GEO DataSets

(Submitter supplied) Genome-wide detection of novel non-coding RNAs in S. cerevisiae by modulating an RNase P pathway through the depletion of a component RPP1. Keywords: time course

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by genome tiling array

Platform:

GPL3471

8 Samples

Download data

(Submitter supplied) GenBank accession numbers: NC_001133-NC_001148, NC_001224 Protocol: Maskless Array Synthesizer (MAS)

Organism:

Saccharomyces cerevisiae

1 Series

8 Samples

Download data

(Submitter supplied) Protein binding is essential to the transport, decay and regulation of almost all RNA molecules. However, the structural preference of protein binding on RNAs and their cellelar functions and dynamics upon changing environmental condictions are poorly understood. Here, we integrated various high-throughput data and introduced a computational framework to describe the global interactions between RNA binding proteins (RBPs) and structured RNAs in yeast at single-nucleotide resolution. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

10 Samples

Download data: BED

(Submitter supplied) We used this array as described in Babak, Blencowe, anf Hughes (2005), to screen novel ncRNA predictions. See author supplementary data for more detailed probe information. Keywords: parallel sample

Organism:

Mus musculus

Type:

Non-coding RNA profiling by array

Platform:

GPL1896

16 Samples

Download data

(Submitter supplied) Compared to other model organisms and despite the clinical relevance of the pathogenic yeast Candida albicans, no comprehensive analysis has been done to provide experimental support of its in silico-based genome annotation. Here we have undertaken a genome-wide experimental annotation to accurately uncover the transcriptional landscape of the pathogenic yeast C. albicans using strand-specific high-density tiling arrays. more...

Organism:

Candida albicans

Type:

Expression profiling by genome tiling array; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL10637 GPL10636

12 Samples

Download data: TXT

(Submitter supplied) The budding yeast Saccharomyces cerevisiae alters its gene expression profile in response to a change in nutrient availability. The PHO-system is a well-studied case in the transcriptional regulation responding to nutritional changes in which a set of genes (PHO genes) is expressed to activate phosphate (Pi) metabolism for adaptation to Pi-starvation. Pi-starvation triggers an inhibition of Pho85 kinase, leading to migration of unphosphorylated Pho4 transcriptional activator into the nucleus enabling expression of PHO genes. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL3723

8 Samples

Download data: CEL

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

Organism:

Saccharomyces cerevisiae

Type:

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

Platforms:

GPL17342 GPL21656

49 Samples

Download data: BIGWIG

(Submitter supplied) Eukaryotic cells utilize several mechanisms to ensure that expression of aberrant non-coding RNAs is limited. Gene looping, chromatin modification or remodeling, and RNA surveillance contribute to ensure the fidelity of transcription and limit non-coding transcripts. Here we identify that in Saccharomyces cerevisiae, the transcription factor Rap1 is critical for limiting the expression of aberrant RNAs, particularly near the highly expressed ribosomal protein genes, and characterize them in the context of other non-coding RNAs regulated by chromatin and transcription related factors.

Organism:

Saccharomyces cerevisiae

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17342

24 Samples

Download data: BIGWIG, TSV

(Submitter supplied) Eukaryotic cells utilize several mechanisms to ensure that expression of aberrant non-coding RNAs is limited. Gene looping, chromatin modification or remodeling, and RNA surveillance contribute to ensure the fidelity of transcription and limit non-coding transcripts. We have identified that the transcription factor Rap1 is critical for limiting the expression of aberrant RNAs, particularly near the highly expressed ribosomal protein genes. more...

Organism:

Saccharomyces cerevisiae

Type:

Other; Expression profiling by high throughput sequencing

Platform:

GPL21656

7 Samples

Download data: BIGWIG

(Submitter supplied) Many active eukaryotic gene promoters exhibit divergent noncoding transcription, but the mechanisms restricting expression of these transcripts are not well understood. Here we demonstrate how a sequence-specific transcription factor represses divergent noncoding transcription at highly expressed genes in yeast. We find that depletion of the transcription factor Rap1 induces noncoding transcription in a large fraction of Rap1 regulated gene promoters. more...

Organism:

Saccharomyces cerevisiae

Type:

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

Platform:

GPL17342

18 Samples

Download data: BIGWIG, TSV

(Submitter supplied) Mitogen Activated Protein Kinase (MAPK) signaling cascades transduce information arising from events external to the cell, such as environmental stresses, to a variety of downstream effectors and transcription factors. The fission yeast stress activated MAP kinase (SAPK) pathway is conserved with the p38 and JNK pathways in humans, and comprises the MAPKKKs Win1, Wis4, the MAPKK Wis1, and the MAPK, Sty1. more...

Organism:

Schizosaccharomyces pombe

Type:

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

Platform:

GPL18570

36 Samples

Download data: TXT

(Submitter supplied) Small RNA produced by Dicer (Dcr1) are used to map dsRNA in wild-type strain and a xrn1-delta mutant of S. cerevisiae, inactivated for the cytoplasmic 5'-3' RNA decay pathway.

Organism:

Saccharomyces cerevisiae

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13272

4 Samples

Download data: TXT

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

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Expression profiling by genome tiling array

Platforms:

GPL7249 GPL9134 GPL7250

24 Samples

Download data: BAR, CEL, TXT

(Submitter supplied) Annotating Low Abundance and Transient RNAs in Yeast using Tiling Microarrays and Ultra High-throughput Sequencing Reveals New Transcripts that are not Conserved Across Closely Related Yeast Species A complete description of the transcriptome of an organism is crucial for a comprehensive understanding of how it functions, how its transcriptional networks are controlled, and may provide insights into the organism’s evolution. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9134

16 Samples

Download data: TXT

(Submitter supplied) A complete description of the transcriptome of an organism is crucial for a comprehensive understanding of how it functions, how its transcriptional networks are controlled, and my provide insights into the organism's evolution. Despite the status of Saccharomyces cerevisiae as arguably the most well understood model eukaryote, we still do not have a full catalog and understanding of all its genes. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by genome tiling array

Platforms:

GPL7249 GPL7250

8 Samples

Download data: BAR, CEL

(Submitter supplied) Glycolytic (G) bodies were purified from hypoxic yeast using differential centrifugation and immunoprecipitation by Pfk2-GFP-Flag in order to determine the RNAs that localize to G bodies by determining the enrichment of RNAs copurified with G bodies over both the flow through and total RNA fractions. We find significant overlap between enriched RNAs and RNAs bound by glycolysis enzymes in normoxic conditions. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL17342

6 Samples

Download data: TXT

(Submitter supplied) This experiment aimed to identify the direct RNA targets of G-body components Pfk2, Eno1, and Fba1 in budding yeast.

Organism:

Saccharomyces cerevisiae

Type:

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

Platform:

GPL13821

3 Samples

Download data: TXT

(Submitter supplied) Protein-RNA interactions are integral components of nearly every aspect of biology including regulation of gene expression, assembly of cellular architectures, and pathogenesis of human diseases. However, studies in the past few decades have only uncovered a small fraction of the vast landscape of the protein-RNA interactome in any organism, and even less is known about the dynamics of protein-RNA interactions under changing developmental and environmental conditions. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

17 Samples

Download data: TXT