biostudies-arrayexpressMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-13606The transcription factor 4 (Tcf4) protein, which is encoded by the Tcf7l2 (transcription factor 7-like 2) gene, 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.biostudies-arrayexpressSample Collection - Mice were sacrificed by cervical dislocation 7 days after tamoxifen treatment. 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.Nucleic Acid Extraction - Total RNA was isolated using RNeasy Micro Kit (Qiagen) as described in the manufacturer’s protocol.Sequencing - Libraries were sequenced on a Illumina NextSeq® 500 instrument using a 76bp single-end configuration.Sample Treatment - Adult Ki67-RFP Tcf7l2-flox/flox Villin-CreERT2 mice were intraorally administered with 5 mg tamoxifen.Library Construction - Libraries were prepared with a SMARTer® Stranded Total RNA-Seq – Pico Input Mammalian library preparation kit v2 (Takara).MINSEQE ScoreAssays and DataProcessed DataorganisationMAGE-TAB FilesData Transformation - Per gene read counts were counted using featureCounts v1.6.4 within nf-core/rnaseq workflow.Sequence Alignment - Sequencing data were quality filtered, adapter trimmed and mapped to reference genome GRCm38 (Ensembl annotation version 98) using nf-core/rnaseq pipeline v1.4.2 with HISAT2 aligner v2.1.0.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsNextSeq 500RNA-seq of coding RNAMus musculusTcf4 regulates secretory cell fate decisions in the small intestine and colon tumors: insights from transcriptomic, histological, and microbiome analyses.ERP155784Lucie JaneckovaJan KubovciakMonika StastnaVladimir KorinekMichal KolarJaneckova 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.falseExpression profiling of RFP-positive cells isolated from Ki67-RFP/Tcf7l2/Villin-CreERT2 mouse small intestinal epithelium 7 days after tamoxifen administration.The transcription factor 4 (Tcf4) protein, which is encoded by the Tcf7l2 (transcription factor 7-like 2) gene, 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.2026-06-29T00:00:00Z2026-06-29T09:58:26.782Z2023-12-05T10:46:33.709ZE-MTAB-13606publ-0-415c-removableERP155784EFO_0002944EFO_0004170EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184EFO_000396910.1186/s13287-025-04280-y