{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Qianhui Yu"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA from single cells"],"organism":["Homo sapiens"],"species":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16821"],"description":["This data provides a single-cell RNA-seq characterization of human intestinal engineered epithelium and its interaction with tissue-resident memory T cells (scRNA-seq) or the pathogen Salmonella Typhimurium (scRNA-seq and scATAC-seq)."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - After single cell dissociation, the singe-cell nucleic acid extraction and subsequent RNA-seq libraries were generated using 10x Genomics Chromium Next GEM Single Cell 3ʹ v3.1 reagents according to user manual CG000315 Rev F. For multiplexed scRNA-seq, single-cell suspensions of 9 biological samples were individually tagged with 10x Genomics 3’ CellPlex Set A reagents according to the Demonstrated Protocol CG000391 Rev B Protocol 1. Equal amounts of tagged cells were pooled together for each sample. Three lanes of Chromium Next GEM Chip G were loaded targeting 30.000 cells per lane. Cell encapsulation and library preparation was performed according to user guide Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 with Feature Barcode technology for Cell Multiplexin","Library Construction - After single cell dissociation, the singe-cell nucleic acid extraction and subsequent RNA-seq libraries were generated using 10x Genomics Chromium Next GEM Single Cell 3ʹ v3.1 reagents according to user manual CG000315 Rev F. For multiplexed scRNA-seq, single-cell suspensions of 9 biological samples were individually tagged with 10x Genomics 3’ CellPlex Set A reagents according to the Demonstrated Protocol CG000391 Rev B Protocol 1. Equal amounts of tagged cells were pooled together for each sample. Three lanes of Chromium Next GEM Chip G were loaded targeting 30.000 cells per lane. Cell encapsulation and library preparation was performed according to user guide Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 with Feature Barcode technology for Cell Multiplexing C","Growth Protocol - For seeding of the chips - hereafter referred to as ‘engineered intestines’ once intestinal epithelial cells are included - approximately 4-day-old human intestinal organoids from various regions of the gastrointestinal tract (duodenum, jejunum, ileum, colon) between passage 5-25 were collected in base-media (Advanced DMEM/F12, HEPES 10mM, Glutamax 1%, Primocin 50ug/mL) and transferred to a 15 mL Falcon tube. Following centrifugation at 300g at 4°C for 4 min, the base-media was aspirated and the pellet was thoroughly resuspended in base-media. After repeating the centrifugation step, organoids were singularized with TrypLE express solution (12604-013, Gibco) containing 250 U/mL DNase I (4536282001, Roche) and 10 µm Y-27632 (72305, Stemcell Technologies) for 8 min at 37°C ","Sample Treatment - Salmonella Typhimurium infection:  The GFP reporter strain of Salmonella enterica subsp. enterica serovar Typhimurium (14028GFP, ATCC), hereafter referred to as S.Tm, was used to infect the epithelial monolayer for 24 h. S.Tm inoculums were grown overnight at 37°C and 230 rpm in 10 mL of BHI (1002417, MP Biomedicals) medium with 100 µg/mL ampicillin (A53542, Sigma-Aldrich) using 50 mL Mini Bioreactor tubes (431720, Corning). Following overnight growth, the OD600 values of the cultures were measured to adjust the bacterial concentration to 10^8 CFU/mL. The bacteria were then pelleted by centrifugation at 3000 rpm for 5 min and washed once with PBS. Subsequently, the pellets were resuspended in 1 mL of chip media (see growth protocol) and serially diluted. The desired numb","Sample Collection - Prior to dissociation, surfaces were cleaned with RNase AWAY™ Decontamination Reagent (10328011, Invitrogen) and all tubes were coated with a coating solution containing HBSS -Ca2+/ -Mg2+ (14175095, Gibco) + 1% BSA (130-091-376, Miltenyi Biotec) at 4°C for at least 15 min. Three independent engineered intestines were pooled for each scRNA-seq and five engineered intestines for scMultiome samples. Intestinal monolayers were detached from the matrix, collected and transferred to DNA LoBind 1.5mL tubes (22431021, Eppendorf) with 1 mL of coating solution using forceps. In the case of the scMultiome experiment, where the epithelium integrity was compromised, the epithelium and hydrogel matrix were apically punched using a 3 mm puncher and transferred to a 1.5 mL tube. The pu","Sequencing - After single cell dissociation, the singe-cell nucleic acid extraction and subsequent RNA-seq libraries were generated using 10x Genomics Chromium Next GEM Single Cell 3ʹ v3.1 reagents according to user manual CG000315 Rev F. For multiplexed scRNA-seq, single-cell suspensions of 9 biological samples were individually tagged with 10x Genomics 3’ CellPlex Set A reagents according to the Demonstrated Protocol CG000391 Rev B Protocol 1. Equal amounts of tagged cells were pooled together for each sample. Three lanes of Chromium Next GEM Chip G were loaded targeting 30.000 cells per lane. Cell encapsulation and library preparation was performed according to user guide Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 with Feature Barcode technology for Cell Multiplexing CG000388 Re"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Marius Harter","Qianhui Yu","Mikhail Nikolaev","J. Gray Camp","Nikolche Gjorevski","Rubén López-Sandoval"],"additional_accession":[]},"is_claimable":false,"name":"Modeling host-microbe interactions in immunocompetent engineered human gut tissues","description":"This data provides a single-cell RNA-seq characterization of human intestinal engineered epithelium and its interaction with tissue-resident memory T cells (scRNA-seq) or the pathogen Salmonella Typhimurium (scRNA-seq and scATAC-seq).","dates":{"release":"2026-08-17T00:00:00Z","modification":"2026-08-17T01:00:46.034Z","creation":"2026-03-27T14:25:55.072Z"},"accession":"E-MTAB-16821","cross_references":{"ENA":["ERP191485"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005684","EFO_0005518","EFO_0004184","EFO_0003969"]}}