Project description:In the bone marrow B cell development occurs in initimate and essential association with stromal cells. Known effects of stromal cells on B cell development have been shown to be mediated through direct contact and by soluble factors produced by stromal cells. Our findings suggest that cell-nonautonomous Hh signaling may play an important role in B cell lymphopoiesis. We therefore interrogated OP9 stromal cells for Hh-dependent transcripts that may confer B lymphopoietic identity. We generated OP9 stromal cells deficient in Hh signaling through targeting the non-redundant, pathway-obligate GPCR Smoothened. OP9 cells were transduced with RNAi pLKO.1-Puro lentiviral particles expressing a scrambled control shRNA (NT) or shRNA targeting Smoothened (Smo-kd). RNA from stable NT and Smo-kd OP9 cells were isolated in triplicate and global changes in transcripts were analyzed using the Affymetrix Mouse Exon 1.0 ST gene chip.
Project description:In the bone marrow B cell development occurs in initimate and essential association with stromal cells. Known effects of stromal cells on B cell development have been shown to be mediated through direct contact and by soluble factors produced by stromal cells. Our findings suggest that cell-nonautonomous Hh signaling may play an important role in B cell lymphopoiesis. We therefore interrogated OP9 stromal cells for Hh-dependent transcripts that may confer B lymphopoietic identity.
Project description:Subcutanesouly tumors from both Bmal1+/+ and Bmal1-/- mice were used to isolated stromal vascular fractions (SVF). Tumor cells with GFP+ signals were exclusive. Remain GFP- cells were collected to do RNAseq.
Project description:We collected whole genome testis expression data from hybrid zone mice. We integrated GWAS mapping of testis expression traits and low testis weight to gain insight into the genetic basis of hybrid male sterility.
Project description:OP9 stromal cells are strong inducers of mesoendodermal differentiation of human embryonic stem cells. They acquire inductive function after prolonged post-confluence culture. The experiment is designed to determine the genes specifically expressed in these highly inductive OP9 cells compared to non-confluent OP9 cultures as well as other stromal cell lines (MS5, S17).
Project description:It is known that ubiquitination is important for T cell receptor (TCR) signaling during T cell activation but the breadth of ubiquitination events triggered during TCR signaling is not completely understood. This dataset utilizes di-glycine remnant profiling combined with mass spectrometry to identify a global landscape of ubiquitination events downstream of the TCR and to quantify changes ubiquitin abundance in response to TCR stimulation. Additionally, whole cell proteomics data were generated to measure protein abundances during TCR stimulation. Mouse primary T cells were isolated, proliferated and either remained resting or stimulated with CD3/CD28 to activate downstream signaling through the TCR and co-stimulatory pathways. Di-glycine remnant profiling and whole cell proteomics was performed on rested cells and cells that had undergone CD3/CD28 TCR stimulation for 4 hours. These data were analyzed to identify the ubiquitination events during TCR activation and to quantify the change in peptide-based ubiquitin abundance and total protein abundance over the course of the 4 hour TCR stimulation. Integration of di-glycine and whole cell proteomics was used to generate protein-specific predictions of whether ubiquitination events downstream of TCR signaling lead to a decrease in associated protein abundance. The analysis of these data suggests that T cell activation leads to an increase in ubiquitination that is not associated with proteasomal or lysosomal degradation.
