Project description:To investigate the effect of co-treatment with deoxynivalenol and acrylamide, rat IEC-6 intestinal cells were treated during four hours with different concentrations of compound alone or together.
Project description:To study the effect of the Grk2 or Ets1 KOs in rat and human CD4+ T cells, in vivo or in vitro respectively, we generated KO CD4+ T cell lines by CRISPR-RNP nucleofection (with an gRNA targeting the gene locus) or control (with a non-targeting gRNA) 3' bulk RNAseq was conducted on CD4+ T-MBP rat cells isolated form spleen or spinal cord parenchyma three days after co-transfer of control and KO cells into the animal. Cells were FACS sorted based on their fluorescent protein reporters, BFP for control, and GFP for KOs. For human experiments, CD4+ T cells were isolated from buffy coats, KOed and restimulated in vitro, and 3' bulk RNAseq was performed. For rats, three biological replicates were used from three different animals, for humans, four biological replicates were used from four different donors
Project description:We conducted RNA-sequencing of lidocaine hydrochloride in treating rat dorsal root ganglion neurons to detect lidocaine’s effect of transcriptome profiling changes compared with control.
Project description:To investigate the effect of increasing 4sU labeling concentrations on quantification bias in nucleotide conversion RNA-seq, we labeled 3 different cell lines with increasing concentrations of 4sU. We then measured 4sU dropout in 4sU samples compared to 4sU naive samples.
Project description:To explore the effect of DEHP on piRNA expression in rat testes, we have employed rat piRNA microarray expression profiling as a discovery platform to identify piRNAs with the potential to study the role of DEHP exposure on piRNA expression in rat testes to provide new insight into DEHP-induced male reproductive injury.
Project description:Microglia are brain-resident, myeloid cells that play important roles in health and brain pathologies. While data on chromatin accessibility in activated murine microglia are available, there is no such data on rat microglia subjected to different stimuli. Herein, we report a comprehensive, replicated, FDR-controlled dataset of DNase-hypersensitive (DHS) open chromatin regions for the rat microglia. We compared open chromatin landscapes in untreated primary microglial cultures and cultures stimulated for 6h with either lipopolysaccharide (LPS) or glioma-conditioned medium (GCM). Glioma-secreted factors induce the pro-invasive and immunosuppressive activation of microglia, in which these cells promote tumor growth. The open chromatin landscape of the rat microglia consisted of 126,640 reproducible DHS regions, of which 12,357 and 2,303 significantly changed openness following the stimulation with LPS and GCM, respectively. Active genes had constitutively open promoters, but there was no direct dependence between cumulative openness of DHS regions near to a gene and its expression. LPS-regulated DHS regions were more frequent in introns, while GCM-regulated regions were more frequent away from gene bodies. GCM and LPS treatment differentially affected open chromatin regions mapped to genes in the pathways of Toll-like-receptor signaling and the Axon guidance, suggesting that the molecular machinery used by migrating microglia is similar to that of growing axons and, moreover, that modulation of these pathways is instrumental for glioma to induce a pro-invasive polarization of microglia. Our dataset of open chromatin regions active in rat microglia will constitute a useful resource for studies of the transcriptional regulation in this system.
Project description:Rat somatic heart cell had different gene expression level compared with that of the adult cells including rat bone marrow cells(BMC) and rat primary ear fibroblasts(PEF). This difference gave the rat somatic heart cell unique characteristics which could then be compared with the rat iPS cells by genes comparison to show the gene expression difference between rat somatic heart cells and rat iPS cells.
Project description:Rat somatic lung cell had different gene expression level compared with that of the adult cells including rat bone marrow cells(BMC) and rat primary ear fibroblasts(PEF). This difference gave the rat somatic lung cell unique characteristics which could then be compared with the rat iPS cells by genes comparison to show the gene expression difference between rat somatic lung cells and rat iPS cells.