ATAC-seq analysis of quiescent and activated primary mouse hepatic stellate cells
Ontology highlight
ABSTRACT: Contrasting chromatin accessibility between activated and quiescent hepatic stellate cells to identify key gene networks for the activation process.
Project description:Contrasting H3K9Me3 binding site number and localisation between activated and quiescent hepatic stellate cells to identify regulation of gene repression.
Project description:Contrasting transcript expression between activated and quiescent hepatic stellate cells to identify key gene networks for the activation process.
Project description:Suberoylanilide hydroxamic acid (SAHA) and valproic acid (VPA) are both histone deacetylases inhibitor (HDACi), and are able to attenuate the activation of hepatic stelllate cells. To explore the underlying molecular mechanisms, we performed gene expression profile analyses of human hepatic stellate cell line LX2 treated with SAHA or VPA for 24 hours. Duplicate experiments were performed: Untreated LX2, SAHA treated LX2 and VPA treated LX2.
Project description:Gene expression of hepatic stellate cells exposed to fetal bovine serum (FBS) (cultured alone and in the presence of Kupffer cells) activated and CCl4 exposure and Bile-duct ligation is characterized. Affymetrix Mouse 430 2.0 gene expression measurements were used to characterize the transcriptomic basis of the effects of the above treatments and genotypes on firbrogenesis. Gene expression of mouse hepatic stellate cells was characterized under the following conditions: A. Quiescent (n=5). B. Activated by FBS (n=3). C. Cocultured with Kupffer cells and activated by FBS (n=3). D. Activate by bile-duct ligation (n=3). E. Activated by CCl4 (n=3).
Project description:Aims: To obtain small non-coding RNA expression profiles of short-term activated and long-term activated hepatic stellate cells (HSCs). To obtain small non-coding RNA expression profiles of small extracellular vesicles (sEVs) from short-term activated and long-term activated HSCs. Methods: Primary rat HSCs were isolated and cultured in vitro. To isolate HSC-derived sEVs, culture media (CMs) from Day 0 to Day 3 and Day 7 to Day 14 were collected. The sEVs from Day 0 to Day 3 HSC CMs were referred to as short-term activated HSC-sEVs (3dHSC-sEVs), and those from Day 7 to Day 14 HSC CMs were referred to as long-term activated HSC-sEVs (14dHSC-sEVs). Day 3 HSCs, Day 14 HSCs, and HSC-sEVs were collected and lysed in TRIzol (Life Technologies) for RNA sample preparation at the indicated time points.
Project description:Gene expression was determined in primary rat hepatic stellate cells during the in vitro activation process in freshly isolated (4h), quiescent (1d), early activated (3d) and fully activated (7d) hepatic stellate cells. The cells were isolated from the liver using density centrifugation and cultured on plastic in DMEM containing serum for the indicated time. RNA was isolated using the Qiagen Rneasy Mini Kit. The Affymetrix Gene Chip Rat Gene 2.0 ST was used for gene expression analysis performed by the genomic core facility of the EMBL (Heidelberg, Germany). All experiments were performed three times with independent animals.
Project description:Gene expression of mouse hepatic stellate cells was characterized under the following conditions: Quiescent (isolated from normal mouse liver) and reverted (isolated from mouse liver treated with 4 injections of carbontetrachloride followed by 45 day rest period) Affymetrix Mouse 1.0ST gene expression measurements were used to characterize the transcriptomic basis in quiescent hepatic stellate cells, isolated from normal liver, and reverted hepatic stellate cells, isolated from liver treated with 4 injections of CCl4 followed by a 45 day rest period. Gene expression of mouse hepatic stellate cells was characterized under the following conditions: A. Quiescent control hepatic stellate cells (n=4). B. Reverted hepatic stellate cells (n=4).
Project description:Extracellular matrix (ECM) deposition and resultant scar play a major role in the pathogenesis and progression of liver fibrosis. Identifying core regulators of ECM deposition may lead to urgently needed diagnostic and therapetic strategies for the disease. The transcription factor Sex determining region Y box 9 (SOX9) is actively involved in scar formation and its prevalence in patients with liver fibrosis predicts progression. In this study, transcriptomic approaches of Sox9-abrogated myofibroblasts identified >30% of genes regulated by SOX9 relate to the ECM.
Project description:Deregulated accumulation of myofibroblasts (MF) is central to liver fibrosis pathogenesis, but the mechanisms controlling myofibroblast fate remain poorly understood. Here we investigated whether Hedgehog (Hh) signaling regulates MF fate by modulating MF metabolism. We performed microarrays to screen hepatic stellate cells (HSC) for transition-associated changes in metabolism. To capture early and late events in their MF transition process, we compared gene expression in freshly isolated primary HSC with gene expression in the same cells after 7 days in culture. We analyzed total RNA from 3 replicates of HSC in the early transition or quiescent state (n=3) as well as in the late phase of transition (MF) (n=3).
Project description:The aim of the experiment was to identify HAND1 target genes and its impact on chromatin accessibility in relation to cardiac development. A HAND1-null hESC line was used, in which a doxycycline-inducible HAND1-T2A-BFP transgene had been integrated in approximately half of the cells for HAND1 rescue / overexpression. The hESCs were differentiated with BMP4, Activin A and CHIR. On day 2.5, doxycycline was added. On day 3, cells were dissociated and sorted by BFP level using FACS. Samples were immediately processed for RNA-seq and ATAC-seq.