ScRNA profiles on hESC-derived lung cells and lung-macrophage co-cultured cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE162996 | GEO | 2022/03/14
REPOSITORIES: GEO
Similar Datasets
Project description:scRNA profiles on hESC-derived lung cells and lung-macrophage co-cultured cells
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Project description:Choroidal atrophy is a common fundus pathological change closely related to the development of age-related macular degeneration (AMD), retinitis pigmentosa, and pathological myopia. Studies suggested that choroidal endothelial cells (CECs) that form the choriocapillaris vessels are the first cells lost in choroidal atrophy. Endothelial cells derived from human pluripotent stem cells (hPSC-ECs) can form blood vessels in vivo and in vitro. We isolated rat choroid and co-cultured with hPSC-ECs. Single-cell RNA-seq (scRNA-seq) studies showed that rat choroid ECs seemed to lose endothelial identity while hPSC-ECs upregulated angiogenesis and hypoxia genes after interacting with choroid.
2024-03-13 | GSE235990 | GEO
Project description:scRNA profiles on hESC-derived lung cells
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Project description:Single-cell RNA-seq (scRNA-seq) on nocodazole and DMSO treated cells before and after differentiation into endoderm. hPSC colonies were treated with DMSO or 100ng/ml nocodazole for 16 hours and induced to differentiate into definitive endoderm for three days. Single cells were subsequently collected in either undifferentiated conditions (Und) or after 3 days of endoderm differentiation (Endoderm) and then sorted onto 384 well plates for Smart-Seq2 processing.
2019-02-09 | E-MTAB-7008 | biostudies-arrayexpress
Project description:Purpose: to analyze change in gene expression of hPSC derived macrophages upon co-culture with hepatic cells including Huh7 and primary human hepatocytes Methods: SMART-seq2 amplified polyA RNA from sorted iMacs in the co-cultures. Results: the transcriptome of iMacs changed after co-culture with Huh7 cells or pHHs, and changed after the HCV infection of the co-cultured Huh7 cells. Conclusions: the gene expression profiles of co-cultured iMacs indicated that the culture conditions and the microenvironments could reprogrammed iMacs to adopt tissue-specific features and perform specifc functions.
2024-05-23 | GSE234572 | GEO
Project description:The development of human pluripotent stem cell (hPSC)- derived small intestinal organoids (HIOs) has led to an improved understanding of human intestinal development and physiology. HIOs generated using directed differentiation lack some cellular populations found in the native organ, including vasculature. We performed single cell RNA sequencing (scRNA-seq) on approximately 13,000 cells at various timepoints (0, 3, 7, and 14 days) across HIO in vitro development and observed a transient population of endothelial-like cells (ECs) present within HIOs early during differentiation. Our data demonstrate that EC-like cells fail to be robustly maintained in long term culture. Here, we have developed a new directed differentiation approach to enhance co-differentiation and maintenance of ECs within HIOs, leading to the development of vascularized HIOs (vHIOs). scRNAseq was used to compare vHIOs to control HIOs after 59d months in culture.
2020-12-20 | E-MTAB-9228 | biostudies-arrayexpress
Project description:Gene expression analysis of hPSC derived macrophages (iMacs) co-cultured with hepatic cells
| PRJNA982074 | ENA
Project description:To mimic more realistic lung tissue conditions, co-cultures of epithelial and immune cells are one comparatively easy-to-use option. To reveal the impact of immune cells on the mode of action (MoA) of CuO nanoparticles (NP) on epithelial cells, A549 cells as a model for epithelial cells have been cultured with or without differentiated THP-1 cells, as a model for macrophages. After 24 h of submerged incubation, cytotoxicity and transcriptional toxicity profiles were obtained and compared between the cell culture systems. Dose-dependent cytotoxicity was apparent starting from 8.0 µg/cm2 CuO NP. With regard to gene expression profiles, no differences between the cell models were observed concerning metal homeostasis, oxidative stress, and DNA damage, confirming the known MoA of CuO NP, i.e., endocytotic particle uptake, intracellular particle dissolution within lysosomes with subsequent metal ion deliberation, increased oxidative stress, and genotoxicity. However, applying a co-culture of epithelial and macrophage-like cells, CuO NP additionally provoked a pro-inflammatory response involving NLRP3 inflammasome and pro-inflammatory transcription factor activation. This study demonstrates that the application of this easy-to-use advanced in vitro model is able to extend the detection of cellular effects provoked by nanomaterials by an immunological response and emphasizes the use of such models to address a more comprehensive MoA.
| S-EPMC8126233 | biostudies-literature
Project description:A comprehensive understanding of the human pluripotent stem cell (hPSC) differentiation process stands as a prerequisite for the development hPSC-based therapeutics. In this study, single-cell RNA-sequencing (scRNA-seq) was performed to decipher the heterogeneity during differentiation of three hPSC lines towards corneal limbal stem cells (LSCs). The scRNA-seq data revealed the presence of nine clusters, among which five clusters followed the anticipated differentiation path of LSCs. The remaining four clusters were linked to previously undescribed cell states that were annotated as either mesodermal or undifferentiated subpopulations, and their prevalence was hPSC line-dependent. Distinct cluster-specific marker genes identified in this study were confirmed by immunofluorescence analysis and employed to purify hPSC-derived LSCs, which effectively minimized the variation in the line-dependent differentiation efficiency. In summary, scRNA-seq offered molecular insights into the heterogeneity of hPSC-LSC differentiation, allowing a data-driven strategy to be adopted for consistent and robust generation of LSCs, essential for future advancement toward clinical translation.
2024-06-26 | GSE248496 | GEO
Project description:Underdeveloped lungs are the primary cause of death in premature infants, however, little is known about stem and progenitor cell maintenance during human lung development. In this study, we have identified that FGF7, Retinoic Acid and CHIR-99021, a small molecule that inhibits GSK3 to activate Wnt signaling, support in vitro maintenance of primary human fetal lung bud tip progenitor cells in a progenitor state. Furthermore, these factors are sufficient to derive a population of human bud tip-like progenitor cells in 3D organoid structures from human pluripotent stem cells (hPSC). Functional studies showed that hPSC-derived bud tip progenitor organoids do not contain any mesenchymal cell types, maintain multilineage potential in vitro and are able to engraft into the airways of injured mice and respond to systemic factors. We performed RNA-sequencing to assess the degree of similarity in global gene expression profiles between the full human fetal lung (59-127 days gestation), isolated human fetal bud tip progenitors, organoids grown from primary fetal bud tip progenitors, and hPSC-derived bud tip organoids. Results showed that hPSC-derived organoids have molecular profiles similar to organoids generated from primary human fetal lung tissue. Gene expression differences between hPSC-derived bud tip organoids and fetal progenitor organoids may be related to the presence of contaminating mesenchymal cells in primary cultures. hPSC-derived bud tip organoids are generated from a well-defined human cell sources, offering a distinct advantage over rare primary tissue as a means to study human specific lung development, homeostasis and disease.<br>Sample Nomenclature - Description<br> -------------------------------------------------------------------------<br> Peripheral fetal lung the distal/peripheral portion of the fetal lung (i.e., distal 0.5 cm) was excised from the rest of the lung using a scalpel. This includes all components of the lung (e.g., epithelial, mesenchymal, vascular). <br>Isolated fetal bud tip the bud peripheral portion of the fetal lung was excised with a scalpel and subjected to enzymatic digestion and microdissection. The epithelium was dissected and separated from the mesenchyme, but a small amount of associated mesenchyme likely remained. <br>Fetal progenitor organoid 3D organoid structures that arose from culturing isolated fetal epithelial bud tips. <br>Foregut spheroid 3D foregut endoderm structure as described in Dye et al. (2015). Gives rise to patterned lung organoid (PLO) when grown in 3F medium. <br> Patterned lung organoid (PLO) lung organoids that were generated by differentiating hPSCs, as described throughout the manuscript. <br> Bud tip organoid organoids derived from PLOs, enriched for SOX2/SOX9 co-expressing cells, and grown/passaged in 3F medium.
2018-11-17 | E-MTAB-6023 | biostudies-arrayexpress