Project description:T cell-specific overexpression of miR-185 caused a developmental block at DN3 stage of thymopoiesis. DN3 stage thymocytes were sorted from the wild type (C57BL/6) and miR-185 Tg mice, followed by total RNA isolation.
Project description:The NOTCH1-driven MYC enhancer (NMe) is essential for T cell development, transformation and the development of acute lymphoblastic leukemia. Here we analyze by RNAseq the gene expression profile of DN3 thymocytes from NMe wild type and NMe GATA site 1 and 2 (GS1+2) homozygous mutant mice. GSEA analysis show a significant enrichment of MYC signature genes, consistent with a deficient function of NMe in GATA site 1 and 2 homozygous mutant thymocytes.
Project description:The NOTCH1-driven MYC enhancer (NMe) is essential for T cell development, transformation and the development of acute lymphoblastic leukemia. Here we analyze chromatin accessibility by ATACseq in DN3 thymocytes and Notch-induced TALL blasts from NMe wild type and NMe GATA site 1 and 2 (GS1+2) homozygous mutant mice.
Project description:Lineage negative, CD44 negative, CD25 positive thymocytes were isolated from wt mice or Miz1 POZ-domain knockout mice to analyze the effect of loss of Miz1 in the DN3 population of T-cells We used the mouse Affymetrix MOE430-2 microarray to characterize global gene expression changes of DN3 thymocytes from Miz1 knockout mice. We performed microarray based gene expression profiling to determine the effect of loss of Miz1 activity on the gene expression pattern of mouse DN3 thymocytes from wt and Miz1-delta-POZ mice.
Project description:Lineage negative, CD44 negative, CD25 positive thymocytes were isolated from wt mice or Miz1 POZ-domain knockout mice to analyze the effect of loss of Miz1 in the DN3 population of T-cells We used the mouse Affymetrix MOE430-2 microarray to characterize global gene expression changes of DN3 thymocytes from Miz1 knockout mice.
Project description:TCF-1 is an HMG family transcription factor which is known to be critical for T cell development. We discovered that it has a unique role in suppressing malignant transformation of developing thymocytes at early stages. We identified ID2 and LEF-1 as key TCF-1 target genens in tumor suppression. We used microarrays to detect gene expression changes in WT and TCF-1 deficient DN3 thymocytes as well as T cell lymphoma cells developed in TCF-1 KO mice. DN3 thymocytes were directly sorted from WT or TCF-1 KO mice. T cell lymphoma blast cells were also sorted from TCF-1 KO mice that developed the disease. RNA was extracted and hybridized to GeneChip Mouse GENE 1.0 ST arrays (Affymetrix).
Project description:We found that naïve T cells from SCD1-/- mice have an intrinsic preference for regulatory T cells differentiation. Such preference was imprinted to DN3 thymocytes developed in SCD1 deficient thymus and persisted to mature T cells. To investigate the potential epigenetic changes underlying the Treg-bias. We employed ATAC-seq to examine the chromatin accessibility of naïve T cells and DN3 thymocytes from SCD1-/- mice and their littermate controls.
