Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq on enriched cardiac fibroblasts from the hearts of Hif-1a conditional knockout or heterozygous mice

ABSTRACT: In this project we explore the role of the master hypoxia regulator, Hypoxia inducible factor-1alpha (Hif-1a), in governing cardiac fibroblast (CF) function in homeostasis. CF-specific Hif-1a conditional knockout (cKO) mice were generated by breeding Pdgfra-merCremer (PdgfraMCM/+) Cre recombinase driver mice with Hif-1a-floxed mice (Hif-1aflox/). In Hif-1afl/-; PdgfraMCM/+ progeny, Hif-1a could be conditionally deleted in adult CFs by tamoxifen (tam) administration. We also introduced a Cre-dependent R26tdTomato reporter allele allowing marking of Pdgfra+ CFs and their progeny. In this experiment, we performed bulk RNA sequencing (RNA-seq) on tdTomato+ cells from the hearts of healthy cKO or heterozygous (HET) adult, male mice.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Mus musculus

SUBMITTER: Ralph Patrick

PROVIDER: E-MTAB-9674 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Single-cell RNA-seq on enriched cardiac fibroblasts from the healthy, sham or MI hearts of Hif-1a conditional knockout or heterozygous mice

Project description:In this project we explore the role of the master hypoxia regulator, Hypoxia inducible factor-1alpha (Hif-1a), in governing cardiac fibroblast (CF) function in homeostasis and following an acute ischaemic injury - myocardial infarction (MI). CF-specific Hif-1a conditional knockout (cKO) mice were generated by breeding Pdgfra-merCremer (PdgfraMCM/+) Cre recombinase driver mice with Hif-1a-floxed mice (Hif-1aflox/). In Hif-1afl/-; PdgfraMCM/+ progeny, Hif-1a could be conditionally deleted in adult CFs by tamoxifen (tam) administration. We also introduced a Cre-dependent R26tdTomato reporter allele allowing marking of Pdgfra+ CFs and their progeny. In this experiment, we first performed single-cell RNA sequencing (scRNA-seq) on tdTomato+ cells from the hearts of healthy cKO or heterozygous (HET) adult, male mice using the 10x Genomics Chromium system. We also performed scRNA-seq on tdTomato+/CD31-/CD45- cells from the hearts of cKO or HET mice at day-3 post-sham or -MI surgery.

2021-11-11 | E-MTAB-9583 | biostudies-arrayexpress

RNA-seq of mitochondrial mass fractions within SCA1+/PDGFRA+/CD31- fibroblasts from adult mouse hearts

Project description:In this project we explore the mitochondrial properties of SCA1+/PDGFRA+/CD31- (S+P+) cardiac fibroblasts (CF) from uninjured adult mouse hearts. We fractionated S+P+ cells on the basis of mitochondrial mass using MitoTracker green-FM and flow cytometry into three fractions: high, mid and low mitochondrial mass as well as total S+P+ cells. Bulk RNA-seq was then performed on each of the fractions.

2021-12-02 | E-MTAB-9675 | biostudies-arrayexpress

Hippo Pathway Deletion in Adult Resting Cardiac Fibroblasts Initiates a Cell State Transition with Spontaneous and Self-Sustaining Fibrosis

Project description:Cardiac fibroblasts (CFs) respond to injury by transitioning through multiple cell states, including resting CFs, activated CFs, and myofibroblasts. We report here that Hippo signaling cell-autonomously regulates CF fate transitions and proliferation, and non-cell-autonomously regulates both myeloid and CF activation in the heart. Conditional deletion of Hippo pathway kinases, Lats1 and Lats2, in uninjured CFs initiated a self-perpetuating fibrotic response in the adult heart that was lethally exacerbated by myocardial infarction (MI). Single cell transcriptomics showed that uninjured Lats1/2 mutant CFs spontaneously transitioned to a myofibroblast cell state. Through gene regulatory network reconstruction, we found that Hippo-deficient myofibroblasts deployed a network of transcriptional regulators of endoplasmic reticulum (ER) stress, and the unfolded protein response (UPR) consistent with elevated secretory activity. Moreover, we observed an expansion of myeloid cell heterogeneity in uninjured Lats1/2 CKO hearts with a striking similarity to cells recovered from infarcted control hearts. Integrated genome-wide analysis of Yap chromatin occupancy revealed that Yap directly activates myofibroblast cell identity genes, the proto-oncogene Myc, and an array of genes encoding pro-inflammatory factors through enhancer-promoter looping. Thus, our data indicate that Lats1/2 maintain the resting CF cell state through restricting the Yap-induced injury response.

2019-10-01 | GSE135296 | GEO

Systematic screening of chromatin factors identifies divergent roles across haematopoiesis and leukaemia [scRNA-Seq]

Project description:Cellular differentiation-trajectories require extensive alterations in chromatin structure and function, elicited by a diverse array of chromatin-factors (CFs). Using haematopoiesis as a model-system, we combined bulk ex vivo and single-cell in vivo CRISPR screens to comprehensively characterise the role of CF families in cell-fate decisions. We uncover marked lineage specificities for many CFs, dissecting specific CF-dependencies in vivo at single-cell resolution. This highlights functional diversity among related CFs (i.e. BAF-subcomplexes, MLL-methyltransferases), but also reveals functional redundancy among unrelated Repressive-complexes that restrain excessive myeloid differentiation. Epigenetic-profiling, molecularly explains CF lineage-dependencies, identifying differentiation stage-specific interactions between individual CFs and lineage-determining Transcription Factors (TFs). Intriguingly, non-canonical BAF remodeler disruption abrogates myeloid-TF function generating a pre-leukaemia phenotype. Screening CF functions in leukemia, we show that leukaemia cells abrogate normal CF function, restraining differentiation trajectories by engaging in novel CF-TF interactions that suggest potential therapeutic avenues. Together, our work greatly elucidates the role of CFs and their TF-partners across normal and malignant haematopoiesis.

2023-05-23 | GSE213511 | GEO

Comparative binding patterns of Chromatin Regulators in normal versus leukemic hematopoiesis [ChIP-Seq]

2023-05-23 | GSE213507 | GEO

Comparative binding patterns of Chromatin Regulators in normal versus leukemic hematopoiesis [ATAC-Seq]

2023-05-23 | GSE213506 | GEO

Single-cell RNA-seq of mouse cardiac interstitial cells 3 & 7 days after sham or myocardial infarction injury

Project description:The aims of the experiment were to profile the cell types in the adult mouse cardiac interstitium (non-myocyte cells) and how they respond to myocardial infarction injury. Adult, male, Pdgfra +/GFP mice were subject to either a myocardial infarction or sham injury, with cells isolated from cardiac ventricles 3 or 7 days following surgery. We obtained scRNA-seq profiles of two cell fractions: total interstitial (non-myocyte) cell population (TIP) and FACS-sorted GFP+/Cd31- cells (GFP).

2019-03-28 | E-MTAB-7376 | biostudies-arrayexpress

Single-cell RNA-seq of Pdgfra+/Sca1+/Cd31- mouse cardiac cells

Project description:Adult mice hearts contain a population of resident mesenchymal stem cell (MSC)-like cells called cardiac colony forming units-fibroblast (cCFU-F). The cCFU-F are housed in a population of non-muscle cardiac cells that are Pdgfra+/Sca1+/Cd31- (S+P+ fraction). The goal of this experiment was to profile the heterogeneity of cell sub-types contained within the S+P+ fraction. We profiled two replicates of S+P+ single-cell transcriptomes from the cardiac ventricles of adult, male, C57BL/6J mice after FACS sorting for live Pdgfra+/Sca1+/Cd31- non-myocyte cells.

2019-03-28 | E-MTAB-7365 | biostudies-arrayexpress

Single-cell RNA-seq of mouse cardiac interstitial cells 3 & 7 days after sham or myocardial infarction injury and PDGF-AB or PBS delivery

Project description:The aims of the experiment were to profile the cardiac interstitial (non-myocyte) cell types in the adult mouse from injured and uninjured hearts and how they respond to modulation of platelet-derived growth factor receptor alpha (PDGFRa) signaling. Adult, male, C57BL/BJ mice were subject to either a myocardial infarction or sham injury, and given either PDGF-AB or PBS treatment via mini-pump, with single-cell RNA-seq profiles obtained from interstitial cells isolated from cardiac ventricles 3 or 7 days following surgery.

2023-05-31 | E-MTAB-7971 | biostudies-arrayexpress

Global genomic profiling of HIF-1a-regulated genes in bone marrow B cells under hypoxia or normoxia

Project description:HIF-1a works as a stress-induced transcription factor to induce target genes mediating cell proliferation, meabolism and inflammation. To gain new insights into HIF-1a biology, we used high-throughput sequencing to analyze global HIF-1a transcriptional networks in WT or HIF-1a deficient bone marrow B cells under hypoxia or normoxia.

2022-02-24 | GSE163848 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data