Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Using tiling arrays to precisely detect DNA targets of THO in yeast

ABSTRACT: Crosslinked DNA from wild type cells or from mutant of the THO complex was analyzed by tiling arrays to precisely detect DNA targets of THO in yeast. DNA coming from SDS-washed DCF pellet and the supernatant SN2k of 2 strains were compared in the study, WT (W303) and mft1 delta (DLY224). The DNA of each condition (Pellet or Supernatant) was labeled either with Cy3 or Cy5 fluorescent dyes and competitively hybridized on 244k agilent arrays. For each strain, the experiment was performed on 2 biological replicates, with dye swap.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: sophie lemoine

PROVIDER: E-GEOD-32980 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

High-frequency promoter firing links THO complex function to heavy chromatin formation.

Mouaikel John J Causse Sébastien Z SZ Rougemaille Mathieu M Daubenton-Carafa Yves Y Blugeon Corinne C Lemoine Sophie S Devaux Frédéric F Darzacq Xavier X Libri Domenico D

Cell reports 20131107 4

The THO complex is involved in transcription, genome stability, and messenger ribonucleoprotein (mRNP) formation, but its precise molecular function remains enigmatic. Under heat shock conditions, THO mutants accumulate large protein-DNA complexes that alter the chromatin density of target genes (heavy chromatin), defining a specific biochemical facet of THO function and a powerful tool of analysis. Here, we show that heavy chromatin distribution is dictated by gene boundaries and that the gene ...[more]

PMID: 24210826

Similar Datasets

Tissue-specific variation in DNA methylation levels along human chromosome 1

Project description:DNA methylation is a major epigenetic modification important for regulating gene expression and suppressing spurious transcription. Most methods to scan the genome in different tissues for differentially methylated sites have focused on the methylation of CpGs in CpG islands, which are concentrations of CpGs often associated with gene promoters. Here, we use a methylation-profiling strategy that is predominantly responsive to methylation differences outside of CpG islands. The method compares the yield from two samples of size-selected fragments generated by a methylation-sensitive restriction enzyme. We profile eight different normal tissues relative to spleen for each of two human donors using a custom array of genomic clones covering the euchromatic portion of human chromosome 1 and representing 8% of the human genome. We observe gross regional differences in methylation states across chromosome 1 between tissues from the same individual, with the most striking differences detected in the comparison of cerebellum and spleen. Profiles of the same tissue from different donors are strikingly similar, as are the profiles of different lobes of the brain. Using DNMT1-deficient cells as a test case, we show that much finer-scale fluctuations in relative fragment yield can be detected when the methylation profiling is performed using a high-resolution oligomer array for chromosome 1. The varied patterns of methylation differences detected between tissues by this method reinforce the potential functional significance of regional differences in methylation levels outside of CpG islands. DNA digested with methylation-sensitive restriction enzyme (HpaII) and size-selected. Eleven human tissue types studied, most from two human individuals, each in triplicate, and one cell line. Two control hybrizations consisting of DNA prepared independently from the same tissue.

2010-05-18 | E-GEOD-12925 | biostudies-arrayexpress

Global Transcription Profiling and Virulence Potential of Streptococcus pneumoniae after Serial Passage

Project description:Alterations in global transcriptional profiles of S. pneumoniae 6304 serotype 4 after 50 passages (50P) and 100 passages (100P) on laboratory media Keywords: Adaptation to unique growth environment Three conditions experiment: Control, single passage strain (1P), 2 biological replicates Experimental 50 passage strain (50P), 2 biological replicates Experimental 100 passage strain (100P), 2 biological replicates All strains independently grown and harvested at OD600 ~ 0.5. Four spot replicates per array.

2010-05-18 | E-GEOD-12607 | biostudies-arrayexpress

Transcription profiling of Escherichia coli strain MG1655 response to NO released from NOC compounds

Project description:Escherichia coli strain MG1655 response to NO released from NOC compounds. Under contiuous steady state chemostat conditions, in chemically defined media.

2006-01-12 | E-MEXP-246 | biostudies-arrayexpress

Transcription profiling of anaerobic transcriptional response of E.coli MG1655 to NO released from NOC compounds

Project description:The transcriptional response of Escherichia coli MG1655 to NO released from NOC-5 and NOC-7 under anerobic conditions in contiuous chemostat culture on chemically defined minimal media

2006-01-14 | E-MEXP-248 | biostudies-arrayexpress

Transcriptional response to stress in serum deprived mouse fibroblasts [RNA-Seq]

Project description:We have employed gene expression profiling in order to identify targets of transcriptional response to stress in resting mouse Swiss 3T3 fibroblasts, either untreated (control) or treated with anisomycin to induce the p38/MAP kinase pathway. Serum starved (72 h 0.2% FCS) mouse 3T3 cells were treated with anisomycin (188.5 nM) for 1 h (in duplicates). Untreated, serum-starved cells were used as a control. RNA was collected and gene expression profiling using strand-specific RNA-seq was performed.

2014-08-12 | E-GEOD-55776 | biostudies-arrayexpress

Shewanella piezotolerans WP3 wild-type strain heat shock for 30 min

Project description:The WP3 strains was cultured at 20Â°C and heat shocked at 40Â°C for 30 min. The transcriptional profiles after and before heat shock were compared. Three biological replicates sample and 6 technical replicates for each experiment

2016-06-15 | E-GEOD-82261 | biostudies-arrayexpress

Shewanella piezotolerans WP3 wild-type strain heat shock for 90 min

Project description:The WP3 strains was cultured at 20Â°C and heat shocked at 40Â°C for 90 min. The transcriptional profiles after and before heat shock were compared. Three biological replicates sample and 6 technical replicates for each experiment

2016-06-15 | E-GEOD-82263 | biostudies-arrayexpress

Shewanella piezotolerans WP3 wild-type strain heat shock for 60 min

Project description:The WP3 strains was cultured at 20Â°C and heat shocked at 40Â°C for 60 min. The transcriptional profiles after and before heat shock were compared. Three biological replicates sample and 6 technical replicates for each experiment

2016-06-15 | E-GEOD-82262 | biostudies-arrayexpress

Transcriptional response to stress in serum deprived mouse fibroblasts in the presence of MSK1/2 inhibitor.

Project description:We have employed gene expression profiling in order to identify targets of transcriptional response to stress in resting mouse Swiss 3T3 fibroblasts, either untreated (control) or treated with anisomycin for 3 or 6 hours to induce the p38/MAP kinase pathway.Â In order determine transcriptional effects dependent on MSK1/2 kinase activity, H89 inhibitor was used in the study. Serum starved (72 h 0.2% FCS) mouse 3T3 cells were treated with anisomycin (188.5 nM) for 3 h or 6h (in duplicates) either with or without 15-min pre-treatment with MSK1/2 inhibitor H89 (10 uM). Untreated, serum-starved cells were used as a control. RNA was collected and gene expression profiling using strand-specific RNA-seq was performed.

2014-08-12 | E-GEOD-58746 | biostudies-arrayexpress

Hybrid wine yeast strains

Project description:This experiment is the analysis of the transcriptomes of several hybrid yeast strains obtained by crossing natural (from wine) isolates of S. cerevisiae and S. uvarum. All isolations have been done from hybrid strains growing in exponential phase in YPD. Keywords: Strain comparison Transcriptomic analysis of three independent replicates of each yeast strain growing in exponential phase. Each replicate has been hybridized on a different macroarray (F19-F22-F24) as indicated in the sample files. A single DNA (S. cerevisiae 3002 wine strain) genomic hybridization, from the same labeling reaction, was done on the same macroarrays for normalization.

2010-06-25 | E-GEOD-9888 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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