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TranscriptomicsThe Saccharomyces cerevisiae genome is highly connected by inter- and intra- chromosomal interactions
Nuclear and mitochondrial organelles must maintain a communication system. Loci on the mitochondrial genome were recently reported to interact with nuclear loci. To determine whether this is part of a DNA based communication system we used genome conformation capture to map the global network of DNA...
ORGANISM(S): Saccharomyces cerevisiae 
2013-01-17 | E-GEOD-33073 | biostudies-arrayexpress
TranscriptomicsInter- and intra- chromosomal interactions change on a global scale according to the metabolic regime employed by Saccharomyces cerevisiae
Nuclear and mitochondrial organelles must maintain a communication system. Loci on the mitochondrial genome were recently reported to interact with nuclear loci. To determine whether this is part of a DNA based communication system we used genome conformation capture to map the global network of DNA...
ORGANISM(S): Saccharomyces cerevisiae 
2013-01-17 | E-GEOD-33074 | biostudies-arrayexpress
TranscriptomicsGlobal spatial organization of M-NM-3 proteobacterial nucleoids is determined by specific long-range interactions (E. coli)
GCC was used to determine the structure of E. coli grown in LB or treated with SHX. The bacterial genome is highly condensed into a nucleoid structure. Here we present global analyses of the genome spatial organization for two M-NM-3-proteobacteria: Escherichia coli and Pseudomonas aeruginosa by Ge...
ORGANISM(S): Escherichia coli 
2013-05-02 | E-GEOD-40603 | biostudies-arrayexpress
TranscriptomicstRNA gene identity acts as a determinant of gene positioning
Here we report that the spatial organization of yeast tRNA genes depends upon both locus position and tRNA identity; supporting the idea that the genomic organization of tRNA loci utilizes tRNA dependent signals within the nucleoprotein-tRNA complexes that form into clusters. We use high-throughput ...
ORGANISM(S): Saccharomyces cerevisiae 
2012-06-13 | E-GEOD-30103 | biostudies-arrayexpress
TranscriptomicsMitochondrial-nuclear DNA interactions contribute to the regulation of nuclear transcript levels as part of the inter-organelle communication system
Nuclear and mitochondrial organelles must maintain a communication system. Loci on the mitochondrial genome were recently reported to interact with nuclear loci. To determine whether this is part of a DNA based communication system we used genome conformation capture to map the global network of DNA...
ORGANISM(S): Saccharomyces cerevisiae 
2013-01-17 | E-GEOD-34132 | biostudies-arrayexpress
ProteomicsScreen Identifies DYRK1B Network as Mediator of Transcription Repression on Damaged Chromatin
The uploaded data are described within "Screen Identifies DYRK1B Network as Mediator of Transcription Repression on Damaged Chromatin". In short, peptides from RPE1 epithelial cells with either normal expression of DYRK1B, over expression, of knockout of the kinase were TMT11 plex labeled and enrich...
ORGANISM(S): Homo sapiens (Human) 
2020-06-18 | PXD019102 | Pride
Human Epithelial Tmt Phosphopeptide Cell culture 
TranscriptomicsRNA-seq of LGR5(+) and LGR5(-) cells isolated from human colon adenoma organoids and targeted DNA-seq of a colorectal biobank
This study has two components: (1) Human colon adenoma organoids (n=4 patients) were dissociated into single cells. Cells were incubated with a magnetic bead bound to an LGR5 antibody and run through a magnetic column. Magnet bound cells and flow through negative (FTN) cells were obtained. Magnet bo...
ORGANISM(S): Homo sapiens 
2020-04-30 | E-MTAB-4698 | biostudies-arrayexpress
TranscriptomicsCharacterization of the autoaggregation response of Fusobacterium nucleatum
Fusobacterium nucleatum is a Gram negative oral bacterial species associated with periodontal disease progression. This species is perhaps best known for its ability to adhere to a vast array of other bacteria and eukaryotic cells. Numerous studies of F. nucleatum have examined various coaggregation...
ORGANISM(S): Fusobacterium nucleatum 
2009-10-15 | E-GEOD-18554 | biostudies-arrayexpress
TranscriptomicsGlobal identification of yeast chromosome interactions using genome conformation capture
The objective of this study was to determine the global chromosomal interaction map for exponentially growing Saccharomyces cerevisiae cells using Genome Conformation Capture. Interactions between chromosomes were identified within a population of yeast cells growing exponentially in a semi-defined ...
ORGANISM(S): Saccharomyces cerevisiae 
2009-07-21 | E-GEOD-13648 | biostudies-arrayexpress
TranscriptomicsChromosome positioning and the clustering of functionally related loci in yeast is driven by chromosomal interactions
In recent years there has been considerable and growing interest in the 3-dimensional organization of genomes. In yeast this has included detailed FISH studies that show a surprising degree of spatial clustering of the tRNA genes, the localization of telomeres, centromere positioning, and global stu...
ORGANISM(S): Saccharomyces cerevisiae 
2012-07-18 | E-GEOD-33018 | biostudies-arrayexpress
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