Haloplasma contractile SSD-17B
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ABSTRACT:
PROVIDER: PRJNA66977 | ENA |
REPOSITORIES: ENA
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Project description:Cutibacterium acnes 17B Genome sequencing and assembly
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Project description:Purpose: Explore IL-17B target genes expression via next-generation sequencing (NGS) in mouse lung tissues. Methods: Overexpress IL-17B in mouse lung tissues via intranasal injection of adenovirus encoding IL-17B (Adv-IL-17B) and empty virus (Adv-EV). Three days after infection lung tisses were removed for RNA collection. Five samples per group were mixed to one sample and used for next RNA purification. RNA samples were then used for high-throughput sequencing according to standard operation based on RNA Hiseq 4000. Results: Using an optimized data analysis workflow, we mapped about 13 million sequence reads per sample to the mouse genome (build mm10) and identified 269 upregulated and 99 downregulated genes in lung after IL-17B overexpression. RNA-seq data had a linear relationship with qRT–PCR for more than four orders of magnitude and a goodness of fit (R2) of 0.8798. Altered expression of 20 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to lung inflammation and infection. Data analysis with BWA and TopHat workflows revealed a significant overlap yet provided complementary insights in transcriptome profiling. Conclusions: Our study represents the first detailed analysis of IL-17B induced downstream genes with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. We conclude that RNA-seq based downstream genes characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
2019-02-19 | GSE106380 | GEO
Project description:Recombinant IL-17B (rIL-17B) promoted the sphere formation ability of CSCs in vitro and enhanced tumor growth and metastasis in vivo. Furthermore, the activation of autophagy was critically involved in IL-17B/IL-17RB-mediated regulation of CSC functions.
2022-01-28 | GSE164038 | GEO
Project description:Compare the expression pattern of 17b-estradiol responsive genes in parent, OHT-resistant and ICI-resistant breast cancer cells. Keywords: 17b-estradiol responsive genes, OHT resistance, Fulvestrand resistance
2007-09-14 | GSE5840 | GEO
Project description:Clostridium botulinum B str. Eklund 17B genome sequencing project.
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Project description:Compare the expression pattern of 17b-estradiol responsive genes in parent, OHT-resistant and ICI-resistant breast cancer cells. Experiment Overall Design: Data for 4 replicate experiments performed with biologically independent samples. Experiment Overall Design: KN01M001v0 DMSO (control) wt MCF7 -> GSM136152 Experiment Overall Design: KN01H002v0 DMSO (control) wt MCF7 -> GSM136148 Experiment Overall Design: KN01H003v0 DMSO (control) wt MCF7 -> GSM136150 Experiment Overall Design: KN01H004v0 DMSO (control) wt MCF7 -> GSM136152 Experiment Overall Design: KN01M005v0 17b-estradiol (10nM 4h) wt MCF7 -> GSM136153 Experiment Overall Design: KN01H006v0 17b-estradiol (10nM 4h) wt MCF7 -> GSM136154 Experiment Overall Design: KN01H007v0 17b-estradiol (10nM 4h) wt MCF7 -> GSM136155 Experiment Overall Design: KN01H008v0 17b-estradiol (10nM 4h) wt MCF7 -> GSM136156
2008-06-14 | E-GEOD-5840 | biostudies-arrayexpress
Project description:YAP and TAZ are transcription cofactors implicated in the contractile and pro-fibrotic activation of fibroblasts. Fibroblast contractile function is important in alveologenesis, as well as in lung wound healing and fibrosis. As paralogs, YAP and TAZ may have independent or redundant roles in regulating transcriptional programs and contractile function. Using IMR-90 lung fibroblasts, microarray analysis and traction microscopy we tested whether independent YAP or TAZ knockdown alone was sufficient to limit transcriptional activation and contraction in vitro.
2021-06-01 | GSE175853 | GEO
Project description:Here, we use a transcriptomic apprach to identify genes associated with variation in muscle contractile physiology differences among different muscles of the same individual.
2022-05-22 | GSE203413 | GEO
Project description:Cardiac contractile strength is recognised as highly pH-sensitive, but less is known about the influence of pH on cardiac gene expression, which may be relevant during changes in myocardial metabolism or vascularization in development or disease. We sought evidence for pH-responsive cardiac genes and a context in which this has physiological relevance. pHLIP, a peptide-based reporter of acidity, revealed a non-uniform pH landscape in early-postnatal myocardium, dissipating in later life. pH-responsive differentially-expressed genes (pH-DEGs) were identified by transcriptomics of neonatal cardiomyocytes cultured over a range of pH. Enrichment analysis indicated “striated muscle contraction” as a pH-responsive biological process. Label-free proteomics verified fifty-four pH-responsive gene-products, including contractile elements and the adaptor protein CRIP2. Using transcriptional assays, acidity was found to inhibit p300/CBP acetylase activity and, as its functional readout, negatively affect myocardin, a co-activator of cardiac gene expression. In cultured myocytes, acid-inhibition of p300/CBP reduced H3K27 acetylation, as demonstrated by chromatin immunoprecipitation. H3K27ac levels were more strongly reduced at promoters of acid-downregulated DEGs, suggesting an epigenetic mechanism of pH-sensitive gene expression. By tandem cytoplasmic/nuclear pH imaging, the cardiac nucleus was found to exercise a degree of control over its pH through Na+/H+ exchangers at the nuclear envelope. Thus, we describe how extracellular pH signals gain access to the nucleus and regulate the expression of a subset of cardiac genes, notably those coding for contractile proteins and Crip2. Acting as a proxy of a well-perfused myocardium, alkaline conditions are permissive for expressing genes related to the contractile apparatus.
2022-04-06 | GSE196438 | GEO