Iso-Seq combined with RNA-Seq analysis provided insight into the molecular response to dietary oxidized fish oil in juvenile Amur sturgeon, Acipenser schrenckii
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Supplementary Table 10 from Characterizing the Impact of Smoking and Lung Cancer on the Airway Transcriptome Using RNA-Seq
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Supplementary Table 3 from Characterizing the Impact of Smoking and Lung Cancer on the Airway Transcriptome Using RNA-Seq
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Supplementary Table 1 from Characterizing the Impact of Smoking and Lung Cancer on the Airway Transcriptome Using RNA-Seq
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Fenneropenaeus chinensis is an important fishery species in China.Hatchery-reared seeds have been released into the wild for improvement of shrimp productivity.Jinzhou bay is the major natural habitat and we used this location to temporally monitor the genetic effects of release of hatchery stocks on local F. chinensis populations across five years.A set of 13 microsatellite markers were used to evaluate genetic patterns across 2015, 2016 and 2019.We observed a significant Hardy-Weinberg disequilibrium across all stocks.The inbreeding coefficient (F is ) was positive (0.121-0.131) for all stocks.A loss of genetic diversity was detected in the 2019 stock and significant differences were observed for number of different alleles, number of effective alleles, allelic richness and unbiased expected heterozygosity in the 2019 stock (P < 0.05).The highest pairwise relatedness and the lowest observed heterozygosity were also observed in 2019 stock.Moreover, a small but significant genetic differentiation was detected between the 2019 stock and the stocks of the previous two years.Given the continuously large scale of artificial enhancements in this area, these data may indicate that releases of hatchery-reared F. chinensis individuals may be associated with inbreeding and potentially the reduction in genetic diversity of the F. chinensis population.
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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.
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The comparison of metabolic pathway in different species is important in detecting a missing gene. There are many visualizations for metabolic pathway. However, Biologists need not only a simple path but also a visualization for comparison. K-Viz is a tool for visualization of metabolic pathway based on KEGG. To compare pathways in different species, K-Viz uses different color for path such as PathComp in KEGG and shows the table of path in pathway. K-Viz helps biologists to understand the comparison of metabolic pathways in different species.
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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.
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Supplementary Table 9 from Characterizing the Impact of Smoking and Lung Cancer on the Airway Transcriptome Using RNA-Seq
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Collembola generally have a positive impact on plant growth and these effects are often attributed to the improvement of soil nutrients availability. However, the involved mechanisms have not been elucidated. We thus performed a comparative transcriptomic analysis of Poa annua in the presence and absence of Folsomia candida. We found that only 6 genes were up-regulated and 1080 down-regulated with Collembola. This first gene ontology analysis could imply that collembola down-regulate protein metabolic processes and defense response to microorganisms of P. annua, and would thus reduce abiotic and biotic stress for plants.
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