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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 04, 2014 |
| Title |
Transcriptome profiling of plaque macrophages during atherosclerosis regression |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by array
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| Summary |
We have carried out a systems biology investigation of regulators controlling arterial plaque macrophage transcriptional changes in response to lipid lowering, in the Reversa mouse model of plaque regression in which poly I:C injections induce recombination-mediated inactivation of Mttp in the liver and (when combined with a switch to chow diet) restore normal lipid levels in an Ldlr-/-Apob100/100 mouse (Lieu et al., 2003, Circulation, v.107(9), pp.1315-21). Twenty-four Reversa mice (12 males, 12 females) were maintained on Western diet for 16 weeks and given injections of either poly I:C or vehicle (saline) and then switched to normal chow. At seven days after the last injection, animals were sacrificed and CD68+ macrophages were isolated from the aortic root plaque using laser-capture microdissection. An additional two Ldlr-/- animals (male) were treated with poly I:C and CD68+ aortic root plaque macrophages were obtained, as a control group for effects of poly I:C independent of Mttp inactivation. RNA isolated from each of the 26 samples was reverse-transcribed, amplified, fragmented, labeled, and then hybridized to the Affymetrix Mouse Exon Array 1.0 ST GeneChip. Probe intensities were analyzed using transcript-level probesets for gene expression profiling, and for each mouse transcript represented on the microarray, a two-factor model (sex and treatment) was used for the analysis of the 24 samples from the Reversa mice, to test for a significant effect of the poly I:C (vs. saline) treatment.
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| Overall design |
Four-week-old Reversa (or for the control group, Ldlr-/-) mice were weaned onto a Western diet for 16 weeks to establish aortic plaque and then switched to a chow diet and injected (i.p.) every other day, for a total of four injections, with either poly I:C or vehicle (saline, only for Reversa mice). In the Reversa mouse, poly I:C is rapidly taken up by the liver where it induces the MX1:Cre transgene, resulting in recombination at the loxP-flanked Mttp alleles and consequent silencing of Mttp expression (Lieu et al., ibid). Animals were sacrificed for arterial tissue collection at seven days after the last poly I:C injection. Hearts were harvested, aortic roots were frozen sectioned, and guide slides were immunostained for CD68. CD68+ cells were isolated by laser capture microdissection and RNA was reverse-transcribed, amplified, fragmented, labeled, and hybridized to the Affymetrix Mouse Exon Array 1.0 ST GeneChip. GeneChips were analyzed for differential expression (between the poly I:C and saline sample groups derived from the Reversa mouse) using transcript-level probesets from the CustomCDF project and using a two-factor model (sex and treatment) with empirical Bayes variance estimates (Limma).
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| Contributor(s) |
Ramsey SA, Vengrenyuk Y, Gold ES, Podolsky I, Aderem A, Fisher EA |
| Citation(s) |
25474352 |
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| Submission date |
Nov 18, 2013 |
| Last update date |
Dec 10, 2014 |
| Contact name |
Stephen Ramsey |
| Organization name |
Oregon State University
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| Department |
Biomedical Sciences
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| Street address |
Dryden Hall 208A
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| City |
Corvallis |
| State/province |
OR |
| ZIP/Postal code |
97331 |
| Country |
USA |
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| Platforms (1) |
| GPL17946 |
[MoEx-1_0-st] Affymetrix Mouse Exon 1.0 ST Array [custom CDF: MoEx10stv1_Mm_ENST ver. 15] |
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| Samples (26)
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| Relations |
| BioProject |
PRJNA229083 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE52482_RAW.tar |
671.6 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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