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Sample GSM403351 Query DataSets for GSM403351
Status Public on May 16, 2009
Title MM-195_GWP
Sample type genomic
 
Source name Human multiple myeloma patient MM-195
Organism Homo sapiens
Characteristics tc classification: TC4
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 multiple myeloma patient MM-195
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

Data table header descriptions
ID_REF
VALUE normalized data

Data table
ID_REF VALUE
SNP_A-1677174 1.996458
SNP_A-1678466 1.996458
SNP_A-1676440 1.996458
SNP_A-1662392 1.996458
SNP_A-1685736 1.996458
SNP_A-1681384 1.996458
SNP_A-1642581 1.996458
SNP_A-1669029 1.996458
SNP_A-1718237 1.996458
SNP_A-1748467 1.996458
SNP_A-1705537 1.996458
SNP_A-1683756 1.996458
SNP_A-1696782 1.996458
SNP_A-1673422 1.996458
SNP_A-1670878 1.996458
SNP_A-1743511 1.996458
SNP_A-1736635 1.996458
SNP_A-1666738 1.996458
SNP_A-1721407 1.996458
SNP_A-1686722 1.996458

Total number of rows: 58613

Table truncated, full table size 1257 Kbytes.




Supplementary file Size Download File type/resource
GSM403351.CEL.gz 14.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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