Project description:Genome-wide patterns of DNA methylation were quantified using the Illumina Infinium HumanMethylationEPIC BeadChip in DNA samples extracted from subpopulations of B cells.
Project description:Solid tumors exhibit significant phenotypic heterogeneity. This phenotypic heterogeneity yields the formation of phenotypically distinct subpopulations of cells within a single tumor. Within the 4T1 murine mammary adenocarcinoma cell line, we observe cells that invade either in collective chains or as single cells. Through this study, we sought to dissect the epigenetic differences between these invasively-distinct subpopulations.
Project description:In this study we mapped H3K27me3, H3K4me3 and H3K9me2 marks in three mammary epithelial subsets: MaSC/basal (MS), luminal progenitor (LP) and mature luminal (ML) in the steady-state. In addition, profiles were generated for H3K4me3 and H3K27me3 marks in the MaSC/basal and luminal populations from the glands of ovariectomized or mid-pregnant (12.5 days) mice as well as from control virgin mice. We used ChIPseq analysis to determine histone modification marks in the MS, LP and ML subsets in the steady-state. We then determined the histone modification profiles of MS and sorted luminal (Lum) cells from pregnant (12.5 dP) or ovariectomized (OVX) mice and compared these with the profiles of control virgin mice in order to study the effect of hormones on the mammary epigenomes.
Project description:We report the development of a bisulfite based whole genome protocol suitable for use on single index sorted primary mammalian cells. Application of this protocol to murine and human hematopoietic stem cells provided quantitative DNA methylation measurements of up to 5.7 million CpGs in a single cell. To analyze the resulting datasets we developed a novel analytical approach designed to detect differences at single CpG resolution and identified epigenetically distinct subpopulations within the highly purified and functionally defined stem and progenitor populations. In silico merging of the methylation states from the single cells residing in each subpopulation allowed us to ascribe functional pathways to these epigenetically distinct subpopulations on the basis of their unique epigenetic states.
Project description:To delineate epithelial subpopulations in mouse mammary tissue, hematopoietic and endothelial cells were depleted from freshly isolated cell suspensions derived from mammary glands using fluorescence-activated cell sorting. The resultant Lin- population was fractionated into four distinct subpopulations using antibodies against CD29, CD24 and CD61. Based on the immunohistochemical phenotype, and in vivo and in vitro functional assays, these subpopulations were identified as fibroblast-containing stromal (CD29loCD24-), mammary stem cell (MaSC)-enriched (CD29hiCD24+CD61+), luminal progenitor (CD29loCD24+CD61+), and mature luminal (CD29loCD24+CD61-) cell subpopulations. Microarray profiling was used to derive gene expression signatures of these 4 subpopulations. The four mammary cell subpopulations were found to have distinct gene expression profiles. Four mammary cell subpopulations from 3-5 pooled mouse tissues were analysed. MS is for the MaSC-enriched cell subpopulation. LP is for the Luminal Progenitor subpopulation. ML is for the Mature Luminal subpopulation.