Caenorhabditis elegans
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA339695 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR4046496.fastq.gz | Fastqsanger.gz | |||
| SRR4046497.fastq.gz | Fastqsanger.gz | |||
| SRR4046498.fastq.gz | Fastqsanger.gz | |||
| SRR4046499.fastq.gz | Fastqsanger.gz |
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Project description:mRNA sequencing in cde-1 mutants versus WT C. elegans infected by the Orsay virus
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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: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: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: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: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:Small RNA sequencing in mutant strains of C. elegans infected by the Orsay virus
| PRJNA318260 | ENA
Project description:Caenorhabditis elegans infected with Enterococcus
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Project description:Genome wide expression analysis of Caenorhabditis elegans cdk-8(tm1238) null mutants (vs. WT N2 worms)
| PRJNA282973 | ENA