{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Alexander Beristain"],"organism":["Homo sapiens"],"software":["Cell Ranger"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16328"],"description":["Placental development occurs in a low oxygen environment, yet how oxygen tension instructs differentiation of progenitor cytotrophoblasts (CTB) along the extravillous versus villous pathways remains incompletely understood. In particular, the role of low oxygen in early extravillous trophoblast (EVT) progenitor expansion and subsequent maturation has been difficult to assess due to the lack of models allowing sequential, high-resolution characterization. Using human trophoblast organoids and single-cell transcriptomics, we examined the effects of ambient (21%) and physiological (2–3%, 8%) oxygen on EVT and SCT differentiation. We show that low oxygen promotes the initial expansion of column CTB-like progenitors but restricts terminal EVT maturation. Conversely, we show that ambient oxygen "],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Organoids were dissociated into single-cells as described in McNeill et. al. https://doi.org/10.1101/2025.10.29.685387","Sequencing - Following library generation,  the samples were sequenced using an Illumina NextSeq 2000 instrument using Illumina NextSeq2000 P2 reagent kit indicated in the table following manufacturer’s protocol.","Library Construction - Manufacturer's protocol was followed to construct single cell RNA libraries using the Chromium Single Cell 3’ v3.1 dual index kit (10x Genomics).","Nucleic Acid Extraction - Single-cell suspensions underwent FACS and live cells were used immediately for preparation of single cell RNA libraries using the Chromium Single Cell 3’ v3.1 kit (10x Genomics) according to the manufacturer's protocol to construct cDNA libraries."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Sequencing reads were aligned to reference genome hg38 using Cell Ranger v6.0.1.","Data Transformation - Generated data was normalized as described in McNeill et. al. https://www.biorxiv.org/content/10.1101/2025.10.29.685387v1."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 2000"],"pubmed_abstract":["<h4>SUMMARY</h4>  Placental development occurs in a low oxygen environment, yet how oxygen tension instructs differentiation of progenitor cytotrophoblasts (CTB) along the extravillous versus villous pathways remains incompletely understood. In particular, the role of low oxygen in early extravillous trophoblast (EVT) progenitor expansion and subsequent maturation has been difficult to assess due to the lack of models allowing sequential, high-resolution characterization. Using human trophoblast organoids and single-cell transcriptomics, we examined the effects of ambient (21%) and physiological (2–3%, 8%) oxygen on EVT and SCT differentiation. We show that low oxygen promotes the initial expansion of column CTB-like progenitors but restricts terminal EVT maturation. Conversely, we show th"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Homo sapiens"],"pubmed_title":["Low oxygen promotes extravillous trophoblast progenitor expansion but restrains maturation"],"pubmed_authors":["Gina L. McNeill, Giada Guntri, Ida Calvi, Alastair H. Kyle, Hans-Rudolf Hotz, Victoria M. Leonard, Willie Wu, Matthew J. Shannon, Andrew I. Minchinton, Keegan Korthauer, Margherita Y. Turco, Alexander G. Beristain","Alexander Beristain","Keegan Korthauer","Gina McNeill"],"additional_accession":[]},"is_claimable":false,"name":"scRNA-seq of human trophoblast organoids EVT-differentiated in 21%, 8%, and 3% oxygen","description":"Placental development occurs in a low oxygen environment, yet how oxygen tension instructs differentiation of progenitor cytotrophoblasts (CTB) along the extravillous versus villous pathways remains incompletely understood. In particular, the role of low oxygen in early extravillous trophoblast (EVT) progenitor expansion and subsequent maturation has been difficult to assess due to the lack of models allowing sequential, high-resolution characterization. Using human trophoblast organoids and single-cell transcriptomics, we examined the effects of ambient (21%) and physiological (2–3%, 8%) oxygen on EVT and SCT differentiation. We show that low oxygen promotes the initial expansion of column CTB-like progenitors but restricts terminal EVT maturation. Conversely, we show that ambient oxygen ","dates":{"release":"2026-09-01T00:00:00Z","modification":"2026-09-01T01:00:40.27Z","creation":"2025-12-02T16:57:08.422Z"},"accession":"E-MTAB-16328","cross_references":{"ENA":["ERP185975"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184"],"doi":["10.1101/2025.10.29.685387"]}}