biostudies-arrayexpressJohan HenrikssonHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16352Single-cell RNA-seq (parse biosciences) of in vitro differentiated human trophoblast stem cells, infected with RVFVbiostudies-arrayexpressGrowth Protocol - hTSC lines were established from isolated villous cytotrophoblasts of human single placentae. hTSC lines were maintained on human fibronectin (Sigma) pre-coated surface in advanced DMEM/F12 (Invitrogen) containing 10 mM HEPES (Gibco), 1×B-27 Supplement (Gibco), 1×Insulin-Transferrin-Selenium-Ethanolamine (ITS-X, Gibco), and 2 mM Glutamine (Gibco), 100 ng/mL recombinant human epidermal growth factor (rhEGF, R&D Systems), 3 μM CHIR99021 (Tocris), and 5 μM Rock Inhibitor (Y-27632, Santa Cruz) at 37°C with 5% CO2.Sample Treatment - hTSCs were infected with RVFV (ZH548 strain) in serum-free advanced DMEM/F12 at an MOI of 1 for 1 hour. The inoculum was then removed, and fresh hTSC culture medium was added.Library Construction - hTSCs were fixed using the Evercode Cell Fixation Kit (PARSE Biosciences) and passed through a 30 µm filter (pluriSelect). Fixed cells were then processed, and single-cell libraries were prepared using the Evercode WT Mini v3 protocol (Parse Biosciences).Sequencing - Pooled libraries were sequenced on an Illumina NovaSeq X using a shared 1.5B flow cell, with a read configuration of R1: 128 cycles and R2: 177 cycles.Nucleic Acid Extraction - Part of library preparationSample Collection - At 24 hours post-infection, single-cell preparation was performed. Briefly, cells were rinsed with PBS and treated with a dissociation buffer containing TrypLE (Invitrogen), DNase (25 µg/mL, Roche), EDTA (0.5 mM, Invitrogen), and RNase inhibitor (1 U/mL, Thermo Scientific) for 10 minutes. Dissociated cells were collected by centrifugation at 400 × g for 5 minutes at 4 °C.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Using the split-pipe v.1.3.1 pipeline (Parse Biosciences), STAR 2.7.11b was used to align FASTQ files to a combined reference genome (Homo_sapiens. GRCh38.112; Genbank accession number for RVFV genome: DQ375406.1, DQ380200.1, DQ380149.1). Single-cell analysis followed a standard workflow using Seurat v.5.3.0 to generate the processed data file, stored using saveRDS in R.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq XRNA-seq of coding RNA from single cellsHomo sapiensMagnus EvanderJohan HenrikssonfalseDissecting placental host-pathogen interactions: Rift Valley fever virus infection in early human trophoblast stem cellsSingle-cell RNA-seq (parse biosciences) of in vitro differentiated human trophoblast stem cells, infected with RVFV2025-12-12T00:00:00Z2026-05-27T15:28:33.137Z2025-12-04T11:42:54.826ZE-MTAB-16352ERP186151EFO_0002944EFO_0004170EFO_0003789EFO_0005684EFO_0005518EFO_0003816EFO_0004184EFO_0003969