Project description:The gDNA of wild type (WT, Col-0), aur2-1 mutant (AAa), and WT trisomy 2 (AAA) were labeled and hybridized with Affymetrix Arabidopsis Tilling 1.0R arrays. The ratio of signal intensity of chromosomes in trisomy (AAa and AAA) to diploid (Col-0) were analyzed. The results indicated that the aur2-1 mutant was a tertiary trisomy (2n + 2L.3S).
Project description:This study aims at identifying non-coding RNA driving AAA pathogenesis and progression.To fish out AAA-relevant circRNA targets, we took advantage of array technology and profiled differentially expressed circRNAs in AAAs vs. non-AAA human tissue specimens. We then focused on studying circRNA-exerted gene expression regulation at the locus of origin and its implication in AAA disease dynamics.
Project description:Abdominal aortic aneurysm (AAA) is a common degenerative cardiovascular disease without clear understanding of its pathobiology. To detect AAA associated variants that may affect gene regulation, we generated H3K27ac HiChIP data for aortic smooth muscle cells (AoSMC) and aortic endothelia cells (HAEC), the two cell types most relevant to the AAA disease. We further implemented cell type-specific REs defined from HiChIP experiments, and observed the consistency between the chromatin accessibility of REs and the expression levels of their target genes. Moreover, the cell type-specific REs contributed to detect the AAA most relevant cell type, AoSMC, and locate the important AAA-related TFs, ERG and KLF family.
Project description:The gDNA of wild type (WT, Col-0), aur2-1 mutant (AAa), and WT trisomy 2 (AAA) were labeled and hybridized with Affymetrix Arabidopsis Tilling 1.0R arrays. The ratio of signal intensity of chromosomes in trisomy (AAa and AAA) to diploid (Col-0) were analyzed. The results indicated that the aur2-1 mutant was a tertiary trisomy (2n + 2L.3S). Three samples (Wild type, WT, Col-0; aur2-1, AAa; WT trisomy 2, AAA) were analyzed.
Project description:We performed two different pools for the 10 AAA patients (n=5 AAA patients in pool A and n=5 AAA patients in pool B) and two different pools for the 10 healthy subjects (n=5 controls in pool C and n=5 controls in pool D). Two replicates of the two microarray experiments were made. Experiment 1: AAA pool A Cy3 labeled vs control pool C Cy5 labeled AAA pool A Cy5 labeled vs control pool C Cy3 labeled (dye swap); Experiment 2: AAA pool B Cy3 labeled vs control pool D Cy5 labeled AAA pool B Cy5 labeled vs control pool D Cy3 labeled (dye swap).
