Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CINS: Cell Interaction Network Inference from Single cell expression data in lungs of yound and aged mice

ABSTRACT: CINS: Cell Interaction Network Inference from Single cell expression data in lungs of yound and aged mice

PROVIDER: PRJNA695254 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR13562807_1.fastq.gz	Fastqsanger.gz
	SRR13562807_2.fastq.gz	Fastqsanger.gz
	SRR13562808_1.fastq.gz	Fastqsanger.gz
	SRR13562808_2.fastq.gz	Fastqsanger.gz
	SRR13562809_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 16

Similar Datasets

CINS: Cell Interaction Network Inference from Single cell expression data in lungs of yound and aged mice

Project description:We report the development of a new computational method to assess differences in cell-cell interactions between conditions through utilizing single-cell RNA sequencing data. The pipeline, known as Cell Interaction Network Inference from Single-cell Expression data (CINS), combines Bayesian network analysis with regression-based modeling to identify differential cell type interactions and the proteins that underlie these interactions.

2022-09-28 | GSE165638 | GEO

Single cell RNA sequencing of myeloid cells from lungs of young and aged mice

Project description:Single cell RNA sequencing from lungs of young (2-3 month old) and aged (20-22 month old) mice.

2021-10-20 | GSE167236 | GEO

scRNA-seq of young and aged lungs following influenza A virus infection

Project description:Aging is known to alter the host repsonse to influenza infection. Here, we use single-cell RNA sequencing (scRNA-seq) to identify cellular changes in the lungs of young (16-week-old) and aged (80-week-old) mice following influenza infection.

2023-09-05 | GSE202325 | GEO

Transcriptome profiling of lungs from young and aged hamster

Project description:Transcriptome profiling of lungs from young and aged hamster

| PRJNA958212 | ENA

Single cell RNA sequencing of myeloid cells from lungs of young and aged mice

Project description:Single cell RNA sequencing of myeloid cells from lungs of young and aged mice

| PRJNA703968 | ENA

Spatial sequencing of young and aged lungs following influenza A virus infection

Project description:Aging is known to alter the host repsonse to influenza infection. Here, we use 10x Visium spatial sequencing to identify spatial changes in mRNA expression of left lungs of young (16-week-old) and aged (80-week-old) mice following influenza infection.

2023-10-16 | GSE202322 | GEO

Bulk RNA-seq of young and aged lungs following influenza A virus infection

Project description:Aging is known to alter the host repsonse to influenza infection. Here, we use bulk RNA sequencing (bulk RNA-seq) to identify cellular changes in the lungs of young (16-week-old) and aged (80-week-old) mice following influenza infection.

2023-09-05 | GSE202324 | GEO

Inference and validation of predictive gene networks from biomedical literature and gene expression data

Project description:Although many methods have been developed for inference of biological networks, the validation of the resulting models has largely remained an unsolved problem. Here we present a framework for quantitative assessment of inferred gene interaction networks using knock-down data from cell line experiments. Using this framework we are able to show that network inference based on integration of prior knowledge derived from the biomedical literature with genomic data significantly improves the quality of inferred networks relative to other approaches. Our results also suggest that cell line experiments can be used to quantitatively assess the quality of networks inferred from tumor samples. Knock-down of eight genes were performed on colorectal cancer cell lines to identify the genes whose expression was significantly affected. These genes were subsequently used to validate the quality of our causal gene interaction network.

2013-12-23 | E-GEOD-53091 | biostudies-arrayexpress

Transcriptome profiling of lungs from young and aged hamster

Project description:Older age is one of the strongest risk factors for COVID-19 morbidity and mortality. Here, we sought to determine whether age-associated cellular senescence contributes to the severity of COVID-19 by studying the well-established golden hamster model of SARS-CoV-2-driven lung disease. We found that aged hamsters (22 months of age) accumulate senescent cells in the lungs and that the senolytic drug ABT-263 depletes these cells at baseline and during a SARS-CoV-2 infection. Relative to young hamsters (2 months of age), aged hamsters had a greater viral load during the acute phase of infection and displayed higher levels of sequelae during the post-acute phase. Interestingly, early treatment with ABT-263 was associated with a significantly lower pulmonary viral load, an effect associated with lower angiotensin converting enzyme 2, the receptor for SARS-CoV-2, and an amelioration of COVID-19-like lung disease in aged (but not young) animals. ABT-263 treatment of aged animals was also associated with lower pulmonary and systemic levels of senescence-associated secretory phenotype factors. Furthermore, early removal of senescent cells reduced the longer-term pulmonary inflammation. These data demonstrate the causative role of age-associated pre-existing senescent cells on the pathologic severity of experimental COVID-19.

2023-04-30 | GSE230301 | GEO

Single cell RNA-sequencing on aged mouse lung mesenchymal cells.

Project description:QC, integration, mesenchymal fraction extraction and purity confirmation were performed as described previously. The mesenchymal cell subpopulations identified in the aged normal and fibrotic lungs were similar to those identified in adult mouse lungs and each cluster showed a distinct gene expression profile.

2021-06-30 | GSE157379 | 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