GEO DataSets

(Submitter supplied) raw RNAseq data from mid-log phase Thermus thermophilus HB27 WT and HB27Δago RNA

Organism:

Thermus thermophilus HB27

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17995

6 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Escherichia coli

Type:

Other

Platform:

GPL18133

36 Samples

Download data: BEDGRAPH, TSV

(Submitter supplied) Members of the conserved Argonaute protein family use small RNA guides to find their mRNA targets to regulate gene expression and suppress mobile genetic elements in eukaryotes. Argonautes are also present in many bacterial and archaeal species. Unlike eukaryotic proteins, several studied prokaryotic Argonautes use small DNA guides to cleave DNA, a process dubbed DNA interference. However, the natural functions and targets of DNA interference are poorly understood and the mechanisms of DNA guide generation and target discrimination remain unknown. more...

Organism:

Escherichia coli

Type:

Other

Platform:

GPL18133

26 Samples

Download data: BEDGRAPH, TSV

(Submitter supplied) Members of the conserved Argonaute protein family use small RNA guides to find their mRNA targets to regulate gene expression and suppress mobile genetic elements in eukaryotes. Argonautes are also present in many bacterial and archaeal species. Unlike eukaryotic proteins, several studied prokaryotic Argonautes use small DNA guides to cleave DNA, a process dubbed DNA interference. However, the natural functions and targets of DNA interference are poorly understood and the mechanisms of DNA guide generation and target discrimination remain unknown. more...

Organism:

Escherichia coli

Type:

Other

Platform:

GPL18133

18 Samples

Download data: BEDGRAPH

(Submitter supplied) SPARTA-related small RNA, long RNA, and DNA

Organism:

Escherichia coli BL21(DE3)

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Other

Platform:

GPL30612

10 Samples

Download data: XLSX

(Submitter supplied) Eukaryotic Argonautes bind small RNAs and use them as guides to find complementary RNA targets and induce gene silencing. Though homologs of eukaryotic Argonautes are present in many bacteria and archaea their small RNA partners and functions are unknown. We found that the Argonaute of Rhodobacter sphaeroides (RsAgo) associates with 15-19 nt small RNAs that correspond to the majority of transcripts. more...

Organism:

Cereibacter sphaeroides ATCC 17029; Escherichia coli BL21(DE3); Cereibacter sphaeroides ATCC 17025

Type:

Non-coding RNA profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

4 related Platforms

16 Samples

Download data: FASTA

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Vanderwaltozyma polyspora; Naumovozyma castellii

Type:

Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL9132 GPL15027

4 Samples

Download data: TXT

(Submitter supplied) The RNA-induced silencing complex, comprising Argonaute and guide RNA, mediates RNA interference. Here we report the 3.2 Å crystal structure of Kluyveromyces Argonaute (KpAGO) fortuitously complexed with guide RNA originating from small-RNA duplexes autonomously loaded by recombinant KpAGO. Despite their diverse sequences, guide-RNA nucleotides 1-8 are positioned similarly, with sequence-independent contacts to bases, phosphates and 2'-hydroxyl groups pre-organizing the backbone of nucleotides 2-8 in a near-A-form conformation. more...

Organism:

Vanderwaltozyma polyspora

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9132

2 Samples

Download data: TXT

(Submitter supplied) The RNA-induced silencing complex, comprising Argonaute and guide RNA, mediates RNA interference. Here we report the 3.2 Å crystal structure of Kluyveromyces Argonaute (KpAGO) fortuitously complexed with guide RNA originating from small-RNA duplexes autonomously loaded by recombinant KpAGO. Despite their diverse sequences, guide-RNA nucleotides 1-8 are positioned similarly, with sequence-independent contacts to bases, phosphates and 2'-hydroxyl groups pre-organizing the backbone of nucleotides 2-8 in a near-A-form conformation. more...

Organism:

Naumovozyma castellii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15027

2 Samples

Download data: TXT

(Submitter supplied) Prokaryotic Argonaute nuclease induces DNA interference between plasmid and chromosomal DNA to promote genome recombineering

Organism:

Escherichia coli

Type:

Other

Platform:

GPL18133

15 Samples

Download data: TSV

(Submitter supplied) Argonaute proteins are programmable nucleases that are found in both eukaryotes and prokaryotes and provide defense against invading genetic elements. Although some prokaryotic Argonautes (pAgos) were shown to recognize RNA targets in vitro, the majority of studied pAgos have strict specificity toward DNA, which limits their practical use in RNA-centric applications. Here, we describe a unique pAgo nuclease, KmAgo, from the mesophilic bacterium Kurthia massiliensis that can be programmed with either DNA or RNA guides and can precisely cleave both DNA and RNA targets. more...

Organism:

Escherichia coli

Type:

Other

Platform:

GPL18133

2 Samples

Download data: BEDGRAPH

(Submitter supplied) microRNAs (miRNAs) act as sequence-specific guides for Argonaute (AGO) proteins, which mediate post-transcriptional silencing of target mRNAs. Despite their importance in many biological processes, rules governing AGO-miRNA targeting are only partially understood. We use a modified AGO HITS-CLIP strategy, termed CLEAR (Covalent Ligation of Endogenous Argonaute-bound RNAs) CLIP that enriches miRNAs ligated to their endogenous mRNA targets. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

31 Samples

Download data: XLSX