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: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: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: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.
Project description:The epigenetic roles in trigeminal neuralgia (TN) still remain unclear. H3K9ac alteration in neuralgia is obscure and controversy. In this study, we established TN rat model via chronic compression, and further treated with 100 mg/kg/d carbamazepine (CBZ). RNA-seq were conducted to investigate the transcriptional profilings in control, TN and TN+CBZ.
Project description:The epigenetic roles in trigeminal neuralgia (TN) still remain unclear. H3K9ac alteration in neuralgia is obscure and controversy. In this study, we established TN rat model via chronic compression, and further treated with 100 mg/kg/d carbamazepine (CBZ). ChIP-seq were conducted to investigate the genome-wide distribution of H3K9ac and HDAC3 in control, TN and TN+CBZ.
Project description:To analyze difference between spleen and mLN TN cells, RNA-seq analysis was performed on TN cells freshly prepared from each organ.
Project description:We have employed whole genome ATAC-seq to profile the chromatin accssibility landscape of naive CD8+ T cells (TN) and these same cells following activation and differentiation to CM/EM and following incubation with homeostatic cytokines, a reverted naive-like phenotype (TNrev). Four umbilical cord blood samples were used to enrich for TN and to produce the respective EM CM and TNrev phenotypes.
Project description:To analyze the influence of IL-1b on TN cells, RNA-seq analysis was performed on spleen TN cells from mice treated or not treated with IL-1b inhibitors.
