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Sample GSM1689838 Query DataSets for GSM1689838
Status Public on Dec 31, 2015
Title Multiple Myeloma patient, diagnosis, rep 1 [MM patient #70]
Sample type genomic
 
Source name CD138+ cell fractions obtained from MM patients' BM
Organism Homo sapiens
Characteristics patient id: MM patient #70
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 AA 0.008318 AA 2310.801514 826.182861
SNP_A-1967418 BB 0.002091 BB 326.292938 757.822266
SNP_A-1969580 BB 0.006812 BB 1021.492188 3370.552246
SNP_A-4263484 BB 0.007120 BB 417.415680 1136.752441
SNP_A-1978185 AA 0.004201 AA 1587.253174 385.314423
SNP_A-4264431 AA 0.000321 AA 2259.696777 372.500336
SNP_A-1980898 BB 0.003131 BB 339.051056 1399.473755
SNP_A-1983139 AA 0.005465 AA 1055.473511 365.698486
SNP_A-4265735 NC 0.594125 AB 410.501434 1003.975830
SNP_A-1995832 BB 0.005612 BB 546.277405 1462.367188
SNP_A-1995893 BB 0.002402 BB 495.119659 2205.105957
SNP_A-1997689 BB 0.026916 BB 877.026978 2928.765625
SNP_A-1997709 AA 0.004535 AA 1025.021240 274.926910
SNP_A-1997896 AA 0.010725 AA 1077.644531 436.497437
SNP_A-1997922 NC 0.125733 BB 592.110352 893.100342
SNP_A-2000230 AA 0.018151 AA 2317.195557 1605.776855
SNP_A-2000332 BB 0.010449 BB 1040.989746 2418.421143
SNP_A-2000337 AA 0.007103 AA 1395.653931 377.125580
SNP_A-2000342 AA 0.009373 AA 3118.220947 1098.517456
SNP_A-4268173 AA 0.005850 AA 1532.512451 368.951447

Total number of rows: 909622

Table truncated, full table size 46162 Kbytes.




Supplementary file Size Download File type/resource
GSM1689838_20090604_MM21_SNP6.0__GenomeWideSNP_6_.CEL.gz 27.6 Mb (ftp)(http) CEL
GSM1689838_20090604_MM21_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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