{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Jan Kubovčiak"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-13731"],"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 key 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 intestinal microbiota and protection against intestinal pathogens. Depletion of Tcf4 in mouse intestinal epithelial cells leads to loss of proliferating cells and dramatic changes in the morophology of the intestinal epithelum. To examine Tcf4 function in more detail, we used the Ki67-RFP Tcf7l2-flox/flox Villin-CreERT2 mouse strain. In this strain, proliferating cells are marked by expression of red fluorescent protein (RFP) and Tcf4 depletion from intestinal epithelial cells is accomplished by administration of tamoxifen. After 7 days, small red structures, i.e. \\\\\"escaped crypts\\\\\", appear in the epithelium, marking proliferative zones that appear to have escaped Tcf4 deletion. We performed gene expression profiling of RFP+ cells from these \\\\\"escaped crypts\\\\\" and from crypts isolated from wild-type epithelium."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Adult Ki67-RFP Tcf7l2-flox/flox Villin-CreERT2 mice were intraorally administered with 5 mg tamoxifen (in EtOH/mineral oil) and sacrificed by cervical dislocation after 7 days. In these mice, proliferating cells are marked by endogenous expression of the red fluorescent protein RFP. The small intestinal epithelium was isolated from the proximal part of jejunum and the single cell suspension was prepared using dispase digestion. Cells were stained with the following antibodies: Hoechst33358, anti-CD45-PacificBlue, anti-CD31-PacificBlue, anti-EpCAM-FITC, anti CD24-APC. Using fluorescent activated cell sorting (FACS), we isolated Hoechst-/CD45-/CD31-/EpCAM+/RFP+/CD24+ cells, i.e. proliferating epithelial crypt cells.","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.","Sequencing - The libraries were sequenced using NextSeq 500 instrument (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol with mRNA fragment read length of 130 nt (samples KO1 and WT1) or 119 nt (sample WT2). Each sample was sequenced in a separate run.","Nucleic Acid Extraction - First-strand cDNA was extracted from cell suspension during library preparation routine using Chromium next gem single-cell 3′ reagent kit (version 3.1)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 500"],"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 RNA-Seq expression profiling of RFP-positive cells isolated from Ki67-RFP/Tcf7l2/Villin-CreERT2 mouse small intestinal epithelium 7 days after tamoxifen administration","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 key 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 intestinal microbiota and protection against intestinal pathogens. Depletion of Tcf4 in mouse intestinal epithelial cells leads to loss of proliferating cells and dramatic changes in the morophology of the intestinal epithelum. To examine Tcf4 function in more detail, we used the Ki67-RFP Tcf7l2-flox/flox Villin-CreERT2 mouse strain. In this strain, proliferating cells are marked by expression of red fluorescent protein (RFP) and Tcf4 depletion from intestinal epithelial cells is accomplished by administration of tamoxifen. After 7 days, small red structures, i.e. \\\\\"escaped crypts\\\\\", appear in the epithelium, marking proliferative zones that appear to have escaped Tcf4 deletion. We performed gene expression profiling of RFP+ cells from these \\\\\"escaped crypts\\\\\" and from crypts isolated from wild-type epithelium.","dates":{"release":"2026-06-29T00:00:00Z","modification":"2026-06-29T10:01:55.394Z","creation":"2024-01-23T18:11:16.463Z"},"accession":"E-MTAB-13731","cross_references":{"pubmed":["publ-1-tdcz-removable"],"ENA":["ERP156824"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0004184"],"doi":["10.1186/s13287-025-04280-y"]}}