GEO DataSets

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

Organism:

Saccharolobus solfataricus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL27060 GPL28445

9 Samples

Download data: WIG

(Submitter supplied) In this study, an exoribonuclease was analyzed by iCLIP. The data documents the role of the archaeal exosome as an exoribonuclease and RNA-tailing enzyme interacting with all RNA classes. Mapping of most reads to mRNAs underlines the role of exosome in mRNA turnover, which is important for adaptation of prokaryotic cells to changing environmental conditions. The clustering of crosslink sites near 5’-ends of genes suggests simultaneous binding of both RNA ends by the S. more...

Organism:

Saccharolobus solfataricus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27060

3 Samples

Download data: CSV

(Submitter supplied) In this study, an exoribonuclease was analyzed by iCLIP. The data documents the role of the archaeal exosome as an exoribonuclease and RNA-tailing enzyme interacting with all RNA classes. Mapping of most reads to mRNAs underlines the role of exosome in mRNA turnover, which is important for adaptation of prokaryotic cells to changing environmental conditions. The clustering of crosslink sites near 5’-ends of genes suggests simultaneous binding of both RNA ends by the S. more...

Organism:

Saccharolobus solfataricus

Type:

Other

Platform:

GPL28445

6 Samples

Download data: WIG

(Submitter supplied) The RNA exosome complex functions in both the accurate processing and rapid degradation of many different classes of RNA. Functional and structural analyses indicate that RNA can either be threaded through the central channel of the exosome or more directly access the active sites of the ribonucleases Rrp44 and Rrp6, but it was unclear how many substrates follow each pathway in vivo. To address this we used UV crosslinking in growing cells to identify transcriptome-wide interactions of RNAs with the major nuclear exosome-cofactor Mtr4 and with individual exosome subunits (Rrp6, Csl4, Rrp41 and Rrp44) along the threaded RNA path. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platforms:

GPL13821 GPL22715

13 Samples

Download data: GTF

(Submitter supplied) Small RNAs and L7Ae co-immunoprecipitated RNA were isolated from the thermophilic archaeon Sulfolobus acidocaldarius and subjected to Illumina sequencing. The sRNome revealed a high abundance of C/D box sRNAs and CRISPR RNAs. The L7Ae-RNA interactome showed enrichment of all known interactors of the L7Ae protein, i.e. C/D box sRNAs, H/ACA box sRNAs, RNaseP, rRNA. A high abundance of reads for the SRP RNA was found, suggesting L7Ae´s interaction with this universal RNA. more...

Organism:

Sulfolobus acidocaldarius

Type:

Other; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL23429 GPL23051

5 Samples

Download data: WIG

(Submitter supplied) RNAPII is responsible for transcription of protein-coding genes and short, regulatory RNAs. In Saccharomyces cerevisiae, termination of RNAPII-transcribed RNAs ≤1000 bases requires the NNS complex (comprised of Nrd1, Nab3, and Sen1) processing by the exosome, and the nuclear specific catalytic subunit, Rrp6. It has been shown that Rrp6 interacts directly with Nrd1, but whether or not Rrp6 is required for NNS-dependent termination is unclear. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18621

8 Samples

Download data: TXT

(Submitter supplied) We studied the differences in RNA accumulation profiles of an rrp6-null mutant and compared it to RNA accumulation in rrp6 catalytic mutants as well as dis3 mutants using RNA-Seq. Rrp6 and Dis3 are exosome exoncleases, therefore this study was used to determine their target RNAs We examined 3' end RNA processing changes by RNA-Seq in wild type, rrp6Δ and rrp6-cat mutants. Libraries were made by 3' adapter ligation

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16192

17 Samples

Download data: TAB, TXT

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

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17970

52 Samples

Download data

(Submitter supplied) The Arabidopsis core exosome (Exo9) has a phosphorolytic activity due to the RRP41 subunit. The goal of this experiment was to determine the role of this intrinsic activity of Exo9 on the degradation of rRNA maturation by-products in Arabidopsis.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17970

26 Samples

Download data: TXT

(Submitter supplied) The Arabidopsis core exosome (Exo9) has a phosphorolytic activity due to the RRP41 subunit. The goal of this experiment was to determine the role of this intrinsic activity of Exo9 on the maturation of the 5.8S rRNA in Arabidopsis.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17970

26 Samples

Download data: TXT

(Submitter supplied) Organisms of the third domain of life, the Archaea, share molecular characteristics both with bacteria and eukarya. These organisms attract scientific attention as research models for regulation and evolution of processes such as transcription, translation and RNA processing. We have reconstructed the primary transcriptome of Sulfolobus solfataricus P2, one of the most widely studied model archaeal organisms. more...

Organism:

Saccharolobus solfataricus P2

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9463

8 Samples

Download data: TXT

(Submitter supplied) Pervasive transcription of the human genome generates an abundance of RNAs that must be processed and degraded. The nuclear RNA exosome is the main RNA degradation machinery in the nucleus. However, nuclear exosome must be recruited to its substrates by targeting complexes, such as NEXT or PAXT. By proteomic analysis, we have identified additional subunits of PAXT, including many orthologs of MTREC found in S. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL16791

26 Samples

Download data: BW

(Submitter supplied) To examine whether the competition between hMTR4 with ALYREF is important for the specific exosome recruitment, we performed stranded RNA-seq using rRNA-depleted nuclear RNAs isolated from ALYREF and control overexpression cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

4 Samples

Download data: TXT

(Submitter supplied) To examine whether the competition between hMTR4 with AlyREF is important for the specific exosome recruitment,we sequenced the RNAs associating with hMTR4 in control and AlyREF overexpression cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL20795

6 Samples

Download data: XLSX

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL20795 GPL11154

27 Samples

Download data

(Submitter supplied) To eliminate the possibility that for a particular gene the increased RNA level is an effect of enhanced transcription. We carried out ChIP-seq for RNAPII to compare transcription of mRNAs and lncRNAs in control, hRRP40 and hMTR4 knockdown cells. Among 15000 RNAPII binding peaks identified in these samples, only less than 50 peaks was significantly increased in hRRP40 or hMTR4 knockdown cells.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

6 Samples

Download data: WIG

(Submitter supplied) To define the in vivo targets of the human nuclear exosome, we performed stranded RNA-seq using polyA RNAs isolated from nuclei of HeLa cells. To compare the RNA levels in each sample in an unbiased fashion, we added spike-in controls to equal amount of total nuclear RNAs.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

6 Samples

Download data: TXT

(Submitter supplied) To define the in vivo targets of the human nuclear exosome, we performed stranded RNA-seq using rRNA-depleted RNAs isolated from nuclei of HeLa cells. To compare the RNA levels in each sample in an unbiased fashion, we added spike-in controls to equal amount of total nuclear RNAs.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

5 Samples

Download data: TXT

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

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL17639 GPL13222

45 Samples

Download data: BED

(Submitter supplied) A key function for RNA-binding proteins in orchestrating plant development and environmental responses is well established. However, the lack of a genome-wide view on their in vivo regulatory landscapes represents a gap in understanding the mode of action of plant RNA-binding proteins. Here, we conducted RNAseq to determine the genome-wide regulation repertoire of the circadian clock-regulated Arabidopsis thaliana glycine-rich RNA-binding protein AtGRP7.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

18 Samples

Download data: TSV