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Sample GSM247741 Query DataSets for GSM247741
Status Public on Dec 01, 2008
Title A34_20h_P
Sample type RNA
 
Source name macrophages
Organism Homo sapiens
Characteristics patient
patient ID_REF: A34
age:42
sex:M
Growth protocol Using immunomagnetic beads (Dynabeads, Invitrogen, Carlsbad, CA), CD14+ monocytes, CD4+ T-cells and CD34+ stem cells were positively isolated for direct cell lysis, while negatively isolated monocytes were split into two fractions for stimulation with 10 ng/ml lipopolysaccharide (LPS) for 3h, or for 20h cell culture towards macrophages.
Extracted molecule total RNA
Extraction protocol Positively isolated monocytes, T-cells and stem cells as well as cultured stimulated monocytes and macrophages were lysed and total RNA was isolated (Absolutely RNA Microprep Kit, Stratagene, La Jolla, CA).
Label biotin
Label protocol Total RNA samples were amplified and biotinylated using the Illumina TotalPrep RNA amplification Kit (Ambion, Austin, TX).
 
Hybridization protocol According to beadchip array manufacturer's protocol
Scan protocol According to beadchip array manufacturer's protocol
Description A34_20h_P
Data processing Array data were extracted using Illumina's BeadStudio software. From 13 controls and 18 patients we analyzed CD14+ monocyte, CD4+ T-cell, LPS-stimulated monocytes and macrophage samples, in total 130 arrays (including 6 technical replicates). From the CD34+ cell samples, only 23 passed quality control and were analyzed by array, giving a grand total of 153 arrays. Normalization and statistical analysis of the bead summary data from the arrays was carried out using the limma package14 and in-house scripts in R/Bioconductor. Bead summary intensities were log2-transformed and then normalized using quantile normalization. To find differentially expressed genes, we performed a linear model analysis. Technical replicates were handled by estimating a common value for the intra-replicate correlation and including it in the linear model. Differential expression between the treatments of interest was assessed using a moderated t-test. This test is similar to a standard t-test for each probe except that the standard errors are moderated across genes to ensure more stable inference for each gene. Resulting p-values were corrected for multiple testing using the Benjamini-Hochberg false discovery rate.
 
Submission date Dec 07, 2007
Last update date Dec 01, 2008
Contact name Stephan Henrik Schirmer
E-mail(s) stephan.schirmer@uks.eu
Organization name Academic Medical Center
Department Cardiology
Street address Meibergdreef 9
City Amsterdam
ZIP/Postal code 1105AZ
Country Netherlands
 
Platform ID GPL6255
Series (1)
GSE9820 Circulating Mononuclear Cell Transcriptomes in Patients with Atherosclerotic Coronary Artery Disease

Data table header descriptions
ID_REF
VALUE log2 normalized signal intensity

Data table
ID_REF VALUE
ILMN_10000 5.926205381
ILMN_10001 11.76559423
ILMN_10002 2.469670682
ILMN_10004 7.43174238
ILMN_10005 3.088242866
ILMN_10006 4.352554655
ILMN_10009 4.91695415
ILMN_1001 6.163713447
ILMN_10010 3.25366603
ILMN_10011 10.59969657
ILMN_10012 3.756543227
ILMN_10013 3.567282314
ILMN_10014 3.830127942
ILMN_10016 5.00155078
ILMN_1002 2.846733878
ILMN_10020 3.310457669
ILMN_10021 6.818745766
ILMN_10022 3.263980049
ILMN_10023 9.270475731
ILMN_10024 4.237782009

Total number of rows: 20589

Table truncated, full table size 454 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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