GEO DataSets

(Submitter supplied) Ribosome profiling measures genome-wide translation dynamics at sub-codon resolution. Cycloheximide (CHX), a widely used translation inhibitor to arrest ribosomes in these experiments, has been shown to induce biases in yeast, questioning its use. However, whether such biases are present in datasets of other organisms including humans is unknown. Here we compare different CHX-treatment conditions in human cells and yeast in parallel experiments using an optimized protocol. more...

Organism:

Schizosaccharomyces pombe; Saccharomyces cerevisiae; Candida albicans; Homo sapiens

Type:

Expression profiling by high throughput sequencing

4 related Platforms

33 Samples

Download data: TXT

(Submitter supplied) In fission yeast, meiosis-specific transcripts are selectively eliminated during vegetative growth by the combined action of the YTH-family RNA-binding protein Mmi1 and the nuclear exosome. Upon nutritional starvation, the master regulator of meiosis Mei2 inactivates Mmi1, thereby allowing expression of the meiotic program. Here, we show that the E3 ubiquitin ligase subunit Not4/Mot2 of the evolutionarily conserved Ccr4-Not complex, which associates with Mmi1, promotes suppression of meiotic transcripts expression in mitotic cells. more...

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20841

7 Samples

Download data: TXT

(Submitter supplied) In the yeast genome, a large proportion of nucleosomes occupy well-defined positions. While the contribution of chromatin remodelers and DNA binding proteins to maintain this organization is well established, the relevance of the DNA sequence to nucleosome positioning in the genomic context remains controversial. Through genome-wide, quantitative analysis of nucleosome positioning and high-resolution mutagenenesis of mononucleosomal DNA, we show that sequence changes distort the nucleosomal pattern at the level of individual nucleosomes. more...

Organism:

Schizosaccharomyces pombe; Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19756 GPL20584

46 Samples

Download data: WIG

(Submitter supplied) The regulation of flocculation, surface adhesion and invasive growth in the fission yeast Schizosaccharomyces pombe has focused primarily at the transcriptional level, but little is known with regards to posttranscriptional control. Here, we identified the Pumilio protein Pfr1 as a novel posttranscriptional regulator of these processes. Deletion of pfr1+ prevented flocculation, surface adhesion and invasive growth under inducing conditions, while overexpression of pfr1+ was sufficient to trigger flocculation. more...

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by array

Platform:

GPL16187

9 Samples

Download data: GPR

(Submitter supplied) Maintenance of the correct level and organization of nucleosomes is crucial for genome function. Here we uncover a role for a conserved bromodomain AAA-ATPase, Abo1, in maintenance of nucleosome architecture in fission yeast. Cells lacking abo1+ experience both a reduction and mis-positioning of nucleosomes at transcribed sequences in addition to increased intragenic transcription, phenotypes that are hallmarks of defective chromatin re-establishment behind RNA polymerase II. more...

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17225 GPL13988

4 Samples

Download data: TXT

(Submitter supplied) Sequencing of mononucleosomal DNA from asynchronous cells of Schizosaccharomyces pombe WT and S2A mutant

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13988

2 Samples

Download data: BW

(Submitter supplied) Domains of heterochromatin play important roles in the maintenance and regulation of eukaryotic genomes. However, the repressive nature of heterochromatin combined with its propensity to self-propagate necessitates the existence of robust mechanisms that limit heterochromatin spreading and thereby avoid silencing of expressed genes. A number of specific sequence elements have been found to serve as barriers to heterochromatin spreading; however, the mechanisms by which spreading is curtailed are generally not well understood. more...

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17225

4 Samples

Download data: BW

(Submitter supplied) We describe the NucleoATAC algorithm for high-resolution nucleosome positioning and occupancy determination using ATAC-seq.

Organism:

Saccharomyces cerevisiae; Homo sapiens; Schizosaccharomyces pombe

Type:

Other

4 related Platforms

32 Samples

Download data

(Submitter supplied) Sequencing of mononucleosomal DNA during asynchronous mitosis in Schizosaccharomyces pombe, Schizosaccharomyces octosporus, Schizosaccharomyces japonicus and Saccharomyces cerevisiae

Organism:

Schizosaccharomyces japonicus; Schizosaccharomyces octosporus; Schizosaccharomyces pombe; Saccharomyces cerevisiae W303

Type:

Genome binding/occupancy profiling by high throughput sequencing

4 related Platforms

4 Samples

Download data: WIG

(Submitter supplied) Poly(A) tails enhance the stability and translation of most eukaryotic messenger RNAs, but difficulties in globally measuring poly(A)-tail lengths have impeded greater understanding of poly(A)-tail function. Here we describe poly(A)-tail length profiling by sequencing (PAL-seq) and apply it to measure tail lengths of millions of individual RNAs isolated from yeasts, cell lines, Arabidopsis thaliana leaves, mouse liver, and zebrafish and frog embryos. more...

Organism:

Schizosaccharomyces pombe; Danio rerio; Saccharomyces cerevisiae; Homo sapiens; Arabidopsis thaliana; Drosophila melanogaster; Xenopus laevis; Mus musculus

Type:

Expression profiling by high throughput sequencing

13 related Platforms

64 Samples

Download data: TXT

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

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by genome tiling array; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by genome tiling array

Platforms:

GPL7715 GPL15167

15 Samples

Download data: CEL, WIG

(Submitter supplied) Sequencing of mononucleosomal DNA during asynchronous mitosis and 0, 3 and 5 hours into meiosis in Schizosaccharomyces pombe.

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL15167

5 Samples

Download data: WIG

(Submitter supplied) Mononucleosomal DNA analysis of atf1D and pcr1D mutants of Schizosaccharomyces pombe and transcription analysis of exponential wild type 972 h-, atf1D, pcr1D and mitotic diploid pat1.114, and synchronous diploid pat1.114 at 0h, 3h and 5h into meiosis

Organism:

Schizosaccharomyces pombe

Type:

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

Platform:

GPL7715

10 Samples

Download data: CEL, WIG

(Submitter supplied) We use high-density tiling DNA microarray technology to obtain the specific transcriptome-wide response induced by 5-Fluorouracil (5FU) in the eukaryotic model Schizosaccharomyces pombe.

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by genome tiling array

Platform:

GPL7715

4 Samples

Download data: CEL, WIG

(Submitter supplied) Here we describe a lariat-sequencing approach, which offers high sensitivity for detecting splicing events, and its application to the unicellular fungus, Schizosaccharomyces pombe, an organism that shares many of the hallmarks of alternative splicing in mammalian systems but for which no previous examples of exon-skipping had been demonstrated. Over 200 previously unannotated splicing events were identified, including examples of regulated alternative splicing.

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15167

2 Samples

Download data: TXT

(Submitter supplied) In Schizosaccharomyces pombe, over 90% of transcription factor genes are nonessential. Moreover, the majority do not exhibit significant growth defects under optimal conditions when deleted, complicating their functional characterization and target gene identification. Here, we systematically overexpressed 99 transcription factor genes with the nmt1 promoter. Screening the overexpression array revealed that 64 transcription factor genes exhibited reduced fitness when ectopically expressed. more...

Organism:

Schizosaccharomyces pombe

Type:

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

Platforms:

GPL16187 GPL16235

20 Samples

Download data: GPR

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

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by genome tiling array; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL7715 GPL13988

5 Samples

Download data: BAR, BED, CEL, WIG

(Submitter supplied) At Schizosaccharomyces pombe centromeres, heterochromatin formation is required for de novo incorporation of the histone H3 variant CENP-A/Cnp1, which in turn directs kinetochore assembly and ultimately chromosome segregation during mitosis. Noncoding RNAs (ncRNAs) transcribed by RNA polymerase II (Pol II) directs heterochromatin formation via the RNAi machinery, but also through RNAiindependent RNA processing factors. more...

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13988

3 Samples

Download data: BED, WIG

(Submitter supplied) In the fission yeast Schizosaccharomyces pombe, the transcriptional-regulatory network that governs flocculation remains poorly understood. Here, we systematically screened an array of transcription factor deletion and overexpression strains for flocculation and performed microarray expression profiling and ChIP-chip analysis to identify the flocculin target genes. We identified five transcription factors that displayed novel roles in the activation or inhibition of flocculation (Rfl1, Adn2, Adn3, Sre2, and Yox1), in addition to the previously-known Mbx2, Cbf11 and Cbf12 regulators. more...

Organism:

Schizosaccharomyces pombe

Type:

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

Platforms:

GPL16187 GPL16235

14 Samples

Download data: GPR

(Submitter supplied) Genome-wide nucleosome position data for wildtype and mutant strains in S. cerevisiae, C. albicans, and S. pombe

Organism:

Saccharomyces cerevisiae; Schizosaccharomyces pombe; Candida albicans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL9134 GPL9854 GPL9133

7 Samples

Download data: TXT, WIG