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

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

PROVIDER: PRJNA563878 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10067161.fastq.gz	Fastqsanger.gz
	SRR10067162.fastq.gz	Fastqsanger.gz
	SRR10067163.fastq.gz	Fastqsanger.gz
	SRR10067164.fastq.gz	Fastqsanger.gz
	SRR10067165.fastq.gz	Fastqsanger.gz

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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.

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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.

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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

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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.

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

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

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