ScRNA-seq of organoids derived from young and old mice livers
Ontology highlight
ABSTRACT: We set up liver-derived organoids to study the ageing progenitor population. We detected epigenetic and transcriptional memory in organoids derived from old mice accompanied by alterations in drug and fatty acid metabolism pathways, similar to phenotypes observed in the liver itself.
Project description:We investigate if the differences in phenotype and transcriptome over age might be explained by an underlying change on the epigenetic level. We performed single-cell ATAC sequencing using the 10x Chromium platform. We profiled 4838 nuclei prepared from 3 young liver tissues and 3361 nuclei from 3 old liver tissues.
Project description:We investigate if the differences in phenotype and transcriptome over age might be explained by an underlying change on the epigenetic level. We performed single-cell ATAC sequencing using the 10x Chromium platform. We profiled 2259 nuclei prepared from 3 young liver tissues and 2490 nuclei from 3 old liver tissues.
Project description:We used cerebral organoids generated from wildtype and CHD8 +/- human ES cells to study the effects of CHD8, one of the top ASD risk genes, on early cortical development. CHD8 +/- hESC were generated using the CRISPR/Cas9 system to create a deletion within the helicase domain. Cerebral organoids were generated according to the protocol from Lancaster et al 2013 with minor modifications.
Project description:Our structural and biochemical studies show that S. cerevisiae RNA Polymerase II (RNAPII) homodimerizes through the stalk domain (formed by the Rpb4-Rpb7 subunits). To explore the biological impact of disrupting this interaction we introduced a triple point mutation at the RNAPII dimerization interface in Rpb7 (Q96A, H97A, F109K). To test the impact of the dimerization mutant on RNA synthesis and 3' end processing in WT and Rpb7-QHF cells, we labelled nascent transcripts with 4tU which enabled subsequent biotinylation and purification of newly-synthesized transcripts. Nascent transcripts were then used to prepare strand-specific RNA-seq libraries.
Project description:Here we provide snRNA-seq datasets from heart failure patients with reduced ejection fraction and snRNA-SEQ of the corresponding LAD mouse model (permanent ligation of the left anterior descending artery)
Project description:To test the role of Mpe1 in transcription termination we inserted a mini-auxin induced degron (mAID) at the C-terminal end of the endogenous MPE1 locus in the yeast Saccharomyces cerevisiae. We treated Mpe1-mAID cells (JRY101) or wild type cells (WT, YMK728) with 1 mM auxin for 30 minutes and labeled the nascent RNA with 4-thiouracil (4tU) for 6 minutes. The nascent RNA fraction was prepared by biotinylating the 4tU-labeled RNA followed purification with streptavidin beads. Nascent and total RNA fractions were depleted of ribosomal RNA and strand-specific libraries prepared. Libraries were single-end sequenced using an Ilummina HiSeq 4000 instrument.
Project description:Streptococcus suis is a zoonotic pathogen that can invade the central nervous system (CNS) and cause meningitis in pigs and humans. The vascularized choroid plexus (ChP) epithelium, known as the blood-cerebrospinal fluid barrier (BCSFB), serves as a route for S. suis invasion of the CNS. In this study, we aimed to use human induced pluripotent stem cells (iPSC)-derived ChP organoids as an in vitro model to investigate S. suis interaction and infection at the BCSFB and the responses of ChP organoids to S. suis using transcriptomics. We also investigated whether the known plasminogen (Plg) binding to S. suis surface enolase and its conversion to proteolytic plasmin (Pln) would facilitate S. suis translocation across the ChP organoid epithelium and alter the ChP response to infection.
Project description:Gene expression profiles of individual bone marrow cells were acquired by Drop-Seq. Total bone marrow (TBM) and weakly depleted bone marrow (DBM; Ter119/Cd45 negative cells) were analysed.
Project description:Identification of cell types in the interphase between muscle and tendon by single-nuclei RNA-seq of three human semitendinous muscle-tendon biopsies. With special focus on the myotendinous junction specific myonuclei, transcripts were identified and confirmed to myotendinous junction with immunofluorescence.