Bulk RNA-seq of sham or alkali injury treated WT and Vegfr3 depletion mouse iris
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1003075 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25555173_1.fastq.gz | Fastqsanger.gz | |||
| SRR25555173_2.fastq.gz | Fastqsanger.gz | |||
| SRR25555174_1.fastq.gz | Fastqsanger.gz | |||
| SRR25555174_2.fastq.gz | Fastqsanger.gz | |||
| SRR25555175_1.fastq.gz | Fastqsanger.gz |
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Project description:We report conditional ablation of lymphatic Vegfr3 alleviated inflammatory process in alkali injured iris. Prox1CreERT2 mice were crossed with Vegfr3fl/fl to selectively target gene expression in Prox1+ lymphatic cells. Injury models were established at 6 weeks postnatally, and Vegfr3 gene depletion was conducted via Tamoxifen injection on the day 13th-17th after corneal alkali injury. Mice were sacrificed 28th days post-injury.
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Project description:Neural stem cells (NSCs) continuously produce new neurons within the adult mammalian hippocampus. However, this process declines with age and this decline correlates with defects in cognitive function and mood. Molecular mechanisms that activate quiescent NSCs to generate progenitor cells in vivo remain poorly understood. Here we show that adult hippocampal NSCs express VEGFR3, a key regulator of vascular and neural development, and are activated by the VEGFR3 ligand VEGF-C to enter the cell cycle and convert into progenitor cells. Conditional deletion of Vegfr3 in NSCs leads to a decline in hippocampal neurogenesis. Functionally, this is associated with increased anxiety behavior and compromised NSC activation in response to VEGF-C and physical activity. These findings establish VEGFR3 expression as a hallmark of adult mouse NSCs and demonstrate a specific requirement for VEGF-C/VEGFR signaling in NSC activation. Enhancing VEGFR3 signaling by VEGF-C may improve neurogenesis and mood during aging. Vegfr3 YFP and Vegfr3 YFP-negative cells were FACS-sorted from two separated groups of Vegfr3::YFP mice (16 mice/ each group; 12-30.10^5 Vegfr3YFP cells/group). Vegfr3 YFP and Vegfr3 YFP-negative cells were suspended in CCMM-BM- were seeded in 24-well plates with or without VEGF-C (50ng/ml). After an 18h-culture period,M-BM- the cells were collected in eppendorf tubes, washed in PBS, and the total RNAs were extracted by Qiagen RNA Micro kit (QIAGEN, Valencia, CA). For each culture condition, the pellets from the two groups of Vegfr3 YFP or Vegfr3 YFP-negative cells were pooled. The RNA integrity number (RIN) of each RNA sample was checked by 2100 Bioanalyzer of Agilent Technologies (Santa Clara, CA). The mRNA library construction were performed by SMARTer Ultra Low RNA Kit for Illumina Sequencing pherchased from Clontech Laboratory (Mountain View, CA) using manufacturer's protocol. And then, the validated libraries were applied to the 75 bp, paired end sequencing process of HiSeq 2500 (Illumina) to generate raw sequencing FASTQ data files. All sequencing procedures from RNA extraction to FASTQ generation were carried out by YCGA (Yale Center for Genome Analysis, West Haven, CT). The quality control check of FASTQ files was carried out by FastQC:ReadQC (version 0.52) analysis in Galaxy web-based platform and the sequences passed on M-bM-^@M-^Xper base sequence qualityM-bM-^@M-^Y were mapped on the UCSC mm10 mouse genome (Dec. 2011 Mus musculus assembly (Genome Reference Consortium Mouse Build 38)) using Tophat-2.0.9 including Bowtie-2-2.1.0 and Samtools-0.1.18. As the option of library type in Tophat, M-bM-^@M-^Xfr-unstrandedM-bM-^@M-^Y for Illumina TruSeq protocol was set as the default and the option of M-bM-^@M-^Xno-novel-juncsM-bM-^@M-^Y was chosen to quantify the reference annotation only. Cuffdiff, a separate program of Cufflinks-2.1.1, analyzed the differentially regulated transcriptional level among the reference transcriptoms of our samples and the results were visualized and further manipulated by CummeRbund-2.12.
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Project description:Alkali stress is an important means of inactivating undesirable pathogens in a wide range of situations, ranging from environmental cleaning of food processing environments, to the phagolysosomal killing of cells engulfed by mammalian phagocytes. Unfortunately, L. monocytogenes can launch an alkaline tolerance response (AlTR), significantly increasing persistence of the pathogen in such environments. This study compared the transcriptome patterns of alkali stressed and non alkali stressed L. monocytogenes 10403S cells, to elucidate the mechanisms by which this important pathogen adapts and/or grows during short or long-term alkali stress. Transcription profiles associated with alkali shock (AS) responses were obtained by DNA microarray analysis of mid-exponential cells suspended in pH 9 media for 15, 30 or 60 min. Transcription profiles associated with alkali adaptation (AA) were obtained by DNA microarray analysis of cells grown to mid-exponential phase in pH 9 media . Comparison of AS and AA transcription profiles with profiles from control (pH 7.0) cells identified over 2,000 genes that were differentially expressed under alkaline conditions. Rapid (15min) changes in expression included upregulation of genes encoding for multiple metabolic pathways, (including those associated with Na+/H+ antiporters), ABC transporters of functional compatible solutes such as carnitine, motility and virulence-associated genes as well as the σB controlled stress resistance network. Slower (30min and more) responses to AS and adaptation during growth in alkaline conditions (AA), included modest changes in mRNA concentrations, and genes involved in proton export. Keywords: Time course study of gene expression response to alkaline shock and adaptation
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Project description:To investigate possible genetic basis of alkali tolerance in rice, we generated an introgressed rice line (K83) with significantly enhanced tolerance to alkali stress than its recipient parental cultivar (Jijing88). By using microarray analysis, we examined global gene expression profiles in K83 and Jijing88, found more than 1,200 genes were constitutively differentially expressed in K83 compared with Jijing88, with 572 up- and 654 down-regulated. Upon alkali treatment, a total of 347 genes in K83 were found up- and 156 down-regulated in K83, compared with 591 and 187 respectively in Jijing88. Seven-day-old uniform-sized seedlings grown in hydroponic medium were transferred to fresh hydroponic medium alone or containing 50 mM alkali salts. Shoots were harvested 24 h after transfer and 10 shoots were pooled for microarray analysis.
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Project description:Neural stem cells (NSCs) continuously produce new neurons within the adult mammalian hippocampus. However, this process declines with age and this decline correlates with defects in cognitive function and mood. Molecular mechanisms that activate quiescent NSCs to generate progenitor cells in vivo remain poorly understood. Here we show that adult hippocampal NSCs express VEGFR3, a key regulator of vascular and neural development, and are activated by the VEGFR3 ligand VEGF-C to enter the cell cycle and convert into progenitor cells. Conditional deletion of Vegfr3 in NSCs leads to a decline in hippocampal neurogenesis. Functionally, this is associated with increased anxiety behavior and compromised NSC activation in response to VEGF-C and physical activity. These findings establish VEGFR3 expression as a hallmark of adult mouse NSCs and demonstrate a specific requirement for VEGF-C/VEGFR signaling in NSC activation. Enhancing VEGFR3 signaling by VEGF-C may improve neurogenesis and mood during aging.
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