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PROVIDER: PRJNA1093225 | ENA |
REPOSITORIES: ENA
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Project description:Purpose:The mud crab Scylla paramamosain is an economically important marine crab in China suffering from severe outbreaks of infectious disease caused by marine bacteria such as Vibrio Parahaemolyticus, resulting in great economic losses. However, the mechanisms involved in the immune response of this crab to bacterial infection are not fully understood. To understand the molecular mechanisms underlying the immune response to such pathogenic bacteria, we used high-throughput deep sequencing technology to investigate the transcriptome and comparative expression profiles of the mud crab S.paramamosain infected with V.parahaemolyticus. Methods: The hemocytes sampled at 0-24h after infection with V.parahaemolyticus were used for transcriptome analysis. The hemocytes sampled at 24 h after injections with V.parahaemolyticus and no injected 0h(as control) were used for gene expression profiling analysis. Results: A total of 52,934,042 reads were obtained and assembled into 186,193 contigs in transcriptional responses of the V.parahaemolyticus-infected mud crab. Via annotation to the NCBI database and the Swissprot database, we obtained 48,934 identified unigenes. In total, 10,139(20.7%) unigenes were classified into Gene Ontology, and 25,349 unigenes were found in 20 KEGG categories. These genes included representatives from almost all functional categories. By using Solexa/Illumina's DeepSAGE, 1213 differentially expressed genes (P value < 0.05) were detected in comparative analysis of the expression profiles between V.parahaemolyticus-infected crabs and control crabs, including 538 remarkably upregulated genes and 675 remarkably downregulated genes. Conclusions: Based on our results, we conclude that the inflammatory response may play an important role in the early stages of infection. The signaling cascades such as the chemokine, JAK-STAT, and MAPK pathways are regulated by V.parahaemolyticus infection. These results revealed changes of multiple signaling pathways involved in immunity during V.parahaemolyticus infection, which will facilitate our comprehensive understanding of the mechanisms involved in the immune response to bacterial infection in the mud crab.
2016-03-21 | GSE45400 | GEO
Project description:We report the de novo assembled transcriptome of Y-organs from two intermolt and two pre-molt blue crabs. Data was obtained from RNAseq, assembled using Trinity, and differential expression was determined using DEseq2 in R.
2020-07-17 | GSE154560 | GEO
Project description:To date, diagnosis of methamphetamine use disorder (MUD) is based primarily on the patient’s self-reports of drug-seeking behaviour and interviews with psychiatrists in the absence of objective biomarkers. As an effective clinical method for diagnosis of MUD is still not available, the development of potential biomarkers for more accurate diagnosis is imperative. Transcription profiling and discovery of biomarkers in the treatment and recovery periods of MUD patients can be used as scientific basis to provide a greater understanding of the disease and to facilitate decisions on whether to continue or not. In this study, RNA sequencing analysis was performed to profile transcripts from hair follicle cells of healthy controls and patients with MUD, and biomarkers were discovered at each transition states to be used to diagnose MUD. This study will present an important information to diagnose MUD using non-invasive biomarkers for human addicts and it will help to develop better pharmacological treatment of MUD in the future.
2023-05-31 | GSE227204 | GEO
Project description:As representatives of n-6 and n-3 fatty acids, many studies have analyzed the use of soybean oil and linseed oil rich in linoleic acid (18:2n-6, LA) and α-linolenic acid (18:3n-3, LNA) as better substitutes for fish oil. In aquatic animals, different dietary ratios of LA and LNA could have significant effects on growth, lipid metabolism, immune response, and reproduction. To assess the nutritive value of these two fatty acids for the Chinese mitten crab (Eriocheir sinensis), we performed transcriptome analysis and proteomic analysis using label-free quantification of the hepatopancreas of mitten crabs fed with LA or LNA diet. Our results provide new insights for further investigation into the replacement of fish oil from mitten crabs with vegetable oils and enable us to better understand the different roles and nutrition value of LA and LNA in mitten crabs.
2019-08-14 | PXD009864 | Pride
Project description:Background: The Scylla paramamosain is a very important aquaculture crustacean species in the southeast coastal areas of China including Shantou. For the past few years, mud crab cultured in Niutianyang of Shantou suffered from serious diseases, especially the bacterial diseases (such as Vibrio parahaemolyticus). In eukaryotes, small RNAs can regulate gene expression in post-transcription to act on host-pathogen interaction system. Aims: V.parahaemolyticus isolated from Shantou Niutianyang crab culture area was injected to S.paramamosains to carry out an essential analysis on global miRNA expression in diverse tissues between two groups by the Illumina Solex deep sequencing technology. Methodology:To examine the relationship between mud crab miRNA expression and the bacterial pathogen, we collected mixed two pools of equal amounts of RNA from 7 different mud crab tissues (mesenteron, heart, liver, gill, brain, muscle and blood) and sequencing by Illumine/Solexa deep sequencing technology under normal conditions and during infection with V.parahaemolyticus. The high throughput sequencing resulted in 19,144,358 and 18,559,070 raw reads corresponding to 17,496,577 and 16,888,096 high-quality mappable reads for the normal and infected mixed pools, respectively. Stem-loop RT-qPCRs were used to confirm the microRNAs expression in different tissues of two pools. The results show that miRNAs might play a key role in regulating gene expression during mud crab S.paramamosain infection with V.parahaemolyticus. Conclusions: We identified a large number of miRNAs during the mud crab Scylla paramamosain infection with V.parahaemolyticus, some of which are differentially expressed between the treatments and the controls. The study provides an opportunity for further understanding of small RNA function in the regulation of molecular response and gives us clues for further studies of the mechanisms of V.parahaemolyticus infection in mud crab.
2012-08-07 | GSE39921 | GEO
Project description:The function of Exosomes of mud crabs Raw sequence reads
| PRJNA669479 | ENA