{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Jan Kubovčiak"],"organism":["Mus musculus"],"software":["10x cellranger v7.1.0"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14489"],"description":["The T-cell factor 4 (Tcf4) protein (encoded by the Tcf7l2 gene) is a nuclear transcription regulator, which plays a key role in maintaining intestinal homeostasis, stem cell self-renewal and epithelial cell differentiation. Tcf4 has been identified as a crucial regulator of Paneth cell function in small intestinal crypts. It controls the expression of antimicrobial peptides and other effector molecules that contribute to the maintenance of the gut microbiota and protection against intestinal pathogens. The Defa6 promoter is active in adult Paneth cells and depletion of Tcf4 in these cells leads to loss of lysozyme production, altered morphology and mislocalization of these cells with the strongest phenotype in the ileum. For deeper understanding of the Tcf4 function in the Paneth cell lineage, we employed the Rosa26-tdTomato Tcf7l2-wt/wt Defa6-iCre mouse strain. In this strain, cells with an active Defa6 promoter are marked by expression of a red fluorescent protein (tdTomato). In parallel, homozygous depletion of the Tcf4 protein was obtained in Tcf7l2-flox/flox littermates. We performed the single cell gene expression profiling of Defa6-tdTomato+ cells from the middle part of the small intestine."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - Single-cell RNA-seq libraries were prepared using Chromium controller instrument and Chromium Next Gem single-cell 3’ reagent kit version 3.1 (both 10X Genomics, Pleasanton, CA, USA) according to the manufacturer’s protocol targeting 4000 cells per sample.","Nucleic Acid Extraction - cDNA was extracted from cell suspension during library preparation routine using Chromium next gem single-cell 3′ reagent kit (version 3.1).","Sequencing - The libraries were sequenced using NextSeq 2000 instrument (Illumina, San Diego, CA, USA) with P2 flowcell according to the manufacturer’s protocol.","Sample Collection - Adult littermates of the Rosa26tdTomato Defa6-iCre mouse strain carrying the Tcf7l2-wt or Tcf4-floxed alleles were sacrificed by cervical dislocation. In these mice, cells expressing Defa6 producing constitutively active Cre recombinase are marked by endogenous expression of the red fluorescent protein tdTomato. The epithelium from the middle part of the small intestine (jejinum) was isolated, and a suspension of single cells was prepared by cleavage using dispase and DNase I. Cells were stained with the following antibodies: Hoechst33358, anti-CD45-PacificBlue, anti-CD31-PacificBlue, anti-EpCAM-FITC. Using fluorescence-activated cell sorting (FACS), we isolated Hoechst-/CD45-/CD31-/EpCAM+/tdTomato+ cells, i.e. Defa6+ cells with either wild-type Tcf4 (WT) or  homozygous loss of Tcf4 protein (cKO)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Fastq files were processed using 10x cellranger software version 7.1.0 using GRCm39 assembly with Ensembl annotation version 109."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 2000"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Mus musculus"],"pubmed_title":["Tcf4 regulates secretory cell fate decisions in the small intestine and colon tumors: insights from transcriptomic, histological, and microbiome analyses."],"pubmed_authors":["Jan Kubovčiak","Vladimír Kořínek","Lucie Janečková","Janeckova L, Stastna M, Hrckulak D, Berkova L, Kubovciak J, Onhajzer J, Kriz V, Dostalikova S, Mullerova T, Vecerkova K, Tenglerova M, Coufal S, Kostovcikova K, Blumberg RS, Filipp D, Basler K, Valenta T, Kolar M, Korinek V.","Monika Šťastná","Michal Kolář"],"additional_accession":[]},"is_claimable":false,"name":"Single cell expression analysis of Defa6+ cells possessing either wild-type Tcf4 or homozygous loss of the Tcf4 protein isolated from mouse small intestinal epithelium","description":"The T-cell factor 4 (Tcf4) protein (encoded by the Tcf7l2 gene) is a nuclear transcription regulator, which plays a key role in maintaining intestinal homeostasis, stem cell self-renewal and epithelial cell differentiation. Tcf4 has been identified as a crucial regulator of Paneth cell function in small intestinal crypts. It controls the expression of antimicrobial peptides and other effector molecules that contribute to the maintenance of the gut microbiota and protection against intestinal pathogens. The Defa6 promoter is active in adult Paneth cells and depletion of Tcf4 in these cells leads to loss of lysozyme production, altered morphology and mislocalization of these cells with the strongest phenotype in the ileum. For deeper understanding of the Tcf4 function in the Paneth cell lineage, we employed the Rosa26-tdTomato Tcf7l2-wt/wt Defa6-iCre mouse strain. In this strain, cells with an active Defa6 promoter are marked by expression of a red fluorescent protein (tdTomato). In parallel, homozygous depletion of the Tcf4 protein was obtained in Tcf7l2-flox/flox littermates. We performed the single cell gene expression profiling of Defa6-tdTomato+ cells from the middle part of the small intestine.","dates":{"release":"2026-06-29T00:00:00Z","modification":"2026-06-29T10:04:52.113Z","creation":"2024-10-01T10:22:21.323Z"},"accession":"E-MTAB-14489","cross_references":{"pubmed":["publ-4-o67l-removable"],"ENA":["ERP164652"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0004917","EFO_0005518","EFO_0004184"],"doi":["10.1186/s13287-025-04280-y"]}}