Project description:Purpose: The goal of this study is to compare endothelial transcriptome affected by OASL knockdown under basal or stimulated conditions by utilizing RNA-seq. Methods: Endothelial mRNA profilies of siCTL or siOASL transfected HUVECs were generated by illumina sequencing method, in duplicate. Following an optimized data analysis workflow, RNA sequence reads were counted using StringTie-2.1.3b and used to identify genes differentially expressed between siCTL- and siOASL-transfected HUVECs treated with or without TNFα and IFNγ. Results: DESeq2 was used to identify genes differentially expressed between siCTL- and siOASL-transfected HUVECs under basal or stimulated conditions. Genes showing <10 read counts total were pre-filtered. Conclusions: Our study represents the first analysis of endothelial mRNA affected by OASL knockdown with biologic replicates, generated by RNA-seq.
Project description:Purpose: The goal of this study is to investigate the responses of HUVECs after the stimulation of conidia of A. fumigatus Methods: HUVECs were stimulated with conidia of Aspergillus fumigatus for 2 and 6 hours. Three biological repeats of stimulated cells or un-stimulated controls were send for RNA sequencing. Results: Using an optimized data analysis workflow, we mapped about 40 million sequence reads per sample to the human genome (build hg38) and identified round 80,000 transcripts in the HUVECs upon stimulation. Conclusions: Our resutls showed the detailed analysis of HUVECs transcriptomes upton conidia of Aspergillus fumigatus stimulation.
Project description:We have generated human induced Pluripotent Stem cells (hiPSc) from two individuals with OPA1 haploinsufficiency, and one control donor, using Sendai virus-mediated delivery of reprogramming factors. hiPSc lines have been screened using SNP array to assess chromosomal stability (alongside the fibroblast lines from which they derived), and validation of the pluripotency of the hiPSc lines is provided by Pluritest assessment of transcriptome datasets, prior to differentiation to dopaminergic neuronal clutures and downstream functional assays. Mitochondrial fragmentation in iPSC-derived dopaminergic neurons with OPA1 haploinsufficiency underpins increased apoptosis and syndromic Parkinsonism.
Project description:Mitochondria are critical for metabolic homeostasis of the liver, and thus, mitochondrial dysfunction is a major cause of liver diseases. Optic atrophy 1 (OPA1) is a mitochondrial fusion protein that also plays a role in cristae shaping. Hence, the OPA1 gene disruption has been shown to cause mitochondrial dysfunction. However, the role of OPA1 in liver function is poorly understood. In this study, we deleted OPA1 in fully developed mouse liver and examined its effect.
Project description:Purpose: The goal of this study is to compare endothelial small RNA transcriptome to identify the target of OASL under basal or stimulated conditions by utilizing miRNA-seq. Methods: Endothelial miRNA profilies of siCTL or siOASL transfected HUVECs were generated by illumina sequencing method, in duplicate. After sequencing, the raw sequence reads are filtered based on quality. The adapter sequences are also trimmed off the raw sequence reads. rRNA removed reads are sequentially aligned to reference genome (GRCh38) and miRNA prediction is performed by miRDeep2. Results: We identified known miRNA in species (miRDeep2) in the HUVECs transfected with siCTL or siOASL. The expression profile of mature miRNA is used to analyze differentially expressed miRNA(DE miRNA). Conclusions: Our study represents the first analysis of endothelial miRNA profiles affected by OASL knockdown with biologic replicates.
Project description:We have generated human induced Pluripotent Stem cells (hiPSc) from two individuals with OPA1 haploinsufficiency, and one control donor, using Sendai virus-mediated delivery of reprogramming factors. hiPSc lines have been screened using SNP array to assess chromosomal stability (alongside the fibroblast lines from which they derived), and validation of the pluripotency of the hiPSc lines is provided by Pluritest assessment of transcriptome datasets, prior to differentiation to dopaminergic neuronal clutures and downstream functional assays. Mitochondrial fragmentation in iPSC-derived dopaminergic neurons with OPA1 haploinsufficiency underpins increased apoptosis and syndromic Parkinsonism.
