Microgravity-induced senescence mechanisms in human stem cell-derived cardiomyocytes
Ontology highlight
ABSTRACT:
INSTRUMENT(S): NextSeq 500
ORGANISM(S): Homo sapiens
SUBMITTER: Aviseka Acharya
PROVIDER: E-MTAB-11159 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:The experiment was carried out to characterize new biological functions of components of the cap-binding complex. A2Lox mouse embryonic stem cells were transfected with Srrt- or Ncbp1-specific siRNA or a non-targeting siRNA control. Total RNAs were extracted at 48 hours post transfection and QC'd. For mRNA-Seq analyses, purified total RNAs were hybridized with oligo(dT) magnetic beads to isolate the poly(A) RNA fraction. Stranded mRNA sequencing libraries were then prepared using the Illumina TruSeq Stranded mRNA Library Kit and sequenced using an Illumina HiSeq 2500 instrument. For 3'mRNA-Seq, sequencing-ready libraries were produced using a QuantSeq 3' mRNA-Seq Library Prep Kit REV and sequenced using an Illumina HiSeq 2500 instrument.
2019-11-27 | E-MTAB-7626 | biostudies-arrayexpress
Project description:We reported previously that chronic treatment with the Cyclooxygenase-2 inhibitor, rofecoxib, increased acute mortality in rats exposed to ischemia/reperfusion injury (I/R). This manifestation of hidden cardiotoxicity was attributed to the proarrhythmic effect of the drug on the ischemic heart. However, rofecoxib also had beneficial effects on ischemic injury, manifesting as decreased infarct size. In the present study, we aimed to identify molecular changes caused by chronic rofecoxib treatment in the heart. Rats were treated with 5.12 mg/kg rofecoxib or its vehicle for four weeks. Messenger RNA (mRNA), microRNA (miRNA) deep sequencing data, and proteomic datasets of left ventricular tissue samples were used for an unbiased differential expression analysis followed by in silico molecular network analysis and experimental target validation. Using mass spectrometry and filtering criteria, 26 proteins were identified that exhibited pronounced changes in protein expression or phosphorylation due to chronic rofecoxib treatment. The transcriptomic analysis showed mild alterations in the heart´s mRNA- and miRNA expression. The posttranscriptional regulation of mRNAs by miRNAs did not result in differential protein expression. This is the first demonstration that chronic rofecoxib treatment affects posttranslational modification and expression of several proteins in the heart. These are potential off-target effects that could account for the hidden cardiotoxic and/or cardioprotective effects of rofecoxib.
2024-10-30 | E-MTAB-13913 | biostudies-arrayexpress
Project description:The lung epithelium contains multiple distinct cell types which are maintained by regionally specific progenitor cell populations in both the airways and in the alveolar compartments. Each of the progenitor populations are known to have varying roles during homeostasis and have increasingly been shown to be deranged in lung diseases. The progenitor cells of the proximal lung epithelium are the basal cells (Krt5+/Krt14+/p63+) which sit at the basement membrane of the trachea, referred to as, proximal progenitors in this study. On the other hand, the distal alveolar epithelium is maintained by alveolar type II cells (Sftpc+), referred to as distal progenitors in this study. Several cell isolation methods are available to isolate each of these populations of proximal and distal progenitors but are traditionally performed separately on mice which is especially important in the context of disease. Methods which allow the isolation of the entire epithelial population from murine lungs, while retaining the capability to perform downstream studies such as organoid assays and air-liquid-interface, would open new possibilities for studying interactions between the proximal and distal airways in lung disease. However, an easy and reproducible method that allows isolation of both cell types simultaneously from an individual mouse has not been previously described. This is in part due to the technical and surgical challenges associated with each isolation method as well as, in part, due to a lack of cell surface markers that are specific and unique to each cell type that could allow their isolation from a single cell suspension of the entire epithelium. Additionally, transgenic models have been shown to be leaky and mark populations other than the target cells. Thus, classical methods that rely on positive or negative selection, coupled by surgical isolation remain the state of the art. In order to facilitate isolation of proximal and distal progenitors from an individual mouse, we developed a 3D printable Lobe Divider (3DLD) that allows for the reproducible separation of the trachea and lung lobes while allowing for controllable and temporal instillation of cell dissociation buffers for both cell isolation procedures. The efficacy of the 3DLD in isolating the two populations and the functionality of the cells isolated with the 3DLD was validated through multiple differentiation assays. Proximal progenitors were differentiated in 2D at air-liquid interface (ALI) culture for 28 days after monolayer formation for 7days. Distal progenitors isolated with the 3DLD or with the equivalent classical tracheal ligation method were differentiated in organoid culture in Matrigel for 14 days while at ALI. Total RNA was isolated from cell pellets of all cell types before differentiation, from ALI cultures of proximal cells, and organoids of distal cells isolated with 3DLD or classic method. Qiagen RNeasy micro kit (74004, QIAGEN, Sweden) was used to isolate total RNA following the manufacturer’s protocol. RNA concentrations were measured using NanoDrop 1000 and Qubit™ RNA HS Assay Kit (Q32852, Fisher Scientific). RNA quality was evaluated by the Agilent 2100 BioAnalyzer. Library preparation was done using the Illumina Stranded mRNA Prep Ligation (20040534, Illumina) with 14 cycles under final PCR amplification and samples were indexed with IDT for Illumina RNA UD Indexes Set B, Ligation (20040554, Illumina) for multiplexing. Clean up steps were automated using the King Fisher FLEX (18-5400620, Thermo Scientific). Library concentration was checked using the QuantIT 1X dsDNA HS Assay Kit (Q33232) and library size and quality were checked using the 5200 Fragment Analyzer™ 12-capillary (M3510AA, Agilent) using the DNF-930 dsDNA Reagent Kit, 75 bp – 20,000 bp(500 Samples) (Part # DNF-930-K0500, Agilent). A library input of 1.25 nM was sequenced using NovaSeq 6000 Sequencing System (20012850, Illumina).
2022-04-30 | E-MTAB-11502 | biostudies-arrayexpress
Project description:We performed bulk RNA-seq on cell lines with and without knock out of the Trex1 gene.
2024-03-12 | E-MTAB-13815 | biostudies-arrayexpress
Project description:Upon virus infections, the transcriptomic profile of host plants markedly changes. The rapid and comprehensive transcriptional reprogramming is critical to ward off virus attack. To learn more about transcriptional reprogramming in tobamovirus-infected pepper leaves, we carried out transcriptome-wide RNA-Seq analyses of pepper leaves following Obuda pepper virus (ObPV) and Pepper mild mottle virus (PMMoV)-inoculations.
2021-07-23 | E-MTAB-10769 | biostudies-arrayexpress
Project description:We investigated the role of NEAT1 knockdown on neuronal excitability in iPSC-derived neurons.
2017-01-26 | E-MTAB-3447 | biostudies-arrayexpress
Project description:The RNA-binding protein AU-rich-element factor-1 (AUF-1) regulates mRNA decay and translation of genes during inflammation and cellular senescence, two pathogenic mechanisms of chronic obstructive pulmonary disease (COPD). Decreased AUF-1 expression was described in bronchiolar epithelium of COPD patients versus controls and in vitro cytokine-challenged airway epithelial cells, prompting the identification of epithelial AUF-1-targeted transcripts and function. RNA immunoprecipitation-sequencing (RIP-Seq) identified, in the human BEAS-2B cell line, 494 AUF-1-bound mRNAs enriched in their 3’-untranslated regions for a Guanine-Cytosine (GC)-rich binding motif, selectively confirmed by biotin pulldown. AUF-1-targets’ steady-state levels were equally affected by partial or near-total AUF-1 loss induced by cytomix (TNF/IL1/IFN/10 nM each) and siRNA, respectively, with differential transcript decay rates. Cytomix-decreased AUF-1 levels in BEAS-2B and primary human small-airways epithelium (HSAEC) associated with cell-cycle arrest, increased lysosomal damage and senescence-associated secretory phenotype (SASP) factors and with increased AUF-1 in extracellular vesicles. In-silico analysis found enriched AUF-1-targets in COPD-related pathways, SASP proteome atlas, transcriptomic COPD databases of HSAEC, lung tissue and single-cell RNA-sequencing. Intracellular and exosomal-associated AUF-1 may mediate airway epithelial inflammatory responses.
2023-04-14 | E-MTAB-12583 | biostudies-arrayexpress
Project description:C57BL6/J mice were treated with anti-PD-1 for 2 or 4 weeks, or with isotype control antibody. In echocardiography, cardiac dysfunction was seen both after 2 and 4 weeks, with decreased ejection fraction and left ventricular dilation. Bulk RNA sequencing of the hearts after treatment was performed to identify the mechanisms of anti-PD-1-induced cardiac dysfunction.
2022-12-03 | E-MTAB-12388 | biostudies-arrayexpress
Project description:We aimed to investigate gene expression changes in intestinal organoids from different mouse genotypes after treatment with interferon-gamma. Wild-type, villinCreER;KrasG12D/+;Trp53fl/flRosa26N1icd/+ (KPN), and villinCreER;Apcfl/fl;KrasG12D/+;Trp53fl/flTgfbrIfl/fl (AKPT) intestinal organoids were plated, and the media was supplemented with 1 ng/mL of recombinant mouse interferon-gamma protein on Day 3. RNA was collected 24h later and processed for RNA sequencing.
2022-06-30 | E-MTAB-11769 | biostudies-arrayexpress
Project description:Human dermal microvascular blood and lymphatic endothelial cells manifest unique profiles of histone modifications.
2021-01-18 | E-MTAB-8951 | biostudies-arrayexpress