An integrated transcriptomic cell atlas of human endoderm-derived organoids
Cite
Xu, Q., Halle, L., Hediyeh-zadeh, S., Kuijs, M., Kilik, U., Yu, Q., Frum, T., Adam, L., Parikh, S., Gander, M. and Kfuri-Rubens, R., 2023. An integrated transcriptomic cell atlas of human endoderm-derived organoids. bioRxiv, pp.2023-11. https://doi.org/10.1038/s41588-025-02182-6
Abstract
Human stem cells can generate complex, multicellular epithelial tissues of endodermal origin in vitro that recapitulate aspects of developing and adult human physiology. These tissues, also called organoids, can be derived from pluripotent stem cells or tissue-resident fetal and adult stem cells. However, it has remained difficult to understand the precision and accuracy of organoid cell states through comparison with primary counterparts, and to comprehensively assess the similarity and differences between organoid protocols. Advances in computational single-cell biology now allow the integration of datasets with high technical variability. Here, we integrate single-cell transcriptomes from 218 samples covering organoids of diverse endoderm-derived tissues including lung, pancreas, intestine, liver, biliary system, stomach, and prostate to establish an initial version of a human endoderm organoid cell atlas (HEOCA). The integration includes nearly one million cells across diverse conditions, data sources and protocols. We align and compare cell types and states between organoid models, and harmonize cell type annotations by mapping the atlas to primary tissue counterparts. To demonstrate utility of the atlas, we focus on intestine and lung, and clarify ontogenic cell states that can be modeled in vitro. We further provide examples of mapping novel data from new organoid protocols to expand the atlas, and showcase how integrating organoid models of disease into the HEOCA identifies altered cell proportions and states between healthy and disease conditions. The atlas makes diverse datasets centrally available, and will be valuable to assess organoid fidelity, characterize perturbed and diseased states, and streamline protocol development.
Datasets
1. human endoderm organoid cell atlas
ExploreSubject ID
Tissue type
Sample ID
Sample source
Sample name
Stem cell source
Tissue (detail)
Timepoint
Protocol
Molecular
Del
Cell type (level 1)
Cell type
Assay
Disease
Sex
Tissue
Leiden clustering
Zeve_NatCommun_2022_EEC_enriched_Organoids14,688 cells Kadur_Nat_2022_LO_Control13,017 cells Augsornworawat_NatCellBio_2023_GSM5979673_week212,080 cells Sarvestani_NatCommun_2021_NL33_iHNO11,428 cells Tran_iScience_2022_GSE164514_AEC_3D10,943 cells Kadur_Nat_2022_LO_EGF_depletion10,909 cells Miller_DevCell_2020_Day_010,765 cells Yoon_NatCommun_2022_salivary_gland_organoids10,505 cells He_Cell_2022_deltaNp63alpha_overexpression10,073 cells Miller_DevCell_2020_Day_39,781 cells Guan_NatCommun_2021_Control_C249,429 cells He_Cell_2022_RFX6_overexpression9,366 cells Augsornworawat_NatCellBio_2023_GSM5979665_scislet19,315 cells Holloway_DevCell_2020_HIO_control_59d9,268 cells He_Cell_2022_PAX9_overexpression9,126 cells Kadur_Nat_2022_LO_Serum_treatement9,004 cells He_Cell_2022_TFAP2A_overexpression8,805 cells Sung_NO_2020_GSM4654340_TNF_free8,756 cells He_Cell_2022_NEUROG3_overexpression8,538 cells Sarvestani_NatCommun_2021_CRL1541_iHNO8,525 cells Rosado_BioRxiv_2021_GSM4984050_LungOD78,462 cells Lim_CellStemCell_2023_Lung_organoid_epithelium8,272 cells Holloway_DevCell_2020_vHIO_59d8,167 cells Augsornworawat_NatCellBio_2023_GSM6571152_month68,082 cells Augsornworawat_NatCellBio_2023_GSM6571154_month127,909 cells Augsornworawat_NatCellBio_2023_GSM5979667_scislet27,848 cells Augsornworawat_NatCellBio_2023_GSM5979675_week37,700 cells Hoffmann_CommunBiol_2022_AO15_pool_16h_control7,039 cells Sarvestani_NatCommun_2021_NL34_iHNO6,574 cells Thispaper_Thispaper_2023_stomach_corpus_organoids5,955 cells He_Cell_2022_wild_type_genotype5,951 cells Augsornworawat_NatCellBio_2023_GSM5979677_week45,743 cells Lim_CellStemCell_2023_Lung_alveolar_organoid_epithelium5,681 cells He_Cell_2022_NEUROD1_overexpression5,529 cells Han_Nat_2021_GSM4451223_hPSC_CO5,516 cells Wiedenmann_NatBME_2021_day135,427 cells Yan_Gut_2020_H019_NOd5,406 cells McCray_AJCEU_2019_Organoid5,375 cells Yoon_NatCommun_2022_salivary_gland_organoids_latepassages5,291 cells McCauley_CMGH_2023_HIO1A_with_EECs5,286 cells Yan_Gut_2020_H019_NO5,277 cells Velazquez_CellSyst_2021_GSM4830979_DesLO_D175,260 cells McCauley_CMGH_2023_HIO1B_with_EECs5,135 cells Elmentaite_DevCell_2020_WNT3Aneg_2206_p2_RSPO5,095 cells Velazquez_CellSyst_2021_GSM4830978_FeLO_D174,972 cells Hoffmann_CommunBiol_2022_AO15_HT2_16h_control4,767 cells Holloway_DevCell_2020_HIO_control_14d4,657 cells Li_StemCR_2020_Stage64,653 cells Charlie_JCI_2023_hfDO_EREG4,521 cells Holloway_DevCell_2020_HIO_control_3d4,417 cells Yan_Gut_2020_H011_NO4,398 cells Augsornworawat_NatCellBio_2023_GSM5979685_txpscislet24,392 cells Sung_NO_2020_GSM4654341_TNF_treat4,369 cells Li_StemCR_2020_Stage54,341 cells Thispaper_Thispaper_2023_fetal_liver_organoids4,338 cells Ouchi_CellMet_2019_Human_liver_organoids4,297 cells Bein_FPhar_2021_all4,261 cells Lamers_EMBOJ_2021_Lung_Bronchioalveolar4,180 cells Blutt_LiverPhys_2021_GSM5075992_HLO24,146 cells Sampaziotis_Science_2021_ORG_CBD_14,119 cells Wiedenmann_NatBME_2021_day144,092 cells Capeling_CellRep_2022_Day14_HIO_EGF_algenate4,083 cells Chan_NatCommun_2022_bronchial_organoids4,073 cells Charlie_JCI_2023_hfDO_EGF4,065 cells He_Cell_2022_ASCL1_overexpression4,011 cells Sampaziotis_Science_2021_ORG_GB_14,007 cells Blutt_LiverPhys_2021_GSM5075993_HLO33,997 cells Capeling_CellRep_2022_Day14_HIO_ENR_algenate3,955 cells Thispaper_Thispaper_2023_UK_Duo893,954 cells Fujii_CellStemCell_2018_hSMO_SB3,786 cells Sampaziotis_Science_2021_ORG_IHD_23,716 cells Elmentaite_DevCell_2020_p1_TIp120383,672 cells Chan_NatCommun_2022_nasopharyngeal_organoids3,576 cells Zhang_JH_2023_PaDLOC_Tenofovir3,575 cells Zhang_JH_2023_PaDLOC_Fialuridine3,487 cells Zhang_JH_2023_PaDLOC_Acetaminophen3,469 cells Zhang_JH_2023_PaDLOC_Tenofovir_InarigivirSoproxil3,457 cells Capeling_CellRep_2022_Day7_HIO_EGF_algenate3,372 cells Kilik_BioRxiv_2021_UK_HIO_NRG13,339 cells Miller_DevCell_2020_Day_213,236 cells Blutt_LiverPhys_2021_GSM5075991_HLO13,223 cells Elmentaite_DevCell_2020_p1_TIp120393,217 cells Sampaziotis_Science_2021_ORG_IHD_13,210 cells Thispaper_Thispaper_2023_suspension_HIO_derived_tHIO3,105 cells Triana_MSB_2021b_Ileum_Organoids_Rev_M3,086 cells Ogawa_NatCommun_2021_GSM5335529_3D_cholangiocyte3,062 cells Thispaper_Thispaper_2023_UK_R5_Duo81_hum_enteroids3,035 cells Hoffmann_CommunBiol_2022_AO16_pool_16h_control2,984 cells Hein_Dev_2022_10_week_iBTO2,950 cells Hoffmann_CommunBiol_2022_AO22_pool_16h_control2,945 cells Fujii_CellStemCell_2018_hSMO_IF2,904 cells Holloway_CellStemCell_2021_hITD_EGF_day132_S882,901 cells Holloway_CellStemCell_2021_hITD_EGF_day132_S902,895 cells Holloway_CellStemCell_2021_hITD_EGF_day132_S912,891 cells Holloway_CellStemCell_2021_hITD_EGF_day132_S892,882 cells Holloway_CellStemCell_2021_hITD_EGF_day105_S42,847 cells Lee_NatCommun_2021A_GSM5399380_GO2,806 cells Hein_Dev_2022_3_week_LPO_Batch22,804 cells Li_StemCR_2020_Stage42,802 cells Holloway_CellStemCell_2021_hITD_EGF_day105_S12,796 cells Kilik_BioRxiv_2021_UK_HIO_EGF2,788 cells Holloway_CellStemCell_2021_hITD_EGF_day105_S22,788 cells Holloway_CellStemCell_2021_hITD_EGF_day105_S32,777 cells Zhang_JH_2023_HLO_Control2,771 cells Hein_Dev_2022_3_week_LPO_Batch12,770 cells Mithal_NatCommun_2020_endodermal_progenitor_day132,744 cells Thispaper_Thispaper_2023_stomach_antrum_organoids2,697 cells Holloway_CellStemCell_2021_hITD_NRG1_day105_S172,624 cells Suzuki_STARProt_2021_LungO_BU3_NGPT_Basal_Cell_Medium_12,613 cells Salahudeen_Nat_2020_GSM2855485_Purified_AT22,560 cells Holloway_CellStemCell_2021_hITD_NRG1_day105_S202,556 cells Holloway_DevCell_2020_HIO_control_7d2,544 cells Holloway_CellStemCell_2021_hITD_NRG1_day105_S192,494 cells Holloway_CellStemCell_2021_hITD_NRG1_day105_S182,478 cells Holloway_CellStemCell_2021_hITD_NRG1_day132_S942,415 cells Holloway_CellStemCell_2021_hITD_NRG1_day132_S922,393 cells Holloway_CellStemCell_2021_hITD_NRG1_day132_S952,368 cells Holloway_CellStemCell_2021_hITD_NRG1_day132_S932,335 cells Sampaziotis_Science_2021_ORG_GB_T1_22,327 cells Sampaziotis_Science_2021_ORG_GB_22,241 cells Suzuki_STARProt_2021_LungO_BU3_NGPT_Basal_Cell_Medium_22,230 cells Sampaziotis_Science_2021_ORG_IHD_T1_12,197 cells Elmentaite_DevCell_2020_WNT3Apos_2206_p2_WNT3A2,190 cells Capeling_CellRep_2022_Day7_HIO_ENR_algenate2,116 cells Holloway_CellStemCell_2021_hITD_EGFNRG1_day105_S162,112 cells Holloway_CellStemCell_2021_hITD_EGFNRG1_day105_S152,097 cells Holloway_CellStemCell_2021_hITD_EGFNRG1_day105_S142,076 cells Holloway_CellStemCell_2021_hITD_EGFNRG1_day105_S132,028 cells Mithal_NatCommun_2020_endodermal_progenitor_day62,018 cells Beumer_Cell_2020_Ile2,003 cells Yan_Gut_2020_H011_NOd1,974 cells Triana_MSB_2021b_Ileum_Organoids_Sort_Mock1,974 cells Wesley_NatCellBio_2022_Hepatoblast_organoids_treated_with_hepatozyme1,954 cells Triana_MSB_2021_Ileum_organoids_Mock1,953 cells Lee_NatCommun_2021B_GSM5399379_LBO1,947 cells Salahudeen_Nat_2020_GSM2855475_Lung_1_21,945 cells Salahudeen_Nat_2020_GSM2855477_Lung_1_41,938 cells Hein_Dev_2022_Spheroids1,924 cells Augsornworawat_NatCellBio_2023_GSM5979683_txpscislet11,857 cells Hoffmann_CommunBiol_2022_AO22_HT2_16h_control1,842 cells Salahudeen_Nat_2020_GSM2855474_Lung_1_11,811 cells Zhang_JH_2023_PaDLOC_Control1,792 cells Salahudeen_Nat_2020_GSM2855476_Lung_1_31,774 cells He_CellStemCell_2022_hSIO_IL22neg1,766 cells Sampaziotis_Science_2021_ORG_CBD_21,763 cells Hein_Dev_2022_6_week_LPO_Batch11,717 cells Wesley_NatCellBio_2022_Fetal_biliary_organoids1,714 cells Beumer_CellRep_2022_all1,671 cells Elmentaite_DevCell_2020_p17_p1720391,670 cells Hein_Dev_2022_4_week_iBTO1,649 cells Romitti_NatCommun_2022_Human_Thyroid_Organoid1,563 cells Triana_MSB_2021_Colon_organoids_Mock1,558 cells Sampaziotis_Science_2021_ORG_CBD_T2_41,548 cells Wesley_NatCellBio_2022_Hepatoblast_organoids1,548 cells Beumer_Cell_2020_Duo1,488 cells Sampaziotis_Science_2021_ORG_CBD_T2_11,468 cells Sampaziotis_Science_2021_ORG_IHD_T2_11,457 cells Sampaziotis_Science_2021_ORG_GB_T2_31,456 cells Thispaper_Thispaper_2023_UK_R6_Duo87_hum_enteroids1,454 cells Romitti_NatCommun_2022_Human_Thyroid_Organoid_day581,436 cells Suzuki_STARProt_2021_LungO_BU3_NGPT_FGF210DCIY_11,405 cells Suzuki_STARProt_2021_LungO_BU3_NGPT_FGF210DCIY_21,311 cells Aizarani_Nat_2019_all1,284 cells Salahudeen_Nat_2020_GSM2855481_Lung_2_41,248 cells Capeling_CellRep_2022_Day3_HIO_alginate1,227 cells Hein_Dev_2022_6_week_LPO_Batch21,200 cells Salahudeen_Nat_2020_GSM2855480_Lung_2_31,195 cells He_CellStemCell_2022_hSIO_IL22pos1,191 cells Salahudeen_Nat_2020_GSM2855478_Lung_2_11,163 cells Roos_CellStemCell_2022_ICO1,113 cells Salahudeen_Nat_2020_GSM2855479_Lung_2_21,111 cells Triana_MSB_2021b_Ileum_Organoids_H4_Live21,078 cells Elmentaite_DevCell_2020_p17_p1720381,037 cells Hein_Dev_2022_10_week_LPO1,020 cells Triana_MSB_2021b_Ileum_Organoids_N_Mock1,014 cells Holloway_DevCell_2020_HIO_control_0d948 cells Augsornworawat_NatCellBio_2023_GSM5979687_txpscislet3899 cells Aguilar_NatCommun_2022_C8811 cells Aguilar_NatCommun_2022_C9762 cells Salahudeen_Nat_2020_GSM2855482_Lung_3_1747 cells Wiedenmann_NatBME_2021_day31_300cells743 cells Triana_MSB_2021b_Ileum_Organoids_Ns_Mock735 cells Roos_CellStemCell_2022_BRCO725 cells Salahudeen_Nat_2020_GSM2855483_Lung_3_2706 cells Beumer_Cell_2020_Col658 cells Wiedenmann_NatBME_2021_day23616 cells Wiedenmann_NatBME_2021_day31_600cells590 cells Wiedenmann_NatBME_2021_day16576 cells Aguilar_NatCommun_2022_A1524 cells Wiedenmann_NatBME_2021_day20488 cells Wiedenmann_NatBME_2021_day27465 cells Salahudeen_Nat_2020_GSM2855484_Lung_3_3464 cells Palikuqi_Nat_2020_GSM4487132_Sample1D449 cells Hoffmann_CommunBiol_2022_AO16_HT2_16h_control410 cells Triana_MSB_2021b_Ileum_Organoids_Ns_NMock_2341 cells Triana_MSB_2021b_Ileum_Organoids_Ns_NMock_1302 cells Hu_Cell_2018B_Human_Chol_Orgs234 cells Camp_Nat_2017_LB172 cells Hu_Cell_2018A_Human_Hep_Orgs148 cells Zeve_NatCommun_2022_EEC_enriched_Organoids14,688 cells Kadur_Nat_2022_LO_Control13,017 cells Augsornworawat_NatCellBio_2023_GSM5979673_week212,080 cells Sarvestani_NatCommun_2021_NL33_iHNO11,428 cells Tran_iScience_2022_GSE164514_AEC_3D10,943 cells Kadur_Nat_2022_LO_EGF_depletion10,909 cells Miller_DevCell_2020_Day_010,765 cells Yoon_NatCommun_2022_salivary_gland_organoids10,505 cells He_Cell_2022_deltaNp63alpha_overexpression10,073 cells Miller_DevCell_2020_Day_39,781 cells Guan_NatCommun_2021_Control_C249,429 cells He_Cell_2022_RFX6_overexpression9,366 cells Augsornworawat_NatCellBio_2023_GSM5979665_scislet19,315 cells Holloway_DevCell_2020_HIO_control_59d9,268 cells He_Cell_2022_PAX9_overexpression9,126 cells Yu_Cell_2021_H9_HIO_1EGF_100NRG1_D409,107 cells Kadur_Nat_2022_LO_Serum_treatement9,004 cells He_Cell_2022_TFAP2A_overexpression8,805 cells Sung_NO_2020_GSM4654340_TNF_free8,756 cells He_Cell_2022_NEUROG3_overexpression8,538 cells Sarvestani_NatCommun_2021_CRL1541_iHNO8,525 cells Rosado_BioRxiv_2021_GSM4984050_LungOD78,462 cells Lim_CellStemCell_2023_Lung_organoid_epithelium8,272 cells Holloway_DevCell_2020_vHIO_59d8,167 cells Augsornworawat_NatCellBio_2023_GSM6571152_month68,082 cells Augsornworawat_NatCellBio_2023_GSM6571154_month127,909 cells Augsornworawat_NatCellBio_2023_GSM5979667_scislet27,848 cells Augsornworawat_NatCellBio_2023_GSM5979675_week37,700 cells Yu_Cell_2021_H9_HIO_0EGF_100NRG1_D407,451 cells Hoffmann_CommunBiol_2022_AO15_pool_16h_control7,039 cells Sarvestani_NatCommun_2021_NL34_iHNO6,574 cells Thispaper_Thispaper_2023_H9_22d_tHIO_8wk_kidneycapsule_HIOEC6,381 cells Thispaper_Thispaper_2023_H9_22d_tHIO_8wk_kidneycapsule_control6,345 cells Yu_Cell_2021_H9_HIO_100EGF_1NRG1_D406,114 cells Thispaper_Thispaper_2023_stomach_corpus_organoids5,955 cells He_Cell_2022_wild_type_genotype5,951 cells Augsornworawat_NatCellBio_2023_GSM5979677_week45,743 cells Lim_CellStemCell_2023_Lung_alveolar_organoid_epithelium5,681 cells He_Cell_2022_NEUROD1_overexpression5,529 cells Han_Nat_2021_GSM4451223_hPSC_CO5,516 cells Wiedenmann_NatBME_2021_day135,427 cells Yan_Gut_2020_H019_NOd5,406 cells McCray_AJCEU_2019_Organoid5,375 cells Yoon_NatCommun_2022_salivary_gland_organoids_latepassages5,291 cells McCauley_CMGH_2023_HIO1A_with_EECs5,286 cells Yu_Cell_2021_H9_HIO_ENR_D145,281 cells Yan_Gut_2020_H019_NO5,277 cells Velazquez_CellSyst_2021_GSM4830979_DesLO_D175,260 cells McCauley_CMGH_2023_HIO1B_with_EECs5,135 cells Elmentaite_DevCell_2020_WNT3Aneg_2206_p2_RSPO5,095 cells Yu_Cell_2021_H9_HIO_ENR_alginate_D285,093 cells Velazquez_CellSyst_2021_GSM4830978_FeLO_D174,972 cells Capeling_CellRep_2022_h9_HIO_Suspension_EGF_28days4,833 cells Hoffmann_CommunBiol_2022_AO15_HT2_16h_control4,767 cells Holloway_DevCell_2020_HIO_control_14d4,657 cells Li_StemCR_2020_Stage64,653 cells Charlie_JCI_2023_hfDO_EREG4,521 cells Yu_Cell_2021_H9_HIO_0EGF_0NRG1_D404,453 cells Holloway_DevCell_2020_HIO_control_3d4,417 cells Yan_Gut_2020_H011_NO4,398 cells Augsornworawat_NatCellBio_2023_GSM5979685_txpscislet24,392 cells Sung_NO_2020_GSM4654341_TNF_treat4,369 cells Li_StemCR_2020_Stage54,341 cells Thispaper_Thispaper_2023_fetal_liver_organoids4,338 cells Ouchi_CellMet_2019_Human_liver_organoids4,297 cells Bein_FPhar_2021_all4,261 cells Yu_Cell_2021_H9_HIO_100EGF_0NRG1_D404,185 cells Yu_Cell_2021_H9_HIO_EGF_alginate_D284,184 cells Lamers_EMBOJ_2021_Lung_Bronchioalveolar4,180 cells Thispaper_Thispaper_2023_H9_22d_tHIO_8wk_mesentery_control4,178 cells Blutt_LiverPhys_2021_GSM5075992_HLO24,146 cells Sampaziotis_Science_2021_ORG_CBD_14,119 cells Yu_Cell_2021_H9_HIO_EGF_matrigel_D284,092 cells Wiedenmann_NatBME_2021_day144,092 cells Capeling_CellRep_2022_Day14_HIO_EGF_algenate4,083 cells Chan_NatCommun_2022_bronchial_organoids4,073 cells Charlie_JCI_2023_hfDO_EGF4,065 cells He_Cell_2022_ASCL1_overexpression4,011 cells Sampaziotis_Science_2021_ORG_GB_14,007 cells Blutt_LiverPhys_2021_GSM5075993_HLO33,997 cells Capeling_CellRep_2022_Day14_HIO_ENR_algenate3,955 cells Thispaper_Thispaper_2023_UK_Duo893,954 cells Thispaper_Thispaper_2023_H9_22d_tHIO_8wk_mesentery_HIOEC3,839 cells Fujii_CellStemCell_2018_hSMO_SB3,786 cells Sampaziotis_Science_2021_ORG_IHD_23,716 cells Elmentaite_DevCell_2020_p1_TIp120383,672 cells Chan_NatCommun_2022_nasopharyngeal_organoids3,576 cells Zhang_JH_2023_PaDLOC_Tenofovir3,575 cells Zhang_JH_2023_PaDLOC_Fialuridine3,487 cells Zhang_JH_2023_PaDLOC_Acetaminophen3,469 cells Zhang_JH_2023_PaDLOC_Tenofovir_InarigivirSoproxil3,457 cells Yu_Cell_2021_H9_HIO_ENR_D283,430 cells Capeling_CellRep_2022_Day7_HIO_EGF_algenate3,372 cells Kilik_BioRxiv_2021_UK_HIO_NRG13,339 cells Yu_Cell_2021_H9_tHIO_WK43,335 cells Miller_DevCell_2020_Day_213,236 cells Blutt_LiverPhys_2021_GSM5075991_HLO13,223 cells Elmentaite_DevCell_2020_p1_TIp120393,217 cells Sampaziotis_Science_2021_ORG_IHD_13,210 cells Yu_Cell_2021_H9_HIO_ENR_D303,200 cells Thispaper_Thispaper_2023_suspension_HIO_derived_tHIO3,105 cells Triana_MSB_2021b_Ileum_Organoids_Rev_M3,086 cells Ogawa_NatCommun_2021_GSM5335529_3D_cholangiocyte3,062 cells Thispaper_Thispaper_2023_UK_R5_Duo81_hum_enteroids3,035 cells Hoffmann_CommunBiol_2022_AO16_pool_16h_control2,984 cells Hein_Dev_2022_10_week_iBTO2,950 cells Hoffmann_CommunBiol_2022_AO22_pool_16h_control2,945 cells Fujii_CellStemCell_2018_hSMO_IF2,904 cells Holloway_CellStemCell_2021_hITD_EGF_day132_S882,901 cells Holloway_CellStemCell_2021_hITD_EGF_day132_S902,895 cells Holloway_CellStemCell_2021_hITD_EGF_day132_S912,891 cells Holloway_CellStemCell_2021_hITD_EGF_day132_S892,882 cells Holloway_CellStemCell_2021_hITD_EGF_day105_S42,847 cells Lee_NatCommun_2021A_GSM5399380_GO2,806 cells Hein_Dev_2022_3_week_LPO_Batch22,804 cells Li_StemCR_2020_Stage42,802 cells Holloway_CellStemCell_2021_hITD_EGF_day105_S12,796 cells Kilik_BioRxiv_2021_UK_HIO_EGF2,788 cells Holloway_CellStemCell_2021_hITD_EGF_day105_S22,788 cells Holloway_CellStemCell_2021_hITD_EGF_day105_S32,777 cells Zhang_JH_2023_HLO_Control2,771 cells Hein_Dev_2022_3_week_LPO_Batch12,770 cells Mithal_NatCommun_2020_endodermal_progenitor_day132,744 cells Yu_Cell_2021_H9_tHIO_WK82,722 cells Thispaper_Thispaper_2023_stomach_antrum_organoids2,697 cells Holloway_CellStemCell_2021_hITD_NRG1_day105_S172,624 cells Suzuki_STARProt_2021_LungO_BU3_NGPT_Basal_Cell_Medium_12,613 cells Salahudeen_Nat_2020_GSM2855485_Purified_AT22,560 cells Holloway_CellStemCell_2021_hITD_NRG1_day105_S202,556 cells Holloway_DevCell_2020_HIO_control_7d2,544 cells Holloway_CellStemCell_2021_hITD_NRG1_day105_S192,494 cells Holloway_CellStemCell_2021_hITD_NRG1_day105_S182,478 cells Holloway_CellStemCell_2021_hITD_NRG1_day132_S942,415 cells Holloway_CellStemCell_2021_hITD_NRG1_day132_S922,393 cells Holloway_CellStemCell_2021_hITD_NRG1_day132_S952,368 cells Holloway_CellStemCell_2021_hITD_NRG1_day132_S932,335 cells Sampaziotis_Science_2021_ORG_GB_T1_22,327 cells 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Salahudeen_Nat_2020_GSM2855477_Lung_1_41,938 cells Hein_Dev_2022_Spheroids1,924 cells Augsornworawat_NatCellBio_2023_GSM5979683_txpscislet11,857 cells Hoffmann_CommunBiol_2022_AO22_HT2_16h_control1,842 cells Salahudeen_Nat_2020_GSM2855474_Lung_1_11,811 cells Zhang_JH_2023_PaDLOC_Control1,792 cells Salahudeen_Nat_2020_GSM2855476_Lung_1_31,774 cells He_CellStemCell_2022_hSIO_IL22neg1,766 cells Sampaziotis_Science_2021_ORG_CBD_21,763 cells Hein_Dev_2022_6_week_LPO_Batch11,717 cells Wesley_NatCellBio_2022_Fetal_biliary_organoids1,714 cells Beumer_CellRep_2022_all1,671 cells Elmentaite_DevCell_2020_p17_p1720391,670 cells Hein_Dev_2022_4_week_iBTO1,649 cells Romitti_NatCommun_2022_Human_Thyroid_Organoid1,563 cells Triana_MSB_2021_Colon_organoids_Mock1,558 cells Sampaziotis_Science_2021_ORG_CBD_T2_41,548 cells Wesley_NatCellBio_2022_Hepatoblast_organoids1,548 cells Beumer_Cell_2020_Duo1,488 cells Sampaziotis_Science_2021_ORG_CBD_T2_11,468 cells Sampaziotis_Science_2021_ORG_IHD_T2_11,457 cells Sampaziotis_Science_2021_ORG_GB_T2_31,456 cells Thispaper_Thispaper_2023_UK_R6_Duo87_hum_enteroids1,454 cells Romitti_NatCommun_2022_Human_Thyroid_Organoid_day581,436 cells Suzuki_STARProt_2021_LungO_BU3_NGPT_FGF210DCIY_11,405 cells Suzuki_STARProt_2021_LungO_BU3_NGPT_FGF210DCIY_21,311 cells Aizarani_Nat_2019_all1,284 cells Salahudeen_Nat_2020_GSM2855481_Lung_2_41,248 cells Capeling_CellRep_2022_Day3_HIO_alginate1,227 cells Hein_Dev_2022_6_week_LPO_Batch21,200 cells Salahudeen_Nat_2020_GSM2855480_Lung_2_31,195 cells He_CellStemCell_2022_hSIO_IL22pos1,191 cells Salahudeen_Nat_2020_GSM2855478_Lung_2_11,163 cells Roos_CellStemCell_2022_ICO1,113 cells Salahudeen_Nat_2020_GSM2855479_Lung_2_21,111 cells Triana_MSB_2021b_Ileum_Organoids_H4_Live21,078 cells Elmentaite_DevCell_2020_p17_p1720381,037 cells Hein_Dev_2022_10_week_LPO1,020 cells Triana_MSB_2021b_Ileum_Organoids_N_Mock1,014 cells Holloway_DevCell_2020_HIO_control_0d948 cells Augsornworawat_NatCellBio_2023_GSM5979687_txpscislet3899 cells Aguilar_NatCommun_2022_C8811 cells Aguilar_NatCommun_2022_C9762 cells Salahudeen_Nat_2020_GSM2855482_Lung_3_1747 cells Wiedenmann_NatBME_2021_day31_300cells743 cells Triana_MSB_2021b_Ileum_Organoids_Ns_Mock735 cells Roos_CellStemCell_2022_BRCO725 cells Salahudeen_Nat_2020_GSM2855483_Lung_3_2706 cells Beumer_Cell_2020_Col658 cells Wiedenmann_NatBME_2021_day23616 cells Wiedenmann_NatBME_2021_day31_600cells590 cells Wiedenmann_NatBME_2021_day16576 cells Aguilar_NatCommun_2022_A1524 cells Wiedenmann_NatBME_2021_day20488 cells Wiedenmann_NatBME_2021_day27465 cells Salahudeen_Nat_2020_GSM2855484_Lung_3_3464 cells Palikuqi_Nat_2020_GSM4487132_Sample1D449 cells Hoffmann_CommunBiol_2022_AO16_HT2_16h_control410 cells Triana_MSB_2021b_Ileum_Organoids_Ns_NMock_2341 cells Triana_MSB_2021b_Ileum_Organoids_Ns_NMock_1302 cells Hu_Cell_2018B_Human_Chol_Orgs234 cells Camp_Nat_2017_LB172 cells Hu_Cell_2018A_Human_Hep_Orgs148 cells Augsornworawat_NatCellBio_202365,825 cells Holloway_CellStemCell_202150,753 cells Thispaper_Thispaper_202345,281 cells Kadur_Nat_202232,930 cells Holloway_DevCell_202030,001 cells Sampaziotis_Science_202129,509 cells Sarvestani_NatCommun_202126,527 cells Miller_DevCell_202023,782 cells Hoffmann_CommunBiol_202219,987 cells Capeling_CellRep_202219,586 cells Zhang_JH_202318,551 cells Elmentaite_DevCell_202016,881 cells Salahudeen_Nat_202016,662 cells Hein_Dev_202216,034 cells Yoon_NatCommun_202215,796 cells Zeve_NatCommun_202214,688 cells Lim_CellStemCell_202313,953 cells Wiedenmann_NatBME_202112,997 cells Li_StemCR_202011,796 cells Blutt_LiverPhys_202111,366 cells Tran_iScience_202210,943 cells McCauley_CMGH_202310,421 cells Velazquez_CellSyst_202110,232 cells Guan_NatCommun_20219,429 cells Charlie_JCI_20238,586 cells Triana_MSB_2021b8,530 cells Rosado_BioRxiv_20218,462 cells Chan_NatCommun_20227,649 cells Suzuki_STARProt_20217,559 cells Fujii_CellStemCell_20186,690 cells Kilik_BioRxiv_20216,127 cells McCray_AJCEU_20195,375 cells Wesley_NatCellBio_20225,216 cells Mithal_NatCommun_20204,762 cells Ouchi_CellMet_20194,297 cells Bein_FPhar_20214,261 cells Lamers_EMBOJ_20214,180 cells Beumer_Cell_20204,149 cells Triana_MSB_20213,511 cells Ogawa_NatCommun_20213,062 cells Romitti_NatCommun_20222,999 cells He_CellStemCell_20222,957 cells Lee_NatCommun_2021A2,806 cells Aguilar_NatCommun_20222,097 cells Lee_NatCommun_2021B1,947 cells Roos_CellStemCell_20221,838 cells Beumer_CellRep_20221,671 cells Aizarani_Nat_20191,284 cells Palikuqi_Nat_2020449 cells EEC_enriched_Organoids14,688 cells GSM5979673_week212,080 cells GSE164514_AEC_3D10,943 cells LO_EGF_depletion10,909 cells salivary_gland_organoids10,505 cells deltaNp63alpha_overexpression10,073 cells RFX6_overexpression9,366 cells GSM5979665_scislet19,315 cells HIO_control_59d9,268 cells PAX9_overexpression9,126 cells H9_HIO_1EGF_100NRG1_D409,107 cells LO_Serum_treatement9,004 cells TFAP2A_overexpression8,805 cells GSM4654340_TNF_free8,756 cells NEUROG3_overexpression8,538 cells GSM4984050_LungOD78,462 cells Lung_organoid_epithelium8,272 cells GSM6571152_month68,082 cells GSM6571154_month127,909 cells GSM5979667_scislet27,848 cells GSM5979675_week37,700 cells H9_HIO_0EGF_100NRG1_D407,451 cells AO15_pool_16h_control7,039 cells H9_22d_tHIO_8wk_kidneycapsule_HIOEC6,381 cells H9_22d_tHIO_8wk_kidneycapsule_control6,345 cells H9_HIO_100EGF_1NRG1_D406,114 cells stomach_corpus_organoids5,955 cells wild_type_genotype5,951 cells GSM5979677_week45,743 cells Lung_alveolar_organoid_epithelium5,681 cells NEUROD1_overexpression5,529 cells GSM4451223_hPSC_CO5,516 cells salivary_gland_organoids_latepassages5,291 cells HIO1A_with_EECs5,286 cells H9_HIO_ENR_D145,281 cells GSM4830979_DesLO_D175,260 cells HIO1B_with_EECs5,135 cells WNT3Aneg_2206_p2_RSPO5,095 cells H9_HIO_ENR_alginate_D285,093 cells GSM4830978_FeLO_D174,972 cells h9_HIO_Suspension_EGF_28days4,833 cells AO15_HT2_16h_control4,767 cells HIO_control_14d4,657 cells H9_HIO_0EGF_0NRG1_D404,453 cells HIO_control_3d4,417 cells GSM5979685_txpscislet24,392 cells GSM4654341_TNF_treat4,369 cells fetal_liver_organoids4,338 cells Human_liver_organoids4,297 cells H9_HIO_100EGF_0NRG1_D404,185 cells H9_HIO_EGF_alginate_D284,184 cells Lung_Bronchioalveolar4,180 cells H9_22d_tHIO_8wk_mesentery_control4,178 cells GSM5075992_HLO24,146 cells H9_HIO_EGF_matrigel_D284,092 cells Day14_HIO_EGF_algenate4,083 cells bronchial_organoids4,073 cells ASCL1_overexpression4,011 cells GSM5075993_HLO33,997 cells Day14_HIO_ENR_algenate3,955 cells H9_22d_tHIO_8wk_mesentery_HIOEC3,839 cells nasopharyngeal_organoids3,576 cells PaDLOC_Tenofovir3,575 cells PaDLOC_Fialuridine3,487 cells PaDLOC_Acetaminophen3,469 cells PaDLOC_Tenofovir_InarigivirSoproxil3,457 cells H9_HIO_ENR_D283,430 cells Day7_HIO_EGF_algenate3,372 cells GSM5075991_HLO13,223 cells H9_HIO_ENR_D303,200 cells suspension_HIO_derived_tHIO3,105 cells Ileum_Organoids_Rev_M3,086 cells GSM5335529_3D_cholangiocyte3,062 cells UK_R5_Duo81_hum_enteroids3,035 cells AO16_pool_16h_control2,984 cells AO22_pool_16h_control2,945 cells hITD_EGF_day132_S882,901 cells hITD_EGF_day132_S902,895 cells hITD_EGF_day132_S912,891 cells hITD_EGF_day132_S892,882 cells hITD_EGF_day105_S42,847 cells 3_week_LPO_Batch22,804 cells hITD_EGF_day105_S12,796 cells hITD_EGF_day105_S22,788 cells hITD_EGF_day105_S32,777 cells 3_week_LPO_Batch12,770 cells endodermal_progenitor_day132,744 cells stomach_antrum_organoids2,697 cells hITD_NRG1_day105_S172,624 cells LungO_BU3_NGPT_Basal_Cell_Medium_12,613 cells GSM2855485_Purified_AT22,560 cells hITD_NRG1_day105_S202,556 cells HIO_control_7d2,544 cells hITD_NRG1_day105_S192,494 cells hITD_NRG1_day105_S182,478 cells hITD_NRG1_day132_S942,415 cells hITD_NRG1_day132_S922,393 cells hITD_NRG1_day132_S952,368 cells hITD_NRG1_day132_S932,335 cells LungO_BU3_NGPT_Basal_Cell_Medium_22,230 cells WNT3Apos_2206_p2_WNT3A2,190 cells Day7_HIO_ENR_algenate2,116 cells hITD_EGFNRG1_day105_S162,112 cells hITD_EGFNRG1_day105_S152,097 cells hITD_EGFNRG1_day105_S142,076 cells hITD_EGFNRG1_day105_S132,028 cells endodermal_progenitor_day62,018 cells Ileum_Organoids_Sort_Mock1,974 cells Hepatoblast_organoids_treated_with_hepatozyme1,954 cells Ileum_organoids_Mock1,953 cells GSM5399379_LBO1,947 cells GSM2855475_Lung_1_21,945 cells GSM2855477_Lung_1_41,938 cells GSM5979683_txpscislet11,857 cells AO22_HT2_16h_control1,842 cells GSM2855474_Lung_1_11,811 cells PaDLOC_Control1,792 cells GSM2855476_Lung_1_31,774 cells 6_week_LPO_Batch11,717 cells Fetal_biliary_organoids1,714 cells Human_Thyroid_Organoid1,563 cells Colon_organoids_Mock1,558 cells Hepatoblast_organoids1,548 cells UK_R6_Duo87_hum_enteroids1,454 cells Human_Thyroid_Organoid_day581,436 cells LungO_BU3_NGPT_FGF210DCIY_11,405 cells LungO_BU3_NGPT_FGF210DCIY_21,311 cells GSM2855481_Lung_2_41,248 cells Day3_HIO_alginate1,227 cells 6_week_LPO_Batch21,200 cells GSM2855480_Lung_2_31,195 cells GSM2855478_Lung_2_11,163 cells GSM2855479_Lung_2_21,111 cells Ileum_Organoids_H4_Live21,078 cells Ileum_Organoids_N_Mock1,014 cells GSM5979687_txpscislet3899 cells GSM2855482_Lung_3_1747 cells Ileum_Organoids_Ns_Mock735 cells GSM2855483_Lung_3_2706 cells GSM2855484_Lung_3_3464 cells GSM4487132_Sample1D449 cells AO16_HT2_16h_control410 cells Ileum_Organoids_Ns_NMock_2341 cells Ileum_Organoids_Ns_NMock_1302 cells intrahepatic_bile_duct10,580 cells common_bile_duct8,898 cells nasopharyngeal3,576 cells biliary cells62,010 cells alveolar type 2 (AT2) cells50,334 cells alveolar type 1 (AT1) cells26,977 cells stellate cells26,220 cells Interstitial cells of Cajal (ICC)16,576 cells stromal 2 (NPY)16,214 cells neuroendocrine cells13,917 cells airway secretory cells12,086 cells pancreatic cells10,845 cells smooth muscle cells (SMC)9,839 cells Microfold cells8,673 cells cycling stromal cells8,125 cells mesoderm 1 (HAND1)8,029 cells mesoderm 2 (ZEB2)8,010 cells ciliated cells6,846 cells enteroendocrine cells5,609 cells mesothelial cells4,690 cells stromal 1 (ADAMDEC1)2,217 cells lymphatic endothelium933 cells cardiovascular cells467 cells BEST4+ epithelial65 cells 10x 3' v3, single-nucleus26,527 cells alveolar sac116,946 cells salivary gland epithelium15,796 cells intrahepatic bile duct10,580 cells common bile duct8,898 cells biliary system6,848 cells prostate gland5,375 cells pyloric antrum2,697 cells 2. human intestine organoid cell atlas
ExploreSample ID
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Zeve_NatCommun_2022_EEC_enriched_Organoids14,688 cells Sarvestani_NatCommun_2021_NL33_iHNO11,428 cells Holloway_DevCell_2020_HIO_control_59d9,268 cells Yu_Cell_2021_H9_HIO_1EGF_100NRG1_D409,107 cells Sung_NO_2020_GSM4654340_TNF_free8,756 cells Sarvestani_NatCommun_2021_CRL1541_iHNO8,525 cells Holloway_DevCell_2020_vHIO_59d8,167 cells Yu_Cell_2021_H9_HIO_0EGF_100NRG1_D407,451 cells Sarvestani_NatCommun_2021_NL34_iHNO6,574 cells Thispaper_Thispaper_2023_H9_22d_tHIO_8wk_kidneycapsule_HIOEC6,381 cells Thispaper_Thispaper_2023_H9_22d_tHIO_8wk_kidneycapsule_control6,345 cells Yu_Cell_2021_H9_HIO_100EGF_1NRG1_D406,114 cells Han_Nat_2021_GSM4451223_hPSC_CO5,516 cells Yan_Gut_2020_H019_NOd5,406 cells McCauley_CMGH_2023_HIO1A_with_EECs5,286 cells Yu_Cell_2021_H9_HIO_ENR_D145,281 cells Yan_Gut_2020_H019_NO5,277 cells McCauley_CMGH_2023_HIO1B_with_EECs5,135 cells Elmentaite_DevCell_2020_WNT3Aneg_2206_p2_RSPO5,095 cells Yu_Cell_2021_H9_HIO_ENR_alginate_D285,093 cells Capeling_CellRep_2022_h9_HIO_Suspension_EGF_28days4,833 cells Holloway_DevCell_2020_HIO_control_14d4,657 cells Charlie_JCI_2023_hfDO_EREG4,521 cells Yu_Cell_2021_H9_HIO_0EGF_0NRG1_D404,453 cells Holloway_DevCell_2020_HIO_control_3d4,417 cells Yan_Gut_2020_H011_NO4,398 cells Sung_NO_2020_GSM4654341_TNF_treat4,369 cells Bein_FPhar_2021_all4,261 cells Yu_Cell_2021_H9_HIO_100EGF_0NRG1_D404,185 cells Yu_Cell_2021_H9_HIO_EGF_alginate_D284,184 cells Thispaper_Thispaper_2023_H9_22d_tHIO_8wk_mesentery_control4,178 cells Yu_Cell_2021_H9_HIO_EGF_matrigel_D284,092 cells Capeling_CellRep_2022_Day14_HIO_EGF_algenate4,083 cells Charlie_JCI_2023_hfDO_EGF4,065 cells Capeling_CellRep_2022_Day14_HIO_ENR_algenate3,955 cells Thispaper_Thispaper_2023_UK_Duo893,954 cells Thispaper_Thispaper_2023_H9_22d_tHIO_8wk_mesentery_HIOEC3,839 cells Fujii_CellStemCell_2018_hSMO_SB3,786 cells Elmentaite_DevCell_2020_p1_TIp120383,672 cells Yu_Cell_2021_H9_HIO_ENR_D283,430 cells Capeling_CellRep_2022_Day7_HIO_EGF_algenate3,372 cells Kilik_BioRxiv_2021_UK_HIO_NRG13,339 cells Yu_Cell_2021_H9_tHIO_WK43,335 cells Elmentaite_DevCell_2020_p1_TIp120393,217 cells Yu_Cell_2021_H9_HIO_ENR_D303,200 cells Thispaper_Thispaper_2023_suspension_HIO_derived_tHIO3,105 cells Triana_MSB_2021b_Ileum_Organoids_Rev_M3,086 cells Thispaper_Thispaper_2023_UK_R5_Duo81_hum_enteroids3,035 cells Fujii_CellStemCell_2018_hSMO_IF2,904 cells Holloway_CellStemCell_2021_hITD_EGF_day132_S882,901 cells Holloway_CellStemCell_2021_hITD_EGF_day132_S902,895 cells Holloway_CellStemCell_2021_hITD_EGF_day132_S912,891 cells Holloway_CellStemCell_2021_hITD_EGF_day132_S892,882 cells Holloway_CellStemCell_2021_hITD_EGF_day105_S42,847 cells Holloway_CellStemCell_2021_hITD_EGF_day105_S12,796 cells Holloway_CellStemCell_2021_hITD_EGF_day105_S22,788 cells Kilik_BioRxiv_2021_UK_HIO_EGF2,788 cells Holloway_CellStemCell_2021_hITD_EGF_day105_S32,777 cells Mithal_NatCommun_2020_endodermal_progenitor_day132,744 cells Yu_Cell_2021_H9_tHIO_WK82,722 cells Holloway_CellStemCell_2021_hITD_NRG1_day105_S172,624 cells Holloway_CellStemCell_2021_hITD_NRG1_day105_S202,556 cells Holloway_DevCell_2020_HIO_control_7d2,544 cells Holloway_CellStemCell_2021_hITD_NRG1_day105_S192,494 cells Holloway_CellStemCell_2021_hITD_NRG1_day105_S182,478 cells Holloway_CellStemCell_2021_hITD_NRG1_day132_S942,415 cells Holloway_CellStemCell_2021_hITD_NRG1_day132_S922,393 cells Holloway_CellStemCell_2021_hITD_NRG1_day132_S952,368 cells Holloway_CellStemCell_2021_hITD_NRG1_day132_S932,335 cells Elmentaite_DevCell_2020_WNT3Apos_2206_p2_WNT3A2,190 cells Capeling_CellRep_2022_Day7_HIO_ENR_algenate2,116 cells Holloway_CellStemCell_2021_hITD_EGFNRG1_day105_S162,112 cells Holloway_CellStemCell_2021_hITD_EGFNRG1_day105_S152,097 cells Holloway_CellStemCell_2021_hITD_EGFNRG1_day105_S142,076 cells Holloway_CellStemCell_2021_hITD_EGFNRG1_day105_S132,028 cells Mithal_NatCommun_2020_endodermal_progenitor_day62,018 cells Beumer_Cell_2020_Ile2,003 cells Yan_Gut_2020_H011_NOd1,974 cells Triana_MSB_2021b_Ileum_Organoids_Sort_Mock1,974 cells Yu_Cell_2021_H9_HIO_ENR_D71,956 cells Triana_MSB_2021_Ileum_organoids_Mock1,953 cells He_CellStemCell_2022_hSIO_IL22neg1,766 cells Beumer_CellRep_2022_all1,671 cells Elmentaite_DevCell_2020_p17_p1720391,670 cells Triana_MSB_2021_Colon_organoids_Mock1,558 cells Beumer_Cell_2020_Duo1,488 cells Thispaper_Thispaper_2023_UK_R6_Duo87_hum_enteroids1,454 cells Capeling_CellRep_2022_Day3_HIO_alginate1,227 cells He_CellStemCell_2022_hSIO_IL22pos1,191 cells Triana_MSB_2021b_Ileum_Organoids_H4_Live21,078 cells Elmentaite_DevCell_2020_p17_p1720381,037 cells Triana_MSB_2021b_Ileum_Organoids_N_Mock1,014 cells Holloway_DevCell_2020_HIO_control_0d948 cells Triana_MSB_2021b_Ileum_Organoids_Ns_Mock735 cells Beumer_Cell_2020_Col658 cells Palikuqi_Nat_2020_GSM4487132_Sample1D449 cells Triana_MSB_2021b_Ileum_Organoids_Ns_NMock_2341 cells Triana_MSB_2021b_Ileum_Organoids_Ns_NMock_1302 cells Holloway_CellStemCell_202150,753 cells Thispaper_Thispaper_202332,291 cells Holloway_DevCell_202030,001 cells Sarvestani_NatCommun_202126,527 cells Capeling_CellRep_202219,586 cells Elmentaite_DevCell_202016,881 cells Zeve_NatCommun_202214,688 cells McCauley_CMGH_202310,421 cells Charlie_JCI_20238,586 cells Triana_MSB_2021b8,530 cells Fujii_CellStemCell_20186,690 cells Kilik_BioRxiv_20216,127 cells Mithal_NatCommun_20204,762 cells Bein_FPhar_20214,261 cells Beumer_Cell_20204,149 cells Triana_MSB_20213,511 cells He_CellStemCell_20222,957 cells Beumer_CellRep_20221,671 cells Palikuqi_Nat_2020449 cells EEC_enriched_Organoids14,688 cells HIO_control_59d9,268 cells H9_HIO_1EGF_100NRG1_D409,107 cells GSM4654340_TNF_free8,756 cells H9_HIO_0EGF_100NRG1_D407,451 cells H9_22d_tHIO_8wk_kidneycapsule_HIOEC6,381 cells H9_22d_tHIO_8wk_kidneycapsule_control6,345 cells H9_HIO_100EGF_1NRG1_D406,114 cells GSM4451223_hPSC_CO5,516 cells HIO1A_with_EECs5,286 cells H9_HIO_ENR_D145,281 cells HIO1B_with_EECs5,135 cells WNT3Aneg_2206_p2_RSPO5,095 cells H9_HIO_ENR_alginate_D285,093 cells h9_HIO_Suspension_EGF_28days4,833 cells HIO_control_14d4,657 cells H9_HIO_0EGF_0NRG1_D404,453 cells HIO_control_3d4,417 cells GSM4654341_TNF_treat4,369 cells H9_HIO_100EGF_0NRG1_D404,185 cells H9_HIO_EGF_alginate_D284,184 cells H9_22d_tHIO_8wk_mesentery_control4,178 cells H9_HIO_EGF_matrigel_D284,092 cells Day14_HIO_EGF_algenate4,083 cells Day14_HIO_ENR_algenate3,955 cells H9_22d_tHIO_8wk_mesentery_HIOEC3,839 cells H9_HIO_ENR_D283,430 cells Day7_HIO_EGF_algenate3,372 cells H9_HIO_ENR_D303,200 cells suspension_HIO_derived_tHIO3,105 cells Ileum_Organoids_Rev_M3,086 cells UK_R5_Duo81_hum_enteroids3,035 cells hITD_EGF_day132_S882,901 cells hITD_EGF_day132_S902,895 cells hITD_EGF_day132_S912,891 cells hITD_EGF_day132_S892,882 cells hITD_EGF_day105_S42,847 cells hITD_EGF_day105_S12,796 cells hITD_EGF_day105_S22,788 cells hITD_EGF_day105_S32,777 cells endodermal_progenitor_day132,744 cells hITD_NRG1_day105_S172,624 cells hITD_NRG1_day105_S202,556 cells HIO_control_7d2,544 cells hITD_NRG1_day105_S192,494 cells hITD_NRG1_day105_S182,478 cells hITD_NRG1_day132_S942,415 cells hITD_NRG1_day132_S922,393 cells hITD_NRG1_day132_S952,368 cells hITD_NRG1_day132_S932,335 cells WNT3Apos_2206_p2_WNT3A2,190 cells Day7_HIO_ENR_algenate2,116 cells hITD_EGFNRG1_day105_S162,112 cells hITD_EGFNRG1_day105_S152,097 cells hITD_EGFNRG1_day105_S142,076 cells hITD_EGFNRG1_day105_S132,028 cells endodermal_progenitor_day62,018 cells Ileum_Organoids_Sort_Mock1,974 cells Ileum_organoids_Mock1,953 cells Colon_organoids_Mock1,558 cells UK_R6_Duo87_hum_enteroids1,454 cells Day3_HIO_alginate1,227 cells Ileum_Organoids_H4_Live21,078 cells Ileum_Organoids_N_Mock1,014 cells Ileum_Organoids_Ns_Mock735 cells GSM4487132_Sample1D449 cells Ileum_Organoids_Ns_NMock_2341 cells Ileum_Organoids_Ns_NMock_1302 cells Interstitial cells of Cajal (ICC)16,005 cells stromal 2 (NPY)12,722 cells cycling stromal cells12,342 cells smooth muscle cells (SMC)8,497 cells mesoderm 1 (HAND1)7,750 cells mesoderm 2 (ZEB2)7,463 cells enteroendocrine cells4,853 cells Microfold cells4,690 cells ciliated cells3,347 cells mesothelial cells2,922 cells cycling endothelial cells1,649 cells stromal 1 (ADAMDEC1)1,568 cells stromal 3 (C7)1,127 cells lymphatic endothelium1,074 cells mature enterocytes37,683 cells Interstitial cells of Cajal (ICC)17,084 cells mature colonocytes17,032 cells stromal 2 (NPY)12,722 cells cycling stromal cells12,342 cells enterocyte precursors10,916 cells myofibroblasts8,497 cells mesoderm 1 (HAND1)7,750 cells mesoderm 2 (ZEB2)7,463 cells MUC2- goblet cells6,877 cells younger goblet cells6,726 cells Microfold cells6,230 cells immature pericytes3,726 cells ciliated cells3,347 cells RGS5 pericytes2,922 cells stromal 1 (ADAMDEC1)2,379 cells cycling endothelial cells1,649 cells stromal 3 (C7)1,127 cells lymphatic endothelium1,074 cells angiogenic pericytes903 cells older goblet cells487 cells colonocyte precursors9 cells stromal 2 (NPY)17,791 cells Interstitial cells of Cajal (ICC)15,347 cells cycling stromal cells9,578 cells smooth muscle cells (SMC)8,967 cells mesoderm 2 (ZEB2)8,290 cells mesoderm 1 (HAND1)5,646 cells ciliated cells4,751 cells enteroendocrine cells4,406 cells Microfold cells4,343 cells mesothelial cells3,068 cells stromal 1 (ADAMDEC1)1,509 cells BEST4+ epithelial1,359 cells stromal 3 (C7)1,119 cells cycling endothelial cells552 cells lymphatic endothelium520 cells mature enterocytes38,381 cells stromal 2 (NPY)17,791 cells Interstitial cells of Cajal (ICC)15,347 cells mature colonocytes15,121 cells enterocyte precursors13,303 cells cycling stromal cells9,578 cells mesoderm 2 (ZEB2)8,290 cells myofibroblasts7,453 cells younger goblet cells7,292 cells MUC2- goblet cells6,400 cells mesoderm 1 (HAND1)5,646 cells ciliated cells4,751 cells Microfold cells4,343 cells immature pericytes3,827 cells RGS5 pericytes2,811 cells older goblet cells2,230 cells angiogenic pericytes1,778 cells stromal 1 (ADAMDEC1)1,509 cells BEST4+ epithelial1,359 cells colonocyte precursors1,314 cells stromal 3 (C7)1,119 cells enterochromaffin cells1,051 cells cycling endothelial cells552 cells lymphatic endothelium520 cells BEST2 goblet cells74 cells contractile pericytes63 cells Zeve_NatCommun_2022_EEC_enriched_Organoids14,688 cells Sarvestani_NatCommun_2021_NL33_iHNO11,428 cells Holloway_DevCell_2020_HIO_control_59d9,268 cells Sung_NO_2020_GSM4654340_TNF_free8,756 cells Sarvestani_NatCommun_2021_CRL1541_iHNO8,525 cells Holloway_DevCell_2020_vHIO_59d8,167 cells Sarvestani_NatCommun_2021_NL34_iHNO6,574 cells Han_Nat_2021_GSM4451223_hPSC_CO5,516 cells Yan_Gut_2020_H019_NOd5,406 cells McCauley_CMGH_2023_HIO1A_with_EECs5,286 cells Yan_Gut_2020_H019_NO5,277 cells McCauley_CMGH_2023_HIO1B_with_EECs5,135 cells Elmentaite_DevCell_2020_WNT3Aneg_2206_p2_RSPO5,095 cells Holloway_DevCell_2020_HIO_control_14d4,657 cells Charlie_JCI_2023_hfDO_EREG4,521 cells Holloway_DevCell_2020_HIO_control_3d4,417 cells Yan_Gut_2020_H011_NO4,398 cells Sung_NO_2020_GSM4654341_TNF_treat4,369 cells Bein_FPhar_2021_all4,261 cells Capeling_CellRep_2022_Day14_HIO_EGF_algenate4,083 cells Charlie_JCI_2023_hfDO_EGF4,065 cells Capeling_CellRep_2022_Day14_HIO_ENR_algenate3,955 cells Thispaper_Thispaper_2023_UK_Duo893,954 cells Fujii_CellStemCell_2018_hSMO_SB3,786 cells Elmentaite_DevCell_2020_p1_TIp120383,672 cells Capeling_CellRep_2022_Day7_HIO_EGF_algenate3,372 cells Kilik_BioRxiv_2021_UK_HIO_NRG13,339 cells Elmentaite_DevCell_2020_p1_TIp120393,217 cells Thispaper_Thispaper_2023_suspension_HIO_derived_tHIO3,105 cells Triana_MSB_2021b_Ileum_Organoids_Rev_M3,086 cells Thispaper_Thispaper_2023_UK_R5_Duo81_hum_enteroids3,035 cells Fujii_CellStemCell_2018_hSMO_IF2,904 cells Holloway_CellStemCell_2021_hITD_EGF_day132_S882,901 cells Holloway_CellStemCell_2021_hITD_EGF_day132_S902,895 cells Holloway_CellStemCell_2021_hITD_EGF_day132_S912,891 cells Holloway_CellStemCell_2021_hITD_EGF_day132_S892,882 cells Holloway_CellStemCell_2021_hITD_EGF_day105_S42,847 cells Holloway_CellStemCell_2021_hITD_EGF_day105_S12,796 cells Holloway_CellStemCell_2021_hITD_EGF_day105_S22,788 cells Kilik_BioRxiv_2021_UK_HIO_EGF2,788 cells Holloway_CellStemCell_2021_hITD_EGF_day105_S32,777 cells Mithal_NatCommun_2020_endodermal_progenitor_day132,744 cells Holloway_CellStemCell_2021_hITD_NRG1_day105_S172,624 cells Holloway_CellStemCell_2021_hITD_NRG1_day105_S202,556 cells Holloway_DevCell_2020_HIO_control_7d2,544 cells Holloway_CellStemCell_2021_hITD_NRG1_day105_S192,494 cells Holloway_CellStemCell_2021_hITD_NRG1_day105_S182,478 cells Holloway_CellStemCell_2021_hITD_NRG1_day132_S942,415 cells Holloway_CellStemCell_2021_hITD_NRG1_day132_S922,393 cells Holloway_CellStemCell_2021_hITD_NRG1_day132_S952,368 cells Holloway_CellStemCell_2021_hITD_NRG1_day132_S932,335 cells Elmentaite_DevCell_2020_WNT3Apos_2206_p2_WNT3A2,190 cells Capeling_CellRep_2022_Day7_HIO_ENR_algenate2,116 cells Holloway_CellStemCell_2021_hITD_EGFNRG1_day105_S162,112 cells Holloway_CellStemCell_2021_hITD_EGFNRG1_day105_S152,097 cells Holloway_CellStemCell_2021_hITD_EGFNRG1_day105_S142,076 cells Holloway_CellStemCell_2021_hITD_EGFNRG1_day105_S132,028 cells Mithal_NatCommun_2020_endodermal_progenitor_day62,018 cells Beumer_Cell_2020_Ile2,003 cells Yan_Gut_2020_H011_NOd1,974 cells Triana_MSB_2021b_Ileum_Organoids_Sort_Mock1,974 cells Triana_MSB_2021_Ileum_organoids_Mock1,953 cells He_CellStemCell_2022_hSIO_IL22neg1,766 cells Beumer_CellRep_2022_all1,671 cells Elmentaite_DevCell_2020_p17_p1720391,670 cells Triana_MSB_2021_Colon_organoids_Mock1,558 cells Beumer_Cell_2020_Duo1,488 cells Thispaper_Thispaper_2023_UK_R6_Duo87_hum_enteroids1,454 cells Capeling_CellRep_2022_Day3_HIO_alginate1,227 cells He_CellStemCell_2022_hSIO_IL22pos1,191 cells Triana_MSB_2021b_Ileum_Organoids_H4_Live21,078 cells Elmentaite_DevCell_2020_p17_p1720381,037 cells Triana_MSB_2021b_Ileum_Organoids_N_Mock1,014 cells Holloway_DevCell_2020_HIO_control_0d948 cells Triana_MSB_2021b_Ileum_Organoids_Ns_Mock735 cells Beumer_Cell_2020_Col658 cells Palikuqi_Nat_2020_GSM4487132_Sample1D449 cells Triana_MSB_2021b_Ileum_Organoids_Ns_NMock_2341 cells Triana_MSB_2021b_Ileum_Organoids_Ns_NMock_1302 cells colon epithelial cell17,041 cells interstitial cell of Cajal16,005 cells mesodermal cell15,213 cells smooth muscle cell8,497 cells enteroendocrine cell4,853 cells mesothelial cell2,922 cells intestinal tuft cell2,203 cells colon endothelial cell1,649 cells endothelial cell1,074 cells hematopoietic cell145 cells 10x 3' v3, single-nucleus26,527 cells 3. human lung organoid cell atlas
ExploreSample ID
Sample source
Sample name
Batch ID
Derive
Time point
Cell type (level_1)
Cell type
Subject ID
Tissue type
Assay
Disease
Tissue
Leiden clustering
Kadur_Nat_2022_LO_Control13,017 cells Kadur_Nat_2022_LO_EGF_depletion10,909 cells Miller_DevCell_2020_Day_010,765 cells He_Cell_2022_deltaNp63alpha_overexpression10,073 cells Miller_DevCell_2020_Day_39,781 cells He_Cell_2022_RFX6_overexpression9,366 cells He_Cell_2022_PAX9_overexpression9,126 cells Kadur_Nat_2022_LO_Serum_treatement9,004 cells He_Cell_2022_TFAP2A_overexpression8,805 cells He_Cell_2022_NEUROG3_overexpression8,538 cells Rosado_BioRxiv_2021_GSM4984050_LungOD78,462 cells Lim_CellStemCell_2023_Lung_organoid_epithelium8,272 cells Hoffmann_CommunBiol_2022_AO15_pool_16h_control7,039 cells Tran_iScience_2022_GSE164514_AEC_3D6,881 cells He_Cell_2022_wild_type_genotype5,951 cells Lim_CellStemCell_2023_Lung_alveolar_organoid_epithelium5,681 cells He_Cell_2022_NEUROD1_overexpression5,529 cells Hoffmann_CommunBiol_2022_AO15_HT2_16h_control4,767 cells Lamers_EMBOJ_2021_Lung_Bronchioalveolar4,180 cells Chan_NatCommun_2022_bronchial_organoids4,073 cells He_Cell_2022_ASCL1_overexpression4,011 cells Chan_NatCommun_2022_nasopharyngeal_organoids3,576 cells Miller_DevCell_2020_Day_213,236 cells Hoffmann_CommunBiol_2022_AO16_pool_16h_control2,984 cells Hein_Dev_2022_10_week_iBTO2,950 cells Hoffmann_CommunBiol_2022_AO22_pool_16h_control2,945 cells Hein_Dev_2022_3_week_LPO_Batch22,804 cells Hein_Dev_2022_3_week_LPO_Batch12,770 cells Suzuki_STARProt_2021_LungO_BU3_NGPT_Basal_Cell_Medium_12,613 cells Salahudeen_Nat_2020_GSM2855485_Purified_AT22,560 cells Suzuki_STARProt_2021_LungO_BU3_NGPT_Basal_Cell_Medium_22,230 cells Lee_NatCommun_2021B_GSM5399379_LBO1,947 cells Salahudeen_Nat_2020_GSM2855475_Lung_1_21,945 cells Salahudeen_Nat_2020_GSM2855477_Lung_1_41,938 cells Hein_Dev_2022_Spheroids1,924 cells Hoffmann_CommunBiol_2022_AO22_HT2_16h_control1,842 cells Salahudeen_Nat_2020_GSM2855474_Lung_1_11,811 cells Salahudeen_Nat_2020_GSM2855476_Lung_1_31,774 cells Hein_Dev_2022_6_week_LPO_Batch11,717 cells Hein_Dev_2022_4_week_iBTO1,649 cells Suzuki_STARProt_2021_LungO_BU3_NGPT_FGF210DCIY_11,405 cells Suzuki_STARProt_2021_LungO_BU3_NGPT_FGF210DCIY_21,311 cells Salahudeen_Nat_2020_GSM2855481_Lung_2_41,248 cells Hein_Dev_2022_6_week_LPO_Batch21,200 cells Salahudeen_Nat_2020_GSM2855480_Lung_2_31,195 cells Salahudeen_Nat_2020_GSM2855478_Lung_2_11,163 cells Salahudeen_Nat_2020_GSM2855479_Lung_2_21,111 cells Hein_Dev_2022_10_week_LPO1,020 cells Salahudeen_Nat_2020_GSM2855482_Lung_3_1747 cells Salahudeen_Nat_2020_GSM2855483_Lung_3_2706 cells Salahudeen_Nat_2020_GSM2855484_Lung_3_3464 cells Hoffmann_CommunBiol_2022_AO16_HT2_16h_control410 cells Kadur_Nat_202232,930 cells Miller_DevCell_202023,782 cells Hoffmann_CommunBiol_202219,987 cells Salahudeen_Nat_202016,662 cells Hein_Dev_202216,034 cells Lim_CellStemCell_202313,953 cells Rosado_BioRxiv_20218,462 cells Chan_NatCommun_20227,649 cells Suzuki_STARProt_20217,559 cells Tran_iScience_20226,881 cells Lamers_EMBOJ_20214,180 cells Lee_NatCommun_2021B1,947 cells LO_EGF_depletion10,909 cells deltaNp63alpha_overexpression10,073 cells RFX6_overexpression9,366 cells PAX9_overexpression9,126 cells LO_Serum_treatement9,004 cells TFAP2A_overexpression8,805 cells NEUROG3_overexpression8,538 cells GSM4984050_LungOD78,462 cells Lung_organoid_epithelium8,272 cells AO15_pool_16h_control7,039 cells GSE164514_AEC_3D6,881 cells wild_type_genotype5,951 cells Lung_alveolar_organoid_epithelium5,681 cells NEUROD1_overexpression5,529 cells AO15_HT2_16h_control4,767 cells Lung_Bronchioalveolar4,180 cells bronchial_organoids4,073 cells ASCL1_overexpression4,011 cells nasopharyngeal_organoids3,576 cells AO16_pool_16h_control2,984 cells AO22_pool_16h_control2,945 cells 3_week_LPO_Batch22,804 cells 3_week_LPO_Batch12,770 cells LungO_BU3_NGPT_Basal_Cell_Medium_12,613 cells GSM2855485_Purified_AT22,560 cells LungO_BU3_NGPT_Basal_Cell_Medium_22,230 cells GSM5399379_LBO1,947 cells GSM2855475_Lung_1_21,945 cells GSM2855477_Lung_1_41,938 cells AO22_HT2_16h_control1,842 cells GSM2855474_Lung_1_11,811 cells GSM2855476_Lung_1_31,774 cells 6_week_LPO_Batch11,717 cells LungO_BU3_NGPT_FGF210DCIY_11,405 cells LungO_BU3_NGPT_FGF210DCIY_21,311 cells GSM2855481_Lung_2_41,248 cells 6_week_LPO_Batch21,200 cells GSM2855480_Lung_2_31,195 cells GSM2855478_Lung_2_11,163 cells GSM2855479_Lung_2_21,111 cells GSM2855482_Lung_3_1747 cells GSM2855483_Lung_3_2706 cells GSM2855484_Lung_3_3464 cells AO16_HT2_16h_control410 cells alveolar type 2 (AT2) cells49,701 cells neuroendocrine cells13,494 cells airway secretory cells12,402 cells alveolar type 1 (AT1) cells4,571 cells ciliated cells2,120 cells Kadur_Nat_2022_LO_Control13,017 cells Kadur_Nat_2022_LO_EGF_depletion10,909 cells Miller_DevCell_2020_Day_010,765 cells He_Cell_2022_deltaNp63alpha_overexpression10,073 cells Miller_DevCell_2020_Day_39,781 cells He_Cell_2022_RFX6_overexpression9,366 cells He_Cell_2022_PAX9_overexpression9,126 cells Kadur_Nat_2022_LO_Serum_treatement9,004 cells He_Cell_2022_TFAP2A_overexpression8,805 cells He_Cell_2022_NEUROG3_overexpression8,538 cells Rosado_BioRxiv_2021_GSM4984050_LungOD78,462 cells Lim_CellStemCell_2023_Lung_organoid_epithelium8,272 cells Hoffmann_CommunBiol_2022_AO15_pool_16h_control7,039 cells Tran_iScience_2022_GSE164514_AEC_3D6,881 cells He_Cell_2022_wild_type_genotype5,951 cells Lim_CellStemCell_2023_Lung_alveolar_organoid_epithelium5,681 cells He_Cell_2022_NEUROD1_overexpression5,529 cells Hoffmann_CommunBiol_2022_AO15_HT2_16h_control4,767 cells Lamers_EMBOJ_2021_Lung_Bronchioalveolar4,180 cells Chan_NatCommun_2022_bronchial_organoids4,073 cells He_Cell_2022_ASCL1_overexpression4,011 cells Chan_NatCommun_2022_nasopharyngeal_organoids3,576 cells Miller_DevCell_2020_Day_213,236 cells Hoffmann_CommunBiol_2022_AO16_pool_16h_control2,984 cells Hein_Dev_2022_10_week_iBTO2,950 cells Hoffmann_CommunBiol_2022_AO22_pool_16h_control2,945 cells Hein_Dev_2022_3_week_LPO_Batch22,804 cells Hein_Dev_2022_3_week_LPO_Batch12,770 cells Suzuki_STARProt_2021_LungO_BU3_NGPT_Basal_Cell_Medium_12,613 cells Salahudeen_Nat_2020_GSM2855485_Purified_AT22,560 cells Suzuki_STARProt_2021_LungO_BU3_NGPT_Basal_Cell_Medium_22,230 cells Lee_NatCommun_2021B_GSM5399379_LBO1,947 cells Salahudeen_Nat_2020_GSM2855475_Lung_1_21,945 cells Salahudeen_Nat_2020_GSM2855477_Lung_1_41,938 cells Hein_Dev_2022_Spheroids1,924 cells Hoffmann_CommunBiol_2022_AO22_HT2_16h_control1,842 cells Salahudeen_Nat_2020_GSM2855474_Lung_1_11,811 cells Salahudeen_Nat_2020_GSM2855476_Lung_1_31,774 cells Hein_Dev_2022_6_week_LPO_Batch11,717 cells Hein_Dev_2022_4_week_iBTO1,649 cells Suzuki_STARProt_2021_LungO_BU3_NGPT_FGF210DCIY_11,405 cells Suzuki_STARProt_2021_LungO_BU3_NGPT_FGF210DCIY_21,311 cells Salahudeen_Nat_2020_GSM2855481_Lung_2_41,248 cells Hein_Dev_2022_6_week_LPO_Batch21,200 cells Salahudeen_Nat_2020_GSM2855480_Lung_2_31,195 cells Salahudeen_Nat_2020_GSM2855478_Lung_2_11,163 cells Salahudeen_Nat_2020_GSM2855479_Lung_2_21,111 cells Hein_Dev_2022_10_week_LPO1,020 cells Salahudeen_Nat_2020_GSM2855482_Lung_3_1747 cells Salahudeen_Nat_2020_GSM2855483_Lung_3_2706 cells Salahudeen_Nat_2020_GSM2855484_Lung_3_3464 cells Hoffmann_CommunBiol_2022_AO16_HT2_16h_control410 cells alveolar sac112,884 cells 
