Deep sequencing of mpox virus (MPOXV)
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ABSTRACT:
PROVIDER: PRJEB64429 | ENA |
REPOSITORIES: ENA
Similar Datasets
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: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:Purpose:MicroRNAs (miRNAs) are members of a rapidly growing class of small endogenous non-coding RNAs that play crucial roles in post-transcriptional regulator of gene expression in many biological processes. Feline Panleukopenia Virus (FPV) is a highly infectious pathogen that causes severe disease in pets, economically important animals and wildlife in worldwide. However, the molecular mechanisms underlying the pathogenicity of FPV have not been completely clear. To study the involvement of miRNAs in the FPV infection process, miRNAs expression profiles were identified via deep sequencing in the feline kidney cell line (F81) infected and uninfected with FPV. Methods:miRNA-sequencing analysis was performed on an Illumina Hiseq 2500 (LC Sciences, USA) following the vendor's recommended protocol Results:As a result, 673 known miRNAs belonging to 210 families and 278 novel miRNAs were identified. Then we found 57 significantly differential expression miRNAs by comparing the results between uninfected and FPV-infected groups. Furthermore, stem-loop qRT-PCR was applied to validate and profile the expression of the randomly selected miRNAs; the results were consistent with those by deep sequencing. Furthermore, the potential target genes were predicted. The target genes of differential expression miRNAs were analyzed by GO and KEGG pathway. Conclusions:The identification of miRNAs in feline kidney cell line before and after infection with Feline Panleukopenia Virus will provide new information and enhance our understanding of the functions of miRNAs in regulating biological processes.
2020-12-20 | GSE122381 | 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.
2023-02-27 | E-MTAB-11811 | biostudies-arrayexpress
Project description:Purpose: The goals of this study are to investigate the differentially expressed miRNAs between ALV-J infected (WRR+) and uninfected (WRR-)chickens spleens by Illumina deep sequencing. Methods: 140-day-old female chickens of White Recessive Rock (WRR) were confirmed as J subgroup avian leukosis virus (ALV-J) infection. Total RNA from three ALV-J-infected spleens (designated: WRR1+, WRR2+, WRR3+) and three uninfected normal spleen samples (designated: WRR1-, WRR2-, WRR3-) was isolated by TRIzol following the manufacturer’s instruction (Invitrogen, CA, USA). RNA samples of three individuals within each group were pooled with equal amounts, and then were subjected to Illumina deep sequencing by Illumina Hiseq 2500. Results: After raw data filtered, 12,150,275 and 15,227,930 reads of 18-32 bp, representing 569,847 and 543,062 unique sequences, were obtained for WRR- and WRR+ libraries, respectively. Through blasting with the chicken reference genome, 360,180 WRR- sequences and 327,391 WRR+ sequences, which accounted for more than 60% of the unique sequences, were perfectly matched.To analyze the miRNA detection efficiency of Illimuna deep sequencing, all the clean reads were blasted with the Rfam data base 10.1, annotated and then removed rRNA, tRNA, snoRNA and other snRNAs. The annotation results revealed that miRNAs accounted for more than 68% of all clean reads in the WRR− and WRR+ libraries. In this study, a total of 476 miRNAs were identified after compared the unique sequences against the chicken miRNAs precursors in miRBase 18.0. Base on unique sequences matched counts, 167 differential expression miRNAs were identified by DEGseq package using Benjamini-q-value of 0.001 as a cut-off. In ALV-J infected spleens, 83 miRNAs showed up-regulated expression and 84 were down-regulated when compared to uninfected samples. Conclusions: Our study represents the first time to analysis of miRNA Expression in Spleen of J Subgroup Avian Leukosis Virus (ALV-J) Infected (WRR+) and Uninfected (WRR-) Broilers. A total of 167 miRNAs were found to be differentially expressed in ALV-J infected spleens when compared to uninfected chickens. These miRNAs can be considered as candidates for further study ALV-J invasion.
2014-12-01 | GSE63676 | GEO
Project description:Recently, we demonstrated that RDRs had a general function to synthesize antisense RNAs from sense transcripts of protein-coding genes. In this study, we analyzed whether RDR-mediated antisense RNAs were processed into small RNAs by deep sequencing using SOLiD. Deep sequencing identified 1,645 RDR1/2/6-mediated smRNA loci in drought stress and control conditions.
2017-07-13 | GSE39024 | GEO
Project description:Whole-genome sequencing of mpox virus in South Kivu, 2023-2024
| PRJEB72662 | ENA
Project description:To evaluate the change of miRNA expression profile in DF-1 cells in respond to Infectious bursal disease virus (IBDV) infection, Deep sequencing was performed by LC Sciences (Hangzhou, China) on DF-1 cells infected with mock or IBDV Lx strain at an MOI of 1 for 24 h.
2017-10-13 | GSE90095 | GEO