RNA-SEQ profiling of dopaminergic neurons from the substantia nigra pars compacta and ventral tegmental area regions of the mouse mid-brain
ABSTRACT: RNA-SEQ profiling of dopaminergic neurons from the substantia nigra pars compacta and ventral tegmental area regions of the mouse mid-brain Murine midbrain dopaminergic neurons from the SNpc and VTA regions
Project description:RNA-SEQ of dopaminergic neurons from the mid-brain of mice that received one daily intraperitoneal injection of MPTP-HCl (30 mg/kg free base per day) or saline for five consecutive days. Samples were taken 4 days. Murine midbrain dopaminergic neurons that were treated with MPTP-HCl
Project description:Background: Microorganisms are the major cause of food spoilage during storage, processing and distribution. Pseudomonas fluorescens is a typical spoilage bacterium that contributes to a large extent to the spoilage process of proteinaceous food. RpoS is considered an important global regulator involved in stress survival and virulence in many pathogens. Our previous work revealed that RpoS contributed to the spoilage activities of P. fluorescens by regulating resistance to different stress conditions, extracellular acylated homoserine lactone (AHL) levels, extracellular protease and total volatile basic nitrogen (TVB-N) production. However, RpoS-dependent genes in P. fluorescens remained undefined. Results: RNA-seq transcriptomics analysis combined with quantitative proteomics analysis basing on multiplexed isobaric tandem mass tag (TMT) labeling was performed for the P. fluorescens wild-type strain UK4 and its derivative carrying a rpoS mutation. A total of 375 differentially expressed genes (DEGs) and 212 differentially expressed proteins (DEPs) were identified in these two backgrounds. The DGEs were further verified by qRT-PCR tests, and the genes directly regulated by RpoS were confirmed by 5’-RACE-PCR sequencing. The combining transcriptome and proteome analysis revealed a role of this regulator in several cellular processes, including polysaccharide metabolism, intracellular secretion and extracellular structures, cell well biogenesis, stress responses, ammonia and biogenic amine production, which may contribute to biofilm formation, stress resistance and spoilage activities of P. fluorescens. Moreover, in this work we indeed observed that RpoS contributed to the production of the macrocolony biofilm’s matrix.
Project description:ATACseq analyses between iEG (ETO2-GLIS2) and CTRL fetal primary cells and myeloid or CD41 iEG cells lines. Briefly, cells were isolated from iEG mice and cultured for 24 hours in RPMI supplemented with 10% FBS, cytokines (mIL3, mIL6, mSCF, mTPO, mFLT3l) and 100 ng/ml Doxycyclin. After cell lysis, transposition and purification step, the transposed DNA fragments were amplified by polymerase chain reaction (PCR) between 12 and 18 depending on the number of cells at the beginning (50,000 to 6,000) using adapters from the Nextera index kit (illumina). PCR purification was performed using Agencourt AMPure XP magnetic beads (Beckman Coulter A63880) in order to remove large fragments and remaining primers. Library quality was assessed using an Agilent 2100 Bioanalyzer using a High Sensitivity DNA chip (Agilent Technologies 5067-4626). Libraries were sequenced using Novaseq-6000 sequencer (Illumina) (50bp paired-end reads). Quality control of reads was performed using FastQC 0.11.7 and multiQC 1.5. The reads were aligned to the reference genome mm10 with bwa (aln 0.7.17). After alignment, we removed reads mapping to the mitochondrial genome, PCR duplicate reads and reads with a mapping quality lower than 20 using samtools (v 1.9). Final read counts for all mouse datasets ranged from 37 to 128 million reads. Mapped reads were normalized to bins per million (BPM) and were converted to bigwig format using deeptools (v3.2.0). Peak calling, differential analysis, annotation and motif analysis was performed using macs2 (V 2.1.2), Diffbind R package (v 2.8.0 in R-3.5.1 with threshold log2(1.5)), and homer (v4.10.4, annotatePeak.pl and findMotifsGenome.pl) respectively.
Project description:Intraepithelilal lymphocytes (IELs) are located at the intestinal barrier where they can offer swift protection against invading pathogens. However, they are kept in a heightened state of activation resembling effector T cells, but without cytokine production or clonal proliferation. They also posses altered metabolic pathways than CD8+ memory T cells from spleen. With differentially expressed gene analysis of intestinal IELs and CD8+ memory T cells from spleen, we confirmed increased expression of metabolic enzymes involved in lipid uptake and lipid metabolism in IELs compared with CD8+ memory T cells. This was particularly the case for enzymes involved in mevalonate, lanosterol and cholesterol synthesis pathways, suggesting increased lipid metabolite generation. Differential gene expression showed also strong predisposition for cytotoxic potential that IELs possess in comparison to CD8+ memory T cell.
Project description:Identifying sex differences in gene expression within the brain is critical for determining why multiple neurological and behavioural disorders differentially affect males and females. Several are more common or severe in males (e.g., autism and schizophrenia) or females (e.g., Alzheimer’s disease and depression). We analyzed transcriptomic data from the mouse hippocampus of six inbred strains (129S1/SvImJ, A/J, C57BL/6J, DBA/1J, DBA/2J and PWD/Ph), to provide a perspective on differences between male and female gene expression. Our data show that: 1) significant gene expression differences in males versus females varies substantially across the strains, 2) 12 genes exist that are differentially expressed across the inbred strains (termed core genes), and 3) there are >2,600 significantly differentially expressed genes (DEGs) among the strains (termed non-core genes). We found that DBA/2J uniquely has a substantial majority (89%) of DEGs that are more highly expressed in females than males; 129/SvImJ is the most strongly male-biased with a majority (69%) of DEGs that are more highly expressed in males. To gain insight into the sex-biased DEGs, we examined gene ontology, pathway and phenotype enrichment and found significant enrichment in phenotypes related to abnormal nervous system morphology and physiology, among others. In addition, several pathways are enriched significantly, including Alzheimer’s disease (AD), with 32 genes implicated in AD, 8 of which are male-biased. Three of the male-biased genes have been implicated in a neuroprotective role in AD. Our transcriptomic data provide new insight into understanding the possible genetic bases for sex-specific susceptibility and severity of brain disorders. Hippocampal mRNA from adult males and females of six inbred strains of mice were analyzed by RNA sequencing of 3 biological replicates using an Illumina HiSeq 2500
Project description:The results of this study demonstrated that esculetin can affect the glucose metabolism by binding to glycolytic proteins, thus playing an anti-tumor role, and the pathway comprising these proteins which have direct interactions are a potential novel targets for tumor treatment by esculetin.
Project description:Exosomes and microvesicles (i.e., extracellular vesicles; EVs) have been identified within ovarian follicular fluid, and recent evidence suggests that EVs are able to elicit profound effects on ovarian cell function. While existence of miRNA within EVs has been reported, it remains unknown if EV size and concentration as well as their cargos (i.e., proteins and RNA) change during antral follicle growth. Extracellular vesicles isolated from follicular fluid of small, medium and large bovine follicles were similar in size, while concentration of EVs decreased progressively as follicle size increased. Electron microscopy indicated a highly purified population of the lipid bilayer enclosed vesicles that were enriched in exosome biomarkers including CD81 and Alix. Small RNA sequencing identified a large number of known and novel miRNAs that changed in the EVs of different size follicles. Ingenuity Pathway Analysis (IPA) indicated that miRNA abundant in small follicle EV preparations were associated with cell proliferation pathways, while those miRNA abundant in large follicle preparations were related to inflammatory response pathways. These studies are the first to demonstrate that EVs change in their levels and makeup during antral follicle development and point to the potential for a unique vesicle-mediated cell-to-cell communication network within the ovarian follicle. Examination of small RNA population in bovine follicular fluid extracellular vesicles isolated from antral follicles
Project description:The study aims to show that Sox9+ Chd1+ mouse embryonic lung progenitors can be isolated and expanded long-term in 3D culture while maintaining their multipotency. in vitro cultured Sox9+ Chd1+ lung progenitors transcriptionally resemble their in vivo counterparts and show significant difference from adult lung epithelial (Cdh1+ and EpCAM+) and non-epithelial (Cdh1- and EpCAM-) cells
Project description:RNA sequencing was performed on sorted populations of Lgr6-positive and Lgr6-negative keratinocytes from the interfollicular epidermis and the hair follicle/sebaceous gland, in order to determine the compartment-specific expression signatures of Lgr6+ progenitor cells.