Ontology highlight
ABSTRACT:
PROVIDER: PRJNA626344 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11566700.fastq.gz | Fastqsanger.gz | |||
| SRR11566701.fastq.gz | Fastqsanger.gz | |||
| SRR11566702.fastq.gz | Fastqsanger.gz | |||
| SRR11566703.fastq.gz | Fastqsanger.gz | |||
| SRR11566704.fastq.gz | Fastqsanger.gz |
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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: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. Examination of miRNA expression in normal Scylla paramamosain group and the Scylla paramamosain infected with Vibrio parahaemolyticus
2012-08-07 | E-GEOD-39921 | biostudies-arrayexpress
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 used the BDA DNBelabC4 platform to conduct single-cell RNA transcriptome sequencing on hemocytes before and after infection with WSSV, and to study the changes in hemocytes composition and antiviral mechanism of a crustacean virus infection represented by mud crab. The blood cells, or hemocytes, of the mud crab (Scylla paramamosain) play crucial roles in its innate immune system. These cells are involved in various immune responses, including phagocytosis, encapsulation, and the production of antimicrobial peptides. The hemocytes can be isolated and characterized using techniques such as flow cytometry, which helps in understanding their functions and interactions within the crab's immune system. White Spot Syndrome Virus (WSSV) is a highly contagious and lethal virus that primarily infects crustaceans, particularly shrimp and crabs. It is an enveloped double-stranded DNA virus, typically oval-shaped, measuring about 320nm in length and 100nm in width, making it one of the largest known viruses. WSSV is the causative agent of White Spot Syndrome, a disease that has caused significant economic losses in the aquaculture industry.
2026-01-12 | GSE289112 | 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