NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM693302 Query DataSets for GSM693302
Status Public on Apr 28, 2011
Title Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN28
Sample type genomic
 
Source name CLL cells from periferal blood sample
Organism Homo sapiens
Characteristics hiearchical model of known recurrent aberrations: No
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from mononuclear cell preparations of obtained from peripheral blood 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 The Arrays were washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
Data processing Quality control (QC), genotype calling and probe level normalization were performed in the Affymetrix GeneChip® Genotyping Analysis Software (GTYPE) 4.1. The Dynamic Model (DM) algorithm was used to perform single sample QC and genotype calls were made using BRLMM (34). Copy number normalization was performed in order to produce log2ratios using the Copy Number Analysis Tool (CNAT) 4.0.1. Eighty-two normal samples analyzed at the Uppsala Array Platform were used as reference set.
Standard Affymetrix CNCHP files with Log2 probe intenisities relative to reference
 
Submission date Mar 17, 2011
Last update date Apr 28, 2011
Contact name Anders Isaksson
E-mail(s) anders.isaksson@medsci.uu.se
Organization name Uppsala University
Street address Akademiska sjukhuset ing61 3tr
City Uppsala
ZIP/Postal code 75185
Country Sweden
 
Platform ID GPL3718
Series (1)
GSE28030 Affymetrix SNP array data for Chronic Lymphocytic Leukemia_diagnostic sample_patient samples

Data table header descriptions
ID_REF
VALUE CN STATE
CHROMOSOME
POSITION
LOG2 RATIO
HMM MEDIAN LOG2 RATIO
NEG LOG10 P-VALUE

Data table
ID_REF VALUE CHROMOSOME POSITION LOG2 RATIO HMM MEDIAN LOG2 RATIO NEG LOG10 P-VALUE
SNP_A-1886933 NC 1 775852 0.106434 0.061253 nan
SNP_A-1902458 NC 1 1120590 -0.040203 0.061253 nan
SNP_A-2131660 NC 1 1145994 0.016072 0.061253 nan
SNP_A-4221087 NC 1 1258710 0.176644 0.061253 nan
SNP_A-1884606 NC 1 1495898 0.132641 0.061253 nan
SNP_A-2235839 NC 1 1711339 -0.270604 0.061253 nan
SNP_A-2218153 NC 1 1743546 0.513899 0.253624 nan
SNP_A-1919019 NC 1 1748886 0.165492 0.253624 nan
SNP_A-1815933 NC 1 1748914 0.253624 0.253624 nan
SNP_A-2115098 NC 1 1813782 -0.021510 0.028648 nan
SNP_A-2264565 NC 1 2094841 -0.232233 0.028648 nan
SNP_A-1788728 NC 1 2095738 -0.094843 0.028648 nan
SNP_A-4218776 NC 1 2145729 0.101908 0.028648 nan
SNP_A-2082194 NC 1 2273173 0.035203 0.028648 nan
SNP_A-2135694 NC 1 2292771 0.130175 0.028648 nan
SNP_A-4220764 NC 1 2296012 0.074300 0.028648 nan
SNP_A-1796345 NC 1 2310562 -0.134832 0.028648 nan
SNP_A-1789472 NC 1 2442429 0.022093 0.028648 nan
SNP_A-1934233 NC 1 2495573 0.084230 0.028648 nan
SNP_A-4207031 NC 1 2536089 -0.601386 -0.601386 nan

Total number of rows: 262217

Table truncated, full table size 13188 Kbytes.




Supplementary file Size Download File type/resource
GSM693302.CEL.gz 26.4 Mb (ftp)(http) CEL
GSM693302.cnchp.gz 3.3 Mb (ftp)(http) CNCHP
Processed data included within Sample table
Processed data provided as supplementary file

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