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Sample GSM1689847 Query DataSets for GSM1689847
Status Public on Dec 31, 2015
Title Multiple Myeloma patient, diagnosis, rep 1 [MM patient #173]
Sample type genomic
 
Source name CD138+ cell fractions obtained from MM patients' BM
Organism Homo sapiens
Characteristics patient id: MM patient #173
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: 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 AB 0.002527 AB 1613.727783 1386.683105
SNP_A-1967418 AB 0.004783 AB 565.388489 492.719147
SNP_A-1969580 BB 0.001958 BB 1311.556274 4102.236816
SNP_A-4263484 BB 0.007408 BB 436.274719 1128.573364
SNP_A-1978185 AA 0.000952 AA 1404.885010 359.967957
SNP_A-4264431 AA 0.002261 AA 2251.199707 329.033661
SNP_A-1980898 BB 0.001128 BB 336.148163 1223.620972
SNP_A-1983139 AA 0.004173 AA 1600.172241 441.963409
SNP_A-4265735 AA 0.022160 AA 782.232910 407.630371
SNP_A-1995832 AA 0.001403 AA 2031.026489 402.347015
SNP_A-1995893 AA 0.002091 AA 2183.219482 939.187256
SNP_A-1997689 BB 0.007290 BB 749.691895 2921.487793
SNP_A-1997709 AA 0.005058 AA 1006.193420 277.855530
SNP_A-1997896 AA 0.000841 AA 1657.000977 472.201385
SNP_A-1997922 AA 0.006831 AA 1112.392334 275.871307
SNP_A-2000230 AA 0.002101 AA 2056.378906 1010.634949
SNP_A-2000332 AA 0.004125 AA 2893.178955 819.800598
SNP_A-2000337 AA 0.002550 AA 1370.471802 261.942841
SNP_A-2000342 AA 0.008842 AA 2930.411377 1042.497681
SNP_A-4268173 AA 0.001878 AA 1662.438354 305.336334

Total number of rows: 909622

Table truncated, full table size 46165 Kbytes.




Supplementary file Size Download File type/resource
GSM1689847_20090728_MART_MM_SNP29__GenomeWideSNP_6_.CEL.gz 27.5 Mb (ftp)(http) CEL
GSM1689847_20090728_MART_MM_SNP29__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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