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Sample GSM1689846 Query DataSets for GSM1689846
Status Public on Dec 31, 2015
Title Multiple Myeloma patient, diagnosis, rep 1 [MM patient #71]
Sample type genomic
 
Source name CD138+ cell fractions obtained from MM patients' BM
Organism Homo sapiens
Characteristics patient id: MM patient #71
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
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 0.001500 BB 598.774475 2557.276123
SNP_A-1967418 BB 0.004429 BB 307.262085 942.990173
SNP_A-1969580 BB 0.000778 BB 1268.439575 4433.477051
SNP_A-4263484 BB 0.003456 BB 589.608154 1717.971558
SNP_A-1978185 AA 0.006012 AA 1668.496460 388.714233
SNP_A-4264431 AB 0.019337 AB 1570.129395 1457.723389
SNP_A-1980898 BB 0.006219 BB 299.367950 1468.552124
SNP_A-1983139 AA 0.001117 AA 1699.454590 557.475586
SNP_A-4265735 AA 0.000534 AA 1313.243042 385.578766
SNP_A-1995832 BB 0.002438 BB 536.768555 1676.855225
SNP_A-1995893 BB 0.001100 BB 473.271820 2490.145508
SNP_A-1997689 BB 0.009883 BB 713.203674 3855.004395
SNP_A-1997709 AA 0.008581 AA 1436.496948 212.050354
SNP_A-1997896 AB 0.000528 AB 1166.510742 1593.696899
SNP_A-1997922 AB 0.013374 AB 873.035461 861.715576
SNP_A-2000230 AA 0.007320 AA 3019.750977 1083.920532
SNP_A-2000332 AA 0.000375 AA 3429.976807 930.551331
SNP_A-2000337 AA 0.008831 AA 1680.872437 236.993256
SNP_A-2000342 AA 0.014575 AA 4611.524414 1063.419556
SNP_A-4268173 AA 0.003455 AA 2177.386230 331.600586

Total number of rows: 909622

Table truncated, full table size 46157 Kbytes.




Supplementary file Size Download File type/resource
GSM1689846_20090728_MART_MM_SNP28__GenomeWideSNP_6_.CEL.gz 28.0 Mb (ftp)(http) CEL
GSM1689846_20090728_MART_MM_SNP28__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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