.539337
SNP_A-4264431 AA 0.001146 AA 2074.809082 349.402313
SNP_A-1980898 AB 0.002329 AB 961.041199 853.757812
SNP_A-1983139 AA 0.000938 AA 1474.509888 496.721344
SNP_A-4265735 AB 0.007024 AB 1126.620361 1217.620483
SNP_A-1995832 AB 0.015537 AB 964.860413 797.311523
SNP_A-1995893 AB 0.005937 AB 1205.172607 1793.824219
SNP_A-1997689 BB 0.007424 BB 684.125488 3675.709961
SNP_A-1997709 AA 0.003817 AA 1069.177002 246.612076
SNP_A-1997896 AB 0.002842 AB 1241.058838 1424.167969
SNP_A-1997922 AA 0.009267 AA 1104.211426 231.884949
SNP_A-2000230 AA 0.012741 AA 3280.352539 1101.320923
SNP_A-2000332 AA 0.003893 AA 2916.164062 830.163269
SNP_A-2000337 AA 0.001442 AA 1535.259766 300.314209
SNP_A-2000342 AA 0.001337 AA 3495.810303 970.380920
SNP_A-4268173 AA 0.002905 AA 2215.812256 418.443970

Total number of rows: 909622

Table truncated, full table size 46158 Kbytes.




Supplementary file Size Download File type/resource
GSM1689840_20090728_MART_MM_SNP20bis__GenomeWideSNP_6_.CEL.gz 28.0 Mb (ftp)(http) CEL
GSM1689840_20090728_MART_MM_SNP20bis__GenomeWideSNP_6_.birdseed-v2.chp.gz 13.2 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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