Methylation profiling of 3T3-L1 Cells: Control vs slincRAD-shRNA8 stable transfected
ABSTRACT: Genome-wide methylation profiling of mouse 3T3-L1 Cells comparing control wildtypes with cells stable transfected with slincRAD shRNA8 (sh8). Two-condition experiment, 3T3-L1 wildtype vs. slincRAD-shRNA8 stable transfected cells before and after Adipogenesis. One replicate per array.
Project description:Selected human sperms with ART technique demonstrate many changes in the genetic and epigenetic aspects. There are many evidances shown that DNA damange and histone retention ratio have significant improved after selection with different methods. These changes may relate with DNA epigenetic changes, however no evidance demonstate these relevance. In this study, MeDIP-ChIP method has been employed to detect DNA methylation loci in human sperm genome processed with density selection. Results demonstrated that DNA methylation changed in specific gene location. comparison the DNA methylation site between 3 pair human sperm DNA samples before or after density selection
Project description:This analysis is part of the study Whole-transcriptome analysis of Staphylococcus aureus under laboratory and infection-mimicking conditions (Mäder, Nicolas et al., to be submitted) where the S. aureus HG001 transcriptome was analyzed under more than 40 different bilogical conditions. Genomic DNA was prepared from four independent cultures of S. aureus HG001 cells; after sonication, DNA was labeled with Cy3 and hybridized to tiling arrays. The data are used in transcriptome studies to compute expression intensities from raw intensity data using a model of shift and drift. genomic DNA from wild type
Project description:Genomic DNA prepared from B. subtilis 168 cells grown to stationary phase was hybridized to tiling arrays. The data are used in transcriptome studies to compute expression intensities from raw intensity data using a model of shift and drift and correcting for probe affinity variations as described in (Nicolas et al., 2009, Bioinformatics 25, 2341-2347). B. subtilis 168 was grown in LB medium to stationary phase. Genomic DNA was prepared from four independent cultures. After sonication, DNA was labeled with Cy3 and hybridized to tiling arrays.
Project description:Obesity is a known risk factor for breast cancer. To identify genes and underlying pathways in human breast cancer cells affected by interaction with mature adipocytes, two estrogen-receptor positive (ER+) breast cancer cell lines, MCF-7 and T47D, and the triple-negative (TN) breast cancer cell line MDA-MB-231 were cultivated in a co-culture system with or without differentiated murine 3T3-L1 adipocytes for the purpose of a microarray gene expression analysis. The use of in vitro differentiated 3T3-L1 adipocytes allowed comparable experimental conditions for each of the co-culture experiments with human breast cancer cell lines. For co-cultivation analyses of 3T3-L1 and breast cancer cells, we set up a two-dimensional transwell system, which enables intercellular communication through soluble factors secreted into the medium but inhibits intermixture of the different cell types. Following 5 days of co-culture with or without differentiated adipocytes, total RNA was isolated from the human breast cancer cells and subjected to microarray gene expression analyses.
Project description:In this experiment, we exposed mice to ethanol injections on postnatal days 4 and 7. We then extracted whole-hippocampus on postnatal day 70. We performed MeDIP-chip using an antibody against 5mC. We also perfomed MEDME anaylsis using a chip with fully methylated DNA to act as a control. We found alterations in both modifications at many sites, including oxidative stress genes and imprinted loci. We also found many affect lipid metabolism pathways. Comparision of neonatal ethanol-injected with saline injected C57BL/6J mouse hippocampus in adulthood (day 70)
Project description:Several studies have suggested that MSCs have pleiotropic immuno-modulatory effects, including inhibition of T cell proliferation, suppression of NK cells proliferation, modulation of cytokine production, and inhibition of dendritic cell (DC) maturation etc. But the exactly mechanism are still largely unclear.We have found that the gene expression profile of psoriatic dermal MSCs was distinct different from normal MSCs. We proposed to investigate the DNA methylation profile of psoriatic MSCs. 6 patients and 6 normal control were inrolled in the study, the DNA methylation profile of dermal MSCs were studied using the microarry.
Project description:Growing evidence indicates that PPARγ agonists, such as rosiglitazone (RSG,), induce adipose mitochondrial biogenesis. Using microarrays, we systematically analyzed nucleus-encoded mitochondrial gene expression in two common murine adipocyte models, 3T3 L1 and C3H/10T1/2 adipocytes, and aimed to further establish the direct role of RSG, and capture the temporal changes in mitochondrial gene transcription during this process. Experiment Overall Design: Fully differentiated 3T3 L1 and C3H/10T1/2 adipocytes were treated with RSG, or DMSO vehicle for 1, 2, 4, 7, 24, and 48 hrs, and total RNA was extracted for microarray analysis.
Project description:The experiment was designed to investigate the regulatory landscape of H3K27me3, a histone methylation form, in the hippocampal neurons upon lead exposure. It reveals that the targeting pathways were altered and migrated throughout the genome, indicating that H3K27me3's sophisticated alterations are responsible for lead-led impairment of hippocampal neurons. Besides, the causes leading to its adaptive changes were figured out.
Project description:We analyzed RING1B binding regions in 3T3-L1 cell lines transduced with the retroviral vector for V5-tagged Fbxl10 or its dF-box mutant. RING1B ChIP-seq in empty, Fbxl10-1, and dF-box mutant vector transduced 3T3-L1 preadipocytes, in duplicate, and V5-Fbxl10 ChIP-seq in Fbxl10 overexpressing 3T3-L1 cells