Project description:An updated representation of S. meliloti metabolism that was manually-curated and encompasses information from 240 literature sources, which includes transposon-sequencing (Tn-seq) data and Phenotype MicroArray data for wild-type and mutant strains.
Project description:Test data used for the evaluation of ESAT performance and results files for data from 3' and 5' end-sequencing RNA-Seq protocols and droplet-based single-cell RNA-Seq.
Project description:Experiment: Establishment of expression profiles in HT, PTC with HT, PTC without HT, and mPTC in comparison to TN samples. TN samples were downloaded as CEL files from the repository of the microarray vendor. Biostatistical analysis focussed in first instance on identifying genes and biofunctions related to HT and PTC with HT.
Project description:Naive CD4 T (TN) cells show some degree of heterogeneity. However, mechanisms that alter TN cells are still largely unknown, and physiological importance in the phenotypic alteration of TN cells is unclear. Thus, to reveal the mechanisms that alter TN cell characteristics, we performed transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) on TN cells from different secondary lymphoid organs with different strength of tonic TCR stimulation.
Project description:By taking advantage of the strong genetic interactions between trans-translation and other ribosome rescue systems, we have employed a transposon sequencing (Tn-Seq) to identify potential novel rescue factors in Bacillus subtilis. In addition to the identification the ArfA-type rescue factor BrfA, as well as the RQC elongation actors RqcP and RqcH, our Tn-Seq screen led to the identification of YlmH, a poorly characterized S4-domain-containing protein, as a potential RQC factor. Binding of YlmH to 50S ribosomal subunit was confirmed by proteomics approach.
Project description:Test data used for the evaluation of ESAT performance and results files for data from 3' and 5' end-sequencing RNA-Seq protocols and droplet-based single-cell RNA-Seq. Quantification and analysis of Tophat-aligned (v2.0.9) samples from mouse bone-marrow derived dendritic cells (mBMDC) timecourse (0, 2, 4 and 6 hours) post LPS stimulation and non-diabetic BBDR rat pancreatic islet cells. Since end-sequencing (3' or 5') is used for all samples, alignments are only required for the R2 (sequence-containing) read.
Project description:To perform Tn-seq experiments random distribution of the transposon in the genome of the recipient cells is essential. In case transposon is delivered into the host cell by conjugation, donor may affect the distribution of the transposon in the genome of the recipient cell. Here, we provide two Tn-seq performed with two different donor strains. FX371 corresponds the Tn-seq using E. coli B-2163 as donor strain. FX442 corresponds to the Tn-seq using E. coli MFDpir as donor strain.
Project description:CD73 (ecto-5'-nucleotidase) is a metabolic immune checkpoint that dephosphorylates AMP to produce adenosine. Adenosine plays a pivotal role in immunosuppressive tumor microenvironment (TME) through adenosine receptors expressed on various immune cells. AB680, a specific CD73 inhibitor, is currently undergoing clinical trials for highly refractory cancers. In this study, we investigated the antitumor effects and mechanisms of AB680 in glioblastoma (GBM). By analyzing the expression pattern of CD73 across all cell types in orthotopic naïve G422<sup>TN</sup>-GBM tumors (d 7), we found that CD73 and its associated adenosine metabolic signaling were significantly elevated in G422<sup>TN</sup>-GBM cells compared to all other cell types. High CD73 expression was also observed in human GBM samples and was correlated with shorter patient survival. Administration of AB680 significantly prolonged survival in G422<sup>TN</sup>-GBM-bearing mice, reduced tumor size, cell proliferation, angiogenesis, and enhanced microglia activation and anti-tumor immune responses. Metabolomic analysis revealed that AB680 markedly increased ADP and AMP levels in the TME of orthotopic G422<sup>TN</sup>-GBM, thereby stimulating the activation of P2RY12<sup>+</sup> microglia to exert their M1-like anti-cancer functions, as confirmed by human GBM scRNA-seq and G422<sup>TN</sup>-GBM snRNA-seq data. Furthermore, AB680 combined with RT/TMZ exhibited synergistic therapeutic effects by reversing RT/TMZ-induced increases in adenosine levels and promoting the transformation of P2RY12<sup>+</sup> microglia. Overall, this study demonstrates that targeting CD73 with AB680 alters purine metabolism in the GBM microenvironment, promotes the transformation of P2RY12<sup>+</sup> microglia, and triggers robust anti-tumor immune responses. These results support the rationale for AB680-based therapeutic clinical trials for GBM.
Project description:To analyze effects of IL-1b on TN cells, RNA-seq analysis was performed on freshly prepared TN cells (0 h) and TN cells cultured with or without recombinamt IL-1b.