Gene expression profile at single cell level of 72 hpf heart cells from wild-type, tnnt2a mutant, and Tnnt2a degron zebrafish larvae.
Ontology highlight
ABSTRACT:
ORGANISM(S): Danio rerio
PROVIDER: GSE232835 | GEO | 2023/12/01
REPOSITORIES: GEO
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Project description:We examined the transcriptional effect of preventing cardiac contraction in zebrafish embryos which can be deprived of circulation without experiencing hypoxia since the fish obtain sufficient oxygen via diffusion. Morpholino antisense knockdown of cardiac troponin T2 (tnnt2) prevented cardiac contraction without affecting vascular development. We concluded that absence of hemodynamic force induces endothelial CXCR4a up-regulation and promotes recovery of blood flow. We used microarrays to define the genetic signatures of the development of collateral vessels in zebrafish. Experiment Overall Design: One cell zebrafish embryos were injected with morpholino antisense against control or cardiac troponin t2, which prevents cardiac development. Whole embryo RNA was extracted at 36, 48, and 60h post fertilization and transcriptionally profiled.
2009-07-05 | E-GEOD-16740 | biostudies-arrayexpress
Project description:We examined the transcriptional effect of preventing cardiac contraction in zebrafish embryos which can be deprived of circulation without experiencing hypoxia since the fish obtain sufficient oxygen via diffusion. Morpholino antisense knockdown of cardiac troponin T2 (tnnt2) prevented cardiac contraction without affecting vascular development. We concluded that absence of hemodynamic force induces endothelial CXCR4a up-regulation and promotes recovery of blood flow. We used microarrays to define the genetic signatures of the development of collateral vessels in zebrafish. Keywords: Time course comparison of wild type zebrafish embryos and morpholino antisense against troponin t2 treated embryos.
2009-06-24 | GSE16740 | GEO
Project description:The ubiquitin-proteasome system plays critical roles in biology by regulating protein degradation. Despite their importance, precise recognition specificity is known for few of the 600 E3s. Here we establish a two-pronged strategy for identifying and mapping critical residues of internal degrons on a genome scale in HEK-293T cells. We employ Global Protein Stability profiling combined with machine learning to identify 15,800 peptides likely to contain sequence-dependent degrons. We combine this with scanning mutagenesis to define critical residues for over 5,000 predicted degrons. Focusing on Cullin-RING ligase degrons, we generated mutational fingerprints for 219 degrons and developed DegronID, a computational algorithm enabling the clustering of degron peptides with similar motifs. CRISPR analysis enabled the discovery of E3-degron pairs of which we uncover 16 pairs that revealed extensive degron variability and structural determinants. We provide the visualization of this data on the public DegronID Data Browser as a resource for future exploration.
2023-09-21 | GSE240610 | GEO
Project description:Study to examine the effect of a demanding 15 minute whole hindlimb isometric contraction protocol in vivo on changes in gene expression, 4 hours post-contraction. Keywords = skeletal muscle Keywords = isometric contractions
2010-06-06 | E-GEOD-1679 | biostudies-arrayexpress
Project description:Background: Hypertensive disorders of pregnancy (HDP) affect 2-8% of pregnancies and are associated postpartum with ongoing, increased cardiovascular disease (CVD) risk. In this study, we aimed to model HDP-induced CVD and decipher systemic mechanisms, using an advanced 3D in vitro cardiac spheroid model. Methods: Human iPSC-derived cardiomyocytes, cardiac fibroblasts and coronary artery endothelial cells were co-cultured to form cardiac spheroids (CS ) in collagen type-1 hydrogels containing 10% patient plasma collected five years postpartum (n=5 per group: normotensive control, gestational hypertension (GH) and preeclampsia). Plasma-treated CS were assessed for cell viability, contractile function and markers of cardiac damage using immunofluorescence staining and imaging. An untargeted, label-free quantitative proteomic analysis of plasma samples was conducted (controls n=24; GH n=5; preeclampsia n=13). Results: Contraction frequency (CF) was increased in preclampsia-treated CS (CF:45.5 contractions/minute, p<0.001) and GH-treated CS (CF:45.7 contractions/minute, p<0.001), compared to controls (CF=21.8 contractions/minute). Only GH-treated CS presented increased fractional shortening (FS) % (FS%=9.5%, p<0.05), compared to controls (FS%=3.7%); this was in conjunction with a reduction in cell viability by ͠ 20% (p<0.05), and an increase in α-SMA expression (p<0.05). Proteomics analysis identified twenty differentially abundant proteins, with haemoglobin A2 the only protein perturbed in both GH and preeclampsia versus control (p<0.05). Conclusions: GH-induced CVD appears linked to an increase in cell death signaling and cardiac remodeling and preeclampsia-induced CVD to vascular and endothelial cell dysfunction. CS could in future be used to assess early changes in cardiac function and as a precision medicine platform for testing post-HDP CVD prevention therapeutics.
2024-11-25 | PXD051288 | Pride
Project description:Study to examine the effect of a demanding 15 minute whole hindlimb isometric contraction protocol in vivo on changes in gene expression, 4 hours post-contraction. Keywords = skeletal muscle Keywords = isometric contractions Keywords: parallel sample
2004-08-17 | GSE1679 | GEO
Project description:Mice were subjected to 50 eccentric contractions (EC) or 50 isometric contractions (IC) using a non-invasive model, and then sacrificed 48 hours later. RNA from the tibialis anterior of 4 animals were pooled and then split into two groups for hybridization onto two separate Affymetrix MGU74Av2 chips. Control samples were contralateral to the exercised legs, and were only subjected to enough contractions to measure isometric torque. Eccentric contractions (ECs), in which a muscle is forced to lengthen while activated, result in muscle injury and, eventually, muscle strengthening and prevention of further injury. Although the mechanical basis of eccentric contraction-induced injury has been studied in detail, muscle's biological response is less well characterized. This study presents the development of a minimally-invasive model of EC injury in the mouse, follows the time course of torque recovery after an injurious bout of ECs, and uses Affymetrix microarrays to compare the gene expression profile 48 hours after ECs to both isometrically stimulated muscles and contralateral muscles. Torque dropped by about 55% immediately after the exercise bout, and recovered to initial levels 7 days later. 36 known genes were upregulated after ECs compared to contralateral and isometrically stimulated muscles, including five muscle specific genes: muscle LIM protein (MLP), Muscle Ankyrin Repeat Proteins (MARP 1 and 2; also known as cardiac ankyrin repeat protein and Arpp/Ankrd2, respectively), Xin, and Myosin Binding Protein H. The time courses of MLP and MARP expression after the injury bout (determined by quantitative real-time polymerase chain reaction) indicate that these genes are rapidly induced, reaching a peak expression level of 6-11 times contralateral values 12-24 hours after the EC bout and returning to baseline within 72 hours. Very little gene induction was seen after either isometric activation or passive stretch, indicating that the MLP and MARP genes may play an important and specific role in the biological response of muscle to EC-induced injury. Keywords = mouse tibialis anterior eccentric contraction muscle
2007-11-06 | E-GEOD-435 | biostudies-arrayexpress
Project description:Mechanical forces are increasingly recognized to regulate morphogenesis, but how this is accomplished in the context of the multiple tissues present within a developing organ remains unclear. Here we use bioengineered “microfluidic chest cavities” to precisely control the mechanical environment of the fetal lung. We show that transmural pressure controls airway branching morphogenesis and regulates the frequency of airway smooth muscle contraction. Next-generation sequencing analysis shows that lungs held at higher pressure are more mature than lungs held at lower pressure. Timelapse imaging reveals that branching events are synchronized across distant locations within the lung, and are preceded by long-duration waves of airway smooth muscle contraction. Higher transmural pressure decreases the interval between systemic smooth muscle contractions and increases the rate of morphogenesis of the airway epithelium. These data reveal that the mechanical properties of the microenvironment instruct crosstalk between tissues to control the rate of development of the embryonic lung.
2017-11-07 | GSE90148 | GEO
Project description:SHM-conduction is a discrete unidirectional model of the human cardiac conduction system. It takes a Boolean input signal from the sinoatrial node (SAN) and includes the refractory behavior of the SAN limiting the maximum signal frequency, the delay between a signal from the SAN and the actual ventricular contraction, and the atrioventricular node generating a signal if no signal has been received for a given period of time.
This project also includes an extension of the model that is able to simulate premature ventricular contractions (PVCs).
2021-03-08 | MODEL2103050002 | BioModels
Project description:Global quantitative proteomics of cells treated with the immunomodulatory drug pomalidomide or dipeptide degrons; global quantitative proteomics of cells treated with heterobifunctional degraders embedded with thalidomide or cyclic imide degrons; gloabl quantitative proteomics of red blood cells to search for the presence of C-terminal cyclic imide modifications on hemoglobin.
2022-07-28 | PXD025413 | Pride