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GenomicsGenome-wide nucleosome position maps in Saccharomyces cerevisiae
Paired-end sequencing study of nucleosomal DNA prepared from budding yeast by micrococcal nuclease digestion. Comparison of control cells with cells treated with 10 mM 3-aminotriazole for 20 minutes
ORGANISM(S): Saccharomyces cerevisiae 
2011-07-20 | E-GEOD-26493 | biostudies-arrayexpress
TranscriptomicsThe CaSm (LSm1) oncogene promotes transformation, chemoresistance, and metastasis of pancreatic cancer cells
The Cancer associated Sm-like (CaSm) oncogene is overexpressed in 87% of human pancreatic tumor samples and CaSm knockdown has demonstrated therapeutic efficacy in murine models of pancreatic cancer. Evidence indicates that CaSm modulates mRNA degradation; however, its target genes and the mechanism...
ORGANISM(S): Homo sapiens 
2015-10-24 | E-GEOD-74319 | biostudies-arrayexpress
GenomicsNovel nucleosomal particles containing core histones and linker DNA but no histone H1
The nucleosome plays a central role in genome regulation. Traditional methods for mapping nucleosomes depend on the resistance of the nucleosome core to micrococcal nuclease (MNase). However, the lengths of the protected DNA fragments are heterogeneous, limiting the accuracy of nucleosome position i...
ORGANISM(S): Synthetic plasmid 
2015-09-23 | E-GEOD-65889 | biostudies-arrayexpress
GenomicsThe PhoP-dependent ncRNA Mcr7 modulates the TAT secretion system in Mycobacterium tuberculosis [ChIP-Seq]
The PhoPR two-component system is essential for virulence in Mycobacterium tuberculosis where it controls expression of approximately 2% of the genes, including those for the ESX-1 secretion apparatus, a major virulence determinant. Mutations in phoP lead to compromised production of pathogen-specif...
ORGANISM(S): Mycobacterium tuberculosis H37Rv 
2014-06-02 | E-GEOD-54239 | biostudies-arrayexpress
TranscriptomicsInhibitory effects of galacturonic acid on Saccharomyces cerevisiae: involvement of hexose transporters
Aim: Analyse inhibitory effects of galacturonic acid, an important constituent of plant biomass hydrolysates, on growing and starving cultures of Saccharomyces cerevisiae CEN.PK113-7D. Method & Results: Biomass yields in aerobic and anaerobic glucose-limited chemostat cultures (pH 3.5) were reduce...
ORGANISM(S): Saccharomyces cerevisiae 
2015-04-14 | E-GEOD-43474 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of mouse cartilage tumours IGFBP-3 reveals is regulated by Gli signaling in cartilage tumors.
Mice that develop benign cartilage lesions due to overexpression of Gli2 in chondrocytes developed lesions similar to chondrosarcomas when also deficient in p53. Gli2 overexpression and p53 deficiency had opposing effects on chondrocyte differentiation, but had additive effects negatively regulatin...
ORGANISM(S): Mus musculus 
2009-03-14 | E-GEOD-15118 | biostudies-arrayexpress
TranscriptomicsNext generation sequencing of Desulfovibrio vulgaris Hildenborough in the presence of Free Nitrous Acid stress
Purpose: Free nitrous acid (FNA) has recently been demonstrated as an antimicrobial agent to a range of microorganisms. However, its antimicrobial mechanism is largely unknown. For this study Desulfovibrio vulgaris Hildenborough was selected to gain a systematic understanding of the antimicrobial me...
ORGANISM(S): Desulfovibrio vulgaris 
2016-07-01 | E-GEOD-78834 | biostudies-arrayexpress
GenomicsGenome-wide nucleosome, histone and Pol II maps for wild type Saccharomyces cerevisiae induced with 3-aminotriazole (3AT)
Paired-end sequencing study of (1) nucleosome core particles and under-digested chromatin from MNase-treated nuclei; (2) ChIP samples for HA-tagged histone H4 and H2B; (3) ChIP for the Rpb3 subunit of Pol II. Nucleosomal DNA and immunopurified sonicated DNA fragments were subjected to paired-end seq...
ORGANISM(S): Saccharomyces cerevisiae 
2014-10-28 | E-GEOD-54524 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of Mycobacterium tuberculosis wild type and BCG strains after knock out of the global transcriptional regulator, CRP
Data is also available from http://bugs.sgul.ac.uk/E-BUGS-61
ORGANISM(S): Mycobacterium tuberculosis 
2008-03-12 | E-BUGS-61 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of brain from mice with multiple sclerosis, Alzheimers disease and permanent mid-cerebral artery occlusion from stroke to compare of gene expression changes characterizing these three different central nervous system pathologies
Three mouse models of human central nervous system pathologies were selected for analyzing gene expression changes compared to wild type normal brain. The selected models are: TgAPP23 for Alzheimerï¾’s disease (see Sturchler-Pierrat, C., Abramowski, D., Duke, M., Wiederhold, K.H., Mistl, C., Rothac...
ORGANISM(S): Mus musculus 
2008-07-12 | E-MTAB-1 | biostudies-arrayexpress
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