Transcriptomic analysis reveals the gene expression profiles in the spleen of spotted knifejaw (Oplegnathus punctatus) infected by Vibrio harveyi
Jie WangZhangfan ChenWenteng XuYangzhen LiSheng LuLei WangSong YuNa WangZhihong GongQian YangSonglin Chen
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Vibrio harveyi
KEGG
Hierarchical clustering
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Profiling (computer programming)
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Abstract The study of gene expression (i.e., the study of the transcriptome) in different cells and tissues allows us to understand the molecular mechanisms of their differentiation, development and functioning. In this article, we describe some studies of gene-expression profiling for the purposes of understanding developmental (age-related) changes in the brain using different technologies (e.g., DNA-Microarray) and the new and increasingly popular RNA-Seq. We focus on advancements in studies of gene expression in the human brain, which have provided data on the structure and age-related variability of the transcriptome in the brain. We present data on RNA-Seq of the transcriptome in three distinct areas of the neocortex from different ages: mature and elderly individuals. We report that most age-related transcriptional changes affect cellular signaling systems, and, as a result, the transmission of nerve impulses. In general, the results demonstrate the high potential of RNA-Seq for the study of distinctive features of gene expression among cortical areas and the changes in expression through normal and atypical development of the central nervous system.
Neocortex
RNA-Seq
Expression (computer science)
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The large yellow croaker (Larimichthys crocea) is an economically important fish species in Chinese mariculture industry. To understand the molecular basis underlying the response to fasting, Illumina HiSeqTM 2000 was used to analyze the liver transcriptome of fasting large yellow croakers. A total of 54,933,550 clean reads were obtained and assembled into 110,364 contigs. Annotation to the NCBI database identified a total of 38,728 unigenes, of which 19,654 were classified into Gene Ontology and 22,683 were found in Kyoto Encyclopedia of Genes and Genomes (KEGG). Comparative analysis of the expression profiles between fasting fish and normal-feeding fish identified a total of 7,623 differentially expressed genes (P < 0.05), including 2,500 upregulated genes and 5,123 downregulated genes. Dramatic differences were observed in the genes involved in metabolic pathways such as fat digestion and absorption, citrate cycle, and glycolysis/gluconeogenesis, and the similar results were also found in the transcriptome of skeletal muscle. Further qPCR analysis confirmed that the genes encoding the factors involved in those pathways significantly changed in terms of expression levels. The results of the present study provide insights into the molecular mechanisms underlying the metabolic response of the large yellow croaker to fasting as well as identified areas that require further investigation.
KEGG
RNA-Seq
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We measured the expression levels of 450 genes during mouse postnatal cerebellar development by quantitative PCR using RNA purified from layers of the cerebellar cortex. Principal component analysis of the data matrix demonstrated that the first and second components corresponded to general levels of gene expression and gene expression patterns, respectively. We introduced 288 of the 450 genes into PC12 cells using a high-throughput transfection assay based on atelocollagen and determined the ability of each gene to promote neurite outgrowth or cell proliferation. Five genes induced neurite outgrowth, and seven genes enhanced proliferation. Evaluation of the functional data and gene expression patterns showed that none of these genes exhibited elevated expression at maturation, suggesting that genes characteristic of mature neurons are not likely to participate in neuronal development. These results demonstrate that functional data can facilitate interpretation of expression profiles and identification of new molecules that participate in biological processes.
Neurite
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The Asian citrus psyllid (ACP), Diaphorina citri Kuwayama, is the principal vector of the Candidatus Liberibacter asiaticus (CLas) bacterium that causes Huanglongbing (HLB) disease. The D. citri salivary glands (SG) is an important barrier to the transmission of CLas. Despite its importance, the transcriptome and proteome of SG defense against CLas are unstudied in D. citri. In the present study, we generated a comparative transcriptome dataset of the SG in infected and uninfected D. citri using an Illumina RNA-Seq technology. We obtained 407 differentially expressed genes (DEGs), including 159 upregulated DEGs and 248 downregulated DEGs. Functional categories showed that many DEGs were associated with the ribosome, the insecticide resistance, the immune response and the digestion in comparison with CLas-infected SG and CLas-free SG. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases confirmed that metabolism and immunity were important functions in the SG. Among the DEGs, 68 genes (35 upregulated and 33 downregulated) encoding putative-secreted proteins were obtained with a signal peptide, suggesting that these genes may play important roles in CLas infection. A total of 673 SG proteins were identified in uninfected D. citri by liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) analysis, and 30 DEGs (15 upregulated and 15 downregulated) were found using the local tBLASTP programs. Among the 30 DEGs, many DEGs mainly involved in the metabolism and cellular processes pathways. This study provides basic transcriptome and proteome information for the SG in D. citri, and helps illuminate the molecular interactions between CLas and D. citri.
KEGG
Diaphorina citri
Proteome
RNA-Seq
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Aging and aging-related diseases are associated with altered patterns of gene expression, involving quantitative and qualitative changes in the abundance of specific transcripts. A complete and simultaneous analysis of gene expression should therefore lead to important insights into the transcriptional mechanisms underlying the aging process. Recently, we have employed high-throughput gene expression profiling to study transcriptional activity in heart. Two technologies, serial analysis of gene expression (SAGE) and gene expression arrays, allow rapid, large-scale expression profiling, which provides information about the dynamics of total gene expression with age and which can be employed to identify candidate genes that may serve as diagnostic and prognostic markers in age-associated cardiac diseases. The accompanying gene predictions from high-throughput gene expression profiling provide a starting point for understanding the function, the complexity of interactions, and the role of genes in promoting cellular/organismal phenotypes during senescence and disease. In this review we describe the current state of transcriptome profiling by SAGE and microarrays and discuss how results generated with these approaches in heart can be applied to the study of aging and the treatment of cardiovascular diseases.
Senescence
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Gene expression fingerprints are already a useful classification tool in tumor biology or drug application. PURPOSE: Similarly, gene expression profiling may provide information for the characterization and understanding of the immunological response to exercise. Microarray expression analysis affords the opportunity to find specific gene expression pattern (fingerprints) and to complete the list of involved genes. METHODS: An inflammation-centered cDNA microarray was used to screen mRNA expression in leukocytes of eight male athletes before (t0), immediately (t1) and 24h after (t2) a half marathon (HM). Differentially regulated gene expression was analyzed using a linear regression-based algorithm. Genes were clustered based upon similarity in gene expression changes with samples from t0 vs t1 and from t0 vs t2. The assumption for a gene to be clustered was that its regulation was identical in all eight athletes at the particular time. Selected genes were evaluated by quantitative Real Time PCR. RESULTS: Comparing t0 with t1, and t0 with t2, 36 and 21 genes respectively, were similarly regulated in all eight athletes. This pattern of identically changed genes can be viewed as a 'gene expression fingerprint' at the particular times post-exercise. Genes were allocated to functional groups such as signal transduction, cell type specific surface markers, cellular interaction and protection, apoptosis, and inflammatory processes. CONCLUSION: Microarray analysis is applicable for exercise-related gene expression profiling in human leukocytes. An exercise-related gene expression fingerprint may become helpful to characterize the immune response to different types of exercise or even to diagnose overtraining.
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Background The brown planthopper (BPH) Nilaparvata lugens (Stål) is one of the most serious insect pests of rice in Asia. However, little is known about the mechanisms responsible for the development, wing dimorphism and sex difference in this species. Genomic information for BPH is currently unavailable, and, therefore, transcriptome and expression profiling data for this species are needed as an important resource to better understand the biological mechanisms of BPH. Methodology/Principal Findings In this study, we performed de novo transcriptome assembly and gene expression analysis using short-read sequencing technology (Illumina) combined with a tag-based digital gene expression (DGE) system. The transcriptome analysis assembles the gene information for different developmental stages, sexes and wing forms of BPH. In addition, we constructed six DGE libraries: eggs, second instar nymphs, fifth instar nymphs, brachypterous female adults, macropterous female adults and macropterous male adults. Illumina sequencing revealed 85,526 unigenes, including 13,102 clusters and 72,424 singletons. Transcriptome sequences larger than 350 bp were subjected to Gene Orthology (GO) and KEGG Orthology (KO) annotations. To analyze the DGE profiling, we mainly compared the gene expression variations between eggs and second instar nymphs; second and fifth instar nymphs; fifth instar nymphs and three types of adults; brachypterous and macropterous female adults as well as macropterous female and male adults. Thousands of genes showed significantly different expression levels based on the various comparisons. And we randomly selected some genes to confirm their altered expression levels by quantitative real-time PCR (qRT-PCR). Conclusions/Significance The obtained BPH transcriptome and DGE profiling data provide comprehensive gene expression information at the transcriptional level that could facilitate our understanding of the molecular mechanisms from various physiological aspects including development, wing dimorphism and sex difference in BPH.
Brown planthopper
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