Similar Datasets
Project description:Duck Tembusu virus (DTMUV) is a newly emerging pathogenic flavivirus that has caused huge economic losses to the duck industry in China since 2010. Moreover, DTMUV can also infect geese, chickens, house sparrows and replicate in in the brain, spleen, liver and kidneys of BALB/c mice, which poses public health concerns. So developing vaccines to combat DTMUV becomes urgent. Baby hamster kidney cell line (BHK-21) is usually employed to produce veterinary vaccine and DTMUV as well as other flaviviruses can be propagated in BHK-21 cells. However, information about mammalian host cell responses to DTMUV infection is limited. In this study, LC–MS/MS coupled to iTRAQ labeling was used to quantitatively identify differentially expressed cellular proteins in DTMUV-infected BHK-21 cells. We identified 192 differentially expressed cellular proteins including 11 upregulated proteins and 8 downregulated at 24 hpostinfection; 25 upregulated proteins and 151 downregulated at 48 h postinfection. Some of these proteins were involved in viral infection.
2017-05-23 | PXD005731 | Pride
Project description:We used RNA-sequencing on the Illumina platform to analyze transcriptome profiles of BHK-21 acutely infected with FMDV. In total, we obtained more than 342.8 million raw sequencing reads. And approximately 336.5 million clean reads (98.14%) were acquired by filtering out the adapters and trimming ambiguous reads. We found that cellular response of BHK-21 is related to certain types of alterations in the host cell transcriptome profiles at 24 h post infection.
2018-12-20 | GSE124122 | GEO
Project description:Rabies virus (RABV) infection led to alteration of microRNA expression in NA and microglia. A sixteen-chip study was performed using total RNA isolated from NA and microglia infected with rabies virus CVS-11 (Challenge virus standard) or mock infected as a control. RNA was isolated from microglia at 12, 24, or 48 hpi and from NA at 24 hpi.
2014-10-10 | E-GEOD-35706 | biostudies-arrayexpress
Project description:Exploiting the power of high-density gene arrays, the simultaneous expression analysis of 5600 cellular genes was executed on proliferating peripheral blood mononuclear cells (PBMCs) from three normal human donors that were infected in vitro with the T cell tropic laboratory strain of HIV-1, RF. Profiles of expressed genes were assessed at 1, 12, 24, 48, and 72 hr postinfection and compared with those of matched uninfected PBMCs. Viral infection resulted in an overall increase in the number of genes expressed with peaks of expression at 1, 12, and 48 hr postinfection. Functional clustering of genes whose expression level in infected PBMCs varied by 2-fold or greater from levels in the controls indicated that cellular activation markers, proteins associated with immune cell function and with transcription and translation, exhibited increased expression subsequent to viral infection. Gene families exhibiting a decline in gene expression were confined to the 72 hr time point and included genes associated with catabolism and a subset of genes involved with cell signaling and synthetic pathways. Self-organizing map (SOM) cluster analysis identified temporal patterns of coordinated gene expression in infected PBMCs including genes associated with the immune response, the cytoskeleton, and ribosomal subunit structural proteins required for protein synthesis. Keywords: other
2003-07-16 | GSE511 | GEO
Project description:Genome wide DNA methylation profiling of normal and trisomic placentas, and maternal blood cell DNA. The aim of this study was to search for methylation differences between maternal and fetal(placenta) cell free DNA, and between normal and trisomic placentas for an optimized methylation based noninvasive prenatal diagnosis of fetal chromosomal aberations. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in DNA samples from Chorionic villus samples(CVS) and DNA samples from whole blood. Samples included 12 Maternal blood cell samples from normal pregnancies, 12 normal CVS, 12 Trisomy 21 CVS, 12 trisomy 18 CVS and 6 trisomy 13 CVS samples.
2015-03-31 | GSE66210 | GEO
Project description:Directed evolution in mammalian cells can facilitate the engineering of mammalian-compatible biomolecules and can enable synthetic evolvability for mammalian cells. We engineered an orthogonal alphaviral RNA replication system to evolve synthetic RNA-based devices, enabling RNA replicase-assisted continuous evolution (REPLACE) in live mammalian cells. To determine the degradation rate of alphaviral RNA in BHK-21 cells, 10 µg of repRNA-v4 RNA was transfected into 4 million wildtype BHK-21 cells via electroporation. Samples were collected at 1-hour, 3-hour, and 12-hour time points for subsequent RNA-seq analysis. The findings revealed that the half-life of alphaviral RNA in the cells was approximately 3.5 hours.
2024-07-07 | GSE235339 | GEO
Project description:The dengue virus (DENV) cause frequent epidemics infecting ~390 million people annually in over 100 countries. There are no approved vaccines or antiviral drugs for treatment of infected patients. However, there is a novel approach to control transmission of DENV by the mosquito vectors, Aedes aegypti and Ae. albopictus, using Wolbachia symbiont. The wMelPop strain of Wolbachia suppresses DENV transmission and shortens the mosquito life span. However, the underlying mechanism is poorly understood. To clarify this mechanism, either naïve Ae. albopictus (C6/36) or wMelPop-C6/36 cells were infected with DENV2. Analysis of host transcript profiles by RNAseq revealed that the presence of wMelPop had profound effects on mosquito host cell transcription in response to DENV2 infection. The viral RNA evolved from wMelPop-C6/36 contained low frequency mutations (~25%) within the coding region of transmembrane domain-1 (TMD1) of E protein. Mutations with >97 % frequencies were distributed within other regions of E, NS5 RNA-dependent RNA polymerase (NS5POL) domain, the TMDs of NS2A, NS2B, and NS4B. Moreover, while DENV2-infected naïve C6/36 cells showed syncytia formation, DENV2-infected wMelPop-C6/36 cells did not. The Wolbachia-induced mutant DENV2 can readily infect and replicate in naïve C6/36 cells; whereas, in the mutant DENV2- infected BHK-21 or Vero cells, the virus replication was delayed. In LLC-MK2 cells, the mutant failed to produce plaques. Additionally, in BHK-21 cells, many mutations in the viral genome reverted to WT and compensatory mutations in NS3 gene appeared. Our results suggest that wMelPop impacts significantly the interactions of DENV2 with mosquito and mammalian host cells.
2019-02-25 | GSE125580 | GEO
Project description:Genome wide DNA methylation profiling of normal and trisomic placentas, and maternal blood cell DNA. The aim of this study was to search for methylation differences between maternal and fetal(placenta) cell free DNA, and between normal and trisomic placentas for an optimized methylation based noninvasive prenatal diagnosis of fetal chromosomal aberations. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in DNA samples from Chorionic villus samples(CVS) and DNA samples from whole blood. Samples included 12 Maternal blood cell samples from normal pregnancies, 12 normal CVS, 12 Trisomy 21 CVS, 12 trisomy 18 CVS and 6 trisomy 13 CVS samples. Bisulphite converted DNA from the 54 samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip.
2015-03-31 | E-GEOD-66210 | biostudies-arrayexpress
Project description:Plant virus infection involves the production of viral small RNAs (vsRNAs) with the potential to associate with distinct Argonaute (AGO)-containing silencing complexes and mediate diverse silencing effects on RNA and chromatin. We used multiplexed, high-throughput pyrosequencing to profile populations of vsRNAs from plants infected with viruses from different genera. Sense and antisense vsRNAs of 20 to 24 nucleotides (nts) spread throughout the entire viral genomes in an overlapping configuration; virtually all genomic nucleotide positions were represented in the dataset. We present evidence to suggest that every genomic position could be a putative cleavage site for vsRNA formation, although viral genomes contain specific regions that serve as preferential sources of vsRNA production. Hotspots for vsRNAs of 21-, 22-, and 24-nt usually coincide in the same genomic regions, indicating similar target affinities among Dicer-like (DCL) enzymes. In the light of our results, the overall contribution of perfectly base paired double-stranded RNA and imperfectly base paired structures within single-stranded RNA to vsRNA formation is discussed. Our census of vsRNAs extends the current view of the distribution and composition of vsRNAs in virus-infected plants, and contributes to define a more comprehensive scenario of vsRNA biogenesis and their regulatory functions in plants Raw data files are available on our FTP site: ftp://ftp.ncbi.nlm.nih.gov/pub/geosup/Series/GSE16996 10 samples examined: Arabidopsis plants infected with TRV, TuMV or CMV; Nicothiana benthamiana plants infected with CymRSV, PVX or PMMoV; Cucumis melo plants infected with MNSV, quimeric MNSV or WMV and Solanum lycopersicum plants infected with TYLCV.
2009-07-09 | E-GEOD-16996 | biostudies-arrayexpress