Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Open chromatin and transcriptome analysis of iPSCs differentiated into lung epithelium at air-liquid interface reveals key transcriptional drivers and processes (ATAC-seq data)

ABSTRACT: Open chromatin and transcriptome analysis of iPSCs differentiated into lung epithelium at air-liquid interface reveals key transcriptional drivers and processes (ATAC-seq data)

PROVIDER: PRJNA563877 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR10067145_1.fastq.gz	Fastqsanger.gz
	SRR10067145_2.fastq.gz	Fastqsanger.gz
	SRR10067146_1.fastq.gz	Fastqsanger.gz
	SRR10067146_2.fastq.gz	Fastqsanger.gz
	SRR10067147_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 32

Similar Datasets

Open chromatin and transcriptome analysis of iPSCs differentiated into lung epithelium at air-liquid interface reveals key transcriptional drivers and processes (RNA-seq data)

Project description:The availability of robust protocols to differentiate induced pluripotent stem cells (iPSCs) into many human cell lineages has transformed research into the origins of human disease. The efficacy of differentiating iPSCs into specific cellular models is influenced by many factors including both intrinsic and extrinsic features. Among the most challenging models is the generation of human bronchial epithelium at air-liquid interface (HBE-ALI), which is the gold standard for many studies of respiratory diseases including cystic fibrosis. Here we perform open chromatin mapping by ATAC-seq and transcriptomics by RNA-seq in parallel, to define the functional genomics of key stages of the iPSC to HBE-ALI differentiation. Within open chromatin peaks the overrepresented motifs include the architectural protein CTCF at all stages, while motifs for the FOXA and GATA pioneer factors families are only seen at early stages, and those regulating key airway epithelial functions, such as EHF, are limited to later stages. The RNA-seq data illustrate dynamic pathways during the iPSC to HBE-ALI differentiation, and also the marked functional divergence of different iPSC lines at the ALI stages of differentiation. Moreover, a comparison of iPSC-derived and lung donor-derived HBE-ALI cultures reveals substantial differences between these models.

2021-01-06 | GSE136858 | GEO

Open chromatin and transcriptome analysis of iPSCs differentiated into lung epithelium at air-liquid interface reveals key transcriptional drivers and processes (ATAC-seq data)

Project description:The availability of robust protocols to differentiate induced pluripotent stem cells (iPSCs) into many human cell lineages has transformed research into the origins of human disease. The efficacy of differentiating iPSCs into specific cellular models is influenced by many factors including both intrinsic and extrinsic features. Among the most challenging models is the generation of human bronchial epithelium at air-liquid interface (HBE-ALI), which is the gold standard for many studies of respiratory diseases including cystic fibrosis. Here we perform open chromatin mapping by ATAC-seq and transcriptomics by RNA-seq in parallel, to define the functional genomics of key stages of the definitive endoderm (DE) to HBE-ALI differentiation. Within open chromatin peaks the overrepresented motifs include the architectural protein CTCF at all stages, while motifs for the FOXA and GATA pioneer factors families are only seen at early stages, and those regulating key airway epithelial functions such as EHF are limited to later stages. The RNA seq data illustrate dynamic pathways during the DE to HBE-ALI differentiation and also the marked functional divergence of different iPSC lines at the ALI stages of differentiation. Moreover, a comparison of iPSC-derived and lung donor-derived HBE cultures reveals substantial differences in these culture models.

2021-01-06 | GSE136857 | GEO

Open chromatin and transcriptome analysis of iPSCs differentiated into lung epithelium at air-liquid interface reveals key transcriptional drivers and processes

Project description:Open chromatin and transcriptome analysis of iPSCs differentiated into lung epithelium at air-liquid interface reveals key transcriptional drivers and processes

| PRJNA563874 | ENA

Air Liquid Interface Model of Gastric Mucosa and H.pylori Infection

Project description:The Air Liquid Interface Model of Gastric Mucosa allows to provide a fully polarized epithelium accessible to infection experiments with H.pylori. The influence of several factors on immune response has been studied.

2018-02-15 | GSE94032 | GEO

Open chromatin and transcriptome analysis of iPSCs differentiated into lung epithelium at air-liquid interface reveals key transcriptional drivers and processes

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-01-06 | GSE136859 | GEO

Open chromatin and transcriptome analysis of iPSCs differentiated into lung epithelium at air-liquid interface reveals key transcriptional drivers and processes (RNA-seq data)

Project description:Open chromatin and transcriptome analysis of iPSCs differentiated into lung epithelium at air-liquid interface reveals key transcriptional drivers and processes (RNA-seq data)

| PRJNA563878 | ENA

Single-cell characterization of human conjunctiva tissue, organoids and air-liquid interface cultures (10X)

Project description:We mapped the cell types present in human conjunctiva tissue, organoids and air-liquid interface cultures exposed or not to IL4/13.

2024-01-11 | GSE242382 | GEO

Liquid Application Dosing Alters the Physiology of Air-Liquid Interface Primary Bronchial Epithelial Cell/Lung Fibroblast Co-Cultures and In Vitro Testing Relevant Endpoints

Project description:Liquid Application Dosing Alters the Physiology of Air-Liquid Interface Primary Bronchial Epithelial Cell/Lung Fibroblast Co-Cultures and In Vitro Testing Relevant Endpoints

2023-08-08 | GSE198884 | GEO

Human ileum stem cell differentiation by air-liquid interface

Project description:Despite major advances with embryonic and induced pluripotent stem cells or lineage-committed, p63-expressing stem cells of stratified epithelia, we know less about the indigenous stem cells of the gastrointestinal tract, pancreas, liver, and other columnar epithelia which collectively resist cloning in their elemental states. Here we demonstrate the cloning of highly immature epithelial stem cells from defined regions of the human intestine and colon. In this study, we have isolated ileal stem cells and performed air-liquid interface method to induce differentiation of human ileal stem cells. The differentiated structure showed villi-like epithelia which contains enterocytes, goblet cells, endocrine cells and paneth cells.

2015-05-29 | GSE66115 | GEO

Strong correlation between air-liquid interface cultures and in vivo transcriptomics of nasal brush biopsy

Project description:Air-liquid interface cultures are extensively used to model chronic respiratory diseases. Comparative transcriptomics between cultured cells and fresh nasal brushings from patients suggests a high degree of correlation.

2020-07-31 | GSE145096 | 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