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Bulk RNA-seq on human pluripotent stem cell-derived type 2 alveolar cell-like cells

ABSTRACT: Bulk RNA-seq on human pluripotent stem cell-derived type 2 alveolar cell-like cells

PROVIDER: PRJNA640646 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12055560.fastq.gz	Fastqsanger.gz
	SRR12055561.fastq.gz	Fastqsanger.gz
	SRR12055562.fastq.gz	Fastqsanger.gz
	SRR12055563.fastq.gz	Fastqsanger.gz
	SRR12055564.fastq.gz	Fastqsanger.gz

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Bulk RNA-seq on human pluripotent stem cell-derived type 2 alveolar cell-like cells

Project description:We reportWe used bulk RNA sequencing technology to profile gene expression in human pluripotent stem cell-derived type 2 alveolar cell-like cells. By obtaining over 15,000 genes, we compared the derived alveolar cell-like cells to H9 embryonic stem cells. We found significant down-regulation of several pluripotency genes whereas activation of lung or alveolus marker genes, and thus suggested successful induction. We treated the derived cells with nano carbon black and sequenced the samples in order to obtain differentially expressed genes due to the treatment. From KEGG analysis, we concluded that expression of most genes inferring lung or alveolus identities were not affected by the treatment. However, pathways such as chemical carcinogenesis and xenobiotic metabolism were significantly promoted. Finally, since organoid culture is trendy, we compared monolayer-derived alveolar cell-like cells to organoid-based derived ones. Results showed overall similarity in gene expression yet organoid culture yielded morphologically and structurally better cells. This study uses bulk RNA sequencing to confirm the alveolar induction from human pluripotent stem cells and provides insights for nano carbon black toxicities in alveolar cells.

2023-06-15 | GSE152854 | GEO

Single-Cell RNA Sequencing Reveals Human iPS Cell-derived Alveolar Type 1 Cells in Alveolar Organoids

Project description:Human induced pluripotent stem cells (hiPSCs) were differentiated into alveolar epithelial cells in the fibroblast-dependent (FD) or fibroblast-free (FF) alveolar organoids (AO). Then the epithelial cells in FD-AOs or FF-AOs were subjected to scRNA-seq. Then, human iPSC-derived AT1 (iAT1) cells were demonstrated to be included in FD-AOs, not in FF-AOs. In addition, XAV-939 increased iAT1 cell population in FD-AOs.

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Project description:We performed bulk transcriptomic profiling of pluripotent stem cell-derived alveolar type 2 cells (iAT2s) and HTII-280-sorted human AT2s cultured with CK+DCI media. We used previously described distal lung directed differentiation protocol to generate alveolar type 2 cells (iAT2s). We used the SPC2-ST-B2 (“SPC2”) line containing a SFTPC-tdTomato knock in reporter. iAT2s were cultured in 3D spheres and at air-liquid interface. Human AT2s were HTII-280-sorted from a pediatric donor lung (13 months old) and an adult, nonsmoker human lung (32 years old) and cultured as spheres in the presence of MRC5s. After deconvolution, we find that iAT2s cultured in ALI correlate more closely to primary cultured AT2s than do iAT2s cultured in 3D spheres on the basis of lung epithelial gene expression.

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