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TranscriptomicsChromatin immunoprecipitation of REST/NRSF
ENCODE ChIP-chip study using 8 diverse human cell lines; 4 of neural origin (NB69, KELLY, SHSY-5Y, U373) and 4 of non-neural origin (HeLa, HepG2, HEK293 and K562) and anti-REST/NRSF antibody (Santa Cruz Biotech; sc-25398 aka H290) to asses REST-genome interactions across 1% of the human genome used...
ORGANISM(S): Homo sapiens 
2009-03-31 | E-TABM-660 | biostudies-arrayexpress
TranscriptomicsM. sedula transcriptional response to ferrous iron and RISC supplements
Abstract: The crenarchaeal order Sulfolobales collectively contains at least five major terminal oxidase complexes. Based on genome sequence information, all five complexes are found only in Metallosphaera sedula and Sulfolobus tokodaii, the two sequenced Sulfolobales capable of iron oxidization. Wh...
ORGANISM(S): Metallosphaera sedula 
2008-10-22 | E-GEOD-12044 | biostudies-arrayexpress
TranscriptomicsM. sedula transcriptional response under heterotrophic, autotrophic, and mixotrophic growth conditions
To study mixotrophy, it is desirable to have an organism capable of growth in the presence and absence of both organic and inorganic carbon sources, as well as organic and inorganic energy sources. Metallosphaera sedula is an extremely thermoacidophilic archaeon which has been shown to grow in the p...
ORGANISM(S): Metallosphaera sedula 
2010-06-20 | E-GEOD-14978 | biostudies-arrayexpress
TranscriptomicsTranscriptional Response of 0.1%YE-grown M. sedula cells to ferrous sulfate
(from abstract): Iron oxidation is a desirable trait of biomining microorganisms, although the mechanism is not well-understood in extreme thermoacidophiles. The complete genome sequence of the extremely thermoacidophilic archaeon Metallosphaera sedula DSM 5348 (2.2 Mb, ~2300 ORFs) provides insights...
ORGANISM(S): Metallosphaera sedula 
2008-05-02 | E-GEOD-11296 | biostudies-arrayexpress
TranscriptomicsComparative analysis of extremely thermophilic Caldicellulosiruptor species reveals common and differentiating cellular strategies for plant biomass utilization
Microbiological, genomic and transcriptomic analyses were used to examine three species from the bacterial genus Caldicellulosiruptor with respect to their capacity to convert the carbohydrate content of lignocellulosic biomass at 70°C to simple sugars, acetate, lactate, CO2 and H2. C. bescii, C. k...
ORGANISM(S): Caldicellulosiruptor kronotskyensis 
2015-07-31 | E-GEOD-68810 | biostudies-arrayexpress
TranscriptomicsReference: MicroRNA expression profiling in adult mouse liver following BaP treatment [Agilent miRNA array]
We have investigated the effect of exposure to 150 mg/kg benzo(a)pyrene (BaP) for 3 days on mRNA and miRNA expression levels in adult mouse liver. We used Agilent miRNA array platforms to assess effects of BaP exposure on miRNA expression levels. Our results indicate a distinct lack of effect of BaP...
ORGANISM(S): Mus musculus 
2010-10-28 | E-GEOD-19438 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of peripheral blood monocytes from healthy humans and from those with Chronic Granulamatous Disease in response to stimulation with peptidoglycan and lipopolysaccharide
Persons with Chronic Granulomatous Disease, are susceptible to a narrow range of infections resulting from the failure of cells to generate toxic reactive oxygen species (ROS) required for phagocytice oxidative killing of microorganisms. For unknown reasons, many inflammatory conditions (inflammato...
ORGANISM(S): Homo sapiens 
2008-11-05 | E-FPMI-9 | biostudies-arrayexpress
TranscriptomicsDigital Karyotyping for Detecting Chromosome Alterations
To establish a method for calling digital karyotypes using the Illumina HumanCoreExome BeadChip, we calculated the percent of cells within a population that were required to detect a chromosome alteration. We performed serial dilutions of an iPSC line with Trisomy 12, 13, 14, 17, 20, and XXY and a g...
ORGANISM(S): Homo sapiens 
2017-04-03 | E-MTAB-5587 | biostudies-arrayexpress
TranscriptomicsM. sedula transcriptional response under "strict" carbon-limited autotrophy compared to carbon "rich" autotrophy and heterotrophy
Metallosphaera sedula is an extremely thermoacidophilic archaeon that grows heterotrophically on peptides, and chemolithoautotrophically on hydrogen, sulfur, or reduced metals as energy sources. During autotrophic growth, carbon dioxide is incorporated into cellular carbon via the 3-hydroxypropionat...
ORGANISM(S): Metallosphaera sedula DSM 5348 
2013-03-05 | E-GEOD-39944 | biostudies-arrayexpress
TranscriptomicsGene expression profiling of novel antigen presenting cells (APC) inducing pathogenic T helper cells of lupus
In lupus autoimmunity, pathogenic IgG autoantibodies that fix complement and bind FcGammaR on inflammatory cells, are produced with help from T helper (Th1 and Th17) cells specific for peptides from nucleosomes of apoptotic cells; and these Th cells also infiltrate vital organs (1-9). Macrophages (...
ORGANISM(S): Mus musculus 
2012-06-20 | E-GEOD-36284 | biostudies-arrayexpress
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