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Sample GSM1689870 Query DataSets for GSM1689870
Status Public on Dec 31, 2015
Title Multiple Myeloma patient, diagnosis, rep 1 [MM patient #199]
Sample type genomic
Source name CD138+ cell fractions obtained from MM patients' BM
Organism Homo sapiens
Characteristics patient id: MM patient #199
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 0.001582 BB 479.704498 2202.493164
SNP_A-1967418 BB 0.000864 BB 286.175659 716.354858
SNP_A-1969580 BB 0.006236 BB 1432.532715 3980.643066
SNP_A-4263484 AB 0.000557 AB 1493.978271 1056.447510
SNP_A-1978185 AA 0.003101 AA 1233.005005 297.463531
SNP_A-4264431 AA 0.001515 AA 2024.995972 355.444611
SNP_A-1980898 BB 0.003419 BB 324.735657 1407.313232
SNP_A-1983139 AA 0.006971 AA 1503.086914 593.583557
SNP_A-4265735 AA 0.003137 AA 1758.950317 461.312073
SNP_A-1995832 BB 0.006127 BB 574.984558 2405.696289
SNP_A-1995893 BB 0.002356 BB 593.583557 2432.080811
SNP_A-1997689 BB 0.004723 BB 523.022583 2211.018555
SNP_A-1997709 AA 0.008496 AA 1678.697388 358.240295
SNP_A-1997896 AB 0.002155 AB 1110.995483 1408.662476
SNP_A-1997922 AB 0.005057 AB 559.430115 566.325562
SNP_A-2000230 AA 0.008722 AA 1540.421021 858.300354
SNP_A-2000332 AA 0.003399 AA 3878.867432 954.144836
SNP_A-2000337 AA 0.005027 AA 1315.088501 238.939346
SNP_A-2000342 AA 0.002242 AA 3098.838867 883.291504
SNP_A-4268173 AA 0.000373 AA 1937.165649 364.113647

Total number of rows: 909622

Table truncated, full table size 46145 Kbytes.

Supplementary file Size Download File type/resource
GSM1689870_20110905_MART_MM_SNP112__GenomeWideSNP_6_.CEL.gz 28.4 Mb (ftp)(http) CEL
GSM1689870_20110905_MART_MM_SNP112__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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