|
| Status |
Public on Dec 31, 2015 |
| Title |
Multiple Myeloma patient, diagnosis, rep 1 [MM patient #116] |
| Sample type |
genomic |
| |
|
| Source name |
CD138+ cell fractions obtained from MM patients' BM
|
| Organism |
Homo sapiens |
| Characteristics |
patient id: MM patient #116
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: SD
|
| 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] |
| GSE69029 |
CD138+ expression and genomic profile obtained from newly diagnosed Multiple Myeloma patients up-front treated with VTD induction therapy |
|
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