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Sample GSM1689827 Query DataSets for GSM1689827
Status Public on May 31, 2016
Title Multiple Myeloma patient, diagnosis, rep 1 [MM patient #174]
Sample type genomic
Source name CD138+ cell fractions obtained from MM patients' BM
Organism Homo sapiens
Characteristics patient id: MM patient #174
disease state: Multiple Myeloma
tumor stage: diagnosis
hh cluster: 2
cell type: mononuclear bone marrow cells
cell subtype: CD138+ cell fractions
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 May 31, 2016
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 (2)
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

Data table header descriptions
VALUE Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

Data table
SNP_A-2131660 NC 0.475829 AB 1950.666016 1036.494019
SNP_A-1967418 AA 0.005788 AA 1111.149536 411.023743
SNP_A-1969580 BB 0.003392 BB 1455.217773 4520.843262
SNP_A-4263484 AB 0.034350 AB 1044.676392 1337.150269
SNP_A-1978185 AA 0.001155 AA 1248.059082 332.139923
SNP_A-4264431 BB 0.021854 BB 1336.405029 1868.538696
SNP_A-1980898 BB 0.009940 BB 310.828461 1569.472168
SNP_A-1983139 AA 0.014078 AA 2152.853760 773.192627
SNP_A-4265735 AA 0.018482 AA 2436.371094 501.321442
SNP_A-1995832 AA 0.019995 AA 1969.962402 937.607300
SNP_A-1995893 AB 0.074905 AB 1924.968628 1492.566406
SNP_A-1997689 BB 0.011874 BB 396.029633 2418.920166
SNP_A-1997709 AA 0.002870 AA 1113.836548 258.339417
SNP_A-1997896 AB 0.026302 AB 1732.401489 1476.611206
SNP_A-1997922 AA 0.004806 AA 1056.145386 346.053162
SNP_A-2000230 AA 0.000725 AA 2477.647461 1108.622437
SNP_A-2000332 NC 0.104436 AB 1890.397461 2952.056396
SNP_A-2000337 AA 0.008271 AA 1061.638062 263.461548
SNP_A-2000342 AA 0.005353 AA 2841.211182 907.925659
SNP_A-4268173 AA 0.013839 AA 2375.353760 918.043274

Total number of rows: 909622

Table truncated, full table size 46161 Kbytes.

Supplementary file Size Download File type/resource
GSM1689827_20090121_MM01_SNP6.0__GenomeWideSNP_6_.CEL.gz 28.5 Mb (ftp)(http) CEL
GSM1689827_20090121_MM01_SNP6.0__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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