Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

High-throughput RNAi screening for genes essential for senecent cell viability

ABSTRACT: High-throughput RNAi screening for genes essential for senecent cell viability

PROVIDER: PRJNA607125 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR11097604.fastq.gz	Fastqsanger.gz
	SRR11097605.fastq.gz	Fastqsanger.gz
	SRR11097606.fastq.gz	Fastqsanger.gz
	SRR11097607.fastq.gz	Fastqsanger.gz
	SRR11097608.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 6

Similar Datasets

High-throughput RNAi screening for genes essential for senecent cell viability

Project description:We carried out the analysis using human skin fibroblast HCA2 (MJ90) cells. Cells were induced to be senescent cells by treatment with nutlin3a + RO3306. The cells were infected with lentiviruses enocoding shRNA against human genes (DECIPHER Human Modules 1-3). As a result, we found some gene candidates involved in senecent cell viability.

2020-02-18 | GSE145414 | GEO

High throughput CRISPR screening identifies genes involved in macrophage viability and inflammatory pathways

Project description:High throughput CRISPR screening identifies genes involved in macrophage viability and inflammatory pathways

| PRJNA577130 | ENA

High throughput CRISPR screening identifies genes involved in macrophage viability and inflammatory pathways II

Project description:High throughput CRISPR screening identifies genes involved in macrophage viability and inflammatory pathways II

| PRJNA577135 | ENA

High throughput CRISPR screening identifies genes involved in macrophage viability and inflammatory pathways I

Project description:High throughput CRISPR screening identifies genes involved in macrophage viability and inflammatory pathways I

| PRJNA577134 | ENA

A novel multiplex cell viability assay for high-throughput RNAi screening.

Project description:Cell-based high-throughput RNAi screening has become a powerful research tool in addressing a variety of biological questions. In RNAi screening, one of the most commonly applied assay system is measuring the fitness of cells that is usually quantified using fluorescence, luminescence and absorption-based readouts. These methods, typically implemented and scaled to large-scale screening format, however often only yield limited information on the cell fitness phenotype due to evaluation of a single and indirect physiological indicator. To address this problem, we have established a cell fitness multiplexing assay which combines a biochemical approach and two fluorescence-based assaying methods. We applied this assay in a large-scale RNAi screening experiment with siRNA pools targeting the human kinome in different modified HEK293 cell lines. Subsequent analysis of ranked fitness phenotypes assessed by the different assaying methods revealed average phenotype intersections of 50.7±2.3%-58.7±14.4% when two indicators were combined and 40-48% when a third indicator was taken into account. From these observations we conclude that combination of multiple fitness measures may decrease false-positive rates and increases confidence for hit selection. Our robust experimental and analytical method improves the classical approach in terms of time, data comprehensiveness and cost.

| S-EPMC3230607 | biostudies-literature

High throughput expression-based phenotyping and RNAi screening reveals novel regulators of planarian stem cells

Project description:The complexity of cell types and states revealed by scRNAseq cell atlases presents a challenge for the systematic analysis of fate determinants using traditional screening methodologies. Differentiation in the planarian Schmidtea mediterranea exemplifies this problem, as these animals continuously produce over 100 differentiated cell types for homeostasis and regeneration using adult pluripotent stem cells termed neoblasts. The signaling factors enabling neoblast self-renewal and selective differentiation of these many fates are still incompletely understood. We developed a method using high-throughput expression profiling by qPCR and whole-animal RNAseq to simultaneously assess numerous cell fate markers as the phenotypic readout in large-scale RNAi screens. Applying this method, we performed an RNAi screen of 400 kinases, receptors, and other regulatory molecules to reveal specific functions for 30 previously unknown factors in neoblast biology. 17 genes were required for neoblast maintenance, including factors likely involved in cell-cycle regulation, nutrient sensing, and chromatin modification. Multidimensional expression information additionally revealed several specific regulators of other neoblast activities, including a mink1 kinase regulating global neoblast differentiation, the energy responsive kinase adenylate kinase-2 regulating intestine specification within the neoblast population, an RNA acetyl transferase nat10 regulating epidermal differentiation, and a pak1 kinase that restricts neoblast localization to prevent tissue outgrowths. These results identify several new regulators of neoblast activities and demonstrate the applicability of expression-based screening for systematic analysis of stem cell phenotypes in whole animals.

2023-08-31 | GSE212136 | GEO

High throughput expression-based phenotyping and RNAi screening reveals novel regulators of planarian stem cells

Project description:High throughput expression-based phenotyping and RNAi screening reveals novel regulators of planarian stem cells

| PRJNA874081 | ENA

Suppressor mutant screening lacking growth-essential tRNA modification in bacteria

Project description:Post-transcriptional modifications are important for transfer RNAs (tRNAs) to be efficient and accurate in translation on the ribosome. The m1G37 modification on a subset of tRNAs in bacteria are generated by a conserved methyltransferase TrmD and is essential for bacterial growth. Previous studies showed that m1G37 has an important role in preventing translational frameshifting and also that this modification is coupled with aminoacylation of tRNAs for proline. Here we performed suppressor screening to isolate a mutant E. coli cell that lacks TrmD but is viable, and the whole-genome sequencing revealed several mutations on prolyl-tRNA synthetase (ProRS) gene conferring cell viability in the absence of TrmD. Biochemical assays confirmed uncoupling of m1G37 modification and aminoacylation, and cell-based assays uncovered the critical role of m1G37 in supporting Wobble decoding.

2022-09-24 | E-MTAB-12178 | biostudies-arrayexpress

High-throughput Drug Screening Identifies Fluoxetine as a Potential Therapeutic Agent for Neuroendocrine Prostate Cancer

Project description:Here, we performed a high-throughput drug screening and identified fluoxetine, originally an FDA-approved antidepressant, as candidate therapeutic agent for NEPC. In vitro experiments revealed that fluoxetine effectively curbed the neuroendocrine differentiation and inhibited the cell viability by targeting the AKT pathway. Altogether, this work repurposed fluoxetine for antitumor application, and supported its clinical development for NEPC therapy, which may provide a promising therapeutic strategy.

2023-04-05 | GSE224715 | GEO

High-throughput transcriptomics platform for screening hepatotoxicants

Project description:High-throughput transcriptomics platform for screening hepatotoxicants

| PRJNA638385 | ENA