Project description:Mouse colonic healing is a unique process distinct from wound healing in other parts of the body. This experiment evaluated the transcriptomic changes that occur in healing mouse colon upon biopsy-induced wounding at multiple time points.
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:This experiment was done to analyze the p53 status in gastrointestinal tumors in the colon and small intestine in APC mice carrying either a wild type p53 or a mutant p53 (R172H) allele and compare colon and small intestine tumors.
Project description:After the library was qualified, the library was pooled according to the effective concentration and the demand of target offline data, and was sequenced by Illumina platform. Since PABPN1L can bind the poly(A) tail, we propose that it participates in the process of post-transcriptional regulation and degradation of maternal mRNA. We investigated the mRNA changes in GV oocytes, MII oocytes, and fertilized eggs using RNA-seq. GV oocytes, MII oocytes and zygotes were collected and mixed from three mice of each genotypes separately.
Project description:PABPN1L participates in the process of post-transcriptional regulation and degradation of maternal mRNA.So,we collect samples of each period from pabpn1l ko and wt female mice during different stages.Then, RNA was extracted and detected.Reverse transcription was performed on the samples that met the effective concentration.After quality inspection, build the library.GV oocytes, MII oocytes and zygotes were collected from three different PABPN1L KO or WT mice separately.
Project description:PABPN1L participates in the process of post-transcriptional regulation and degradation of maternal mRNA.We collect samples of each period from pabpn1l ko and wt female mice during different stages. Each group contained a total of 30 oocytes or zygotes. In the initial step, we spiked 2 × 106 mRNA-EGFP, transcribed in vitro, into each group.Then, RNA was extracted and detected.Reverse transcription was performed on the samples that met the effective concentration.After quality inspection, build the library.GV oocytes, MII oocytes and zygotes were collected from three different PABPN1L KO or WT mice seperately.
Project description:We aim to establish NAFLD model of Zebrafish. Zebrafish larvae fed with high cholesterol diet,high fructose diet and overfeed diet to induce liver steatosis. RNA-seq was employed to analyze the effects of different diets on NAFLD development.
Project description:Vascular Innate immune cells, such as macrophages, elicit long-term T cell-, and B cell- immune responses, by expressing danger-associated molecular pattern (DAMP) receptors, T cell co-stimulation receptors and presenting antigens to the adaptive system through major histocompatibility complex (MHC)-II. Here, we investigated whether human aortic endothelial cells (HAECs) could also be “transdifferentiated” into innate immune cells after treatment of hyperlipidemia-upregulated DAMP molecules, lysophosphatidylinositol (LPI). HAECs were treated with vehicle control or lysophosphatidylinositol (16:0) (10µM) for 18 hours.
Project description:To shed lights on the potential candidate genes and molecular pathways in vitiligo pathomechanism and therapeutics, we compared the transcriptomes between depigmented and normal skin in Ets-1 knockout mice that spontaneously exhibit human vitiligo-like depigmentation. We performed gene expression profiling analysis using data obtained from RNA-seq of 1 depigmented and 1 pigmented skins of Ets-1 KO mice, and 1 normal skins of wild-type mice.