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Series GSE21419 Query DataSets for GSE21419
Status Public on Nov 03, 2011
Title Laser Capture Microdissection of Hyperlipidemic Mouse Aorta Atherosclerosis
Organism Mus musculus
Experiment type Expression profiling by array
Summary Atherosclerosis is a transmural chronic inflammatory condition of small and large arteries that is associated with adaptive immune responses at all disease stages. However, impacts of adaptive immune reactions on clinically apparent atherosclerosis such as intima lesion (plaque) rupture, thrombosis, myocardial infarction, and aneurysm largely remain to be identified. It is increasingly recognized that leukocyte infiltrates in plaque, media, and adventitia are distinct but their specific roles have not been defined. To map these infiltrates, we employed laser capture microdissection (LCM) to isolate the three arterial wall laminae using apoE-/- mouse aorta as a model. RNA from LCM-separated tissues was extracted and large scale whole genome expression microarrays were prepared. We observed that the quality of the resulting gene expression maps was compromised by tissue RNA carried over from adjacent laminae during LCM. To account for these flaws, we established quality controls and algorithms to improve the predictive power of LCM-derived microarray data. Our approach creates robust transcriptome atlases of normal and atherosclerotic aorta. Assessing LCM transcriptomes for immunity-related mRNAs indicated markedly distinctive gene expression patterns in the three laminae of the atherosclerotic aorta. These mouse mRNA expression data banks can now be mined to address a wide range of questions in cardiovascular biology.
Overall design Wild-type and apoE-deficient mice on the C57BL/6J genetic background were maintained on a standard mouse chow. Total aortae were removed at the age of 78 weeks, abdominal aorta was separated from the remainder of the tissue and arterial wall laminae were separated by laser capture microdissection as described (Beer et al. 2011). Following RNA quality controls, microarrays were prepared following MIAME guidelines as described previously (Uzonyi et al. 2006; Graebner et al. 2009; Lotzer et al. 2010).
Contributor(s) Beer M, Doepping S, Habenicht A, Graebner R
Citation(s) 16179593, 16606835, 19139167, 20139367, 21761324
Submission date Apr 21, 2010
Last update date May 04, 2018
Contact name Andreas Johann Richard Habenicht
Organization name Ludwig Maximilians Universität München
Department Medicine
Lab Institute for Cardiovascular Disease Prevention
Street address Pettenkoferstraße 9a
City Munich
State/province Bavaria
ZIP/Postal code 80336
Country Germany
Platforms (1)
GPL8321 [Mouse430A_2] Affymetrix Mouse Genome 430A 2.0 Array
Samples (19)
GSM252007 apoE-adv.lesion-78-weeks-1
GSM252008 apoE-adv.lesion-78-weeks-2
GSM252009 apoE-adv.lesion-78-weeks-3
BioProject PRJNA126367

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE21419_RAW.tar 35.0 Mb (http)(custom) TAR (of CEL)
Raw data provided as supplementary file
Processed data included within Sample table

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