Spatio-temporal mRNA tracking in the early zebrafish embryo
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA666689 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR12749591_1.fastq.gz | Fastqsanger.gz | |||
| SRR12749591_2.fastq.gz | Fastqsanger.gz | |||
| SRR12749592_1.fastq.gz | Fastqsanger.gz | |||
| SRR12749592_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 15 |
Similar Datasets
Project description:Early stages of embryogenesis depend on subcellular localization and transport of maternal mRNA. However, systematic analysis of these processes is hindered by a lack of spatio-temporal information in single-cell RNA sequencing. Here, we combine spatially-resolved transcriptomics and single-cell RNA labeling to perform a spatio-temporal analysis of the transcriptome during early zebrafish development. We measure spatial localization of mRNA molecules within the one-cell stage embryo, which allows us to identify a class of mRNAs that are specifically localized at an extraembryonic position, the vegetal pole. Furthermore, we establish a method for high-throughput single-cell RNA labeling in early zebrafish embryos, which enables us to follow the fate of individual maternal transcripts until gastrulation. This approach reveals that many localized transcripts are specifically transported to the primordial germ cells. Finally, we acquire spatial transcriptomes of two xenopus species and compare evolutionary conservation of localized genes as well as enriched sequence motifs.
| S-EPMC8184788 | biostudies-literature
Project description:We performed spatially resolved transcriptomics with sub-single-cell resolution in zebrafish embryos at the one-cell stage, which allowed us to identify a class of mRNAs that is specifically localized at an extraembryonic position in the yolk sac, the vegetal pole. The 3’ UTRs of these localized genes are enriched in specific sequence motifs. Comparison to two frog species revealed relatively low conservation of localized genes, but high conservation of sequence motifs. In vivo RNA labeling followed by scRNA-seq revealed that a large number of the localized transcripts are specifically transported to the primordial germ cells.
2020-12-07 | GSE158849 | GEO
Project description:Embryogenesis in rice shows a non-stereotypic cell division pattern, the formation of dorsal-ventral polarity, and endogenous initiation of the radicle, which differs from most dicotyledonous plants. To reveal the transcriptional features associated with developmental events during early embryogenesis in rice, we obtained transcriptome data, including the spatial and temporal data sets, using microarray experiments combined with a laser microdissection. We could predict the spatial expression foci of each expressed gene in the globular embryo, which revealed that the expression bias along the apical-basal and dorsal-ventral axes was correlated with temporal changes in expression levels during early embryogenesis. The spatial expression patterns of transcripts was suggestive of a potential contribution of phytohormone-related genes to early embryogenesis and was a characteristic feature of transcription factor genes. We also analyzed the relationship between expression sites of the genes in the globular embryo and those in embryonic organs at later stages. Based on in silico prediction of gene expression sites, we developed potential marker genes expressed in specific domains of the early embryo. The results and database will provide a framework for spatio-temporal gene expression in rice embryogenesis and increase our understanding of developmental diversity of plant embryogenesis.
2014-11-08 | GSE63110 | GEO
Project description:Spa sulfurous water metagenomes: spatio-temporal study
| PRJEB35095 | ENA
Project description:Spatio-temporal transcriptional profiling of leaf development in rice
| PRJNA667479 | ENA
Project description:Functional specification of mammalian tissues is a result of precise regulation of gene expression during development. Although previous transcriptomic and proteomic analyses have provided great biological insight into tissue specific gene expression and their physiological relevance in development, our understanding of translational regulation in developing tissues is lacking. Here, we report a spatio-temporally resolved translatome analysis of six mouse tissues at embryonic and adult stages to quantify the effects of translational regulation and identify new translational components. We quantified the spatial and temporal divergence of gene expression and showed specific changes in gene expression and pathways underlying the divergence. We further showed dynamic translational control by modulating translational efficiency, enhancing tissue specificity during development. We discovered thousands of actively translated upstream open read frames (ORFs) that exhibited spatio-temporal patterns and demonstrated their regulatory roles in translational regulation. Finally, we identified known and novel micropeptides encoded by small ORFs from long non-coding RNAs with functional relevance to tissue development. Our data and analyses facilitate a better understanding of complex translational regulation across tissue and developmental spectra and serve as a useful resource of mouse translatome.
2020-03-10 | GSE94982 | GEO
Project description:Here we profile the expression of circRNA in 6 different brain tissues at up to 6 different time-points during fetal porcine development, constituting the first report of circRNA in a large animal. An unbiased analysis reveals a highly complex regulation pattern of thousands of circular RNAs, with a distinct spatio-temporal expression profile. The amount and complexity of the circRNA expression was most pronounced in cortex day 60 from gestation. Here we find 4,634 unique circRNAs expressed from 2,195 genes out of a total of 13,854 expressed genes. These data demonstrate that circRNAs are highly abundant and dynamically expressed in a spatio-temporally manner in porcine fetal brain, suggesting important functions during mammalian brain development.
2015-10-06 | GSE71832 | GEO
Project description:We aim to monitor global transcriptomic changes during the HR in Arabidopsis Col-0 leaf upon localized infiltration of Pst DC3000 (avrRpm1) (5*107cfu/mL) and mock (10 Mm MgCl2) in a spatio-temporal manner. The infiltrated cells were harvested in parallel with the immediately adjacent uninfected cells. Samples were collected at 0,1,2,4,6 post-inoculation in three biological replicates.
2022-05-23 | GSE198022 | GEO
Project description:Metabolism of the adult liver in mice and human is spatially zonated with hepatocytes along the axis from each portal vein to the nearest central vein expressing enzymes in a zonated manner. Upstream of that functional zonation, interactions of Wnt and Hh signaling are orchestrating and self-organizing the spatial expression patterns. This spatio-temporal model is derived from experimental data and explores the interacting signaling pathways. To run this model, use the free, open-source software Morpheus (download for Windows, macOS, Linux from https://morpheus.gitlab.io).
2021-09-30 | MODEL2009110001 | BioModels
Project description:A method for the factor-specific spatio-temporal control of splicing
| PRJNA756193 | ENA