Bulk RNA sequencing for various tissues using SENCR-BAC transgenic mice
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ABSTRACT:
PROVIDER: PRJNA1311519 | ENA |
REPOSITORIES: ENA
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Project description:SENCR is a vascular-restricted long noncoding RNA specifically expressed in humans. To investigate its biological role in vivo, we generated a transgenic mouse line by introducing a ~220 kb genomic locus encompassing SENCR and its antisense neighbor FLI1, using a bacterial artificial chromosome (BAC clone: RP11-744N12) in combination with PiggyBAC technology. To assess whether SENCR-BAC mice recapitulate the human tissue-specific expression pattern, we collected multiple tissues, including the aorta, heart, brain, kidney, liver, lung, spleen, and stomach, and performed bulk RNA sequencing to evaluate SENCR expression levels across different tissues. The clean reads were mapped to genome using human genome database, but not mouse genome database, due to the objective of this experiment is focused on comparing the level of SENCR, which is human specific.
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Project description:We generated mice with a transgenic BAC on a B6 background. The BAC contains Glo1, and the transgenic mice were found to overexpress Glo1. We performed a microarray on whole-brain RNA of adult mice to identify differentially expressed genes resulting from Glo1 overexpression. Wild type (WT) and transgenic (Tg) littermates were used. Mice were adult males, and RNA was extracted from whole brains.
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Project description:We generated a transgenic mouse line which express EGFP in the retina driven by the Crx promoter using BAC transgenesis. We sorted EGFP-positive photoreceptor precursors at E17.5 using FACS, and subsequently performed microarray analysis of the FACS-sorted cells.
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Project description:A novel missense mutation has been identified in a human pain-insensitive family in the gene ZFHX2. We modelled this mutation in mice by changing the orthologous amino acid and carried out pain behaviour tests in mutant BAC transgenic mice. These showed a phenotype of hyposensitivity to noxious thermal stimuli. ZFHX2 has enriched expression in dorsal root ganglia neurons, and so we carried out microarray analyses in mutant vs wild type controls from lumbar DRG to see which genes were deregulated by the mutant ZFHX2 protein. To understand which genes are differentially expressed in lumbar DRG (L1-6) between Zfhx2 p.R1907K BAC transgenic mice (n=5, genomic BAC copy number of 4) and wild-type controls (n=7). Complementary ChIP-seq data for this study have also been deposited at ArrayExpress under accession number E-MTAB-5651 ( https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5651 ).
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Project description:Glial cells have been proposed as an endogenous source of progenitors for the treatment of neural deficits. However, the cellular and molecular mechanisms underpinning the neurogenic potential of certain populations of adult glial cells, are not known. Previous studies have indicated that chemical injury of the gut by benzalkonium chloride (BAC) of the gut can activate neuronal markers. To examine whether gut injury can induce in EGCs neurogenic programs similar to those expressed by early ENS progenitors in vivo, we performed bulk RNA-seq of enteric glia isolated from mouse guts 48 hours after BAC treatment. We isolated tdT+ cells (=EGCs) and tdT- cells (=non-glia cells) from the TM of control and BAC-treated Sox10CreERT2;Rosa26tdTomato mice and subjected the samples to bulk RNAseq analysis.
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Project description:P. aeruginosa is the leading cause of death in patients with cystic fibrosis patients and one of the most problematic bacterial pathogens responsible for hospital-acquired infections. This pathogen has a high capacity to form biofilms on inert and living surfaces. This lifestyle allows it to persist in various hospital niches or on medical device which become vectors of contamination. Chronic infections are extremely complicated to eradicate due to the remarkable antimicrobial resistance of biofilms leading to a persistence in the tissue and an immune system exhaustion. It is therefore becoming essential to understand the mechanisms of biofilm formation to find new therapeutic targets in order to develop effective antibiofilm strategies. We previously identified in P. aeruginosa PA01 biofilms an accumulation of a hypothetical protein named PA3731 and its deletion impacted the biofilm formation. Similarly, to PspA, a protein from the well-known Psp system of E. coli, PA3731 is a has a predicted structure mostly helical, a PspA/IM30 domain and was accumulated during an osmotic shock. In P. aeruginosa genome, PA3731 appears to form a cluster with 3 genes (PA3732 to PA3729) that we named BAC system for “Biofilm Associated Cluster”. Here we worked on the PA14 strain and focus our study on PA14_16140, the PA3732 homologue. Using a ∆16140 mutant and phenotypic approach, we confirmed the role of the BAC system in the virulence and biofilm formation. We added supplementary genes coding the BAC system and demonstrate that altogether they form an operonic structure regulates by RpoN. We get further insight the role PA14_16140 by proteomic quantitative approach revealing an accumulation of the BAC system proteins in ∆16140 biofilms suggesting its regulatory role of the bac operon. Moreover, we present here the first crystallographic structure of PA14_16140. To summarise, according to our studies, and although further analysis is still required, this newly discovered operon appears composed firstly of its regulator and then of a homologous PspA.
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