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Sample GSM247813 Query DataSets for GSM247813
Status Public on Dec 01, 2008
Title A4_T_C
Sample type RNA
 
Source name T cells
Organism Homo sapiens
Characteristics control
patient ID_REF: A4
age:44
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 A4_T_C
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 7.082593239
ILMN_10001 11.24919758
ILMN_10002 2.535699462
ILMN_10004 5.465828826
ILMN_10005 4.687081728
ILMN_10006 4.91695415
ILMN_10009 4.140954896
ILMN_1001 3.302949971
ILMN_10010 2.913815225
ILMN_10011 8.508760023
ILMN_10012 2.644859075
ILMN_10013 2.935030998
ILMN_10014 4.239697374
ILMN_10016 4.452165731
ILMN_1002 2.954128162
ILMN_10020 7.618183357
ILMN_10021 7.171074811
ILMN_10022 3.708865184
ILMN_10023 2.876619644
ILMN_10024 2.902733885

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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