biostudies-arrayexpressVasileios BekiarisMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16692This study investigates the post-thymic maturation and transcriptional programming of intestinal γδ T cells across early life. Single-cell RNA sequencing of FACS-sorted small-intestinal lamina propria γδ T cells was performed at four developmental stages: newborn, day 7, day 21, and post-weaning (day 42) in order to characterize dynamic changes in cell composition, activation, and effector programs. Mice carried a RORγt-Cre allele, cIAP1 floxed alleles, and a full cIAP2 knockout. Both Cre⁺ and Cre⁻ γδ T cells were sorted; Cre⁻ cells served as wild-type controls and were used to define the normal developmental trajectory (aim 1), while Cre⁺ cells, which lack cIAP proteins, were analyzed alongside their Cre⁻ littermates controls to determine how cIAP deficiency affects γδ T cell development and transcriptional profile (aim 2).biostudies-arrayexpressSample Collection - Small intestines and colons were dissected from adult mice and were flushed with 20 mL HBSS-HEPES to remove intestinal contents. Fat and Peyer’s patches were removed, the tissues were opened longitudinally and cut into small pieces of approximately 1 cm. Tissue was washed 4 times in HBSS-EDTA buffer at 37°C while shaking at 400 rpm and then digested using 60 µg/ml LiberaseTM (Roche) and 40 µg/ml DNase (Sigma-Aldrich) per sample in supplemented RPMI for 45 minutes at 37°C on a magnetic stirrer (800 rpm). The resulting cell suspensions were filtered through 70 μm cell strainers and washed once in supplemented RPMI. Lymphocytes were separated on a 40/70 Percoll gradient. Cells from the interphase were collected and washed once before use. For neonatal gut samples, the Percoll gradient was omitted. Cells from Cre- and Cre+ RORγt-CRE-cIAP1F/F-cIAP2KO were stained in cold PBS containing bovine serum albumin (0.5%) and sorted using a BD FACSAria Fusion III. Each genotype was differentially hashed with TotalSeq anti-mouse antibodies (C0304, C0305; 1 µg per million cells; Biolegend).Nucleic Acid Extraction - RNA and cDNA was isolated and prepared following the Chromium Next GEM Single Cell 5' v2 (Dual Index) User Guide (version F) from 10X Genomics.Library Construction - Libraries were prepared following the Chromium Next GEM Single Cell 5' v2 (Dual Index) User Guide (version F) from 10X Genomics. Library quality control and quantification was performed using a 2100 Bioanalyzer equipped with a High Sensitivity DNA kit (Agilent, 5067-4626).Sequencing - Libraries were sequenced on an Illumina NextSeq 6000 instrument at the Flow Cytometry & Single Cell Core Facility at the University of Copenhagen, Denmark following the sequencing depth and read-length cycles recommended by 10X Genomics in the Chromium Next GEM Single Cell 5' v2 (Dual Index) User Guide (version F).OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - The data was Log Normalized with default parameters from Seurat.UnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNA from single cellsMus musculusVasileios BekiarisfalseSingle-cell RNA-seq of intestinal γδ T cells from cIAP2-deficient and RORγt-Cre–mediated cIAP1 conditional knockout mice across developmental stagesThis study investigates the post-thymic maturation and transcriptional programming of intestinal γδ T cells across early life. Single-cell RNA sequencing of FACS-sorted small-intestinal lamina propria γδ T cells was performed at four developmental stages: newborn, day 7, day 21, and post-weaning (day 42) in order to characterize dynamic changes in cell composition, activation, and effector programs. Mice carried a RORγt-Cre allele, cIAP1 floxed alleles, and a full cIAP2 knockout. Both Cre⁺ and Cre⁻ γδ T cells were sorted; Cre⁻ cells served as wild-type controls and were used to define the normal developmental trajectory (aim 1), while Cre⁺ cells, which lack cIAP proteins, were analyzed alongside their Cre⁻ littermates controls to determine how cIAP deficiency affects γδ T cell development and transcriptional profile (aim 2).2026-03-14T00:00:00Z2026-03-14T02:03:46.99Z2026-02-26T14:34:25.447ZE-MTAB-16692ERP189680E-MTAB-16691E-MTAB-16690E-MTAB-16689EFO_0002944EFO_0004170EFO_0005684EFO_0005518EFO_0003816EFO_0004184