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TranscriptomicsTranscription analysis of biofilm grown in different depth
Using DNA-microarrays analysis 39 differentially expressed genes were identified in 200 vs. 100 microns biofilms, which might be associated with thickness of S. mutans biofilm. Using DNA-microarrays analysis 29 differentially expressed genes were identified in 400 vs. 100 microns biofilms of S. muta...
ORGANISM(S): Streptococcus mutans 
2010-05-06 | E-GEOD-12496 | biostudies-arrayexpress
TranscriptomicsThe S-adenosyl-homosteine hydrolase inhibitor DZNeP unspecifically affects histone methylation patterns in embryos and results in developmental aberrations
3-deazaneplanocin A (DZNeP) is a promising cancer drug affecting the methylation status of histone lysine residues. To investigate the specificity and mode of action of DZNeP, zebrafish embryos displaying high histone methyltransferase activity were cultured with DZNeP and histone methylation (H3K4m...
ORGANISM(S): Danio rerio 
2014-11-21 | E-GEOD-53209 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of FOXL2 over-expression in human KGN cells
In order to identify novel FOXL2 targets, we have transfected KGN cells using an expression vector containing the coding sequence of FOXL2 or, as a reference, the empty vector (mock transfection). The transcriptome perturbation induced by FOXL2 overexpression was then followed by DNA chips (i.e. FOX...
ORGANISM(S): Homo sapiens 
2007-03-02 | E-MEXP-985 | biostudies-arrayexpress
TranscriptomicsMapping of H3K4 and H3K27 trimethylation in zebrafish cells (ChIP-chip)
The genomic distribution of post-translationally modified histones in the zebrafish (Danio rerio) genome remain largely unraveled. The objective of this study was to (1) design a microarray covering all zebrafish gene promoters and 5' end of coding regions, and (ii) using these arrrays, map the geno...
ORGANISM(S): Danio rerio 
2011-02-08 | E-GEOD-23691 | biostudies-arrayexpress
TranscriptomicsEpigenetic environment of histone H3.3 on promoters revealed by integration of imaging, ChIP-chip, and MeDIP-chip data
Epigenetic environment of histone H3.3 on promoters revealed by integration of imaging and genome-scale chromatin and methyl-DNA immunoprecipitation information. Chromatin regions with different transcriptional outputs are distinguished by the deposition of histone variants. Histone H3.3 is incorpor...
ORGANISM(S): Homo sapiens 
2010-05-12 | E-GEOD-17053 | biostudies-arrayexpress
TranscriptomicsExpression data from esd7-1 mutant vs wt (Ler)
We have characterized a mutation affecting the Arabidopsis EARLY IN SHORT DAYS 7 (ESD7) gene encoding the catalytic subunit of the DNA polymerase epsilon (e), AtPOL2A. esd7-1 mutations causes early flowering independently of photoperiod, shortened inflorescence internodes and altered leaf and root d...
ORGANISM(S): Arabidopsis thaliana 
2010-10-14 | E-GEOD-18603 | biostudies-arrayexpress
TranscriptomicsMapping of H3K4 and H3K27 trimethylation in zebrafish cells
This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
ORGANISM(S): Danio rerio 
2011-02-08 | E-GEOD-23872 | biostudies-arrayexpress
TranscriptomicsAffymetrix SNP array data for 4 MYC-negative B-cell lymphoma cases and 2 B-cell lymphoma cell lines (SU-DHL-5 and HT)
Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from blood samples and cell lines Copy number analysis of Affymetrix SNP 6.0 arrays was performed for 4 MYC-negative B-cell lymphoma and 2 B-cell lymphoma cell lines
ORGANISM(S): Homo sapiens 
2014-01-10 | E-GEOD-47507 | biostudies-arrayexpress
TranscriptomicsGenome-wide analysis of DNA methylation and gene expression patterns in purified, uncultured human liver cells and activated hepatic stellate cells
The human liver contains multiple cell types whose epigenetic patterns are undetermined. We examined the promoter methylome of purified and uncultured hepatic stellate cells (HSCs), hepatocytes (HEPs) and liver sinusoidal endothelial cells (LSECs), by methylated DNA immunoprecipitation (MeDIP) and a...
ORGANISM(S): Homo sapiens 
2015-12-21 | E-GEOD-66796 | biostudies-arrayexpress
TranscriptomicsDevelopmental features of DNA methylation during activation of the embryonic zebrafish genome
Zygotic genome activation (ZGA) occurs at the mid-blastula transition (MBT) in zebrafish and is a period of chromatin remodeling. Genome-scale gametic demethylation and remethylation occurs after fertilization, during blastula stages, but how ZGA relates to promoter DNA methylation states is unknown...
ORGANISM(S): Danio rerio 
2012-07-05 | E-GEOD-33236 | biostudies-arrayexpress
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