GEO DataSets

(Submitter supplied) The eukaryotic RNA exosome is a ubiquitously expressed complex of nine core proteins (EXOSC1-9) and associated nucleases responsible for RNA processing and degradation. Autosomal recessive mutations in EXOSC3, EXOSC8, EXOSC9 and the exosome cofactor RBM7 cause pontocerebellar hypoplasia and motor neuronopathy. To understand the importance of the exosome in neurodegeneration, we investigated the consequences of exosome mutations on RNA metabolism and cellular survival in zebrafish and human cell models. more...

Organism:

Danio rerio; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18413 GPL16791

108 Samples

Download data: TXT

(Submitter supplied) Recessive mutations in EXOSC3, encoding a subunit of the human RNA exosome complex, cause Pontocerebellar hypoplasia type 1b (PCH1B). We report a boy with severe muscular hypotonia, psychomotor retardation, progressive microcephaly, and cerebellar atrophy. Biochemical abnormalities comprised mitochondrial Complex I and PDHc deficiency. Whole exome sequencing uncovered a known EXOSC3-mutation p.(D132A) as the underlying cause. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Third-party reanalysis

Platform:

GPL23227

1 Sample

Download data: XLSX

(Submitter supplied) RNA exosomopathies, a growing family of tissue-specific diseases, are linked to missense mutations in genes encoding the structural subunits of the conserved 10-subunit exoribonuclease complex, the RNA exosome. Such mutations in the cap subunit gene EXOSC2 cause the novel syndrome SHRF (Short stature, Hearing loss, Retinitis pigmentosa and distinctive Facies). In contrast, exosomopathy mutations in the cap subunit gene EXOSC3 cause pontocerebellar hypoplasia type 1b (PCH1b). more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21656

6 Samples

Download data: TXT

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

Organism:

Danio rerio; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL14875 GPL18573

20 Samples

Download data

(Submitter supplied) The development of a differentiated and functional vasculature requires coordinated control of cell fate specification, lineage differentiation and vascular network growth. Cellular proliferation is spatiotemporally regulated in developing vessel networks but how this is achieved and differentially controlled in specific lineages is unknown. Using a zebrafish forward genetic screen for mutants that form blood vessels but fail to form lymphatic vessels, we uncovered a mutant for the RNA helicase Ddx21. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

12 Samples

Download data: CSV

(Submitter supplied) In our RIP-seq experiment, RNAs were purified from the E12.5 WT mouse cortex. By sequencing of the Exosc10-bound RNAs, binding enrichment of Exosc10 on 3159 transcripts was identified (adjusted p-value < 0.05). GO analysis revealed that the Exosc10-bound transcripts participate in various processes of brain development.

Organism:

Mus musculus

Type:

Other

Platform:

GPL21103

8 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

Other; Expression profiling by high throughput sequencing

Platform:

GPL13112

22 Samples

Download data: NARROWPEAK

(Submitter supplied) The RNA exosome is a ten-subunit complex that mediates both RNA processing and degradation. This complex is evolutionarily conserved, ubiquitously expressed, and required for fundamental cellular functions, including rRNA processing. The RNA exosome plays many roles in regulating gene expression and protecting the genome, including modulating the accumulation of R-loops at sites of transcription. The RNA exosome interacts with specific target RNAs for decay or processing by interacting proteins termed cofactors. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

9 Samples

Download data: TXT

(Submitter supplied) The RNA exosome is a ten-subunit complex that mediates both RNA processing and degradation. This complex is evolutionarily conserved, ubiquitously expressed, and required for fundamental cellular functions, including rRNA processing. The RNA exosome plays many roles in regulating gene expression and protecting the genome, including modulating the accumulation of R-loops at sites of transcription. The RNA exosome interacts with specific target RNAs for decay or processing by interacting proteins termed cofactors. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL13112

13 Samples

Download data: NARROWPEAK

(Submitter supplied) Analysis of transcriptional profiles in Sbds(ATG) MO-injected embryos with and without coinjection of p53(ATG) MO. We identified a large number of changes in transcript abundance associated with loss of Sbds. Among the 24,278 annotated zebrafish genes in the platform, 4,892 significantly differentially expressed genes were identified.

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL14688

16 Samples

Download data: TXT

(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) The RNA exosome is fundamental for the degradation of RNA in eukaryotic nuclei. Substrate targeting is facilitated by its co-factor Mtr4p/hMTR4, which links to RNA-binding protein adaptors. One such activity is the human Nuclear EXosome Targeting (NEXT) complex, composed of hMTR4, the Zn-finger protein ZCCHC8 and the RNA-binding factor RBM7. NEXT primarily targets early and unprocessed transcripts, demanding a rationale for how the nuclear exosome recognizes processed RNAs. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL11154

36 Samples

Download data: BW

(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) The nuclear RNA exosome is an essential multi-subunit complex that controls RNA homeostasis. Congenital mutations in exosome genes are associated with neurodegenerative diseases. Here, we show that transient depletion of nuclear RNA exosome subunits in epithelial cells inhibits influenza virus replication. Similarly, viral biogenesis was suppressed in cells derived from mice with conditional ablation of the RNA exosome subunit Exosc3. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL16791 GPL17021

28 Samples

Download data: TXT

(Submitter supplied) Individual-nucleotide resolution UV-crosslinking and immunoprecipitation (iCLIP) followed by high-throughput sequencing of RBM7-associated transcripts. Note: these data relate to Figure 1, 2, 3, 4, 5 and 6 in Lubas, Andersen et al., Cell Reports 2014

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL11154

4 Samples

Download data: WIG