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Sample GSM368490 Query DataSets for GSM368490
Status Public on Mar 01, 2010
Title CLLCEC MG
Sample type RNA
 
Channel 1
Source name UHR
Organism Homo sapiens
Characteristics Universal Human Reference RNA (UHR) (Stratagene, Cedar Creek, TX), consisted of equal amount of total RNA from 10 human cancer cell lines, was used as reference control in all microarray gene-profiling experiments. Amplified reference cRNA was labelled with cyanine 3-CTP (Agilent Technologies) in each experiment.
Extracted molecule total RNA
Extraction protocol COMMERCIAL RNA
Label CY3
Label protocol Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies, Palo alto, CA, USA)
 
Channel 2
Source name CLLCEC MG
Organism Homo sapiens
Characteristics CIRCULATING ENDOTHELIAL CELLS FROM CLL PATIENT
Extracted molecule total RNA
Extraction protocol RNeasy Mini Kit (QIAGEN, Valencia, CA, USA)
Label CY5
Label protocol Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies, Palo alto, CA, USA)
 
 
Hybridization protocol 825 ng of Cy5-labelled cRNA were mixed with the same amount of Cy3-labeled reference cRNA and then cRNA mixtures were fragmented to an average size of 50-100 nt by incubation at 60°C for 30 min using in situ Hybridization kit-plus (Agilent Technologies). Samples were hybridized for 17 h at 65°C on 4x44K Whole Human Genome Microarray (Agilent Technologies), comprising over 33’000 (60-mer) experimentally validated oligonucleotide probes and then scanned using a confocal laser scanner (Agilent Technologies).
Scan protocol Fluorescence data were analyzed with Feature Extraction Software v.9.1 (Agilent Technologies).
Description circulating endothelial cells (CEC), chronic lymphocytic leukemia (CLL),
Data processing Result data from each scan (Log10 Cy5/Cy3) were imported into the gene expression analysis software Luminator (Rosetta Bio software, Seattle, WA, USA). Two-dimensional clustering analysis was performed using an agglomerative algorithm with an average link heuristics and a correlation with mean subtraction.The identification of genes differentially expressed between subgroups was performed using both Significant Analysis of Microarray (SAM) algorithm with false discovery ratio (FDR)<5% and enhanced Analysis of Variance (ANOVA) with p-value <0.001. To increase the statistical power, the enhanced ANOVA uses as input data both expression level and the estimated technology error associated with the expression level. As a result, the false-positive rate is reduced when the number of replicates is small and, then, sensitivitydetection is increased.
 
Submission date Feb 09, 2009
Last update date Dec 28, 2009
Contact name Rossana Maffei
E-mail(s) rossana.maffei@unimore.it
Phone +39 059 4222715
Organization name University of Modena and Reggio Emilia
Department Dept of Hematology and Oncology
Lab Lab of Molecular Hematology
Street address Via del Pozzo 71
City Modena
State/province Modena
ZIP/Postal code 41100
Country Italy
 
Platform ID GPL4133
Series (1)
GSE14853 Circulating endothelial cells in patients with chronic lymphocytic leukemia: clinical and biological characterization

Data table header descriptions
ID_REF
VALUE Normalized log10 ratio Cy5/Cy3
gProcessedSignal CY3 SIGNAL
rProcessedSignal CY5 SIGNAL

Data table
ID_REF VALUE gProcessedSignal rProcessedSignal
1 0.58 60015 227476
2 0.00 13 19
3 0.00 13 19
4 0.00 13 19
5 0.00 13 19
6 0.00 13 19
7 0.00 13 19
8 0.00 13 19
9 0.00 13 19
10 0.00 14 19
11 0.00 14 19
12 -0.40 1326 525
13 0.48 17 53
14 0.21 2092 3413
15 0.04 55 60
16 -0.42 33358 12727
17 -1.13 284 21
18 0.03 272 295
19 0.20 133872 210838
20 0.23 13 22

Total number of rows: 45015

Table truncated, full table size 850 Kbytes.




Supplementary file Size Download File type/resource
GSM368490.txt.gz 12.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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