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Sample GSM1689841 Query DataSets for GSM1689841
Status Public on Dec 31, 2015
Title Multiple Myeloma patient, diagnosis, rep 1 [MM patient #375]
Sample type genomic
 
Source name CD138+ cell fractions obtained from MM patients' BM
Organism Homo sapiens
Characteristics patient id: MM patient #375
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: CR
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 BB 0.002239 BB 656.271667 2593.253906
SNP_A-1967418 BB 0.004769 BB 351.835541 934.550354
SNP_A-1969580 BB 0.001973 BB 1326.944336 4144.102051
SNP_A-4263484 AB 0.002307 AB 1565.073853 1026.617310
SNP_A-1978185 AA 0.006806 AA 1701.855591 387.630646
SNP_A-4264431 AB 0.002622 AB 1509.272827 1028.756348
SNP_A-1980898 BB 0.001408 BB 309.976532 1306.202881
SNP_A-1983139 AA 0.003894 AA 1271.241089 482.938049
SNP_A-4265735 BB 0.001491 BB 400.320740 1376.569946
SNP_A-1995832 BB 0.005260 BB 530.176697 1466.595459
SNP_A-1995893 AB 0.004416 AB 1255.416382 1786.364502
SNP_A-1997689 BB 0.005867 BB 767.356567 3462.581055
SNP_A-1997709 AA 0.001992 AA 1462.358643 262.332550
SNP_A-1997896 AA 0.001015 AA 1551.283203 518.904663
SNP_A-1997922 AB 0.004369 AB 810.923279 636.743530
SNP_A-2000230 AA 0.024108 AA 2949.248535 1781.262207
SNP_A-2000332 AA 0.014540 AA 2523.289307 1029.516357
SNP_A-2000337 AA 0.005321 AA 1678.509399 273.182434
SNP_A-2000342 AA 0.002622 AA 3249.760254 975.169250
SNP_A-4268173 AB 0.001332 AB 1062.146851 1045.779297

Total number of rows: 909622

Table truncated, full table size 46151 Kbytes.




Supplementary file Size Download File type/resource
GSM1689841_20090728_MART_MM_SNP23bis__GenomeWideSNP_6_.CEL.gz 28.4 Mb (ftp)(http) CEL
GSM1689841_20090728_MART_MM_SNP23bis__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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