Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A platform for screening microbial effects on primary epithelial cells

ABSTRACT: A platform for screening microbial effects on primary epithelial cells

PROVIDER: PRJNA967000 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR24422583_1.fastq.gz	Fastqsanger.gz
	SRR24422583_2.fastq.gz	Fastqsanger.gz
	SRR24422584_1.fastq.gz	Fastqsanger.gz
	SRR24422584_2.fastq.gz	Fastqsanger.gz
	SRR24422585_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 30

Similar Datasets

A platform for screening microbial effects on primary epithelial cells

Project description:CACO2 cells were exposed to four bacteria ( LGG, BB-12, Bifidobacterium infantis DSM33361(hereafter referred to as DSM33361), and Bifidobacterium breve Bif195 (hereafter called Bif195)), and control (untreated)

2023-05-15 | GSE231605 | GEO

High-throughput transcriptomics platform for screening hepatotoxicants

Project description:High-throughput transcriptomics platform for screening hepatotoxicants

| PRJNA638385 | ENA

High-throughput transcriptomics platform for screening hepatotoxicants

Project description:We introduce a new high-throughput transcriptomics (HTTr) platform comprised of a collagen sandwich primary rat hepatocyte culture and the TempO-Seq assay for screening and prioritizing potential hepatotoxicants. We selected 14 chemicals based on their risk of drug-induced liver injury (DILI) and tested them in hepatocytes at two treatment concentrations. HTTr data was generated using the TempO-Seq whole transcriptome and S1500+ assays. The HTTr platform exhibited high reproducibility between technical replicates (r>0.9) but biological replication was greater for TempO-Seq S1500+ (r>0.85) than for the whole transcriptome (r>0.7). Reproducibility between biological replicates was dependent on the strength of transcriptional effects induced by a chemical treatment. Despite targeting a smaller number of genes, the S1500+ assay clustered chemical treatments and produced gene set enrichment analysis (GSEA) scores comparable to those of the whole transcriptome. Connectivity mapping showed a high-level of reproducibility between TempO-Seq data and Affymetrix GeneChip data from the Open TG-GATES project with high concordance between the S1500+ gene set and whole transcriptome. Taken together, our results provide guidance on selecting the number of technical and biological replicates and support the use of TempO-Seq S1500+ assay for a high-throughput platform for screening hepatotoxicants.

2021-09-01 | GSE152128 | GEO

High-Throughput Transcriptomics Platform for Screening Environmental Chemicals

Project description:High-Throughput Transcriptomics Platform for Screening Environmental Chemicals

| PRJNA683595 | ENA

A safety screening platform for individualized cardiotoxicity assessment

Project description:A safety screening platform for individualized cardiotoxicity assessment

| PRJNA971626 | ENA

A cyanobacterial screening platform for mutant variants of a Form II Rubisco

Project description:Cyanobacterial Form II Rubisco screening platform

| PRJEB79580 | ENA

Ex-vivo screening platform to identify tumor-specific therapies

Project description:Ex-vivo screening platform to identify tumor-specific therapies

| PRJNA417676 | ENA

Glioma-propagating cells as an in vitro screening platform: PLK1 as a case study

Project description:Gliomas are the most devastating of primary adult malignant brain tumors. These tumors are highly infiltrative and can arise from cells with extensive self-renewal capability and chemoresistance, frequently termed glioma-propagating cells (GPCs). GPCs are thus the plausible culprits of tumor recurrence. Treatment strategies that eradicate GPCs will greatly improve disease outcome. Such findings support the use of GPCs as in vitro cellular systems for small molecule screening. However, the nuances in utilizing GPCs as a cellular screening platform are not trivial. These slow-growing cells are typically cultured as suspension, spheroid structures in serum-free condition supplemented with growth factors. Consequently, replenishment of growth factors throughout the screening period must occur to maintain cells in their undifferentiated state, as the more lineage-committed, differentiated cells are less tumorigenic. We will present a case study of a small molecule screen conducted with GPCs and explain how unique sphere activity assays were implemented to distinguish drug efficacies against the long-term, self-renewing fraction, as opposed to transient-amplifying progenitors, latter of which are detected in conventional viability assays. We identified Pololike kinase 1 as a regulator of GPC survival. Finally, we leveraged on public glioma databases to illustrate GPC contribution to disease progression and patient survival outcome. Total RNA from primary neurosphere culture of brain tumor specimens were hybridized in baseline condition. Specimens were obtained from 11 patients and replicate arrays were performed for all 11 neurosphere cultures.

2012-08-01 | E-GEOD-36782 | biostudies-arrayexpress

Open-source electrophilic fragment screening platform for UCHL1 covalent inhibitors

Project description:Data in support of the manuscript "Open-source electrophilic fragment screening platform for UCHL1 covalent inhibitors"

2024-12-06 | MSV000096608 | MassIVE

SEUSS: A scalable screening platform to assess transcriptomic and fitness effects of transcription factor overexpression

Project description:Understanding the complex effects of genetic perturbations on cellular state and fitness in human pluripotent stem cells (hPSCs) has been challenging using traditional pooled screening techniques which typically rely on unidimensional phenotypic readouts. Here, we use barcoded open reading frame (ORF) overexpression libraries with a coupled single-cell RNA sequencing (scRNA-seq) and fitness screening approach, a technique we call SEUSS (ScalablE fUnctional Screening by Sequencing), to establish a comprehensive assaying platform. Using this system, we perturbed hPSCs with a library of developmentally critical transcription factors (TFs), and assayed the impact of TF overexpression on fitness and transcriptomic cell state across multiple media conditions. We further leveraged the versatility of the ORF library approach to systematically assay mutant gene libraries and also whole gene families. From the transcriptomic responses, we built genetic co-perturbation networks to identify key altered gene modules. Strikingly, we found that KLF4 and SNAI2 have opposing effects on the pluripotency gene module, highlighting the power of our method to characterize the effects of genetic perturbations. From the fitness responses, we identified ETV2 as a driver of reprogramming towards an endothelial-like state.

2018-09-24 | GSE107185 | 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