Ontology highlight
ABSTRACT:
PROVIDER: PRJNA508444 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8284434_1.fastq.gz | Fastqsanger.gz | |||
| SRR8284434_2.fastq.gz | Fastqsanger.gz | |||
| SRR8284435_1.fastq.gz | Fastqsanger.gz | |||
| SRR8284435_2.fastq.gz | Fastqsanger.gz | |||
| SRR8284436_1.fastq.gz | Fastqsanger.gz |
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Project description:The cestodes Echinococcus granulosus and Echinococcus multilocularis, as the pathogens of cystic echinococcosis and alveolar echinococcosis respectively, can cause significant health problems to the host and considerable socio-economic losses as a consequence. Based on the genomic data regarding these two species available in public database recently, we carried out high-throughput mRNA and small RNA transcriptomic sequencing of them and generate enormous transcriptomic datasets. A total of 34,717,856 reads (79.79%) mapped to E. granulosus genome, and 38,882,179 reads (87.61%) mapped to E. multiloculari genome. A total of 24,550 (7,925 known and 16,625 novel transcripts) and 23,771 transcripts (8,432 known and 15,339 novel transcripts) were assembled for E. granulosus and E. multilocularis respectively, and the assembly yielded 11,330 genes (6,815 known and 4,515 novel genes) for E. granulosus and 10,101 genes (7,051 known and 3,050 novel genes) for E. multilocularis, compared with the reference genome data. Bioinformatic analysis identified 6,826 AS events from 3,774 E. granulosus genes (33.31%) and 6,644 AS events in 3,611 E. multilocularis genes (35.75%). A total of 76,674 distinct microRNAs of E. granulosus and 115,742 of E. multilocularis were also obtained from small RNA transcriptome sequencing reads. Of these, there were 20 microRNAs of E. granulosus and 22 microRNAs of E. multilocularis that belonged to 19 and 21 microRNA families common to other metazoan lineages separately. 76 and 90 novel microRNAs so far unique to E. granulosus and E. multilocularis were also identified respectively. This study represents an extensive mRNA and small RNA transcriptome dataset obtained from the deep sequencing of these two cestode species. The findings will facilitate a more fundamental understanding of cestode biology, evolution, the host-parasite interplay, and provide new insights into the pathophysiology of echinococcosis, contributing to the development of improved interventions for disease control.
2017-06-26 | GSE59173 | GEO
Project description:Echinococcosis is a disease resulting from infection by flatworms of the Echinococcus genus. The vast majority of cystic echinococcosis cases in Southern Brazil are caused by Echinococcus granulosus and Echinococcus ortleppi. Here, we surveyed the protein contents of the hydatid fluid compartment of E. granulosus and E. ortleppi pulmonary bovine cysts, in an attempt to compare their molecular arsenal in this host-parasite interface. We detected some molecular players equally in E. granulosus and E. ortleppi, such as proteolytic enzymes and development signaling molecules, while some activities were more evident in one species, such as apoptosis in E. ortleppi, and cysteine protease activity in E. granulosus.
2022-04-04 | PXD019314 | Pride
Project description:Echinococcus granulosus small RNA Transcriptome
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Project description:MicroRNAs (miRNAs) are important post-transcriptional regulators which control growth and development in eukaryotic animals. The cestode Echinococcus granulosus has a complex life-cycle involving different development stages but the mechanisms underpinning this development, including the involvement of miRNAs, remain unknown. Using Illumina deep-sequencing technology, we sequenced at the genome-wide level three small RNA populations from the adult, protoscolex and cyst membrane of E. granulosus. A total of 94 miRNA candidates (coding 100 mature miRNAs and 30 miRNA*s) were predicted by a computational pipeline, of which 25 mature miRNAs and 2 miRNA*s were identified experimentally. Through comparison of expression profiles, we found 48 mature miRNAs and 17 miRNA*s expressed in different patterns in the three life stages examined and 31 of them were validated by real-time PCR. Most of the differentially expressed miRNAs exhibited obvious up-regulated expressions in the adult stage and down-regulation in the hydatid cyst. A total of 3,622 genes were predicted to be targets of 126 mature miRNAs and 50 miRNA*s. Further analysis of the differentially expressed miRNAs and their potential targets indicated that they may be involved in bi-directional development, nutrient metabolism and nervous system development in E. granulosus. This study has, for the first time, provided a comprehensive description of the different expression patterns of miRNAs in the three distinct life cycle stages of E. granulosus. Understanding the regulatory processes involving miRNAs in E. granulosus may help in the exploration of the mechanism of interaction between this parasitic worm and its definitive and intermediate hosts and provide new information to develop new intervention strategies for control of cystic echinococcosis. Examination of small RNA populations in 3 different life stages of Echinococcus granulosus
2015-01-16 | E-GEOD-54180 | biostudies-arrayexpress
Project description:Project to investigate gene and small RNA expression of tapeworms (including Echinococcus multilocularis, E. granulosus, Hymenolepis microstoma).This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
2013-12-13 | E-ERAD-236 | biostudies-arrayexpress
Project description:Echinococcus granulosus granulosus isolate:Echinococcus granulosus | breed:Eukaryotic breed Genome sequencing and assembly
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Project description:Echinococcus granulosus Genome sequencing
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Project description:Echinococcus granulosus granulosus Genome sequencing and assembly
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Project description:TGF-β is a crucial cytokine participate in the interplay between the intermediate host and helminthes. TGF-β receptors were discovered in many cestode, and could bind the human TGF-β. However, the function of host TGF-β on the Echinococcus is still not elucidated, and this paper aim to explore the question at transcription level. Microarray analysis was used to investigate differential expression genes in protoscolices of Echinococcus granulosus cultured in the presence or absence of human TGF-β at different time points (4h, 8h and 24h) in vitro. A total of 523 genes were up- or down-regulated in response to TGF-β, compared with control group, 390 genes were up-regulated and 47 genes were down-regulated at 8h, and 376 genes were up-regulated and 19 genes were down-regulated at 12h, including 310 differential genes were regulated at both time point. Only 1 gene down-regulated at 4 h. Gene ontology (GO) analysis showed that the biological process of the up-regulated genes in protoscolex were predominantly involved in DNA packaging, nucleosome assembly, chromatin assembly, etc. And the cellular component gene were located in cell nucleus. TGF-β appeared to promote growth or development of the protoscolex by up-regulated the gene related with mitosis. In addition, the study also indicated that TGF-β has a multiple influence on the protoscolex, as reflected in the increased stimulation of gene expression of the ErbB signaling pathway, MAPK signaling pathway, Notch signaling pathway and VEGF signaling pathway. Isolated E. granulosus protoscoleces were treated with human TGF-β at different time points (4h, 8h and 24h) in vitro, and replicated 3 times. Each samples independently grown and harvested. And was extracted of total RNA using the TRIZOL Reagent according to the manufacturer's instructions. Gene-expression profiling was performed for each RNA sample separately on the GeneChip of Echinococcus granulosus Genome Array (Capitalbio) at CapitalBio Corporation (Beijing, China). The reference samples are protoscoleces treated by human TGF-β(0 h)
2014-06-03 | E-GEOD-58134 | biostudies-arrayexpress
Project description:Cystic echinococcosis (CE) is a common zoonotic parasitic disease that seriously impacts public health. However, the full spectrum of immune cell changes in Echinococcus granulosus (E. granulosus) infection, especially the negative immune regulation of subpopulations of regulatory T cells (Treg), are not yet well understood. In this study, we aimed to identify the panoramic landscape of changes in immune cells and molecules and the distinct alterations in Treg subpopulations in mice infected with E. granulosus. We used single-cell RNA sequencing and single-cell T/B cell receptor sequencing to analyze 53,298 cells from the spleen and peripheral blood mononuclear cells (PBMCs) of healthy and E. granulosus-infected mice. We used immunofluorescence combined with RNA fluorescence in situ hybridization and quantitative real-time polymerase chain reaction to verify the sequencing results. Our results showed organ-specific immune system alterations in mice infected with E. granulosus. E. granulosus-infected mice induced a subpopulation of CD4+ cells with type I interferon production potential. Furthermore, there were seven different Treg cell subpopulations in vivo at three stages of differentiation, and Treg subpopulations of different classes and different stages of differentiation showed tissue specificity. After infection, the Lag3hi Treg and Gpr83+Igfbp4+ naïve Treg subpopulations were specifically induced in PBMCs and spleen, respectively. Furthermore, T follicular helper 2(Tfh2) cells with high expression of Cxxc5 and Spock2 were found in E. granulosus-infected mice. Additionally, combined single-cell immunome repertoire sequencing analysis revealed that gene fragment expression of multiple VJ-paired combinations of T cell receptor β chains were downregulated after infection. Our data uncovered changes in the full spectrum of immune cells in mice following E. granulosus infection, including subpopulations of cells that have not been emphasized in previous studies. These results further enrich the study of the bidirectional immunomodulatory mechanism and offer a different perspective for subsequent studies of E. granulosus infection.
2023-03-08 | GSE216347 | GEO