GEO DataSets

(Submitter supplied) In Saccharomyces cerevisiae, the maturation of both pre-rRNA and pre-small nucleolar RNAs (pre-snoRNAs) involves common factors, thereby providing a potential mechanism for the coregulation of snoRNA and rRNA synthesis. In this study, we examined the global impact of the double-stranded-RNA-specific RNase Rnt1p, which is required for pre-rRNA processing, on the maturation of all known snoRNAs. In silico searches for Rnt1p cleavage signals, and genome-wide analysis of the Rnt1p-dependent expression profile, identified seven new Rnt1p substrates. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL90

8 Samples

Download data: CEL, CHP

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

Organism:

Saccharomyces cerevisiae

Type:

Non-coding RNA profiling by high throughput sequencing; Expression profiling by genome tiling array

Platforms:

GPL16028 GPL7250

9 Samples

Download data: BED, CEL, TXT

(Submitter supplied) Here we present complete genomic and biochemical annotations of the signals required for RNA degradation by the dsRNA specific ribonuclease III (Rnt1p) and examine its impact on transcriptome stability. Rnt1p cleavage signals are randomly distributed in the yeast genome and encompass wide variety of sequence indicating that transcriptome stability is not determined by the recurrence of a fixed cleavage motif. more...

Organism:

Saccharomyces cerevisiae

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16028

2 Samples

Download data: BED, TXT

(Submitter supplied) Here we present complete genomic and biochemical annotations of the signals required for RNA degradation by the dsRNA specific ribonuclease III (Rnt1p) and examine its impact on transcriptome expression. Rnt1p cleavage signals are randomly distributed in the yeast genome and encompass wide variety of sequence indicating that transcriptome stability is not determined by the recurrence of a fixed cleavage motif. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by genome tiling array

Platform:

GPL7250

4 Samples

Download data: BED, CEL, CSV, TXT

(Submitter supplied) Here we present complete genomic and biochemical annotations of the signals required for RNA degradation by the dsRNA specific ribonuclease III (Rnt1p) and examine its impact on transcriptome stability. Rnt1p cleavage signals are randomly distributed in the yeast genome and encompass wide variety of sequence indicating that transcriptome stability is not determined by the recurrence of a fixed cleavage motif. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by genome tiling array

Platform:

GPL7250

3 Samples

Download data: CEL, TXT

(Submitter supplied) Transcription termination of messenger RNA (mRNA) is normally achieved by polyadenylation followed by Rat1p dependent 5’-3’ exoribonuleolytic degradation of the downstream transcript. Here we show that the yeast orthologue of the dsRNA-specific ribonuclease III (Rnt1p) may trigger Rat1p dependent termination of RNA transcripts that fail to terminate near polyadenylation signals. Rnt1p cleavage sites were found downstream of several genes and the deletion of RNT1 resulted in transcription read-through. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL4131

5 Samples

Download data: GPR, TIFF

(Submitter supplied) We show that in S. cerevisiae pre-snoRNA processing by the endonuclease Rnt1 occurs co-transcriptionally, removing the m7G cap to facilitate the formation of box C/D snoRNA. Failure to remove m7G cap from box C/D pre-snoRNA affects 3’ end processing, ribonucleoprotein complex formation and causes mislocalization to the cytoplasm. Consequently, Rnt1-dependent 5’ end processing of box C/D snoRNA is critical for snoRNA-dependent methylation of ribosomal RNA. more...

Organism:

Saccharomyces cerevisiae

Type:

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

Platforms:

GPL18249 GPL21656

11 Samples

Download data: BED, BW

(Submitter supplied) Introns in pre-mRNAs must be spliced out prior to their translation. During splicing, introns are removed in the form of a lariat, in which the 5' end is linked to the 2' hydroxyl of an internal adenosine. Lariat degradation is initiated by an 2'-5' phosphodiester-specific RNA endonuclease which debranches these lariat RNAs to linear form. Deletion of the debranching enzyme is yeast results in the accumulation of lariat introns. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by genome tiling array

Platform:

GPL4065

6 Samples

Download data: CEL

(Submitter supplied) Numerous RNAs copurify with RNase P and are affected by temperture sensitive mutations in conserved residues with the essential RNA and protein subunits. Specifically, RNase P physically interacts with ribosomal protein mRNAS and the intron-encoded box C/D snoRNAs. Keywords: RNA copurification, temperature sensitive mutants

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL6424

10 Samples

Download data: GPR

(Submitter supplied) Small nucleolar RNAs (snoRNAs) are highly abundant non-coding RNAs whose canonical function is to guide the 2’-O-ribose methylation or pseudouridylation of ribosomal RNAs. They are often encoded in longer genes referred to as their host genes, the expression of which is required for their own biogenesis. Due to their very stable structure, reverse transcription of snoRNAs using standard viral reverse transcriptases is very inefficient, and does not provide an adequate view of the abundance of these small RNAs. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

8 Samples

Download data: TSV

(Submitter supplied) The differentiation of cells into distinct cell types, each of which is heritable for many generations, underlies many biological phenomena. White and opaque cells of the fungal pathogen Candida albicans are two such heritable cell types, each thought to be adapted to unique niches within their human host. To systematically investigate the differences between the two cell types, we performed strand-specific massively-parallel sequencing of RNA from C. more...

Organism:

Candida albicans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10314

7 Samples

Download data: PDF, TXT, WIG

(Submitter supplied) Changes in RNA levels during osmotic stress were investigated. Total RNA was extracted from a wild-type yeast strain before and after treatment with 0.4 M NaCl and the corresponding cDNAs were hybridazed on Tiling arrays. In particular, for all the intron-containing genes, the changes in the levels of intron signal in stressed cells related to the intron signal in the non-stressed cells, and the changes in the levels of exon signal in stresses cells related to the exon signal in non-stressed cells were investigated. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by genome tiling array

Platform:

GPL7250

6 Samples

Download data: BAR, CEL, TXT

(Submitter supplied) Background: Small nucleolar RNAs (snoRNAs) are mid-size non-coding RNAs required for ribosomal RNA modification, implying a ubiquitous tissue distribution linked to ribosome synthesis. However, increasing numbers of studies identify extra-ribosomal roles of snoRNAs in modulating gene expression, suggesting more complex snoRNA abundance patterns. Therefore, there is a great need for mapping the snoRNome in different human tissues as the blueprint for snoRNA functions. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL18573

12 Samples

Download data: CSV

(Submitter supplied) Eukaryotic RNAs with premature termination codons (PTCs) are eliminated by nonsense-mediated decay (NMD). While human nonsense RNA degradation can be initiated either by an endonucleolytic cleavage event near the PTC or through decapping, the individual contribution of these activities on endogenous substrates has remained unresolved. Here we unambiguously establish that SMG6-catalyzed endonucleolysis is the primary initiating step in human nonsense RNA decay. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

9 Samples

Download data: BW, TXT

(Submitter supplied) Eukaryotic RNA polymerase II (RNAPII) transcribes mRNA genes and non-protein coding RNAs (ncRNAs) including small nuclear and nucleolar RNAs (sn/snoRNAs). In metazoans, RNAPII transcription of sn/snoRNAs is facilitated by a number of specialized complexes, but no such complexes have been discovered in yeast. It has been proposed that yeast sn/snoRNA promoters use the same factors as mRNA promoters, but the extent to which regulators of mRNA genes function at yeast sn/snoRNA genes is unclear. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL19756

7 Samples

Download data: BW

(Submitter supplied) A comprehensive genome-wide binding profile for Hmt1 was obtained through the method of ChIP-chip using NimbleGen high-resolution tiling microarrays. Of the approximately 1000 Hmt1-binding sites found, the majority fall within or proximal to an ORF. However, Hmt1 occupancy is found at a number of other genomic features such as tRNA and snoRNA genes, thereby implicating a regulatory role in the biogenesis of these non-coding RNAs. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL15469

3 Samples

Download data: TXT

(Submitter supplied) RNA synthesis and decay rates determine the steady-state levels of cellular RNAs. Metabolic tagging of newly transcribed RNA by 4-thiouridine (4sU) can reveal the relative contributions of RNA synthesis and decay rates. The kinetics of RNA processing, however, so far remained unresolved. Here, we show that ultra-short 4sU-tagging not only provides snap-shot pictures of eukaryotic gene expression but, when combined with progressive 4sU-tagging and RNA-seq, reveals global RNA processing kinetics at nucleotide resolution. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9138

7 Samples

Download data: RPKM

(Submitter supplied) Analysis of noncoding RNA processing phenotypes in mutant yeast strains, with isogenic wildtype strains as controls two-color microarrays, total RNA labeled directly with Alexa Ulysis 546 and 648 dyes, dye-swap, eight replicates of each oligo per slide, Lowess smoother, Hedge et al. 2002 protocols, see Peng, Robinson et al., 2003. Keywords: other

Organism:

Saccharomyces cerevisiae

Type:

Non-coding RNA profiling by array

Platform:

GPL337

597 Samples

Download data

(Submitter supplied) We have previously shown that C/D box snoRNAs transcribed from the DLK1-DIO3 locus on human chromosome 14 (14q32) are associated with cardiovascular disease. DLK1-DIO3 snoRNAs are ‘orphan snoRNAs’ that have no known targets. We aimed to identify RNA targets and elucidate the mechanism-of-action of human SNORD113-6 (AF357425 in mice). As AF357425-knockout cells were non-viable, we induced overexpression or inhibition of AF357425 in primary murine fibroblasts and performed RNA-Seq. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL28457

4 Samples

Download data: TSV

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

Organism:

Saccharomyces cerevisiae

Type:

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

Platforms:

GPL18085 GPL17342

14 Samples

Download data: BW, TXT