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Sample GSM1689897 Query DataSets for GSM1689897
Status Public on Dec 31, 2015
Title Multiple Myeloma patient, diagnosis, rep 1 [MM patient #278]
Sample type genomic
Source name CD138+ cell fractions obtained from MM patients' BM
Organism Homo sapiens
Characteristics patient id: MM patient #278
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
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 0.006927 BB 445.595276 1451.779907
SNP_A-1967418 BB 0.024037 BB 291.195007 439.776306
SNP_A-1969580 BB 0.005840 BB 1346.208008 3789.461914
SNP_A-4263484 BB 0.004443 BB 379.054596 1386.656738
SNP_A-1978185 AA 0.004659 AA 1041.506958 313.310242
SNP_A-4264431 AA 0.005932 AA 1788.100220 386.957336
SNP_A-1980898 AA 0.009597 AA 1094.305420 222.308899
SNP_A-1983139 AA 0.004174 AA 1477.419189 414.490387
SNP_A-4265735 AB 0.005606 AB 754.292542 683.582031
SNP_A-1995832 AB 0.003005 AB 1274.045898 1141.528931
SNP_A-1995893 AB 0.008063 AB 1177.009888 1388.490723
SNP_A-1997689 BB 0.012199 BB 417.816711 1719.456055
SNP_A-1997709 AA 0.001970 AA 1443.771118 260.420959
SNP_A-1997896 AB 0.002587 AB 1077.133301 1674.323364
SNP_A-1997922 AA 0.005661 AA 710.771179 273.514496
SNP_A-2000230 AA 0.008740 AA 1538.546509 878.717896
SNP_A-2000332 AA 0.002674 AA 3732.328857 862.441711
SNP_A-2000337 AA 0.005392 AA 1327.026978 234.912964
SNP_A-2000342 AA 0.008048 AA 2656.821777 902.289368
SNP_A-4268173 AA 0.011263 AA 1424.231201 336.650208

Total number of rows: 909622

Table truncated, full table size 46162 Kbytes.

Supplementary file Size Download File type/resource
GSM1689897_20111121_MART_MM_SNP139_GenomeWideSNP_6_.CEL.gz 28.3 Mb (ftp)(http) CEL
GSM1689897_20111121_MART_MM_SNP139_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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