Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Robust transcriptional indicators of plant immune cell death revealed by spatio-temporal transcriptome analyses

ABSTRACT: Robust transcriptional indicators of plant immune cell death revealed by spatio-temporal transcriptome analyses

PROVIDER: PRJNA813448 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR18254700_1.fastq.gz	Fastqsanger.gz
	SRR18254700_2.fastq.gz	Fastqsanger.gz
	SRR18254701_1.fastq.gz	Fastqsanger.gz
	SRR18254701_2.fastq.gz	Fastqsanger.gz
	SRR18254702_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 120

Similar Datasets

Robust transcriptional indicators of plant immune cell death revealed by spatio-temporal transcriptome analyses

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

Spa sulfurous water metagenomes: spatio-temporal study

Project description:Spa sulfurous water metagenomes: spatio-temporal study

| PRJEB35095 | ENA

A spatio-temporal translatome of mouse tissue development

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

Microbial indicators

Project description:Microbial indicators for rehabilitation of post-minings substrate

| PRJEB10826 | ENA

Spatio-temporal regulation of circular RNA expression during porcine embryonic brain development

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

Spatio-temporal transcriptional profiling of leaf development in rice

Project description:Spatio-temporal transcriptional profiling of leaf development in rice

| PRJNA667479 | ENA

Spatio-temporal mRNA tracking in the early zebrafish embryo

Project description:Spatio-temporal mRNA tracking in the early zebrafish embryo

| PRJNA666689 | ENA

A method for the factor-specific spatio-temporal control of splicing

Project description:Precursor messenger RNA splicing is a highly regulated process, mediated by a complex RNA-protein machinery, the spliceosome, that encompasses several hundred proteins and five small nuclear RNAs in human. Emerging evidence suggests that the spatial organization of splicing factors and their spatio-temporal dynamics participate in the regulation of splicing. For instance, Cajal bodies and nuclear speckles function as centers for snRNP assembly and recycling or storage, respectively, whereas the assembly of spliceosomes on nascent pre-mRNAs predominantly occurs in peri-chromatin fibrils. So far, methods to manipulate the spatial distribution of splicing factors in a temporally defined manner in living cells are missing. Here, we describe such an approach that takes advantage of a reversible chemical dimerizer, and outline the requirements for efficient, reversible re-localization of splicing factors to selected sub-nuclear compartments. In a proof-of-principle study, the partial re-localization of the PRPF38A protein to the nuclear lamina induced a moderate increase in intron retention. Our approach allows fast and reversible re-localization of splicing factors, has few side effects and can be applied to any splicing factor by fusion of a protein tag through genome engineering. Apart from the systematic analysis of the spatio-temporal aspects of splicing regulation, the approach has a large potential for the fast induction and reversal of splicing switches and can reveal mechanisms of splicing regulation in native nuclear environments.

2022-06-18 | GSE182412 | GEO

Kolbe2019 - Spatio-temporal liver zonation

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

Spatio-temporal transcriptional profiling of early embryogenesis in rice

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

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