Project description:Memory B cells represent one of the pillar of humoral protection and are found in the circulation and secondary lymphoid organs several decades after initial pathogen or vaccine encounter. The exact cellular and biological mechanisms allowing long-term survival of quiescent cells in such a fluctuating microenvironment remain poorly understood. scRNA-seq analysis of long-lived Vaccinia-specific and total IgG+ memory B cells had helped us identify two subsets of quiescent switched memory B cells in the spleen of adult donors, separated by the expression of CR2(CD21). To better understand the relationship between these two resting splenic memory B cell subsets, we sorted CD21hiCD20hi and CD21intCD20int IgG+ memory B cells from the live IgD-CD27+IgG+CD20+CD3-CD14-CD16- compartment of the spleen of four organ donors, collected between 2015 and 2019. For all donors, both IgG+ memory B cell subsets were sorted alongside naïve B cells (IgD+CD27-CD38-CD24-CD20+CD3-CD14-CD16-). Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) was performed on 50000 cells of each sorted population, according to published methods (Buenrostro, Nature Methods, 2013, PMID: 24097267) and sent for library sequencing by Integragen (Evry, France) (See linked experiment). RNA was extracted from remaining cells and sent for library preparation and sequencing by Integragen (Evry, France).
Project description:Memory B cells represent one of the pillar of humoral protection and are found in the circulation and secondary lymphoid organs several decades after initial pathogen or vaccine encounter. The exact cellular and biological mechanisms allowing long-term survival of quiescent cells in such a fluctuating microenvironment remain poorly understood. scRNA-seq analysis of long-lived Vaccinia-specific and total IgG+ memory B cells had helped us identify two subsets of quiescent switched memory B cells in the spleen of adult donors, separated by the expression of CR2(CD21). To better understand the relationship between these two resting splenic memory B cell subsets, we sorted CD21hiCD20hi and CD21intCD20int IgG+ memory B cells from the live IgD-CD27+IgG+CD20+CD3-CD14-CD16- compartment of the spleen of four organ donors, collected between 2015 and 2019. For all donors, both IgG+ memory B cell subsets were sorted alongside naïve B cells (IgD+CD27-CD38-CD24-CD20+CD3-CD14-CD16-). Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) was performed on 50000 cells of each sorted population, according to published methods (Buenrostro, Nature Methods, 2013, PMID: 24097267) and sent for library sequencing by Integragen (Evry, France). In parallel, RNA was extracted from remaining cells and sent for library preparation and sequencing by Integragen (Evry, France) (see related accession number).
Project description:Transcriptional abundance in each of senescent populations from three cell lines (WS1, WI38 and BJ) is compared with abundance in isogenic early passage proliferating cells and also with abundance in early passage quiescent cells.
Project description:A defining characteristic of quiescent cells is their low level of gene activity compared to growing cells. Using a yeast model for cellular quiescence, we compared the genome-wide profiles of multiple histone modifications between growing and quiescent cells, and correlated these profiles with the presence of RNA polymerase II and its transcripts. Quiescent cells retained several forms of histone methylation normally associated with transcriptionally active chromatin and had many transcripts in common with growing cells. Quiescent cells also contained high levels of RNA polymerase II, but only low levels of the canonical initiating and elongating forms of the polymerase. The data suggest that the transcript and histone methylation marks in quiescent cells were either inherited from growing cells or established early during the development of quiescence and then retained in this non-growing cell population. This might ensure that quiescent cells can rapidly adapt to a changing environment to resume growth. RNA-seq analysis was performed in yeast Log-phase cells and purified Quiescent yeast cells and the transcriptomes in each were compared. The RNA data was correlated with genomic RNA polymerase II and histone H3 methylation occupancy profiles in the log and quiescent cells.
Project description:Quiescent MRC-5 fibroblasts were compared to young fibroblasts 6 samples: 3 biological replicates for each age group: young and quiescent MRC-5 cells. 50bp, single-end reads, no strand-specific reads