Orsay Virus infection is neither systemic nor transgenerational
Ontology highlight
ABSTRACT:
ORGANISM(S): Caenorhabditis elegans
PROVIDER: GSE60020 | GEO | 2015/01/01
SECONDARY ACCESSION(S): PRJNA257304
REPOSITORIES: GEO
Similar Datasets
Project description:Comparison of small RNAs between virus-infected animals and their progeny Sequencing of small RNAs (15-30nt)
2015-01-01 | E-GEOD-60020 | biostudies-arrayexpress
Project description:This experiment investigates the temporal dynamics in gene expression upon Orsay virus infection in the nematode Ceanorhabditis elegans. Three different strains were infected: JU1580, N2, and CB4856. Of these, JU1580 is highly susceptible, N2 moderately susceptible, and CB4856 the most resistant strain. The goal of the experiment was to identify genes that show different expression dynamics over the time-course of the infection. We (mock-)infected 40h-old C. elegans populations with Orsay virus and took samples over a 32-hour spanning time-course. For each treatment-strain combination 12 samples were collected. Thereafter RNA was isolated, labelled, and hybridized on microarray. The gene-expression dynamics of previously identified genes (e.g. from literature and from a highly replicated N2 versus CB4856 experiment) were analyzed.
2020-07-14 | E-MTAB-7573 | biostudies-arrayexpress
Project description:Aim: We question relative mRNA levels in cde-1 mutants versus WT C. elegans (N2 strain) infected by the Orsay virus Methods: Approximately 200 cde-1 (tm1021) mutants or N2 animals were infected for 48 hours from the L2 stage to the adult stage with 20 µl filtrate of the Orsay virus on 50mm plate seeded with HB101 bacteria, in biological triplicates. Animals were then washed in M9 and resuspended in 1 ml TRIsure (Bioline). Samples were freeze-thaw three times using liquid nitrogen and RNA purification was performed according to Bioline’s guidelines. mRNA libraries were prepared using the NEBNext Ultra directional RNA library kit (NEB) with poly(A) selection and deep sequencing was produced with an Illumina HiSeq machine (single read 50). For differential expression analysis, genes were only included in the analysis if they had at least 1 count per million in all of the control samples or all of the experiment samples. After applying this filter, differentially expressed genes were then called using EdgeR (Robinson, et al. 2010). For the correlation matrix, Pairwise Pearson correlation values were calculated between all samples.
2018-01-31 | GSE76901 | GEO
Project description:This experiment investigates changes in gene expression upon Orsay virus infection and between males and hermaphrodites in the nematode Ceanorhabditis elegans. The laboratory reference strain N2 was used. For this strain, males are less susceptible to Orsay virus infection than hermaphrodites. The goal of the experiment was to identify genes that show different expression patterns for both sexes upon Orsay virus infection. We mock-treated or infected 48h-old C. elegans populations with Orsay virus and took samples 30-hours after infection. For each treatment-sex combination 8 samples were collected. Thereafter RNA was isolated, labelled, and hybridized on microarray. The gene-expression dynamics of previously identified genes (e.g. from literature and from a highly replicated N2 versus CB4856 experiment) were analyzed.
2020-09-13 | E-MTAB-9561 | biostudies-arrayexpress
Project description:Background information: According to our observations, cde-1 (tm1021) null C. elegans animals show increased susceptibility to the Orsay virus (which has a bipartite positive RNA genome), compared to WT (N2 strain). Viral infection seems limited to intestinal cells. CDE-1 is a terminal uridylyltransferase (TUT). TUTs have been shown to promote RNA decay by 3’ end uridylation in various contexts and organisms. We hypothesize that CDE-1 serves as an antiviral factor by uridylating the viral RNA genome. Aims: We question small RNA populations in cde-1 mutants versus WT after two days of infection by the Orsay virus. Methods: Approximately 200 C. elegans animals were infected for 48 hours from the L2 stage to the adult stage with 20 µl filtrate of the Orsay virus on 50mm plate seeded with HB101 bacteria, in biological duplicates, for the following genetic backgrounds: N2 (+), drh-1 (ok3495), rde-1 (ne219), cde-1 (mj414), cde-1 (tm1021), cde-1 (tm1021);drh-1 (ok3495), cde-1 (tm1021);rde-1 (ne219). Animals were then washed in M9 and resuspended in 1 ml TRIsure (Bioline). Samples were freeze-thaw three times using liquid nitrogen and RNA purification was performed according to Bioline’s guidelines. Purified RNA was either directly used for library preparation (5’ dependent libraries) or was first submitted to 5’ polyphosphatase treatment (5’ independent libraries) as in Ashe, et al. 2013. sRNA libraries were prepared using the TruSeq Small RNA Library Preparation Kit (Illumina) according to manufacturer’s instructions (with size selection between 20 and 35 nt, adapters excluded) and deep sequencing was produced with an Illumina HiSeq machine (single read 36).
2019-04-12 | GSE80169 | GEO
Project description:This experiment investigates the gene expression differences upon Orsay virus infection in the Caenorhabdits elegans strains N2 and CB4856. Assays measuring viral load found that the N2 strain displays higher viral loads upon infection than the CB4856 strain. The goal of the experiment was to identify gene-expression differences that could explain the differences in viral load. We (mock-)infected 26h-old C. elegans populations with Orsay virus and took samples after 30h of infection. For each treatment-strain combination 8 samples were collected. Thereafter RNA was isolated, labelled, and hybridized on microarray.
2020-07-08 | E-MTAB-7574 | biostudies-arrayexpress
Project description:Aim: We question non-templated transcript 3ʹ tails in cde-1 mutants versus WT C. elegans (N2 strain) infected by the Orsay virus Methods: Approximately 200 cde-1 (tm1021) mutants or N2 animals were infected for 48 hours from the L2 stage to the adult stage with 20 µl filtrate of the Orsay virus on 50mm plate seeded with HB101 bacteria, in biological duplicates. Animals were then washed in M9 and resuspended in 1 ml TRIsure (Bioline). Samples were freeze-thaw three times using liquid nitrogen and RNA purification was performed according to Bioline’s guidelines. TAILseq preparation and sequencing was performed as described in Chang, et al. Moll. Cell 2014. Tail-seq libraries were processed using Tailseeker 2 (Chang et al. Moll. Cell 2014). The 5ʹ and 3ʹ libraries were subsequently adapter trimmed using cutadapt 1.10 (Martin. EMBnet.journal 2011) with Illumina small RNA-seq adapters and filtered to a minimum length of 5bp. Trimmed 5’ reads were mapped with STAR 2.5.2a (Dobin, et al. Bioinformatics 2013) against a combined meta-genome consisting of the C. elegans reference genome WBcel235 (Harris, et al. Nucleic Acids Res. 2014) and the Orsay virus genome (Felix, et al. Plos Bio. 2011). Mapping was performed in end-to-end mode allowing no mismatches and a gap opening and extension penalty of 10000. Reads were assigned to genes with bedtools 2.26.0 (Quinlan and Hall. Bioinformatics 2010). Subsequently, 3ʹ reads without poly(A) tail or too many dark cycles were removed from the data. For the subsequent analysis, all C. elegans tags with poly(A) tail length equal to zero were discarded. Average poly(A) tail lengths and uridylation lengths for each sample were calculated as the arithmetic mean weighted by the support for each tag, reported by Tailseeker.
2019-08-19 | GSE85893 | GEO
Project description:This explorative study investigated the transcriptional response of C. elegans wild types N2 and CB4856 after Orsay virus infection and Heat shock (n=1). Each strain had a sample that was heat-shocked and infected, one that was heat-shocked and mock-infected, one that was only infected and one that only underwent a mock infection. Age synchronized worms were treated separately according to different treatments mentioned before. After flash freezing, RNA was isolated, labeled and hybridized on oligo microarray (Agilent) slides.
2021-03-08 | E-MTAB-10214 | biostudies-arrayexpress
Project description:Following pathogen infection, plants have developed diverse mechanisms of defense that enhance their immune system for more robust induction of defense responses against recurrent environmental stresses. This induced resistance can be heritable to the progeny, rendering them more tolerant to stressful events. Although within-generational induction of tolerance to abiotic stress is a well-documented phenomenon in virus-infected plants, the transgenerational inheritance of tolerance to abiotic stresses in their progenies has not been explored. Here, we show that infection of Nicotiana benthamiana plants by Potato virus X (PVX) and by a chimeric Plum pox virus (PPV) expressing the P25 protein of PVX (PPV-P25), but not by PPV, conferred tolerance to both salt and osmotic stresses to the progeny, which correlated with the level of virulence of the pathogen. This transgenerational tolerance to abiotic stresses in the progeny was partially sustained even if the plants experience a virus-free generation. Moreover, progenies from a Dicer-like3 mutant, irrespective whether their parents were infected or not, mimicked the enhanced tolerance to abiotic stress observed in progenies of PVX-infected wild-type plants, suggesting the involvement of 24-nt small interfering RNAs in the transgenerational tolerance to abiotic stress induced by virus infection. RNAseq analysis supported the upregulation of genes related to protein folding and response to stress in the progeny of PVX-infected plants. From an environmental point of view, the significance of virus-induced transgenerational tolerance to abiotic stress could be questionable, as its induction was offset by major reproductive costs arising from a detrimental effect on seed production
2022-10-14 | GSE214636 | GEO
Project description:Dissection of the small RNA pathway required for generation of an antiviral small RNA response Small non-coding RNA (~15-30nt) was extracted from animals infected with the Orsay virus
2013-06-01 | E-GEOD-41693 | biostudies-arrayexpress