|
| Status |
Public on May 16, 2009 |
| Title |
PCL-004_GWP |
| Sample type |
genomic |
| |
|
| Source name |
Human multiple myeloma patient PCL-004
|
| Organism |
Homo sapiens |
| Characteristics |
tc classification: PCL
|
| Treatment protocol |
Plasma cells were purified from bone marrow samples using CD138 immunomagnetic microbeads according to the manufacturer's instructions (MidiMACS system, Miltenyi Biotec); the purity of the positively selected PCs was assessed by morphology and flow cytometry and was > 90% in all cases.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA extraction was performed using Wizard® Genomic DNA Purification kit according to the manufacturer's instructions (Promega).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 nanograms of genomic DNA.
|
| |
|
| Hybridization protocol |
Following fragmentation, 40 micrograms of biotin-labeled DNA were hybridized for 16 hr at 48°C on GeneChip Human Mapping 50K XbaI Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
Human Mapping 50K XbaI arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix).
|
| Description |
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human plasma cell leukemia patient PCL-004
|
| Data processing |
The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using DNAcopy package for R Bioconductor on raw data. FBN procedure was finally applied to infer exact local copy number as described in the mentioned Reference.
|
| |
|
| Submission date |
May 15, 2009 |
| Last update date |
May 22, 2011 |
| Contact name |
Luca Agnelli |
| E-mail(s) |
luca.agnelli@istitutotumori.mi.it, luca.agnelli@gmail.com
|
| Phone |
+390223903581
|
| Organization name |
IRCCS Istituto Nazionale dei Tumori
|
| Department |
Department of Advanced Diagnostics
|
| Street address |
Venezian 1
|
| City |
MILAN |
| ZIP/Postal code |
20133 |
| Country |
Italy |
| |
|
| Platform ID |
GPL2005 |
| Series (2) |
| GSE16121 |
Integrated genomics approach to detect allelic imbalances in multiple myeloma, SNP data |
| GSE16122 |
A SNP microarray and FISH-based procedure to detect allelic imbalances in multiple myeloma |
|
