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MetabolomicsDiel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms
Dynamic environmental factors such as light, nutrients, salt, and temperature continuously affect chlorophototrophic microbial mats, requiring adaptive and acclimative responses to stabilize composition and function. Quantitative metabolomics analysis can provide insights into metabolite dynamics fo...
2024-02-23 | MTBLS187 | MetaboLights
TranscriptomicsHigh-resolution analysis of the m-xylene/toluene biodegradation subtranscriptome of Pseudomonas putida mt-2 [RNA-seq]
Pseudomonas putida mt-2 metabolizes m-xylene and other aromatic compounds through the enzymes encoded by the xyl operons of the TOL plasmid pWW0 along with other chromosomally-encoded activities. Tiling arrays of densely overlapping oligonucleotides were designed to cover every gene involved in this...
ORGANISM(S): Pseudomonas putida 
2016-07-07 | E-GEOD-71852 | biostudies-arrayexpress
GenomicsCpG island-mediated global gene regulatory modes in mouse embryonic stem cells
In order to identify the regions occupied by transcription factors, we performed bio-ChIP followed by massive parallel sequencing (bioChIP-Seq) in mouse ES cells. A total of seven DNA transcription factors including Myc module (Myc, Max, E2F4, Tip60 and Dmap1) and Core module transcription factors (...
ORGANISM(S): Mus musculus 
2014-11-24 | E-GEOD-48666 | biostudies-arrayexpress
TranscriptomicsmRNA-Seq of head tissue from Drosophila mojavensis
We sequenced mRNA from head tissue of females and male of Drosophila mojavensis to identify genes differentially expressed between the sexes and sex-specific alternative splicing events. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pa...
ORGANISM(S): Drosophila mojavensis 
2010-04-11 | E-GEOD-20882 | biostudies-arrayexpress
TranscriptomicsAuxin stimulates brassinosteroid biosynthesis in Arabidopsis roots
We found that auxin stimulates gene expression of DWF4, which encodes a rate-dertermining step in brassinosteroid biosynthesis pathways. This increased gene expressioin subsequently led to elevation of the biosynthetic flux in Arabidopsis roots. To determine the list of genes that are regulated by a...
ORGANISM(S): Arabidopsis thaliana 
2011-02-15 | E-GEOD-12964 | biostudies-arrayexpress
ProteomicsEpigenetic Silencing by SETDB1 Suppresses Tumor-cell Intrinsic Immunogenicity
Griffin GK, Wu J, Iracheta-Vellve A, Patti JC, Hsu J, Davis T, Dele-Oni D, Du PP, Halawi A, Ishizuka JJ, Kim S, Klaeger S, Knudsen NH, Miller BC, Nguyen T, Olander K, Papanastasiou M, Rachimi S, Robitschek EJ, Schneider EM, Yeary M, Zimmer M, Jaffe JD, Carr SA, Doench JG, Haining WN, Yates KB, Mangu...
ORGANISM(S): Mus Musculus (ncbitaxon:10090) 
2020-12-11 | MSV000086580 | MassIVE
TranscriptomicsExpression of M-CSF from cryopreserved teeth-derived human periodontal ligament cells with different freezing protocols
This study investigated which genes regarding root resorption are upregulated by cryopreservation and whether cryopreservation affects the expression of Macrophage M-bM-^@M-^Scolony stimulating factor. We manufactured the customized template which was made of genes selected regarding root resorption...
ORGANISM(S): Homo sapiens 
2013-01-19 | E-GEOD-43611 | biostudies-arrayexpress
TranscriptomicsDeep sequencing of endogenous mRNA from Caenorhabditis elegans in the presence of 2-deoxy-D-glucose (DOG) at 4 different time points
Background: C. elegans fed with a chemical inhibitor of glucose, namely 2-deoxy-D-glucose (DOG), exhibit considerably extended life span. DOG, in contradiction to D-glucose, cannot be metabolized in the glycolytic pathway. This results in the fact that less glucose is available for ATP production, a...
ORGANISM(S): Caenorhabditis elegans 
2013-11-06 | E-GEOD-46344 | biostudies-arrayexpress
TranscriptomicsmRNA-Seq of head tissue from Drosophila melanogaster
We sequenced mRNA from head tissue of females and male of Drosophila melanogaster to identify genes differentially expressed between the sexes and sex-specific alternative splicing events. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/...
ORGANISM(S): Drosophila melanogaster 
2010-04-08 | E-GEOD-20348 | biostudies-arrayexpress
TranscriptomicsThe role of the Ras- and cAMP-signaling pathways in stress response and sterol biosynthesis in Cryptococcus neoformans
The cAMP-pathway plays a central role in regulation of growth, differentiation, and virulence of human pathogenic fungi, including Cryptococcus neoformans. Three major upstream signaling regulators of the adenylyl cyclase (Cac1), Ras, Aca1 (Adenylyl cyclase-associated protein 1) and G-alpha subunit ...
ORGANISM(S): Cryptococcus neoformans var. grubii H99 
2010-05-22 | E-GEOD-17338 | biostudies-arrayexpress
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