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TranscriptomicsStrand-specific RNA-seq of 13 human tissues from Michael Snyder's lab for the ENCODE project
This ArrayExpress experiment contains RNA-seq data from human tissues, generated by Michael Snyder's lab at Stanford University as part of the ENCODE project ( https://www.encodeproject.org/search/?type=Experiment ). Sample information was obtained from the ENCODE data coordination center and proto...
ORGANISM(S): Homo sapiens 
2016-01-21 | E-MTAB-4344 | biostudies-arrayexpress
MetabolomicsThe metabolic background is a global player in Saccharomyces gene expression epistasis
The regulation of gene expression in response to nutrient availability is fundamental to the genotype-phenotype relationship. The metabolic-genetic make-up of the cell, as reflected in auxotrophy, is hence likely to be a determinant of gene expression. Here, we address the importance of the metaboli...
2016-12-16 | MTBLS168 | MetaboLights
TranscriptomicsTranscription profiling of yeast treated with rapamycin in a 7-part time series
This experiment was a 7-part time series (or, 2x7 factorial design) examining the effect of rapamycin on gene expression in Saccharomyces cerevisiae. Treated and untreated cultures were compared at 0, 20, 40, 60, 120, 240, and 360 minutes. In the paper, expression ratios (mRNA) at each time point ...
ORGANISM(S): Saccharomyces cerevisiae 
2010-02-05 | E-TABM-639 | biostudies-arrayexpress
TranscriptomicsDivergent functions of hematopoietic transcription factors in lineage priming and differentiation during erythro-megakaryopoiesis
Combinatorial actions of relatively few transcription factors control hematopoietic differentiation. To investigate this process in erythro-megakaryopoiesis, we correlated the genome-wide chromatin occupancy signatures of four master hematopoietic transcription factors (GATA1, GATA2, TAL1, and FLI1)...
ORGANISM(S): Mus musculus 
2014-11-14 | E-GEOD-51337 | biostudies-arrayexpress
TranscriptomicsElectric current induced genes in Escherichia coli
The control of cellular processes by direct electronic interface will facilitate the development of biosensors, synthetic biology, and nanobiotechnology by providing the means to pass information from synthetic to living elements of hybrid systems. To investigate the potential of manipulating cellu...
ORGANISM(S): Escherichia coli 
2010-06-25 | E-GEOD-5192 | biostudies-arrayexpress
TranscriptomicsDivergent functions of hematopoietic transcription factors in lineage priming and differentiation during erythro-megakaryopoiesis
Combinatorial actions of relatively few transcription factors control hematopoietic differentiation. To investigate this process in erythro-megakaryopoiesis, we correlated the genome-wide chromatin occupancy signatures of four master hematopoietic transcription factors (GATA1, GATA2, SCL/TAL1 and FL...
ORGANISM(S): Mus musculus 
2013-08-09 | E-GEOD-49664 | biostudies-arrayexpress
TranscriptomicsIPC knockout, 14 day old female flies, 48h yeast feeding
Background Insulin signaling pathway is conserved from worms to humans. In Drosophila, three insulin-like peptides (dilps) are expressed in the insulin producing cells (IPCs) in the brain. In order to identify target genes of insulin signaling, the IPCs of female flies were destroyed during develop...
ORGANISM(S): Drosophila melanogaster 
2010-06-25 | E-GEOD-10625 | biostudies-arrayexpress
TranscriptomicsDifferential control of Zap1-regulated genes in response to zinc deficiency in Saccharomyces cerevisiae
The Zap1 transcription factor is a central player in the response of yeast to changes in zinc status. Zap1 acts as both a positive and negative regulator of its target genes. We previously used transcriptome profiling with DNA microarrays to identify 46 potential Zap1 target genes in the yeast gen...
ORGANISM(S): Saccharomyces cerevisiae 
2008-07-04 | E-GEOD-11983 | biostudies-arrayexpress
TranscriptomicsA Signaling Lipid Associated with Alzheimer’s Disease Promotes Mitochondrial Dysfunction
Fundamental changes in the composition and distribution of lipids within the brain are believed to contribute to the cognitive decline associated with Alzheimer’s disease (AD). The mechanisms by which these changes in lipid composition affect cellular function and ultimately cognition are not well...
ORGANISM(S): Saccharomyces cerevisiae 
2016-01-21 | E-GEOD-40814 | biostudies-arrayexpress
TranscriptomicsBand-array detection of chromosomal rearrangements in diploid yeast cells exposed to ionizing radiation
At the organismal level, genome rearrangements are usually deleterious and are often associated with disease. Yet, on an evolutionary scale, they can be beneficial as they provide for rapid genetic diversification. DNA lesions, particularly double-strand breaks (DSBs), are sources of genome instab...
ORGANISM(S): Saccharomyces cerevisiae 
2010-06-11 | E-GEOD-6991 | biostudies-arrayexpress
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