Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ATAC-seq analysis of quiescent and activated primary mouse hepatic stellate cells

ABSTRACT: Contrasting chromatin accessibility between activated and quiescent hepatic stellate cells to identify key gene networks for the activation process.

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Mus musculus

SUBMITTER: Ian Donaldson

PROVIDER: E-MTAB-12908 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

CUT&Tag analysis of H3K9Me3 binding quiescent and activated primary mouse hepatic stellate cells

Project description:Contrasting H3K9Me3 binding site number and localisation between activated and quiescent hepatic stellate cells to identify regulation of gene repression.

2023-10-11 | E-MTAB-12907 | biostudies-arrayexpress

RNA-seq analysis of quiescent and activated primary mouse hepatic stellate cells

Project description:Contrasting transcript expression between activated and quiescent hepatic stellate cells to identify key gene networks for the activation process.

2023-10-11 | E-MTAB-12909 | biostudies-arrayexpress

Expression data from human hepatic stellate cell line LX2 treated with suberoylanilide hydroxamic acid (SAHA) or valproic acid (VPA)

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.

2016-04-07 | E-MTAB-3764 | biostudies-arrayexpress

Gene expression changes in hepatic stellate cells in response to fibrogenic agents.

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).

2014-12-19 | E-GEOD-34640 | biostudies-arrayexpress

ATACseq in BMEL cells invalidated or not for the expression of the three HP1 isoforms (CBX1, CBX3, CBX5)

Project description:Chromatin accessibility assay by ATACseq in BMEL cells. Three clones (TKO1, TKO2, TKO3) of BMEL TKO cells invalidated for the expression of the three HP1 isoforms (Cbx1-/-; Cbx3-/-; Cbx5-/-) were compared to three clones (Het1, Het32, Het35) of BMEL Het cells (Cbx1+/+; Cbx3+/+; Cbx5+/-) as controls.

2026-03-31 | E-MTAB-15197 | biostudies-arrayexpress

Small RNA-Seq for primary rat hepatic stellate cells and hepatic stellate cell-derived small extracellular vesicles

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.

2024-08-29 | E-MTAB-12764 | biostudies-arrayexpress

ATAC-Seq from Primate iPSC derived Astrocytes (iAstrocytes)

Project description:ATAC-seq experiments were performed to map the open chromatin regions of human, chimpanzee and macaque iAstrocytes. This experiment allowed to compare evolutionary changes according to chromatin activity.

2025-03-06 | E-MTAB-13253 | biostudies-arrayexpress

ATAC-seq of synovial tissues from mice with Antigen Induced Arthritis (AIA) showing distinct hallmarks of synovitis heterogeneity

Project description:Joint pathology in rheumatoid arthritis is broadly classified as fibroblast-rich, myeloid-rich, or lymphoid-rich synovitis. How these pathotypes evolve is unknown. Based on the clinical efficacy of biological medicines and targeted inhibitors, we hypothesise that cytokines instruct this process, affecting the rate of onset, severity, and course of disease. These include cytokine signals that define the organisation and maintenance of lymphocyte sentinels in lymphoid-rich synovitis, and others that guide a pauci-immune pathology involving activated stromal cells in fibroblast-rich synovitis. With a long-standing interest in the IL-6 cytokine family, we have identified distinct roles for Jak-STAT signalling in shaping synovitis heterogeneity. Establishing new mouse models that mimic fibroblast-rich, myeloid-rich, and lymphoid-rich synovitis in humans, we propose that wild-type (WT), Il6ra-/-, and Il27ra-/- mice with AIA share hallmarks of these pathotypes. The reported RNA-seq now profiles the transcriptional profile of synovitis in WT, Il6ra-/-, and Il27ra-/- mice with AIA and provides datasets captured at day-3 and day-10 AIA reflecting early and established disease.

2026-03-26 | E-MTAB-16747 | biostudies-arrayexpress

Profiling of the transcriptome during culture-induced activation of rat hepatic stellate cells.

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.

2017-10-23 | E-MTAB-5404 | biostudies-arrayexpress

ATAC-seq from mouse embryonic stem cell and their derivative neural stem cells

Project description:ATAC-seq experiments were performed to map the open chromatin regions of embryonic stem cells and neural stem cells.

2025-06-13 | E-MTAB-13559 | biostudies-arrayexpress