Deep sequencing of mpox virus (MPOXV)
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB64429 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| ERR11734989_1.fastq.gz | Fastqsanger.gz | |||
| ERR11734989_2.fastq.gz | Fastqsanger.gz | |||
| ERR11734990_1.fastq.gz | Fastqsanger.gz | |||
| ERR11734990_2.fastq.gz | Fastqsanger.gz |
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Project description:The mpox outbreak of 2022–2023 involved rapid global spread in men who have sex with men. We infected 18 rhesus macaques with mpox by the intravenous, intradermal, and intrarectal routes and observed robust antibody and T cell responses following all three routes of infection. Numerous skin lesions and high plasma viral loads were observed following intravenous and intradermal infection. Skin lesions peaked on day 10 and resolved by day 28 following infection. On day 28, we re-challenged all convalescent and 3 naive animals with mpox. All convalescent animals were protected against re-challenge. Transcriptomic studies showed upregulation of innate and inflammatory responses and downregulation of collagen formation and extracellular matrix organization following challenge, as well as rapid activation of T cell and plasma cell responses following re-challenge. These data suggest key mechanistic insights into mpox pathogenesis and immunity. This macaque model should prove useful for evaluating mpox vaccines and therapeutics.
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Project description:Generation of recombinant mpox viruses expressing fluorescent proteins
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Project description:To investigate specific miRNA expression profiles of Marek's disease virus (MDV)-infected samples, we performed deep sequencing for miRNAs in four small RNA libraries, including MDV-infected tumorous spleen, MD lymphoma from liver, and non-infected spleen and lymphocytes from controls. A total of 7.76x106, 6.36x106, 6.36x106, and 7.60x106 counts were obtained in four libraries, respectively. The sequences were blasted with chicken and MDV genomes and miRBase 16.0 to identify known and novel miRNAs. In total, 187 and 16 known mature miRNAs were identified in the chicken and MDV, respectively. Deep sequencing detected 942 novel chicken miRNA candidates, of which 646 were in tumorous spleen. These results indicate that MDV infection induced new host miRNA candidates and increased diversity of miRNAs. Of 942 miRNA candidates, 276 of 533 were verified by customized microarray, and 17 of them were further confirmed by qPCR. Four samples examined: MDV-infected tumorous spleen, MD lymphoma from liver, Non-infected spleen, Non-infected lymphocytes
2013-12-30 | E-GEOD-31349 | biostudies-arrayexpress
Project description:To investigate specific miRNA expression profiles of Marek's disease virus (MDV)-infected samples, we performed deep sequencing for miRNAs in four small RNA libraries, including MDV-infected tumorous spleen, MD lymphoma from liver, and non-infected spleen and lymphocytes from controls. A total of 7.76x106, 6.36x106, 6.36x106, and 7.60x106 counts were obtained in four libraries, respectively. The sequences were blasted with chicken and MDV genomes and miRBase 16.0 to identify known and novel miRNAs. In total, 187 and 16 known mature miRNAs were identified in the chicken and MDV, respectively. Deep sequencing detected 942 novel chicken miRNA candidates, of which 646 were in tumorous spleen. These results indicate that MDV infection induced new host miRNA candidates and increased diversity of miRNAs. Of 942 miRNA candidates, 276 of 533 were verified by customized microarray, and 17 of them were further confirmed by qPCR.
2013-12-30 | GSE31349 | GEO
Project description:A total of 52 patients were analyzed: 21 of them monoinfected with HCV and 31 coinfected with HIV (HCV/HIV). HCV patients were recruited from Hospital Italiano and Hospital José María Ramos Mejía from Buenos Aires, Argentina, and HCV/HIV patients from Hospital Universitario La Paz, Hospital Infanta Leonor, Hospital Universitario La Princesa, Hospital Puerta de Hierro, from Madrid, Spain. All samples were processed at the National Center for Microbiology (Madrid). Patients were naıve of treatment for HCV. CHC infection was defined by the presence of anti-HCV antibodies in serum and detectable HCV RNA in plasma samples in at least 2 separate occasions. All HIV+ patients had HIV antibodies, CD4+ T-cells counts ≥ 500 cel/mm3 for at least one year before sample collection, and undetectable HIV viral load since they received suppressive antiretroviral treatment (ART) for at least one year. Plasma extracellular vesicles isolation and RNA purification was performed using the ExoRNeasy Serum/Plasma Midi kit (QIAGEN, Cat #77044). EVs were phenol-lysed and total RNA was purified by ethanol-based membrane binding into spin columns. Quality and integrity were evaluated by the Bioanalyzer 2100 with Agilent RNA 6000 Nano kit (Agilent). Small RNA library synthesis and sequencing were performed at Centre for Genomic Regulation (CRG) at Barcelona (Spain). Small RNA libraries were constructed with Illumina’s TruSeq Small RNA kit v.4 (Illumina) and 50nts (1x50) were sequenced in an Illumina HiSeq2500, with a single read approach.
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Project description:Whole-genome sequencing of mpox virus in South Kivu, 2023-2024
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Project description:In this research, to discover the interactions of mpox-A5 with host proteins, HEK293T cells were utilized and transfected with pCAGGS-HA-A5L plasmid (or pCAGGS-HA plasmid), harvested at 24h, Heterologous expression of MPXV A5L in HEK293T cells was performed for Co-IP with anti-HA beads, and Immunoblotting was conducted to verify the protein expression. The Co-IP products were subjected to liquid chromatography-tandem mass spectrometry (LC-MS/MS).
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