Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Decoding the interplay between m6A modification and stress granule stability by live-cell imaging

ABSTRACT: Decoding the interplay between m6A modification and stress granule stability by live-cell imaging

PROVIDER: PRJNA1141493 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR30033248_1.fastq.gz	Fastqsanger.gz
	SRR30033248_2.fastq.gz	Fastqsanger.gz
	SRR30033249_1.fastq.gz	Fastqsanger.gz
	SRR30033249_2.fastq.gz	Fastqsanger.gz
	SRR30033250_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

Decoding the interplay between m6A modification and stress granule stability by live-cell imaging

Project description:We present a spatiotemporal m6A imaging system (SMIS) that can monitor the m6A modification and the translation of mRNAs with high specificity and sensitivity in a single live cell. The SMIS system contains a m6A-modified reporter mRNA and fluorescence resonance energy transfer (FRET) biosensors. To quantify the methylation viariation achieved at m6A sites in the reporter mRNA after STM2457 treatment, a classical METTL3 inhibitor, we performed m6ACE-seq to measure the relative m6A level with single-base-resolusion.

2024-10-11 | GSE273366 | GEO

Combined multiphoton live-cell imaging and molecular systems approaches reveal mosaic contribution of dynamic transiently signaling INPs to the adult Dentate Gyrus NSC niche

Project description:Here we directly compare for the first time how the longstanding static model of mouse Dentate Gyrus (DG) development compares with a comprehensive high-resolution live-cell multiphoton (live-MPM) imaging approach. We took advantage of multiple fluorescent protein-based cell-type specific reporters to identify Neural Stem Cells (NSC), Intermediate Neurogenic Progenitors (INPs), and Granule Neurons (GNs) to generate live 4D cellular datasets across embryonic, postnatal and adult ages. Live-MPM revealed that INPs and NSCs migrated long distances along multiple routes to seed the SGZ from multiple directions, and from mosaic progenitor zones along the septo-temporal axis of the hippocampus. We found that dynamic INPs processes and interactions contributed to the architecture of both transient and permanent NSC niches during embryonic development, and that INP cellular plasticity is maintained in the adult SGZ NSC niche. We also used a Molecular Systems (MS) approach to determine the basis for maintained INP cellular plasticity that revealed an overlapping signaling network infrastructure based largely on Rho-family mediated regulation of cytoskeletal dynamics. Our combined strategies revealed that dynamic INPs are a major molecular signaling transition state in the adult SGZ, and that Tbr2 expression defines the initial stage of GN commitment. Our novel findings reveal fundamental new insight into one of the most well studied brain regions key for normal cognitive function, and the importance of analyzing the development of live stem cell niches in vivo. In concert with live-cell imaging, we used microarray analysis to identify genes that may be involved in the development of the Dentate Gyrus NSC niche.

2014-08-01 | E-GEOD-50148 | biostudies-arrayexpress

Live-animal imaging of native hematopoietic stem and progenitor cells

Project description:Live-animal imaging of native hematopoietic stem and progenitor cells

| PRJNA476466 | ENA

Quantitative live-cell imaging of secretion activity reveals dynamic immune responses

Project description:Quantitative live-cell imaging of secretion activity reveals dynamic immune responses

| PRJNA1064034 | ENA

Integrating single-cell RNA-seq and imaging with SCOPE-seq2

Project description:Live cell imaging allows direct observation and monitoring of phenotypes that are difficult to infer from the transcriptome. However, existing methods for linking microscopy and single-cell RNA-seq (scRNA-seq) have limited scalability. Here, we describe an upgraded version of Single Cell Optical Phenotyping and Expression (SCOPE-seq2), which builds on our earlier efforts to combine single-cell imaging and expression profiling, with substantial improvements in throughput, molecular capture efficiency, linking accuracy, and compatibility with standard microscopy instrumentation. We introduce improved optically decodable mRNA capture beads and implement a more scalable and simplified optical decoding process. We demonstrated the utility of SCOPE-seq2 for fluorescence, morphological, and expression profiling of individual primary cells from a human glioblastoma (GBM) surgical sample, revealing relationships between simple imaging features and cellular identity, particularly among malignantly transformed tumor cells.

2020-06-28 | GSE151137 | GEO

Combined multiphoton live-cell imaging and molecular systems approaches reveal mosaic contribution of dynamic transiently signaling INPs to the adult Dentate Gyrus NSC niche

2014-08-01 | GSE50148 | GEO

Pooled CRISPR screens with imaging on microRaft arrays reveals stress granule-regulatory factors

Project description:Pooled CRISPR screens with imaging on microRaft arrays reveals stress granule-regulatory factors

| PRJNA587094 | ENA

Quantitative live-cell imaging of secretion activity reveals dynamic immune responses

Project description:Quantification of cytokine secretion has facilitated advances in the field of immunology, yet the dynamic and varied secretion profiles of individual cells, particularly those obtained from limited human samples, remain obscure. Herein, we introduce a new technology for quantitative live-cell imaging of secretion activity (qLCI-S) that enables high-throughput and dual-color monitoring of secretion activity at the single-cell level over several days, followed by transcriptome analysis of individual cells based on their phenotype. The efficacy of qLCI-S was demonstrated by visualizing the characteristic temporal pattern of cytokine secretion of group 2 innate lymphoid cells, which constitute less than 0.01% of human peripheral blood mononuclear cells, and by revealing minor subpopulations with enhanced cytokine production. The underlying mechanism of this feature was linked to the gene expression of stimuli receptors. This new technology paves the way for exploring gene expression signatures linked to the spatiotemporal dynamic nature of various secretory functions.

2024-02-01 | GSE253100 | GEO

Transcription profiling of human primary liver tumours vs. universal human reference reveals that dynamic imaging traits in non-invasive computed tomography (CT) systematically correlate with the global gene expression programs of primary human liver cancer

Project description:Segal et al., 2007, Nature Biotechnology (doi:10.1038/nbt1306): Decoding global gene expression programs in liver cancer by noninvasive imaging. ABSTRACT: Paralleling the diversity of genetic and protein activities, pathologic human tissues also exhibit diverse radiographic features. Here we show that dynamic imaging traits in non-invasive computed tomography (CT) systematically correlate with the global gene expression programs of primary human liver cancer. Combinations of twenty-eight imaging traits can reconstruct 78% of the global gene expression profiles, revealing cell proliferation, liver synthetic function, and patient prognosis. Thus, genomic activity of human liver cancers can be decoded by noninvasive imaging, thereby enabling noninvasive, serial and frequent molecular profiling for personalized medicine.

2007-06-06 | E-SMDB-3992 | biostudies-arrayexpress

Decoding global gene expression programs in liver cancer by noninvasive imaging

Project description:ABSTRACT: Paralleling the diversity of genetic and protein activities, pathologic human tissues also exhibit diverse radiographic features. Here we show that dynamic imaging traits in non-invasive computed tomography (CT) systematically correlate with the global gene expression programs of primary human liver cancer. Combinations of twenty-eight imaging traits can reconstruct 78% of the global gene expression profiles, revealing cell proliferation, liver synthetic function, and patient prognosis. Thus, genomic activity of human liver cancers can be decoded by noninvasive imaging, thereby enabling noninvasive, serial and frequent molecular profiling for personalized medicine. Keywords: disease_state_design

2007-04-07 | GSE7474 | 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