{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Charles Girardot"],"instrument_platform":["NextSeq 2000"],"study_type":["RNA-seq of coding RNA"],"organism":["Homo sapiens"],"species":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14937"],"description":["This dataset comprises bulk RNA sequencing (RNA-seq) data generated from primary human brain microvascular endothelial cells (HBMECs), induced pluripotent stem cell (iPSC)-derived iBMEC-like cells, and ETS-transcription factor-guided iPSC-derived endothelial cells (ETS-iBMEC). Cells were cultured as monolayers and exposed to egress products from ruptured Plasmodium falciparum schizonts (5x107 schizonts/ml) or a media control. The experimental design included exposure durations of 8 and 24 hours to examine transcriptional responses over time. RNA was extracted from these samples and subjected to library preparation and bulk RNA sequencing using a NextSeq 2000 platform (P3 flow cell, 50 bp single-end reads, no barcoding). This dataset provides valuable insights into the transcriptional responses of endothelial cell types to P. falciparum egress products and serves as a resource for studying the host-pathogen interactions at the brain-endothelial interface and for endothelial profiling of the three cell types."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Total RNA isolation At the end of the experimental timeline, each sample was fixed in Buffer RLT, and total RNA was extracted using the RNeasy QIAGEN Mini Kit, following the manufacturer's instructions, including on-column DNase digestion. RNA quality and concentration were assessed using the Tapestation system (Agilent Technologies). The final samples were adjusted to ~100 ng total RNA and stored at -80°C.","Library Construction - This protocol prepares stranded mRNA-seq libraries from total RNA using the NEBNext RNA Ultra II Kit with polyA enrichment. NEBNext RNA Ultra II Kit for bulkRNA library prepIndividually barcoded stranded mRNA-seq libraries were prepared from high quality total RNA samples (~100 ng/sample) using the New England Biolabs NEBNext RNA Ultra II Kit combined with the polyA-enrichment module, according to the manufacturers instructions with 12 PCR cycles,implemented on the liquid handling robot Beckman i7. Obtained libraries that passed the QC step were pooled in equimolar amounts; 650 pM solution of this pool was loaded on the Illumina sequencer NextSeq 2000 and sequenced uni-directionally, generating 1980 million reads, each 80 bases long.","Sequencing - single-end sequencing on illumina NextSeq 2000","Sample Collection - This protocol describes the culturing and experimental conditions for hbmec and ibmec used for bluk RNASeq. iBMEC and hBMEC culture for bulk RNASeq   Human brain microvascular endothelial cells (hBMEC) hBMECs (Cell Systems, lot 376.11.04.01.2F) were cultured according to the manufacturer's instructions. Cells were seeded at 3 × 104 passage 7 hBMECs per well in 24-well plates and grown with daily media changes for 3 days.   iBMEC (DOX-induced and not DOX-induced)  Human IMR90-4 induced pluripotent stem cells (iPSCs) (WiCell, lot WB65316) were cultured following the manufacturer's instructions. This genetically modified cell line contains a PiggyBac insertion of a Tet-On motif, enabling DOX-inducible upregulation of the ETS transcription factors ETV2, ERG, and FLI1. The B6 clone was used for differentiation and experiments. Differentiation was performed according to Park et al., Nat Commun, 2019, with the following modification: On day 6, DOX induction was applied to generate the DOX cell line, while no induction was applied for the noDOX cell line. On day 8, the resulting cell populations were purified through subpassaging and washing on collagen-fibronectin-coated plates. Cells were then seeded into 24-well plates at 7.5 × 104 DOX-induced and 1 × 105 non-DOX-induced cells per well.   P. falciparum egress media exposure Parasite egress media was prepared as described in Long et al., bioRxiv, 2024, and applied to the respective samples at a concentration of 5 × 107 egressed parasites per mL for 8 or 24 hours."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Charles Girardot","Francois Korbmacher","Maria Aznar"],"additional_accession":[]},"is_claimable":false,"name":"Bulk RNA-seq of HBMEC, iBMEC-like cells, and ETS-iBMEC in Response to Plasmodium falciparum Egress Products","description":"This dataset comprises bulk RNA sequencing (RNA-seq) data generated from primary human brain microvascular endothelial cells (HBMECs), induced pluripotent stem cell (iPSC)-derived iBMEC-like cells, and ETS-transcription factor-guided iPSC-derived endothelial cells (ETS-iBMEC). Cells were cultured as monolayers and exposed to egress products from ruptured Plasmodium falciparum schizonts (5x107 schizonts/ml) or a media control. The experimental design included exposure durations of 8 and 24 hours to examine transcriptional responses over time. RNA was extracted from these samples and subjected to library preparation and bulk RNA sequencing using a NextSeq 2000 platform (P3 flow cell, 50 bp single-end reads, no barcoding). This dataset provides valuable insights into the transcriptional responses of endothelial cell types to P. falciparum egress products and serves as a resource for studying the host-pathogen interactions at the brain-endothelial interface and for endothelial profiling of the three cell types.","dates":{"release":"2026-03-05T00:00:00Z","modification":"2026-03-05T02:02:44.037Z","creation":"2025-03-10T17:49:02.177Z"},"accession":"E-MTAB-14937","cross_references":{"ENA":["ERP170149"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003738","EFO_0004184"]}}