Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Analysis of 3' 2'-O-methylated small RNAs in Caenorhabditis elegans

ABSTRACT: To identify methylated small RNAs in C. elegans, we deep sequenced both β-eliminated and untreated small RNAs isolated from wild type C. elegans.

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE34321 | GEO | 2011/12/10

SECONDARY ACCESSION(S): PRJNA156417

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Analysis of 3' 2'-O-methylated small RNAs in Caenorhabditis elegans

Project description:To identify methylated small RNAs in C. elegans, we deep sequenced both β-eliminated and untreated small RNAs isolated from wild type C. elegans. Small RNAs were isolated from larval and adult stage C. elegans and either subjected to β-elimination or no treatment. Small RNA cDNA libraries were sequenced on an Illumina HiSeq instrument, and enrichment or depletion of small RNAs by β-elimination was assessed after library size normalization based on the number of mappable reads in each library.

2011-12-10 | E-GEOD-34321 | biostudies-arrayexpress

Analysis of 22G siRNA triggered siRNA amplification and 3' 2'-O-methylated small RNAs in Caenorhabditis elegans

Project description:Small RNAs, including piRNAs, miRNAs and endogenous siRNAs, bind Argonaute proteins to form RNA-silencing complexes that target coding genes, transposons and aberrant RNAs. To assess the requirements for endogenous siRNA formation and activity in C. elegans, we developed a GFP-based sensor for the endogenous siRNA 22G siR-1, one of a set of abundant siRNAs processed from a precursor RNA mapping to the X chromosome, the X-cluster. Silencing of the sensor is also dependent on the partially complementary, unlinked 26G siR-O7 siRNA. We show that 26G siR-O7 acts in trans to initiate 22G siRNA formation from the X-cluster. The presence of several mispairs between 26G siR-O7 and the X-cluster mRNA, as well as mutagenesis of the siRNA sensor, indicates that siRNA target recognition is permissive to a degree of mispairing. From a candidate reverse genetic screen, we identified several factors required for 22G siR-1 activity, including the Argonaute ergo-1 and the 3' methyltransferase henn-1. Quantitative RT-PCR of small RNAs in a henn-1 mutant and deep sequencing of methylated small RNAs indicate that siRNAs and piRNAs that associate with PIWI clade Argonautes are methylated by HENN-1, while siRNAs and miRNAs that associate with non-PIWI clade Argonautes are not. Thus, PIWI-class Argonaute proteins are specifically adapted to associate with methylated small RNAs in C. elegans. This SuperSeries is composed of the following subset Series: GSE34320: Analysis of 22G siRNA triggered siRNA amplification in Caenorhabditis elegans GSE34321: Analysis of 3' 2'-O-methylated small RNAs in Caenorhabditis elegans Refer to individual Series

2012-02-03 | E-GEOD-35550 | biostudies-arrayexpress

Analysis of 22G siRNA triggered siRNA amplification and 3' 2'-O-methylated small RNAs in Caenorhabditis elegans

2012-02-03 | GSE35550 | GEO

Caenorhabditis elegans

Project description:Analysis of 3' 2'-O-methylated small RNAs in Caenorhabditis elegans

| PRJNA156417 | ENA

Caenorhabditis elegans

Project description:C. elegans small RNAs

| PRJNA117887 | ENA

High-throughput sequencing of small RNAs from Caenorhabditis elegans

Project description:High-throughput sequencing of mixed-stage Caenorhabditis elegans small RNAs. total RNA, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH Keywords: high-throughput 454 sequencing

2006-10-15 | GSE5990 | GEO

Caenorhabditis elegans

Project description:Illumina sequencing of small RNAs from C. elegans embryos

| PRJNA119753 | ENA

Identification of non-coding RNAs expressed by Burkholderia cenocepacia during Caenorhabditis elegans infection

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

Caenorhabditis elegans

Project description:Mutant analysis of C. elegans small RNAs with 5p monophosphates

| PRJNA109169 | ENA

Caenorhabditis elegans

Project description:Deep sequencing of small RNAs from C. elegans during aging

| PRJNA132585 | ENA