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Invertebrate gut metagenome

ABSTRACT: The intestinal microbiome in C. elegans deficient to RDE-1 upon Orsay virus infection

PROVIDER: PRJNA382464 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5436390_1.fastq.gz	Fastqsanger.gz
	SRR5436390_2.fastq.gz	Fastqsanger.gz
	SRR5436391_1.fastq.gz	Fastqsanger.gz
	SRR5436391_2.fastq.gz	Fastqsanger.gz
	SRR5436392_1.fastq.gz	Fastqsanger.gz

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Microarray on mock-treated or Orsay virus infected males and hermaphrodites of Caenorhabditis elegans

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

Small RNA sequencing in mutant strains of C. elegans infected by the Orsay virus

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

Microarray on Caenorhabditis elegans N2 and CB4856 infected with Orsay virus

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

Microarray on an infection time-series of Orsay virus in three Caenorhabditis elegans genotypes

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

Transcriptome analysis of C. elegans embryos lacking ADARs and the 26G pathway

Project description:Adenosine deaminases that act on RNA (ADARs) catalyze the conversion of adenosine to inosine in dsRNA. C. elegans ADARs, ADR-1 and ADR-2, promote the expression of genes containing dsRNA structures by preventing their processing into siRNAs and silencing by RNAi. The 26G endogenous siRNA (endo-siRNA) pathway generates a subset of siRNAs distinct from those made in adr-1;adr-2 mutants, but using many of the same factors. We found that adr-1;adr-2;rrf-3 mutants, lacking both ADARs and the RNA-dependent RNA polymerase RRF-3 required for the 26G pathway, display a bursting phenotype rescued by the RNAi factors RDE-1 and RDE-4. To determine what gene expression changes underlie the synthetic phenotype of adr-1;adr-2;rrf-3 mutants, we sequenced poly(A)+ RNA from adr-1;adr-2;rrf-3 embryos, their parent strains, and strains rescued with mutations in rde-1 and rde-4. We found that genes associated with edited structures were robustly downregulated in adr-1;adr-2;rrf-3 mutants in a manner partially dependent on rde-1 and rde-4. Additionally, genes induced during Orsay virus infections were induced in rrf-3 mutants and further upregulated in adr-1;adr-2;rrf-3 mutants, again dependent in part on rde-1 and rde-4.

2018-02-23 | GSE106647 | GEO

Role of STA-1 and SID-3 upon Orsay virus infection in C. elegans

Project description:Role of STA-1 and SID-3 upon Orsay virus infection in C. elegans

| PRJNA376445 | ENA

Characterization of the transcriptional response to Orsay RNA1

Project description:We used RNA-seq to identify gene expression changes in C. elegans ectopically expressing Orsay virus RNA1(wt) or RNA1(RDRP defective mutant), in both wt and drh-1 mutant backgrounds

2019-10-04 | GSE138268 | GEO

Caenorhabditis elegans

Project description:Role of STA-1 and SID-3 upon Orsay virus infection in C. elegans (ChIP-Seq)

| PRJNA376451 | ENA

Caenorhabditis elegans

Project description:Role of STA-1 and SID-3 upon Orsay virus infection in C. elegans (RNA-Seq)

| PRJNA376450 | ENA

Microarray of C. elegans wild types N2 and CB4856 after Orsay virus infection and heat-shock treatment.

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

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