Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

12 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide nucleosome position data for 3 yeast species

ABSTRACT: Genome-wide nucleosome position data for wildtype and mutant strains in S. cerevisiae, C. albicans, and S. pombe Illumina sequencing of mononucleosomal DNA isolated from mid-log cultures grown in rich medium (abbreviated CM, in house recipe). S. pombe samples were grown in YES medium at permissive temperature (30C) and restrictive temperature (35C)

ORGANISM(S): Candida albicans

SUBMITTER: Alex Tsankov

PROVIDER: E-GEOD-28839 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization.

Tsankov Alex A Yanagisawa Yoshimi Y Rhind Nicholas N Regev Aviv A Rando Oliver J OJ

Genome research 20110913 11

The packaging of eukaryotic genomes into nuclesomes plays critical roles in chromatin organization and gene regulation. Studies in Saccharomyces cerevisiae indicate that nucleosome occupancy is partially encoded by intrinsic antinucleosomal DNA sequences, such as poly(A) sequences, as well as by binding sites for trans-acting factors that can evict nucleosomes, such as Reb1 and the Rsc3/30 complex. Here, we use genome-wide nucleosome occupancy maps in 13 Ascomycota fungi to discover large-scale ...[more]

PMID: 21914852

Similar Datasets

Genome-wide nucleosome position data for 12 yeast species

Project description:We mapped nucleosome positions genome-wide in 12 Ascomycetes Illumina sequencing of mononucleosomal DNA isolated from mid-log cultures grown in rich medium (abbreviated CM, in house recipe)

2010-07-06 | E-GEOD-22211 | biostudies-arrayexpress

The role of nucleosome positioning in the evolution of gene regulation

Project description:This SuperSeries is composed of the following subset Series: GSE22191: Absolute expression level of Debaryomyces hansenii genes GSE22192: Absolute expression level of Yarrowia lipolytica genes GSE22193: Absolute expression level of Saccharomyces paradoxus genes GSE22194: Absolute expression level of Candida glabrata genes GSE22197: Absolute expression level of Candida albicans genes GSE22198: Absolute expression level of Kluyveromyces lactis genes GSE22199: Absolute expression level of Kluyveromyces waltii genes GSE22200: Absolute expression level of Saccharomyces castellii genes GSE22201: Absolute expression level of Saccharomyces mikatae genes GSE22202: Absolute expression level of Saccharomyces kluyveryii genes GSE22204: Absolute expression level of Saccharomyces cerevisiae genes GSE22205: Absolute expression level of Saccharomyces bayanus genes GSE22211: Genome-wide nucleosome position data for 12 yeast species Refer to individual Series

2010-07-05 | E-GEOD-21960 | biostudies-arrayexpress

A species-specific nucleosomal signature defines a periodic distribution of amino acids in proteins

Project description:Sequencing of mononucleosomal DNA during asynchronous mitosis in Schizosaccharomyces pombe, Schizosaccharomyces octosporus, Schizosaccharomyces japonicus and Saccharomyces cerevisiae Samples from mononucleosomal DNA from asynchronous mitosis of four species of budding (Saccharomyces cerevisiae W303-1a) and fission yeasts (S. pombe wild type 972h-, S. octosporus CBS1804, S. japonicus var. japonicus ade12- FY53) were sequenced (Illumina Genome Analyzer IIx and HiSeq 2500) using the single read and paired end protocol.

2015-04-10 | E-GEOD-52170 | biostudies-arrayexpress

Promoter nucleosome dynamics regulated by signaling through the CTD code

Project description:Sequencing of mononucleosomal DNA from asynchronous cells of Schizosaccharomyces pombe WT and S2A mutant Mononucleosomal DNA from asynchronous S. pombe WT (1 sample) and S2A mutant cells (2 samples) were sequenced (Illumina HiSeq 2000) using the single-end read protocol

2015-06-22 | E-GEOD-59768 | biostudies-arrayexpress

Drosophila melanogaster S2 cells nucleosome occupancy data after simulation by heat killed Staphylococcus aureus

Project description:The innate immune response is among the strongest genomic responses and is conserved across all metazoa. Although transcription during the innate immune response has been well studied, the associated chromatin reorganizations are largely uncharacterized. Here we show that Drosophila S2 cells stimulated with Staphylococcus aureus display a dynamic change in genome-wide nucleosome occupancy and sensitivity. We found a widespread and transient nucleosomal loss peaking at 30 minutes post stimulation, and we demonstrated that the regulatory potentials of nucleosomes differ following stimulation. In addition, we identified differentially sensitive nucleosomes with response-specific potentials. Our results provide high-resolution nucleosome-distribution maps of the fly genome, revealing chromatin's role in: the innate immune response to Gram-positive bacteria, response-specific regulatory-factor binding, and nucleosome sensitivity. We identify functional chromatin regulatory features associated with immune response, and lay a foundation for a framework linking general and locus-specific roles for nucleosomes in immune regulation. Drsophila S2 cells at 0hr, 30minutes, 1hr and 4hr post heat-killed Staphylococcus aureus stimulation

2015-02-28 | E-GEOD-66367 | biostudies-arrayexpress

The Nucleosome Map of the Mammalian Liver

Project description:We report the genome-wide map of nucleosome positions in the mouse liver, with emphasis on transcriptional start sites, CpG islands, Foxa2 binding sites, and their correlation with gene expression. Despite the heterogeneity of liver tissue, we could clearly discern the nucleosome pattern of the predominant liver cell, the hepatocyte. By analyzing nucleosome occupancy and the distributions of heterochromatin protein 1 (Hp1), CBP, and p300 in Foxa1/2-deficient livers we find, surprisingly, that the maintenance of nucleosome position and chromatin structure surrounding Foxa2 binding sites is independent of Foxa1/2. Examination of nucleosome map and Foxa2 binding in the mouse liver.

2011-04-30 | E-GEOD-26729 | biostudies-arrayexpress

Clustered regulatory signals at nucleosome-depleted regions punctuate a constant nucleosomal landscape in Schizosaccharomyces pombe

Project description:Sequencing of mononucleosomal DNA during asynchronous mitosis and 0, 3 and 5 hours into meiosis in Schizosaccharomyces pombe. Two samples from mononucleosomal DNA from asynchronous mitosis (haploid 972 h- and diploid pat1.114) and three samples from 0, 3 and 5 hours into meiosis (from diploid pat1.114) were sequenced (Illumina Genome Analyzer IIx) using the single-end read protocol.

2013-11-25 | E-GEOD-41772 | biostudies-arrayexpress

The nucleoporin Nup170p is required for subtelomeric chromatin structure and gene silencing. [MNase-Seq]

Project description:Transcriptionally silent heterochromatin preferentially localizes at the nuclear periphery, but, despite this, certain budding yeast genes relocate to the nuclear periphery following gene activation, implicating the nuclear envelope in both transcriptional activation and silencing. It is unclear how these distinct chromatin domains are established, maintained and distinguished from one another at the nuclear envelope. Here we report that nuclear pore complexes (NPCs) facilitate the transition between chromatin states by providing a platform to which chromatin-remodeling and chromatin-modifying complexes bind. In particular, we show that the RSC chromatin-remodeling complex associates with NPCs and that the nucleoporin Nup170p nucleates heterochromatin formation at telomeres through recruitment of Sir4p. Deletion of NUP170 altered subtelomeric chromatin structure, reduced SIR complex binding at telomeres, impaired telomeric silencing and abated telomere tethering. These results support a model in which telomeric heterochromatin formation occurs through telomere-NPC interactions that both promote Sir4p binding at telomeres and permit chromatin-remodeling complexes to mediate the transition between chromatin states. Examination of genome-wide nucleosome positions in WT and nup170∆ cells via next-generation sequencing of mononucleosomal DNA.

2013-02-28 | E-GEOD-36792 | biostudies-arrayexpress

Genome-wide maps of nucleosome positions in Saccharomyces strains bearing heterologous DNA on yeast artificial chromosomes

Project description:We identify the cis and trans determinants of nucleosome positioning using a functional evolutionary approach involving S. cerevisiae strains containing large genomic regions from other yeast species. In a foreign species, nucleosome depletion at promoters is maintained over poly(dA:dT) tracts, whereas internucleosome spacing and all other aspects of nucleosome positioning tested are not. Interestingly, the locations of the +1 nucleosome and RNA start sites shift in concert. Strikingly, in a foreign species, nucleosome-depleted regions occur fortuitously in coding regions, and they often act as promoters that are associated with a positioned nucleosome array linked to the length of the transcription unit. nucleosome mapping for 3 strains bearing yeast artificial chromosomes from Kluyveromyces lactis and 2 strains with Debaryomyces hansenii artificial chromosomes in Saccharomyces cerevisiae

2012-06-30 | E-GEOD-39011 | biostudies-arrayexpress

Comprehensive nucleosome mapping of the human genome in cancer progression

Project description:Altered chromatin structure is a hallmark of cancer, and inappropriate regulation of chromatin structure may represent the origin of transformation. Several important studies have mapped human nucleosome distributions genome wide, but the genome-wide role of chromatin structure in cancer progression has not been addressed. We developed a MNase-Sequence Capture method, mTSS-seq, to map genome-wide nucleosome distribution in primary human lung and colon adenocarcinoma tissue. Here, we confirm that nucleosome redistribution is an early, widespread event in lung (LAC) and colon (CRC) adenocarcinoma. These altered nucleosome architectures are consistent between LAC and CRC patient samples indicating that they may serve as important early adenocarcinoma markers. We demonstrate that the nucleosome alterations are driven by the underlying DNA sequence and potentiate transcription factor binding. We conclude that DNA-directed nucleosome redistributions are widespread early in cancer progression. We have proposed an entirely new hierarchical model for chromatin-mediated genome regulation. â Nucleosome distribution mapping in primary patient tissue at all transcription start sites in the human genome Please note that two processed data files '4137N_ALLcombined.bed' and '4137T_ALLcombined.bed' (linked as Series supplementary file) are processed bed files combined from three 4137N_*_hiseq samples (total 6 raw data files) and three 4137T_*_hiseq samples (total 6 raw data files), respectively.

2015-10-27 | E-GEOD-74340 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data