GEO DataSets

(Submitter supplied) Splicing is an important step of gene expression regulation in eukaryotes, as there are many mRNA precursors that can be alternatively spliced in different tissues, at different cell cycle phases or under different external stimuli. We have developed several life constructs that allow the quantification of fission yeast splicing in vivo on intact cells, and we have compared their splicing efficiency in a wild type strain and in a prp2-1 (U2AF65) genetic background, showing a clear dependency between Prp2 and a consensus signal at 5’ splicing site (5’SS). more...

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30658

6 Samples

Download data: TXT

(Submitter supplied) Eukaryotes employ a set of conserved transcription elongation factors to modulate the behavior of RNA polymerase II (RNAPII). Disruptions of one such factor, the Paf1 complex (Paf1C), generate subunit-specific phenotypes, including distinct changes to co-transcriptional histone modifications. How individual Paf1C subunits impact transcription and coupled processes remains ambiguous. By comparing conditional depletion and steady-state deletion of Paf1C subunits, we determine direct and indirect contributions of Paf1C to gene expression in Saccharomyces cerevisiae. more...

Organism:

Saccharomyces cerevisiae; Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28173

12 Samples

Download data: BW

(Submitter supplied) Eukaryotes employ a set of conserved transcription elongation factors to modulate the behavior of RNA polymerase II (RNAPII). Disruptions of one such factor, the Paf1 complex (Paf1C), generate subunit-specific phenotypes, including distinct changes to co-transcriptional histone modifications. How individual Paf1C subunits impact transcription and coupled processes remains ambiguous. By comparing conditional depletion and steady-state deletion of Paf1C subunits, we determine direct and indirect contributions of Paf1C to gene expression in Saccharomyces cerevisiae. more...

Organism:

Saccharomyces cerevisiae; Schizosaccharomyces pombe

Type:

Other

Platform:

GPL28173

50 Samples

Download data: BW

(Submitter supplied) RNA-seq on total RNA of wild type (WT) and set2 mutant (set2d). To determine the changes in transcriptome profile when set2 gene is delete in comparision to WT cells.

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13988

4 Samples

Download data: TXT

(Submitter supplied) Our characterization of Mug174 using genetic and biochemical approaches revealed that Mug174 is the Coilin (an integral component of the Cajal body in multicellular organisms) ortholog in the fission yeast S. pombe. To investigate the Mug174 role in shaping transcriptome, we delete the mug174 gene and performed RNA-seq. We found that intron and exon-intron junction reads were elevated in mug174∆, indicating that pre-mRNA splicing is compromised in the absence of Mug174. more...

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30067

6 Samples

Download data: XLS

(Submitter supplied) Visualizing and measuring molecular-scale interactions in living cells represents a major challenge, but recent advances in microscopy are bringing us closer to achieving this goal. Single-molecule super-resolution microscopy enables high-resolution and sensitive imaging of the positions and movement of molecules in living cells. HP1 proteins are important regulators of gene expression because they selectively bind and recognize H3K9 methylated (H3K9me) histones to form heterochromatin-associated protein complexes that silence gene expression. more...

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20584

5 Samples

Download data: BW

(Submitter supplied) We explored transcriptional responses of the fission yeast to DNA damage. RNA-seq was used to characterize changes in expression profiles of all known lncRNAs and mRNAs in wild type cells and cells treated by four DNA damage agents: Camptothecin, Hydroxyurea, Methyl methanesulfonate and Phleomycin.

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28961

10 Samples

Download data: TXT

(Submitter supplied) RNA-seq analysis compares gene expression of the snf22∆ and snf22-(D996A-E997A) mutants to the wild-type fission yeast (Schizosaccharomyces pombe).

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28961

9 Samples

Download data: XLSX

(Submitter supplied) To investigate the differential analysis of gene expression of mutations at different sites of H2B, we constructed six strains with point mutations at different positions of H2B, and then, we performed the gene expression analysis from the RNA-Seq data.

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17225

24 Samples

Download data: TXT

(Submitter supplied) Chromatin-based epigenetic memory relies on the accurate distribution of parental histone tetramers to newly replicated DNA strands, serving as templates for chromatin structure duplication. Mcm2, a subunit of the replicative helicase, and the Dpb3/4, subunits of polymerase epsilon, govern parental histone deposition to the lagging and leading strands, respectively. However, their contribution to epigenetic inheritance remains controversial. more...

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20584

112 Samples

Download data: BW, TAR

(Submitter supplied) he RNA polymerase II carboxy-terminal domain (CTD) consists of conserved repeats of the consensus sequence Y1-S2-P3-T4-S5-P6-S7, which can be phosphorylated to influence distinct stages of the transcription cycle, including RNA processing. Although affinity purification coupled with mass spectrometry has defined CTD-associated proteins, phospho-dependent CTD interactions have remained largely elusive. more...

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22682

8 Samples

Download data: BW, TXT

(Submitter supplied) The RNA polymerase II carboxy-terminal domain (CTD) consists of conserved repeats of the consensus sequence Y1-S2-P3-T4-S5-P6-S7, which can be phosphorylated to influence distinct stages of the transcription cycle, including RNA processing. Although affinity purification coupled with mass spectrometry has defined CTD-associated proteins, phospho-dependent CTD interactions have remained largely elusive. more...

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL22682 GPL20584

53 Samples

Download data: BW

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

Organism:

Schizosaccharomyces pombe

Type:

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

Platforms:

GPL22682 GPL20584

61 Samples

Download data: BW

(Submitter supplied) Schizosaccharomyces pombe Clp1 is a Cdc14-family phosphatase that reverses mitotic Cdk1 phosphorylation. Despite evolutionary conservation, Clp1’s mammalian orthologs do not share this function. Rather, higher eukaryotic Cdc14 enzymes act in DNA repair, ciliogenesis, and gene regulation. To examine if Clp1 regulates gene expression, we compared the transcriptional profiles of cells lacking Clp1 function to that of wildtype. more...

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by array

Platform:

GPL34165

8 Samples

Download data: TXT

(Submitter supplied) We did transcription profiling on the effect of PAT1 (moonlight protein whose most studied function is to degrade mRNA.) deletion in genes involved in Congo Red response (2 hours of treatment).

Organism:

Schizosaccharomyces pombe; Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL2529

12 Samples

Download data: CEL

(Submitter supplied) Centromeric chromatin is crucial for supporting kinetochore assembly and chromosome segregation. To specify centromeres, the histone H3 variant CENP-A is loaded by the conserved chaperone Scm3/HJURP. The amino-terminus of Scm3/HJURP interacts with CENP-A, while the carboxyl-terminus contains a small domain that interacts with the Mis18 holocomplex, which facilitates centromere localization. Fungal Scm3 proteins contain an additional conserved cysteine-rich domain (CYS) with unknown function. more...

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16192

4 Samples

Download data: BEDGRAPH

(Submitter supplied) We explored transcriptional profiles of the fission yeast Schizosaccharomyces pombe. RNA-seq was used to characterize changes in expression profiles of all known lncRNAs and mRNAs in wild type cells.

Organism:

Schizosaccharomyces pombe

Type:

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

Platform:

GPL28961

1 Sample

Download data: TXT

(Submitter supplied) We explored transcriptional responses of the fission yeast Schizosaccharomyces pombe to DNA damage. RNA-seq was used to characterize changes in expression profiles of all known lncRNAs and mRNAs in response to four DNA damage agents: Camptothecin, Hydroxyurea, Methyl methanesulfonate, Phleomycin.

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28961

4 Samples

Download data: TXT

(Submitter supplied) Circular RNAs (circRNAs) are natural outputs of eukaryotic transcription and RNA processing and have emerged as critical regulators in physiology and human diseases. Although a series of cis-elements and trans-factors are reported to globally regulate circRNA biogenesis, most of these regulations are unconserved or at most mammalian conserved. Here, using a genome-wide CRISPR knockout screen, we have identified an evolutionarily conserved polyadenosine RNA-binding protein ZC3H14 to regulate circRNA biogenesis in eukaryotes. more...

Organism:

Homo sapiens; Mus musculus; Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL24247 GPL24676 GPL28961

19 Samples

Download data: TXT

(Submitter supplied) Condensin drives mitotic chromosome assembly by folding chromatin into loops and is enriched in the vicinity of highly expressed genes, but the significance of such proximity with respect to condensin activity has remained unclear. Here, by modulating the occupancy of RNA Pol II in vivo, we show that transcription plays no role in the steady state association of condensin with DNA. Rather, transcription stalls and even displaces condensin, hindering its ability to fold chromatin and to support chromosome segregation. more...

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL28961

34 Samples

Download data: BIGWIG, COOL