biostudies-arrayexpressMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-13730The 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. To further investigate the function of Tcf4 in Paneth cells, 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, heterozygous or homozygous deletion of the Tcf4 protein was obtained in Tcf7l2-flox/wt and Tcf7l2-flox/flox littermates, respectively. We performed gene expression profiling of Defa6-tdTomato+ cells from the distal part of the small intestine.biostudies-arrayexpressSample 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 distal part of the small intestinal epithelium was isolated, and a suspension of single cells was prepared by dispase cleavage. 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 or heterozygous and homozygous loss of Tcf4 protein.Nucleic Acid Extraction - Total RNA was isolated using RNeasy Micro Kit (Qiagen) as described in the manufacturer’s protocol.Library Construction - Libraries were prepared with a SMARTer® Stranded Total RNA-Seq – Pico Input Mammalian library preparation kit v2 (Takara).Sequencing - Libraries were sequenced on Illumina NextSeq 2000 instrument using P2 flowcell with fragment read length of 122 nt.MINSEQE ScoreAssays and DataorganisationMAGE-TAB FilesMetabolomicsUnknownTranscriptomicsGenomicsProteomicsNextSeq 2000RNA-seq of coding RNAMus musculusERP156823Jan KubovčiakVladimír KořínekLucie JanečkováKateřina VečerkováMonika ŠťastnáMichal KolářfalseRna-Seq expression profiling of Defa6+ cells possessing either wild-type Tcf4 or heterozygous and homozygous loss of Tcf4 protein isolated from mouse small intestinal epitheliumThe 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. To further investigate the function of Tcf4 in Paneth cells, 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, heterozygous or homozygous deletion of the Tcf4 protein was obtained in Tcf7l2-flox/wt and Tcf7l2-flox/flox littermates, respectively. We performed gene expression profiling of Defa6-tdTomato+ cells from the distal part of the small intestine.2026-05-01T00:00:00Z2026-05-01T01:03:25.699Z2024-01-23T18:08:32.592ZE-MTAB-13730ERP156823EFO_0002944EFO_0004170EFO_0005518EFO_0003738EFO_0004184