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Temporal Expression Profiling of Global Long Noncoding RNA and mRNA during Development in Pig Whole-blood

ABSTRACT: Temporal Expression Profiling of Global Long Noncoding RNA and mRNA during Development in Pig Whole-blood

PROVIDER: PRJNA510331 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8327870_1.fastq.gz	Fastqsanger.gz
	SRR8327870_2.fastq.gz	Fastqsanger.gz
	SRR8327861_1.fastq.gz	Fastqsanger.gz
	SRR8327861_2.fastq.gz	Fastqsanger.gz
	SRR8327862_1.fastq.gz	Fastqsanger.gz

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Temporal Expression Profiling of Global Long Noncoding RNA and mRNA during Development in Pig Whole-blood

Project description:Blood is the pipeline of the immune system. Assessing changes in transcript abundance in blood on a genome-wide scale affords a comprehensive view of the status of the immune system during development. However, little is known about the changes of gene expression in blood across multiple developmental stages in pigs. In this study, we performed transcriptomic analysis of messenger RNA (mRNA) and long noncoding RNA (lncRNA) expressed in whole-blood tissue from pigs of natal, suckling, weaning, sexual maturity and adult stages. A total of 5,946 lncRNA and 12,354 mRNA transcripts were identified to be substantially expressed. Short time-series expression miner (STEM) and functional enrichment analysis showed that genes with the greatest variation of expression levels between suckling period (0, 7 and 28 days) and the late stage of development (180 days and 2 years) might function in transcription, immune function, and apoptotic process. Functional prediction indicated the expression correlation and functional relatedness between mRNAs and lncRNAs. Additionally, a number of T cell-related genes were continuously up-regulated during lactation, suggesting this phase is significant for the establishment of piglet adaptive immunity. Notably, the TCONS_00192752 and TCONS-00086451 lncRNA might promote blood immune development by up-regulating the tumor necrosis factor receptor-associated factor 3 (TRAF3) and nuclear factor of activated T-cells cytoplasmic 2 (NFATC2) expression, respectively. Our research provides the first catalog of the developing pig whole-blood, and will accelerate clinical researches of immune system development with pig models.

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Assessment Of Long Noncoding RNA CCAT1 In Colorectal Cancer Patients

Project description:1. Evaluate the diagnostic value of long noncoding RNA (CCAT1) expression by RT-PCR in peripheral blood in colorectal cancer patients versus normal healthy control personal. 2. Evaluate the clinical utility of detecting long noncoding RNA (CCAT1) expression in diagnosis of colorectal cancer patients & its relation to tumor staging. 3. Evaluate the clinical utility of detecting long noncoding RNA (CCAT1) expression in precancerous colorectal diseases. 4. Compare long noncoding RNA (CCAT1) expression with traditional marker; carcinoembryonic antigen (CEA) and Carbohydrate antigen 19-9 (CA19-9) in diagnosis of colorectal cancer.

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Expression profiling of long noncoding RNAs and mRNAs in mouse heart, whole blood (WB), and plasma.

Project description:Long noncoding RNA profile in the heart, whole blood, and plasma before and heart failure (HF). In the study presented here, we mixed the five pairs of mouse hearts, whole blood, and plasma before and after HF and identified the genome-wide expression level of lncRNAs.

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Expression profiling of long noncoding RNAs and mRNAs in mouse heart, whole blood (WB), and plasma.

Project description:Long noncoding RNA profile in the heart, whole blood, and plasma before and heart failure (HF).

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Transcriptional perturbations by long noncoding RNAs with distinct spatio-temporal expression in the mammalian brain

Project description:Long noncoding RNAs (lncRNAs) have been implicated in numerous cellular processes including brain development. Yet the in vivo expression dynamics and molecular pathways regulated by these molecules are less well understood. Here, we leveraged a cohort of 13 lncRNA null-mutant mouse models to investigate the spatio-temporal expression of lncRNAs in the developing and adult brain. We observed a wide range of different spatio-temporal expression profiles in the brain. Several lncRNAs are differentially expressed both in time and space, and others present highly restricted expression in only selected brain regions. We further explore the consequent transcriptome alterations after loss of these lncRNA loci, and demonstrate altered regulation of a large variety of cellular pathways and processes. We further found that 6/13 lncRNA null-mutant strains significantly affect the expression of several neighboring protein-coding genes, in a cis-like manner. This resource provides insight into the expression patterns and potential effect of lncRNA loci in the developing and adult mammalian brain, and allows future examination of the specific functional relevance of these genes in neural development, brain function, and disease. We have sequenced wildtype and mutant whole brains from a cohort of 13 lncRNA knockout mouse strains at two developmetal timepoints (E14.5 and adult).

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Project description:Men are more prone to acute kidney injury (AKI) and chronic kidney disease (CKD), progressingto end-stage renal disease (ESRD) than women. Severity and capacity to regenerate after AKI are important determinants of CKD progression, and of patient morbidity and mortality in the hospital setting. To determine sex diferences during injury and recovery we have generated a female and male renal ischemia/reperfusion injury (IRI) pig model, which represents a major cause of AKI. This study was conducted using farm pigs, hybrids between Large White and Landrace. Five females and five males of four months old, free of specifc pathogens, between 30 and 40 kg of weight were included in this study. This age range was chosen due to the sexual maturity of the animal, allowing hormone efects. Using microarray assays, global transcriptomic analyses of kidney biopsies from this IRI pig model was conducted and revealed a sexual dimorphism in the temporal regulation of genes and pathways relevant for kidney injury and repair. Overall, this study constitutes an extensive characterization of the time and sex diferences occurring during renal IRI and recovery at gene expression level.

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Analysis of long noncoding RNA expression profile in the whole blood of neonatal Hypoxic Ischemic Encephalopathy

Project description:Long noncoding RNAs (lncRNA) have been proved to participate in many biological processes. To investigate the expression profile of lncRNAs and their potential functions in neonatal hypoxic ischemic encephalopathy (HIE). We detected the lncRNA and mRNA expression in the peripheral blood samples in HIE and relative control using microarray. A total of 376 lncRNAs and 126 mRNAs were detected to be differentially expressed between HIE and the non-HIE samples (fold change>2). Quantitative real-time PCR were used to validation of microarray data. Gene ontology (GO) enrichment and KEGG pathway analysis were used to determine the gene function. Furthermore, the co-expression network of lncRNA-mRNA were conducted to predicted the potential the targets of lncRNAs. In conclusion, our study first demonstrated the differentially expression profile of lncRNAs in the whole blood of neonatal HIE and may provide a new view of distinct lncRNAs functions in HIE.

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