Optogenetic perturbations of RNA expression in tissue space
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA767388 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR16119402.fastq.gz | Fastqsanger.gz | |||
| SRR16119403.fastq.gz | Fastqsanger.gz | |||
| SRR16119404.fastq.gz | Fastqsanger.gz | |||
| SRR16119405.fastq.gz | Fastqsanger.gz | |||
| SRR16119406_1.fastq.gz | Fastqsanger.gz |
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Project description:Quantifying gene expression in space, for example by spatial transcriptomics, is essential for describing the biology of cells and their interactions in complex tissues. Perturbation experiments, at single-cell resolution and conditional on both space and time, are necessary for dissecting the molecular mechanisms of these interactions. To this aim, we combined optogenetics and CRISPR technologies to activate or knock-down RNA of target genes, at single-cell resolution and in programmable spatial patterns. As a proof of principle, we optogenetically induced Sonic Hedgehog (SHH) signaling at a distinct spatial location within human neural organoids. This robustly induced known SHH spatial domains of gene expression – cell-autonomously and across the entire organoid. In principle, our approach can be used to induce or knock down RNAs from any gene of interest in specific spatial locations or patterns of complex biological systems.
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Project description:Microarray Analysis of Space-flown Murine Thymus Tissue Reveals Changes in Gene Expression Regulating Stress and Glucocorticoid Receptors. We used microarrays to detail the gene expression of space-flown thymic tissue and identified distinct classes of up-regulated genes during this process. We report here microarray gene expression analysis in young adult C57BL/6NTac mice at 8 weeks of age after exposure to spaceflight aboard the space shuttle (STS-118) for a period of 13 days. Upon conclusion of the mission, thymus lobes were extracted from space flown mice (FLT) as well as age- and sex-matched ground control mice similarly housed in animal enclosure modules (AEM). mRNA was extracted and an automated array analysis for gene expression was performed. Examination of the microarray data revealed 970 individual probes that had a 1.5 fold or greater change. When these data were averaged (n=4), we identified 12 genes that were significantly up- or down-regulated by at least 1.5 fold after spaceflight (p≤0.05). Together, these data demonstrate that spaceflight induces significant changes in the thymic mRNA expression of genes that regulate stress, glucocorticoid receptor metabolism, and T cell signaling activity. These data explain, in part, the reported systemic compromise of the immune system after exposure to the microgravity of space.
2010-03-10 | GSE18388 | GEO
Project description:Optogenetics is a rapidly advancing technology that combines photochemical, optical and synthetic biology techniques to control cellular behaviour and physiology. Combining sensitive light responsive optogenetic intervention tools with human pluripotent stem cell differentiation models has the potential to refine differentiation and unpick the processes by which morphogenetic signals direct tissue patterning, organisation and cell specification. Here, we utilised an optogenetic bone morphogenetic protein (BMP) signalling system (optoBMP) to drive chondrogenic differentiation of human embryonic stem cells (hESCs). We initially engineered light-sensitive hESCs through CRISPR/Cas9-mediated integration of the optoBMP system into the AAVS1 locus. Activation of optoBMP with blue light in lieu of BMP family growth factors during differentiation resulted in activation of BMP signalling pathway mechanisms and upregulation of a chondrogenic phenotype, with significant transcriptional differences compared to cells left in the dark. Furthermore, cells differentiated with light were capable of forming chondrogenic pellets consisting of a hyaline-like cartilaginous matrix.
2023-11-09 | E-MTAB-13377 | biostudies-arrayexpress
Project description:Expression of tissue-restricted human genes following signaling or chromatin perturbations
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Project description:Optogenetic neural stem cells microarray
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Project description:The goal of the study was to determine whether perturbations in signaling pathways or chromatin regulators were sufficient to induce the illegitimate expression of tissue-restricted genes in primary human cells
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Project description:The goal of the study was to determine whether perturbations in signaling pathways or chromatin regulators were sufficient to induce the illegitimate expression of tissue-restricted genes in primary human cells
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Project description:We elucidate the transcriptome effects of optogenetics on developing neural stem cells population. The application of optogenetics in neural stem cell (NSC), allow photo-modulation of NSC in an activity-dependent manner. This provided spatio-temporal tool for studying activity dependent neurogenesis, including the potential of regulating the differentiation and maturation process of transplanted NSC. Currently, this is mainly driven by virally transfected of Channelrhodopsin-2 (ChR2) gene, which also requires high irradiance and complex in vitro stimulation systems. Additionally, despite the extensive application of optogenetics in neuroscience, the question of what transcriptome changes does optogenetic stimulation induced in developing NSCs have not been elucidated yet. To address these questions, we established a NSC line, expressing high light-sensitivity step-function opsin (SFO) variant of the chimeric channelrhodopsin, ChRFR(C167A) (~40x higher than ChR2), via the non-viral piggyBac transposon system. We set up a simple low-irradiance optogenetics stimulation-incubation system, which sufficiently induced depolarization in differentiating NSCs. We significantly enhance neurogenesis with low power optogenetic stimulation by 3 folds. Through microarray analysis, we have identified the genes and signaling pathways in axonal remodeling, synaptic plasticity and microenvironment modulation from optogenetic stimulation. Our results elucidate the transcriptome effects of optogenetics and the ability to drive neurogenesis with low irradiance optogenetics.
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Project description:Rationale: Monitoring and controlling cardiomyocyte activity with optogenetic tools offers exciting possibilities for fundamental and translational cardiovascular research. Genetically encoded voltage indicators may be particularly attractive for minimal invasive and repeated assessments of cardiac excitation from the cellular to the whole heart level. Objective: To test the hypothesis that cardiomyocyte-targeted voltage-sensitive fluorescence protein 2.3 (VSFP2.3) can be exploited as optogenetic tool for the monitoring of electrical activity in isolated cardiomyocytes and the whole heart as well as function and maturity in induced pluripotent stem cell (iPSC)-derived cardiomyocytes. Methods and Results: We first generated mice with cardiomyocyte-restricted expression of VSFP2.3 and demonstrated distinct sarcolemmal localization of VSFP2.3 without any signs for associated pathologies (assessed by echocardiography). Optically recorded VSFP2.3 signals correlated well with membrane voltage measured simultaneously by patch-clamping. The utility of VSFP2.3 for human action potential recordings was confirmed by simulation of immature and mature action potentials in murine VSFP2.3 cardiomyocytes. Optical cardiograms (OCGs) could be monitored in whole hearts ex vivo and minimally invasively in vivo via fiber optics at physiological heart rate (10 Hz) and under pacing-induced arrhythmia. Finally, we reprogrammed tail-tip fibroblasts from transgenic mice and used the VSFP2.3 sensor for benchmarking functional and structural maturation in iPSC-derived cardiomyocytes. Conclusions: We introduce a novel transgenic voltage-sensor model as a new method in cardiovascular research and provide proof-of-concept for its utility in optogenetic sensing of physiological and pathological excitation in mature and immature cardiomyocytes in vitro and in vivo. Determination of transgene (VSFP2.3) cardiotoxicity
2015-09-02 | E-GEOD-69190 | biostudies-arrayexpress
Project description:Expression of tissue-restricted human genes following signaling or chromatin perturbations [sirna screen]
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