Long non-coding RNAs and mRNAs profiling during spleen development in pig
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: PRJNA416652
ORGANISM(S): Sus scrofa domesticus Sus scrofa
PROVIDER: GSE106381 | GEO | 2018/02/16
REPOSITORIES: GEO
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Project description:Genome-wide transcriptomic studies in humans and mice have become extensive and mature. However, a comprehensive and systematic understanding of protein-coding genes and long non-coding RNAs (lncRNAs) expressed during pig spleen development has not been achieved. LncRNAs are known to participate in regulatory networks for an array of biological processes. Here, we constructed 18 RNA libraries from developing fetal pig spleen (55 days before birth), postnatal pig spleens (0, 30, 180 days and 2 years after birth), and the samples from the 2-year-old Wild Boar. A total of 15,040 lncRNA transcripts were identified among these samples. We found that the temporal expression pattern of lncRNAs was more restricted than observed for protein-coding genes. Time-series analysis showed two large modules for protein-coding genes and lncRNAs. The up-regulated module was enriched for genes related to immune and inflammatory function, while the down-regulated module was enriched for cell proliferation processes such as cell division and DNA replication. Co-expression networks indicated the functional relatedness between protein-coding genes and lncRNAs, which were enriched for similar functions over the series of time points examined. We identified numerous differentially expressed protein-coding genes and lncRNAs in all five developmental stages. Notably, ceruloplasmin precursor (CP), a protein-coding gene participating in antioxidant and iron transport processes, was differentially expressed in all stages. This study provides the first catalog of the developing pig spleen, and contributes to a fuller understanding of the molecular mechanisms underpinning mammalian spleen development.
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Project description:Long non-coding RNAs and mRNAs profiling during spleen development in pig
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Project description:We report the application of high-throughput RNA sequencing for comparing the expression levels of the coding and long noncoding RNAs (lncRNAs) in leaf samples from a glossy mutant nwgl and its wild-type (WT) in cabbage. By obtaining over 163.35 Gb cleaned data generated from six libraries (on average, more than 26.48 Gb clean data for each sample replicate), we identified 1247 differential expressed genes (DEGs) and 148 differential expressed lncRNAs in nwgl leaves relative to WT. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that the DEGs and cis-regulated target genes for differential expressed lncRNAs were significantly enriched in wax and lipid biosynthetic and/or metabolic processes. Our results provide the novel foundation to explore the complex molecular basis of cuticular wax biosynthesis.
2019-07-26 | GSE130405 | GEO
Project description:In order to systematically identify the possible regulatory roles of (long nocoding RNAs) lncRNAs and (circular RNAs) cirRNAs in the rice photo-thermosensitive genic male sterile (PTGMS) line that were involved in fertility transition, 18 RNA libraries from rice young panicles of the Wuxiang S sterile line rice (WXS (S)) and its fertile line rice (WXS (F)) at the pollen mother cell (PMC) formation stage (P2), the meiosis stage (P3), and the microspore formation stage (P4) were constructed, with three biological replicates for each condition. These libraries were sequenced using an Illumina Hiseq 2500 platform, and approximately 214.54 Gb clean reads were generated. we performed genome-wide identification and characterization of lncRNAs circRNAs using high-throughput strand-specific RNA sequencing (ssRNA-seq) technology and bioinformatics tools to investigate the expression profiles of circRNAs in the PTGMS rice line WXS and their potential roles in the fertility transition.A total of 3948 lncRNAs and 9994 circRNAs were indentifiled in WXS rice, and our findings clearly revealed that lnRNAs and circRNAs might be endogenous noncoding regulators of flower and pollen development in the PTGMS rice line.
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Project description:We report the application of Illumina RNA sequencing for characterization and discovery of genes and transcripts in Italian Large Whtie pig backfat tissue.
2016-03-15 | GSE68007 | GEO
Project description:The dysregulation of long non-coding RNAs (lncRNAs) is associated with the development of various diseases. However, little is known about the regulatory function of lncRNAs in peritendinous fibrosis. Therefore, the expression profiles of lncRNAs and mRNAs in normal tendon and fibrotic peritendinous tissues were analyzed in this study using RNA sequencing. In total, 219 lncRNAs and 3403 mRNAs were identified that were differentially expressed between the two sets of tissues. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed that the dysregulated mRNAs were mainly associated with immune regulation, inflammation, extracellular matrix (ECM) production and remodeling, and cell cycle regulation. An lncRNA-mRNA co-expression network revealed 181 network pairs comprising eight dysregulated lncRNAs and 146 mRNAs. The results of the bioinformatics analysis indicated that the dysregulated lncRNAs play a role in fibrogenesis through regulation of the cell cycle, inflammation, and ECM production. Furthermore, silencing the lncRNA dnm3os prevented transforming growth factor (TGF)-?1-induced tenocyte proliferation and expression of genes related to fibrogenesis. These findings provide a basis for investigations into the regulatory mechanisms underlying the development and progression of peritendinous fibrosis.
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Project description:We report the application of Illumina RNA sequencing for characterization and discovery of genes and transcripts in Italian Large Whtie pig backfat tissue. RNAs sequencing for long RNA quantification, discovery, characterisation and differential expression evaluation.
2016-03-15 | E-GEOD-68007 | biostudies-arrayexpress
Project description:Age-related decline in olfactory function affects the quality of life in elderly people and also potentially represents an early clinical symptom of neurodegenerative disorder. Olfactory bulb (OB) plays a central role in olfactory information transmitting and signal processing. The mechanisms underlying this impairment remain unclear. In the current study, microarray was used to investigate differentially expressed protein coding genes (PCGs) and long non-coding RNAs (lncRNAs) in OBs from three groups of mice of different ages (2 months-old young adults, 6 months-old mature adults and 20 months-old aged adults), for their potential roles in olfactory impairment. Gene Ontology and pathway analysis results showed that the differentially expressed PCGs in the OBs from aged mice were mainly associated with signal transduction, regulation of gene expression and cellular microenvironment. Similarly, gene set enrichment analysis identified two differentially and inversely expressed lncRNAs (NONMMUT004524 and NONMMUT000384), both of which were significantly associated with neuroactive ligand-receptor interaction pathway in the OBs of aged mice. These findings suggest that a decline of olfactory function in aged mice may be linked to differential expression of specific lncRNAs and their potentially adverse effects on the neuroactive ligand-receptor interaction pathway in the OB.
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Project description:BackgroundTo explore long non-coding RNA (lncRNA), mRNA and circular RNA (circRNA) expression profiles and their biological functions in the pathogenesis of kidney stones in ethylene glycol-induced urolithiasis rats.ResultsThe expression of 1440 lncRNAs, 2455 mRNAs and 145 circRNAs was altered in the kidneys of urolithiasis rats. GO and KEGG biological pathway analysis were performed to predict the functions of differentially expressed lncRNAs, circRNAs and co-expressed potential targeting genes. Co-expression networks of lncRNA-mRNA and circRNA-miRNA were constructed based on correlation analysis between differentially expressed RNAs. mRNAs coexpressed with lncRNAs were involved in many kidney diseases, e.g., Ephb6 was associated with the reabsorption ability of the kidney. Arl5b was associated with the dynamic changes in the podocyte foot process in podocyte injury. miRNAs co-expressed with circRNAs, such as rno-miR-138-5p and rno-miR-672-5p, have been proven to be functional in hypercalciuria urolithiasis.ConclusionThe expression profile provided a systematic perspective on the potential functions of lncRNAs and circRNAs in the pathogenesis of kidney stones. Differentially expressed lncRNAs and circRNAs might serve as treatment targets for kidney stones.
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Project description:Lung adenocarcinoma (LUAD) is the primary subtype in lung cancer, which is the leading cause of cancer-related death worldwide. This study aimed to investigate the aberrant expression profiling of long non-coding RNA (lncRNA) in TNM I stage (stage I) LUAD. The lncRNA/mRNA/miRNA expression profiling of stage I LUAD and adjacent non-tumor tissues from 4 patients were measured by RNA-sequencing. Total of 175 differentially expressed lncRNAs (DELs), 1321 differentially expressed mRNAs (DEMs) and 94 differentially expressed microRNAs (DEMIs) were identified in stage I LUAD. DEMI-DEM regulatory network consisted of 544 nodes and 1123 edge; miR-200 family members had high connectivity with DEMs. In DEL-DEM co-expression network, CDKN2B-AS1, FENDRR and LINC00312 had the high connectivity with DEMs, which co-expressed with 105, 63 and 61 DEMs, respectively. DEL-DEMI-DEM network depicted the links among DELs, DEMI and DEMs. Identified DEMs were significantly enriched in cell adhesion molecules, focal adhesion and tight junction of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways; and enriched in cell adhesion, angiogenesis and regulation of cell proliferation of Gene Ontology biological processes. Quantitative real-time polymerase chain reaction results were generally consistent with our bioinformatics analyses. LINC00312 and FENDRR had diagnostic value for LUAD patients in The Cancer Genome Atlas database. Our study might lay the foundation for illumination of pathogenesis of LUAD and identification of potential therapeutic targets and novel diagnosis biomarkers for LUAD patients.
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