Caenorhabditis elegans
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA157963 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We utilized high-throughput RNA-seq to uncover the intermediate-sized noncoding RNAs invovled in UV-DNA Damage Responses in C. elegans. 450 novel transfrags were discovered, some of which show dramatic expression change between the UV irradiation and control. This study should lead to a better understanding of the role of is-ncRNAs invovled in UV-DDR. Examination of intermediate-sized transcripts (70-500nt) in L4 larvae of C. elegans strains, including wild-type (N2), UV-irradiated (N2-UV100J/m2) and NER-deficient mutant (xpa-1) strains.
2012-05-01 | E-GEOD-37063 | biostudies-arrayexpress
Project description:We utilized high-throughput RNA-seq to uncover the intermediate-sized noncoding RNAs invovled in UV-DNA Damage Responses in C. elegans. 450 novel transfrags were discovered, some of which show dramatic expression change between the UV irradiation and control. This study should lead to a better understanding of the role of is-ncRNAs invovled in UV-DDR.
2012-05-01 | GSE37063 | GEO
Project description:Expression profile analysis of C. elegans intermediate sized non-coding transcriptome
| PRJNA130269 | ENA
Project description:This project aims to identify novel RNA binding proteins in the nematode, Caenorhabditis elegans. Since interactions between RNAs and proteins may be transient, these animals were crosslinked with UV light at 254 nm which promotes the covalent link between proteins and RNAs. After this, polyadenylated mRNAs were purified via oligo(dT) coupled to magentic beads under stringent conditions. Finally, samples were subjected to mass spectrometry analysis. To rule out the possibility of RNA-independent binding we also analysed other samples: i) samples digested with RNase one; ii) samples where we performed competition assays with polyadenylic acid
2015-10-26 | PXD002226 | Pride
Project description:We have adapted the eXcision Repair-sequencing (XR-seq) method to generate single-nucleotide resolution dynamic repair maps of UV-induced cyclobutane pyrimidine dimers (CPD) photoproducts in the Caenorhabditis elegans (C. elegans) genome.
2024-04-02 | GSE262486 | GEO
Project description:The nematode Caenorhabditis elegans has evolutionarily conserved EV signaling pathways. In this study, we apply a recently published method for high specificity purification of EVs from C. elegans to carry out target-independent proteomic and RNA analysis of EVs from C. elegans. Our experiments uncovered diverse coding and non-coding RNA transcripts as well as protein cargo types commonly found in human EVs.
2020-08-05 | GSE146973 | GEO
Project description:We have adapted the eXcision Repair-sequencing (XR-seq) method to generate single-nucleotide resolution dynamic repair maps of UV-induced cyclobutane pyrimidine dimers (CPD) photoproducts in the Caenorhabditis elegans (C. elegans) genome. We focus on the C. elegans ortholog of the human XPC-deficient strain (xpc-1) and its exclusive use of transcription-coupled repair. We provide evidence demonstrating the utility of xpc-1 XR-seq as a remarkable tool for detecting nascent transcription and identifying new transcripts. The integration of epigenetic markers, chromatin states, and non-coding RNA annotations supports the robust detection of intergenic nascent transcription by XR-seq. Overall, our results provide a comprehensive view of the transcription-coupled repair landscape in C. elegans, highlighting their potential contributions to our understanding of DNA repair mechanisms and non-coding RNA biology.
2023-11-21 | GSE245181 | GEO
Project description:One of the most abundant RNA modifications is N6-methyladenosine (m6A). RNA from all forms of life, including viruses, contain m6A. This modification has been detected in many types of RNAs, such as mRNA, ribosomal RNA, long non-coding RNAs, small nuclear RNAs and microRNAs. Diverse set of proteins have been characterized to methylate, demethylate and specifically bind to this modification in different organisms. C. elegans is a unique model organism with abundant m6A modification, although its genome does not code for orthologs of the well characterized m6A methyltransferase METTL3/METTL14 complex or the demethylases FTO or ALKBH5. Furthermore, orthologs of the YTH family m6A reader proteins seem to be absent from the worm genome as well. To gain insights into how this modification is installed in this organism, we set out to identify enzymes that contribute to the abundant level of m6A in C. elegans. We designed a targeted RNAi screen by which the expression of 22 candidate putative RNA methyltransferase genes are knocked down. We measured global RNA methylation level by HPLC-MS/MS analysis after two generations of RNAi-mediated knock down. The knock down of two candidate methyltransferases resulted in a decrease in global m6A level in total RNA. The first methyltransferase, F33A8.4, is an ortholog of the human ZCCHC4 gene. The second methyltransferase, C38D4.9, is an ortholog of the human METTL5 gene. In order to determine if ZCCHC4 or METTL5 are involved in the deposition of m6A at the mRNA level, m6A-RIP-seq experiments were performed in mRNA derived from WT (N2), ZCCHC4 KO, METTL5 KO and ZCCHC4/METTL5 dKO C. elegans embryos.
2021-04-06 | GSE148786 | GEO
Project description:We investigated the transcriptome of B. cenocepacia under infection of the nematode Caenorhabditis elegans. RNAs fractions extracted from C. elegans infected with B. cenocepacia were used for Illumina high throughput sequencing using the CappableSeq method. The main objective of this work was to identify small non-coding RNAs (sRNAs) expressed by B. cenocepacia under infection conditions.
2024-01-10 | E-MTAB-12592 | biostudies-arrayexpress