Virus Dataset Detail

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Dataset Information
Accession GSE197949
Status 2022/7/8
Title Human alveolar progenitors generate dual lineage bronchioalveolar organoids
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Mechanisms of epithelial renewal in the alveolar compartment remain incompletely understood. To this end, we aimed to characterize alveolar progenitors. Single-cell RNA-seq (scRNA-seq) analysis of the HTII-280 positive and HTII-280+ /EpCAM+populations from total 6 donors from periferal tissue was performed, and analysis revealed subclusters enriched for stem cell signature genes. We found that these alveolar progenitors in organoid culture in vitro show phenotypic lineage plasticity as they can yield alveolar or bronchial cell type progeny. The direction of the differentiation is dependent on the presence of the GSK-3β inhibitor, CHIR99021. By RNA-seq analysis of GSK-3 βknockdown organoids, we identify additional functional candidate target genes and pathways which contribute to alveolar differentiation independent of Wnt signaling
Samples
GSM ID Sample info Characteristics Description
GSM5934385 AO13_pool_batch1_control tissue:bronchial organoid; batch:1; treatment:control single-cell polyA RNA;organoids_pool.rds
GSM5934386 AO13_pool_batch2_control tissue:bronchial organoid; batch:1; treatment:control single-cell polyA RNA;organoids_pool.rds
GSM5934387 AO15_HT2_16h_control tissue:alveolar organoid; batch:3; treatment:control single-cell polyA RNA;organoids_all.rds;organoids_HT2.rds
GSM5934388 AO15_HT2_16h_H3N2 tissue:alveolar organoid; batch:3; treatment:IAV-infection single-cell polyA RNA;organoids_all.rds
GSM5934389 AO15_pool_16h_control tissue:bronchial organoid; batch:3; treatment:control single-cell polyA RNA;organoids_all.rds;organoids_pool.rds
GSM5934390 AO15_pool_16h_H3N2 tissue:bronchial organoid; batch:3; treatment:IAV-infection single-cell polyA RNA;organoids_all.rds
GSM5934391 AO15_pool_batch2_control tissue:bronchial organoid; batch:2; treatment:control single-cell polyA RNA;organoids_pool.rds
GSM5934392 AO16_HT2_16h_control tissue:alveolar organoid; batch:4; treatment:control single-cell polyA RNA;organoids_all.rds
GSM5934393 AO16_HT2_16h_H3N2 tissue:alveolar organoid; batch:4; treatment:IAV-infection single-cell polyA RNA;organoids_all.rds
GSM5934394 AO16_pool_16h_control tissue:bronchial organoid; batch:4; treatment:control single-cell polyA RNA;organoids_all.rds;organoids_pool.rds
GSM5934395 AO16_pool_16h_H3N2 tissue:bronchial organoid; batch:4; treatment:IAV-infection single-cell polyA RNA;organoids_all.rds
GSM5934396 AO18_pool_batch1_control tissue:bronchial organoid; batch:1; treatment:control single-cell polyA RNA;organoids_pool.rds
GSM5934397 AO22_HT2_16h_control tissue:alveolar organoid; batch:4; treatment:control single-cell polyA RNA;organoids_all.rds
GSM5934398 AO22_HT2_16h_H3N2 tissue:alveolar organoid; batch:4; treatment:IAV-infection single-cell polyA RNA;organoids_all.rds
GSM5934399 AO22_HT280 tissue:HT280+ cells; treatment:control single-cell polyA RNA;HT280_Epcam.rds
GSM5934400 AO22_pool_16h_control tissue:bronchial organoid; batch:4; treatment:control single-cell polyA RNA;organoids_all.rds;organoids_pool.rds
GSM5934401 AO22_pool_16h_H3N2 tissue:bronchial organoid; batch:4; treatment:IAV-infection single-cell polyA RNA;organoids_all.rds
GSM5934402 AO23_HT280 tissue:HT280+ cells; treatment:control single-cell polyA RNA;HT280_Epcam.rds
GSM5934403 AO34_HT280_Epcam tissue:HT280+/Epcam+ cells; treatment:control single-cell polyA RNA;HT280_Epcam.rds
GSM5934404 AO35_HT280_Epcam tissue:HT280+/Epcam+ cells; treatment:control single-cell polyA RNA;HT280_Epcam.rds
GSM5934405 AO36_HT280_Epcam tissue:HT280+/Epcam+ cells; treatment:control single-cell polyA RNA;HT280_Epcam.rds
GSM5934406 AO37_HT280_Epcam tissue:HT280+/Epcam+ cells; treatment:control single-cell polyA RNA;HT280_Epcam.rds
GSM5934407 ctrl_CHIR_1 tissue:alveolar organoid; batch:1; treatment:shctrl_CHIR bulk polyA RNA
GSM5934408 GSK3kd_ctrl_1 tissue:alveolar organoid; batch:1; treatment:shGSK3hp1_ctrl bulk polyA RNA
GSM5934409 GSK3kd_ctrl_2 tissue:alveolar organoid; batch:2; treatment:shGSK3hp2_ctrl bulk polyA RNA
GSM5934410 GSK3kd_CHIR_2 tissue:alveolar organoid; batch:2; treatment:shGSK3hp2_CHIR bulk polyA RNA
GSM5934411 ctrl_ctrl_1 tissue:alveolar organoid; batch:1; treatment:shctrl_ctrl bulk polyA RNA
GSM5934412 ctrl_CHIR_2 tissue:alveolar organoid; batch:2; treatment:shctrl_CHIR bulk polyA RNA
GSM5934413 GSK3kd_CHIR_1 tissue:alveolar organoid; batch:1; treatment:shGSK3hp1_CHIR bulk polyA RNA
GSM5934414 ctrl_ctrl_2 tissue:alveolar organoid; batch:2; treatment:shctrl_ctrl bulk polyA RNA
Platform GPL18573  : Illumina NextSeq 500 (Homo sapiens)
Literature 36008580  
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scRNA-seq UMAP