Human respirovirus 3
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA524147 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8618853.fastq.gz | Fastqsanger.gz | |||
| SRR8861325.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 2 of 2 |
Similar Datasets
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
Project description:Organoid models have been one of the most exciting advancements in stem cell research of the past decade. Here we describe a strategy for directed differentiation of human pluripotent stem cells into distal lung organoids that can be used to model interstitial lung disease, viral infection and human endoderm and lung development. This protocol entails five stages that recapitulate lung development. hPSCs are sequentially specified to definitive endoderm, anterior foregut endoderm, ventral anterior foregut endoderm, lung bud organoids, and finally branching lung organoids that can be maintained, while progressively maturing up to the a stage consistent with the second trimester of human gestation, for more than 180 days. This protocol is conducted in defined, serum-free conditions and does not require lineage-specific reporters or cell purification. We also provide a protocol for the generation of single cell suspensions for single cell RNAseq, and for clearing and 3D light sheet fluorescence imaging.
2023-10-17 | GSE215825 | GEO
Project description:A distal lung organoid model to study interstitial lung disease, viral infection and human lung development.
| PRJNA890673 | ENA
Project description:We established the differentiation method of a limb bud organoid from mouse embryonic stem cells (mESCs) using SFEBq. mESCs-derived limb bud organoid selectively differentiate into forelimb or hindlimb by adjusting the retinoic acids activity. To evaluate a correlation of gene expression between limb bud organoid and embryonic tissues (limb bud, branchial arch, cardiac, and tail bud), we performed comparative transcriptome analysis using RNA-seq.
2019-05-01 | GSE126387 | GEO
Project description:A platform for generating expandable, branching and gene-editable ureteric bud organoid from primary mouse and human ureteric bud progenitor cells and human pluripotent stem cells, and its maturation into collecting duct organoid.
2021-05-11 | GSE149109 | GEO
Project description:Taste stem/progenitor cells from the mouse posterior tongue have been recently used to generate taste bud organoids. However, the inaccessible location of the taste receptor cells is observed in conventional organoids. Here, we established a suspension culture method for fine tuning of taste bud organoid by apicobasal polarity alteration to form the accessible localization of taste receptor cells in organoid. Compared to conventional Matrigel-embedded organoids, suspension-cultured organoids showed comparable differentiation and renewal rates to those of taste buds in vivo and exhibited functional taste receptor cells and cycling progenitor cells. Accessible taste receptor cells on the outer region of taste bud organoids enabled the direct application of calcium imaging for evaluating the taste response. Moreover, suspension-cultured organoids could be genetically altered using gene editing methods. Suspension-cultured taste bud organoid harmoniously integrated with the recipient lingual epithelium; maintained the taste receptor cells and gustatory innervation capacity. Thus, we propose that suspension-cultured organoids may provide efficient model for taste research including taste bud development, regeneration and transplantation
2021-12-25 | GSE191169 | GEO
Project description:The distal lung contains terminal bronchioles and alveoli that facilitate gas exchange. Three-dimensional in vitro human distal lung culture systems would strongly facilitate investigation of pathologies including interstitial lung disease, cancer, and SARS-CoV-2-associated COVID-19 pneumonia. We generated long-term feeder-free, chemically-defined culture of distal lung progenitors as organoids derived from single adult human alveolar epithelial type II (AT2) or KRT5+ basal cells. AT2 organoids exhibited AT1 transdifferentiation potential while basal cell organoids developed lumens lined by differentiated club and ciliated cells. Single cell analysis of basal organoid KRT5+ cells revealed a distinct ITGA6+ITGB4+ mitotic population whose proliferation further segregated to a TNFRSF12Ahi subfraction comprising ~10% of KRT5+ basal cells, residing in clusters within terminal bronchioles and exhibiting enriched clonogenic organoid growth activity. Distal lung organoids were created with apical-out polarity to display ACE2 on the exposed external surface, facilitating SARS-CoV-2 infection of AT2 and basal cultures and identifying club cells as a novel target population. This long-term, feeder-free organoid culture of human distal lung, coupled with single cell analysis, identifies unsuspected basal cell functional heterogeneity and establishes a facile in vitro organoid model for human distal lung infections including COVID-19-associated pneumonia.
2020-11-01 | GSE106850 | GEO
Project description:The lack of a robust system to reproducibly propagate HRV-C substantially hampered our understanding of the common respiratory virus. We sought to develop an organoid-based system to reproducibly propagate HRV-C and characterize virus-host interaction using the respiratory organoids established by our team. We demonstrated that airway organoids sustained serial virus passage with the aid of CYT-387-mediated immunosuppression; nasal organoids, an organoid model more closely simulating the human upper airway, achieved this without any intervention. Nasal organoids were more susceptible to HRV-C than airway organoids. Intriguingly, we observed a more intensive innate immune response in airway organoids than nasal organoids upon HRV-C infection, which was reproduced in a Poly (I:C) stimulation assay. Treatment with an anti-CDHR3 and two antivirals significantly reduced HRV-C viral growth in nasal organoids. An organoid-based immunofluorescence assay was established to titrate HRV-C infectious particles. Collectively, we developed an organoid-based system to reproducibly propagate the previously uncultivable HRV-C, which enabled an in-depth elucidation of HRV-C infection and innate immunity unprecedentedly. The organoid-based HRV-C infection model can be extended for developing antiviral strategies. More importantly, our study has paved a new avenue for propagating and studying other uncultivable human and animal viruses.
2024-11-18 | GSE254400 | GEO
Project description:Genetic diversity of Human parainfluenza virus 3 in Latin America
| PRJNA237303 | ENA
Project description:Human respirovirus 3 neutralizing antibody escape mutants and their fitness
| PRJNA1083633 | ENA