NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM278944 Query DataSets for GSM278944
Status Public on Nov 11, 2008
Title GE110_GWP
Sample type genomic
 
Source name Human B-cell chronic lymphocytic leukemia patient GE110
Organism Homo sapiens
Characteristics Legend: VH status = IgVH mutational status (Fais et al. J Clin Invest, 1998)
Sex: F; VH status: mut
Treatment protocol Peripheral blood mononuclear cells from B-CLL patients were isolated by Ficoll-Hypaque (Seromed, Biochrom KG, Berlin, Germany) density-gradient centrifugation and the proportion of CD5/CD19/CD23 triple positive B cells in the suspension was determined by direct immunofluorescence performed using a FACS-sort flow cytometer (Becton Dickinson & Co, Sunnyvale, CA) with antibodies to: CD19 FITC/PE, CD23 PE and CD5 Cy-Chrome (Becton Dickinson). If B-CLL cells were less than 90%, T cells, NK cells and monocytes were removed by negative selection using CD3, CD56, CD16, and CD14 monoclonal antibody (mAb) treatment (Becton Dickinson) followed by magnetic beads (Goat Anti-Mouse IgG Dynabeads, Dynal Biotech ASA, Oslo, Norway).
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 DNA were prepared according to the standard Affymetrix protocol starting 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 Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient GE110
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 1 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1.
 
Submission date Apr 03, 2008
Last update date Nov 11, 2008
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)
GSE11036 Molecular and transcriptional characterization of chromosome 17p loss in chronic lymphocytic leukemia, experiment B
GSE11038 Molecular and transcriptional characterization of chromosome 17p loss in chronic lymphocytic leukemia

Data table header descriptions
ID_REF
VALUE HMM Median Log2 copy number - Genomic Bandwith Smoothing 1 Mb
LOC Physical position

Data table
ID_REF VALUE LOC
SNP_A-1677174 -0.01 836727
SNP_A-1678466 -0.01 2915399
SNP_A-1676440 -0.01 2926730
SNP_A-1662392 -0.01 2941104
SNP_A-1685736 -0.01 2941694
SNP_A-1681384 -0.01 2963436
SNP_A-1642581 -0.01 3116997
SNP_A-1669029 -0.01 3127559
SNP_A-1718237 -0.01 3178003
SNP_A-1748467 -0.01 3178365
SNP_A-1705537 -0.01 3671541
SNP_A-1683756 -0.01 3671691
SNP_A-1696782 -0.01 3754076
SNP_A-1673422 -0.01 3797248
SNP_A-1670878 -0.01 3966540
SNP_A-1743511 -0.01 3966641
SNP_A-1736635 -0.01 4073701
SNP_A-1666738 -0.01 4215064
SNP_A-1721407 -0.01 4242464
SNP_A-1686722 -0.01 4276892

Total number of rows: 58613

Table truncated, full table size 1593 Kbytes.




Supplementary file Size Download File type/resource
GSM278944.CEL.gz 13.9 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap