GEO DataSets

(Submitter supplied) To determine the genome-wide changes in gene expression associated with depletion of sulfur in S. cerevisiae, we performed transcriptional profiling using RNA-seq before and at three time points after tranfer in medium without sulfur. Genes downregulated and upregulated were identified by differential gene expression analysis of the RNA-seq data using DESeq2.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26302

12 Samples

Download data: CSV

(Submitter supplied) Abstract: Protein-protein interactions (PPIs) regulate many cellular processes, and engineered PPIs have cell and gene therapy applications. Here we introduce massively parallel protein-protein interaction measurement by sequencing (MP3-seq), an easy-to-use and highly scalable yeast-two-hybrid approach for measuring PPIs. In MP3-seq, DNA barcodes are associated with specific protein pairs, and barcode enrichment can be read by sequencing to provide a direct measure of interaction strength. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platforms:

GPL26302 GPL17143

36 Samples

Download data: CSV, XLSX

(Submitter supplied) We report on how the absence of expansion segment 7S from the yeast ribosome alters A-site occupancy along transcripts. This has consequence for local translation rates and protein fidelity.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL26302

11 Samples

Download data: TXT

(Submitter supplied) Nonsense and missense mutations in the transcription factor PAX6 cause a wide range of eye development defects, including aniridia, microphthalmia and coloboma. To understand how changes of PAX6:DNA binding cause these phenotypes, we combined saturation mutagenesis of the paired domain of PAX6 with a yeast one-hybrid (Y1H) assay in which expression of a PAX6-GAL4 fusion gene drives antibiotic resistance. more...

Organism:

Saccharomyces cerevisiae; synthetic construct

Type:

Other

Platforms:

GPL31112 GPL26302 GPL33815

15 Samples

Download data: CSV, TSV

(Submitter supplied) Cotranslational protein folding depends on general chaperones that engage highly diverse nascent chains at the ribosomes. Here we find that the universal cotranslational machinery adapts to accommodate the challenging biogenesis of abundantly expressed eukaryotic translation elongation factor 1A (eEF1A). During eEF1A synthesis, chaperone Chp1 is recruited to the ribosome with the help of the nascent polypeptide-associated complex (NAC), where it safeguards eEF1A biogenesis. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL26302

16 Samples

Download data: H5

(Submitter supplied) The variant histone H2A.Z is inserted into nucleosomes immediately downstream of promoters and is important for transcription. The site-specific deposition of H2A.Z is catalyzed by SWR, a conserved chromatin remodeler with affinity for promoter-proximal nucleosome depleted regions (NDRs) and histone acetylation. By comparing the genomic distribution of H2A.Z in wild-type and SWR-deficient cells, we found that SWR is also responsible for depositing H2A.Z at thousands of non-canonical sites not directly linked to NDRs or histone acetylation. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26302

16 Samples

Download data: BED, BW

(Submitter supplied) A key step towards defining the structure-function relationship of the genome is to identify the molecular mechanisms that drive higher-order genome folding. To this end, we reconstituted five S. cerevisiae chromosomes in vitro and developed a high-resolution MNase-based chromosome conformation capture assay to measure their 3D organization. We show that the formation of regularly spaced and phased nucleosome arrays is sufficient to drive higher-order genome folding into domains that resemble in vivo genome organization and thereby demonstrate that neither loop extrusion nor transcription are required for domain formation. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26302

47 Samples

Download data: BED

(Submitter supplied) A key step towards defining the structure-function relationship of the genome is to identify the molecular mechanisms that drive higher-order genome folding. To this end, we reconstituted five S. cerevisiae chromosomes in vitro and developed a high-resolution MNase-based chromosome conformation capture assay to measure their 3D organization. We show that the formation of regularly spaced and phased nucleosome arrays is sufficient to drive higher-order genome folding into domains that resemble in vivo genome organization and thereby demonstrate that neither loop extrusion nor transcription are required for domain formation. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL26302

26 Samples

Download data: TXT

(Submitter supplied) A key step towards defining the structure-function relationship of the genome is to identify the molecular mechanisms that drive higher-order genome folding. To this end, we reconstituted five S. cerevisiae chromosomes in vitro and developed a high-resolution MNase-based chromosome conformation capture assay to measure their 3D organization. We show that the formation of regularly spaced and phased nucleosome arrays is sufficient to drive higher-order genome folding into domains that resemble in vivo genome organization and thereby demonstrate that neither loop extrusion nor transcription are required for domain formation. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26302

26 Samples

Download data: BW

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

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL26302

99 Samples

Download data: BW, TXT

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

Organism:

Saccharomyces cerevisiae

Type:

Other; Expression profiling by high throughput sequencing; Genome variation profiling by high throughput sequencing

Platform:

GPL26302

45 Samples

Download data: CSV, TXT

(Submitter supplied) Whether synthetic genomescan power life has attracted broad interest in the synthetic biology field, especially when the synthetic genomes are extensively modified with thousands of designer features. Here we reportde novosynthesis of the largest eukaryotic chromosome thus far, synIV, a 1,454,621-bpSaccharomyces cerevisiaechromosome resulting from extensive genome streamlining and modification. During the construction ofsynIV, we developed megachunk assembly combined with a hierarchical integration strategy, which significantly increased the accuracy and flexibility of synthetic chromosome construction and facilitated chromosome debugging. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome variation profiling by high throughput sequencing

Platform:

GPL26302

6 Samples

Download data: CSV

(Submitter supplied) Whether synthetic genomescan power life has attracted broad interest in the synthetic biology field, especially when the synthetic genomes are extensively modified with thousands of designer features. Here we reportde novosynthesis of the largest eukaryotic chromosome thus far, synIV, a 1,454,621-bpSaccharomyces cerevisiaechromosome resulting from extensive genome streamlining and modification. During the construction ofsynIV, we developed megachunk assembly combined with a hierarchical integration strategy, which significantly increased the accuracy and flexibility of synthetic chromosome construction and facilitated chromosome debugging. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26302

30 Samples

Download data: TXT

(Submitter supplied) Whether synthetic genomescan power life has attracted broad interest in the synthetic biology field, especially when the synthetic genomes are extensively modified with thousands of designer features. Here we reportde novosynthesis of the largest eukaryotic chromosome thus far, synIV, a 1,454,621-bpSaccharomyces cerevisiaechromosome resulting from extensive genome streamlining and modification. During the construction ofsynIV, we developed megachunk assembly combined with a hierarchical integration strategy, which significantly increased the accuracy and flexibility of synthetic chromosome construction and facilitated chromosome debugging. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL26302

9 Samples

Download data: TXT

(Submitter supplied) Cytoplasmic poly(A)-binding protein (PABPC, yeast Pab1) is involved in various stages of mRNA post-transcriptional control, including translation initiation, translation termination, and mRNA decay regulation. Due to the multi-functional properties of PABPC, attempts to define a specific role for PABPC in vivo by deleting, depleting, overexpressing, or mutating the protein has led to conflicting models of PABPC's function. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platforms:

GPL26302 GPL19756

9 Samples

Download data: CSV, WIG

(Submitter supplied) We present two sets of 5P-Seq experiments: i) comparison of wt and new1-KO S. cerevisiae ii) analysis of New1:80S pulldown samples. Collectively our results unravel codon-dependent nature of ribosomal stalling in S. cerevisiae lacking New1.

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL26302

20 Samples

Download data: WIG

(Submitter supplied) Regulation of gene expression in biological systems is a complex, nonlinear process composed of context specific interactions, from signaling and transcription to genome modification. Modeling gene regulatory networks (GRNs) can be limited due to a lack of direct measurements of regulatory features in genome-wide screens. Most GRN inference methods are consequently forced to model covariance between regulatory genes and their targets as a proxy for causal interactions. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26302

3 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; Methylation profiling by high throughput sequencing; Other

Platforms:

GPL26302 GPL19756 GPL31112

25 Samples

Download data: BED

(Submitter supplied) “Biological noise” is defined as functionally insignificant events that occur in living cells due to imperfect fidelity of biological processes. Distinguishing between biological function and biological noise is often difficult, and experiments to measure biological noise have not been performed. Here, we measure biological noise in yeast cells by analyzing chromatin structure and transcription of an 18 kb region of DNA whose sequence was randomly generated and hence is functionally irrelevant. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL26302

6 Samples

Download data: BED

(Submitter supplied) “Biological noise” is defined as functionally insignificant events that occur in living cells due to imperfect fidelity of biological processes. Distinguishing between biological function and biological noise is often difficult, and experiments to measure biological noise have not been performed. Here, we measure biological noise in yeast cells by analyzing chromatin structure and transcription of an 18 kb region of DNA whose sequence was randomly generated and hence is functionally irrelevant. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL26302

5 Samples

Download data: BED