Project description:We want to investigate how cells in the specific zones in murine liver are affected by age-related changes of the microenvironment. To this end, we generated high-quality scRNA-seq dataset of hepatocytes using Smart-seq3express from 2 young (3-5 months) and 2 old (18-20 months) male mice. Livers were perfused and viable hepatocytes were FACS-sorted based on size. In addition, we recorded ploidy levels of hepatocytes. We retained 545 hepatocytes in total after initial filtering.
Project description:Aging is known to alter the host repsonse to influenza infection. Here, we use bulk RNA sequencing (bulk RNA-seq) to identify cellular changes in the livers of young (16-week-old) and aged (80-week-old) mice following influenza infection.
Project description:Purpose: We used RNA-seq to compare daily rhythms of gene expression in livers of young and old mice. Methods: Livers of young and old mice were processed for RNA-seq at 4-h interval across 2 days. Gene expression level was analyzed by hisat2 and StringTie. Results: We obtained ~10 million high quality sequencing reads per time point per sample after quality control and alignment. Gene expression levels of ~19,000 transcripts were obtained for both age groups. We found genome-wide differenes in gene expression level as well as rhythms in gene expression. Conclusions: Our study revealed genomwide differences in the level and rhythm of liver gene expression between young and old mice.
Project description:Here, we used single cell RNA-sequencing (scRNA-seq) to profile pluripotent stem cell derived human intestinal organoids (HIOs) grown in matrigel or a non-adhesive alginate hydrogel after 28 days of in vitro growth. Additionally, we used scRNA-seq to profile HIOs derived in the presence of Neuregulin 1 (NRG1) and/or EGF after 40 days of in vitro growth.
Project description:Here, we used single-cell RNA-sequencing (scRNA-seq) to profile intestinal epithelial only organoids (also known as enteroids) from human fetal duodenum after one passage of in vitro growth. Organoids were grown in the standard 25% LWRN media with either 100 ng/ml of epidermal growth factor (EGF) or 1 ng/ml of EPIREGULIN (EREG) added.