Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Spatially-structured inflammatory response in the presence of a uniform stimulus: RNAseq screen

ABSTRACT: Spatially-structured inflammatory response in the presence of a uniform stimulus: RNAseq screen

PROVIDER: PRJNA1204318 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR31854000.fastq.gz	Fastqsanger.gz
	SRR31854001.fastq.gz	Fastqsanger.gz
	SRR31854002.fastq.gz	Fastqsanger.gz
	SRR31853995.fastq.gz	Fastqsanger.gz
	SRR31853996.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

Spatially-structured inflammatory response in the presence of a uniform stimulus: RNAseq screen

Project description:Inflammatory responses occur within the complex spatial context of tissues and organs, and many questions remain about how tissue structure and cellular communication shape their spatiotemporal dynamics. Here, we used single-cell RNA sequencing to screen for genes differentially expressed under LPS (lipopolysaccharide) and vehicle control conditions in epithelial cells in zebrafish larvae. We used this data to choose candidate genes for spatial gene expression analysis.

2025-02-07 | GSE285534 | GEO

Spatially uniform establishment of chromatin accessibility in the early Drosophila embryo

Project description:Spatially uniform establishment of chromatin accessibility in the early Drosophila embryo

| PRJNA414230 | ENA

Transcription profiling of human leukocytes after an inflammatory stimulus (bacterial endotoxin) to identify significant functional modules perturbed in response to this stimulus using network analysis

Project description:Oligonucleotide and complementary DNA microarrays are being used to subclassify histologically similar tumours, monitor disease progress, and individualize treatment regimens. However, extracting new biological insight from high-throughput genomic studies of human diseases is a challenge, limited by difficulties in recognizing and evaluating relevant biological processes from huge quantities of experimental data. Here we present a structured network knowledge-base approach to analyse genome-wide transcriptional responses in the context of known functional interrelationships among proteins, small molecules and phenotypes. This approach was used to analyse changes in blood leukocyte gene expression patterns in human subjects receiving an inflammatory stimulus (bacterial endotoxin). We explore the known genome-wide interaction network to identify significant functional modules perturbed in response to this stimulus. Our analysis reveals that the human blood leukocyte response to acute systemic inflammation includes the transient dysregulation of leukocyte bioenergetics and modulation of translational machinery. These findings provide insight into the regulation of global leukocyte activities as they relate to innate immune system tolerance and increased susceptibility to infection in humans.

2007-10-02 | E-GEOD-3284 | biostudies-arrayexpress

Uniform response to aneuploidy in human cells

2014-02-19 | GSE47830 | GEO

Uniform response to aneuploidy in human cells

Project description:There are many different types and origins of aneuploidy, but whether there is a uniform cellular response to aneuploidy in human cells has not been addressed so far. To uncover a uniform transcriptional response to aneuploidy we evaluted the transcription profiles of trisomic and tetrasomic cell lines and cell lines with complex aneuploid karyotypes. mRNA expression analysis of aneuploid cell lines derived from HCT116 compared to the HCT116 diploid cell line. With the exception of HCT116 3/3, three biological replicates of the Microarray experiment were performed.

2014-02-19 | E-GEOD-47830 | biostudies-arrayexpress

Spatially uniform dynamics in equilibrium colloidal gels.

Project description:Gels of DNA nanostars, besides providing a compatible scaffold for biomedical applications, are ideal model systems for testing the physics of equilibrium colloidal gels. Here, using dynamic light scattering and photon correlation imaging (a recent technique that, by blending light scattering and imaging, provides space-resolved quantification of the dynamics), we follow the process of gel formation over 10 orders of magnitude in time in a model system of tetravalent DNA nanostars in solution, a realization of limited-valence colloids. Such a system, depending on the nanostar concentration, can form either equilibrium or phase separation gels. In stark contrast to the heterogeneity of concentration and dynamics displayed by the phase separation gel, the equilibrium gel shows absence of aging and a remarkable spatially uniform dynamics.

| S-EPMC8641940 | biostudies-literature

miRNA expression in spatially-sorted hepatocytes

Project description:The mammalian liver is composed of repeating hexagonal units termed lobules. Spatially-resolved single-cell transcriptomics revealed that about half of hepatocyte genes are differentially expressed across the lobule. Technical limitations impede reconstructing similar global spatial maps of other hepatocyte features. Here, we used zonated surface markers to sort hepatocytes from defined lobule zones with high spatial resolution. We applied transcriptomics, miRNA array measurements and Mass spectrometry proteomics to reconstruct spatial atlases of multiple zonated hepatocyte features. We found that protein zonation largely overlapped mRNA zonation, with the periportal HNF4α as an exception. We identified zonation of miRNAs such as miR-122, and inverse zonation of miRNAs and their hepatocyte target genes, implying potential regulation through zonated mRNA degradation. These targets included the pericentral Wnt receptors Fzd7 and Fzd8 and the periportal Wnt inhibitors Tcf7l1 and Ctnnbip1. Our approach facilitates reconstructing spatial atlases of multiple cellular features in the liver and other structured tissues.

2019-07-26 | GSE134827 | GEO

SNAI1 knockdown under VEGF stimulus in HUVECs

Project description:SNAI1 knockdown under VEGF stimulus in HUVECs

| PRJNA436851 | ENA

Structured elements drive extensive circular RNA translation

Project description:Structured elements drive extensive circular RNA translation

| PRJNA740184 | ENA

Potent and uniform fetal hemoglobin induction via base editing

Project description:Potent and uniform fetal hemoglobin induction via base editing

| PRJNA951684 | ENA