GEO DataSets

(Submitter supplied) We report the TSSs of transcripts derived from in vitro chromatin transcription

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL17143

4 Samples

Download data: TXT

(Submitter supplied) We present Micrococcal Nuclease digestion maps of S. cerevisiae through the progression of the Yeast Metabolic Cycle. We demonstrate that nucleosome positions at many promoters are dynamic, and remodeling events at promoters have significant consequences with respect to gene expression.

Organism:

Saccharomyces cerevisiae

Type:

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

Platform:

GPL13821

24 Samples

Download data: WIG, XLSX

(Submitter supplied) Histone post-translational modifications (PTMs) alter chromatin structure by promoting the interaction of chromatin-modifying complexes with nucleosomes. The majority of chromatin-modifying complexes contain multiple domains that preferentially interact with modified histones, leading to speculation that these domains function in concert to target nucleosomes with distinct combinations of histone PTMs. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13821 GPL17342

16 Samples

Download data: WIG

(Submitter supplied) In S. cerevisiae, histone variant H2A.Z is deposited in euchromatin at the flanks of silent heterochromatin to prevent its ectopic spread. The degree to which H2A.Z is found and functions elsewhere is unknown. Here we show that H2A.Z nucleosomes are found at promoter regions of nearly all genes in euchromatin. They generally occur as two positioned nucleosomes that flank a nucleosome-free region (NFR) that contains the transcription start site. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL2626

5 Samples

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

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

28 Samples

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(Submitter supplied) Modifications on histone tails largely affect chromatin associated processes. Previous studies have shown the existence of asymmetrically modified nucleosomes in promoters in multiple cell types. However, whether modifications on both sister histones contribute equally to chromatin dynamics remains elusive. Here we devised a bivalent nucleosome system which allows for the constitutive assembly of asymmetrically modified sister histone H3 in nucleosomes in vivo. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

12 Samples

Download data: TXT

(Submitter supplied) Histone tail modificationscan greatly influencechromatin-associated processes. Asymmetrically modified nucleosomes exist inmultiple cell types; however,whether modifications on both sister histones contribute equally to chromatin dynamicsremainselusive. Here, we devised a bivalent nucleosome system thatallowedfor the constitutive assembly of asymmetrically modified sister histone H3s in nucleosomes inSaccharomyces cerevisiae. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

16 Samples

Download data: TXT

(Submitter supplied) We tracked the fate of labelled nucleosomes through DNA replication, and established that nucleosomes present at a locus remembered their position during DNA replication. The replication-associated histone chaperones DPB3 and MCM2 were essential for nucleosome position memory, and in the absence of both DPB3 and MCM2 histone chaperone activity nucleosomes did not remember their position. Using the same approach, we tested the model that transcription results in retrograde transposition of nucleosomes along a transcription unit. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21656 GPL22715

81 Samples

Download data: BEDGRAPH

(Submitter supplied) To investigate the role of DNA topoisomerases in transcription, we have studied global gene expression in Saccharomyces cerevisiae cells deficient for topoisomerases I and II and performed single-gene analyses to support our findings. The genome-wide studies show a general transcriptional down-regulation upon lack of the enzymes, which correlates with gene activity but not gene length. Furthermore, our data reveal a distinct subclass of genes with a strong requirement for topoisomerases. more...

Organism:

Saccharomyces cerevisiae; Schizosaccharomyces pombe

Type:

Expression profiling by array

Platform:

GPL2529

12 Samples

Download data: CEL

(Submitter supplied) Carbon source is the basic nutrition and is essential for yeast growth. We grew the yeast cells (BY4741 strain) under different carbon sources including glucose with different concentration, galactose and raffinose. We generated bulk-cell RNA-seq data and investigated the dynamics of gene expression profiles under different growth conditions. We also generated single-cell RNA-seq data for yeast cells under 2% glucose, and explored the heterogeneity of gene expression within a cell population.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21656

22 Samples

Download data: CSV, TXT

(Submitter supplied) We present an approach (native elongating transcript sequencing, NET-seq), based on deep sequencing of 3’ ends of nascent transcripts associated with RNA polymerase, to monitor transcription at nucleotide resolution. Application of NET-seq in Saccharomyces cerevisiae reveals that while promoters are generally capable of divergent transcription, the Rpd3S deacetylation complex enforces strong directionality to most promoters by suppressing antisense transcript initiation. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL9377

7 Samples

Download data: WIG

(Submitter supplied) Compared to the initiation and elongation stages of transcription, the role of chromatin in transcription termination is poorly understood. Through a yeast genetic screen, we identified histone H3 and H4 substitutions that cause transcription to read through the terminator of a small noncoding gene. The substitutions map to the nucleosome DNA entry-exit site, a region that controls nucleosome stability and certain histone modifications. more...

Organism:

Saccharomyces cerevisiae

Type:

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

Platform:

GPL19756

24 Samples

Download data: BW

(Submitter supplied) A strain harboring two copies of RAP1 is used for a competition-ChIP experiment. One copy of RAP1 is expressed from the endogenous RAP1 promoter and a c-terminal 3X FLAG epitiope tag and the other is expressed from a weakened Galactose inducible promoter and a c-terminal 9X MYC tag. Following induction by 2% galactose Rap1-Myc and Rap1-Flag levels are determined genome wide using ChIP-chip.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL14612

24 Samples

Download data: GFF, PAIR, TXT

(Submitter supplied) A strain harboring two copies of RAP1 is used for a competition-ChIP experiment. One copy of RAP1 is expressed from the endogenous RAP1 promoter and a c-terminal 3X FLAG epitiope tag and the other is expressed from a weakened Galactose inducible promoter and a c-terminal 9X MYC tag. Following induction by 2% galactose Rap1-Myc and Rap1-Flag levels are determined genome wide using ChIP-chip.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by array

Platform:

GPL4414

41 Samples

Download data: GPR

(Submitter supplied) Open chromatin provides access to a wide spectrum of DNA binding proteins for DNA metabolism processes such as transcription, repair, recombination, and replication. In this regard, open chromatin profiling has been widely used to identify the location of regulatory regions, including promoters, enhancers, insulators, silencers, replication origins, and recombination hotspots. Regulatory DNA elements are made accessible by nucleosome-depeleted states. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9134

2 Samples

Download data: BED

(Submitter supplied) We performed a fluorescent reporter based screen to identify factors determining transcriptional directionality from bidirectional promoters that give rise to a coding and a non-coding transcript. Promoters like these are most frequent in many organisms and non-coding transcription from this origin represents a large fraction of total long non-coding transcripts. We applied NET-seq to compare nascent transcription in yeast wild-type and mutations in the three members of the CAF-I complex. more...

Organism:

Saccharomyces cerevisiae

Type:

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

Platform:

GPL13821

8 Samples

Download data: TXT

(Submitter supplied) The Saccharomyces cerevisiae Snf/Swi complex has been previously demonstrated to control transcription and chromatin structure of particular genes in vivo and to remodel nucleosomes in vitro. We have performed whole-genome expression analysis, using DNA microarrays, to study mutants deleted for a gene encoding one conserved (Snf2) or one unconserved (Swi1) Snf/Swi component. This analysis was performed on cells grown in both rich and minimal media. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Datasets:

GDS105 GDS106

Platforms:

GPL57 GPL67 GPL65

12 Samples

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Whole-genome expression analysis of mutants deleted for a gene encoding one conserved (Snf2) or one unconserved (Swi1) Snf/Swi component. The Snf/Swi complex controls transcription and chromatin structure.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, log ratio, 2 growth protocol, 2 strain sets

Platform:

GPL65

Series:

GSE21

8 Samples

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Whole-genome expression analysis of mutants deleted for a gene encoding one conserved (Snf2) or one unconserved (Swi1) Snf/Swi component. The Snf/Swi complex controls transcription and chromatin structure.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, log ratio, 2 strain sets

Platform:

GPL67

Series:

GSE21

2 Samples

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(Submitter supplied) Poly(A) and CUT RNA fractions are compared using 3 'Long-SAGE deep-sequencing. ArrayExpress Release Date: 2008-12-19 Publication Title: Widespread bidirectional promoters are the major source of cryptic transcripts in yeast Publication Author List: Helen Neil, Christophe Malabat, Yves d'Aubenton-Carafa, Zhenyu Xu, Lars M. Steinmetz and Alain Jacquier Person Roles: submitter Person Last Name: Malabat Person First Name: Christophe Person Mid Initials: Person Email: [email protected] Person Phone: Person Address: Unité de Génétique des Interactions Macromoléculaires; CNRS, URA2171,F-75015, Paris, France Person Affiliation: Institut Pasteur

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11160

2 Samples

Download data: FNA, QUAL, TXT