HAC1 protein arrays
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE33750 | GEO | 2012/11/15
SECONDARY ACCESSION(S): PRJNA154357
REPOSITORIES: GEO
Similar Datasets
Project description:Binding of in vitro synthesized HAC1 mRNA was studied using protein microarray. 3 replicates, plus 3 reverse dye replicates An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract. is_reverse: no: HAC1 mRNA Cy5 labeled; yes: HAC1 mRNA Cy3 labeled all_pairs
2012-11-15 | E-GEOD-33750 | biostudies-arrayexpress
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Project description:We performed expression profiling experiments on two-week old rice leaf tissues grown in light and dark condition with the rice 47k array. Four biological replicates and a dye-swap were used. To generate more consistent results on light vs dark response in rice, biological replicates were prepared from 4 different varieties such as Kitaake, Nipponbare, Tapei309 and IR24 because individual genetic background can affect to expression profile (Townsend et al., 2003). Gene expression was assayed by probing the microarray with pooled Cy3 and Cy5 labeled cDNAs derived from 0.5-1.0ug high quality mRNA prepared from leaf samples. Keywords: Direct comparison
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Project description:The gene expression profiles of the differentiating xylem of 91 Eucalyptus grandis backcross individuals were characterized following a loop design (Churchill, G.A. Nat Genet. 2002 Dec;32 Suppl:490-5). In this design, RNA from genotype 1666 (labeled with Cy5) was hybridized with RNA from genotype 1667 (labeled with Cy3) on the first slide(GEO accession number GSM7637); the same genotype 1667 (now labeled with Cy5) was compared with genotype 1669 (Cy3) on the second slide (GSM7638), and so on. The loop was completed when genotype 1666 (Cy3) was contrasted to individual 1796 (Cy3) on slide GSM7727. Therefore, 91 individuals (genotypes) from the E. grandis backcross population were analyzed in two replicates, one with RNA labeled with Cy3 and the other with Cy5. Keywords = Eucalyptus, xylem, microarray Keywords: ordered
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Project description:Transcriptional profiling of hac1 deletion mutant compared to wild type (control). Wild type vs. hac1 deletion mutant of Ogataea angusta DL1 strain in exponential growth. Two biological replicates, with dye-swaps.
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Project description:The goal of this study is to gain a better understanding of the transcriptional responses of M. hyopneumoniae under norepinephrine stress. Six independent RNA samples from norepinephrine-exposed cultures were paired with six independent RNA samples from control cultures for hybridization to six two-color microarrays. For three arrays, the control RNA sample was labeled with Cy3 dye and the experimental RNA sample was labeled with Cy5 dye, the dyes were reversed for the other three arrays to overcome dye bias. Keywords: stress response
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Project description:Both in situ synthesized long oligo arrays from Agilent Technologies and short oligo arrays from Affymetrix were used to meausre differential gene expression in RNA samples generated from human neural stem cells treated with vehicle (EtOH, 0.01%) and tert-butylhydroquinone (tBHQ, 20µM) for 24h. For Affymetrix technology, RNAs from vehicle or tBHQ treated groups were analyzed separately. There are three replicates (GSM 11755, 11756, 11780, 11781, 11782, and 11783) which represent the RNA preps harvested at three different time (Jan 16, 2002, Jan 24, 2002, and Feb 20, 2002). For Agilent arrays, amplified cRNAs generated from vehicle or tBHQ treated groups were labeled with cy3 or cy5 and were competitively hybridized with Hu 1A oligo arrays. The same RNA preps used for Affymetrix array analysis were also used for Agilent array analysis. Finally, three replicates (GSM 11803, 11804 and 11809) were generated. Keywords: parallel sample
2003-10-22 | GSE759 | GEO
Project description:Both in situ synthesized long oligo arrays from Agilent Technologies and short oligo arrays from Affymetrix were used to measure differential gene expression in RNA samples generated from human neuroblastoma cells treated with vehicle (EtOH, 0.01%) and tert-butylhydroquinone (tBHQ, 10µM) for 24h. For Affymetrix technology, RNAs from vehicle or tBHQ treated groups were analyzed separately. There are three replicates (GSM 11865, 11866, 11858, 11857, 11870, and 11871) which represent the RNA preps harvested at three different time (April 17, 2001, March 15, 2001, and Feb 21, 2001). For Agilent arrays, amplified cRNAs generated from vehicle or tBHQ treated groups were labeled with cy3 or cy5 and were competitively hybridized with Hu 1A oligo arrays. The RNA prep used for Agilent array analysis was not the same as the one used for Affymetrix array analysis. Finally, three replicates (GSM 11828, 11831 and 11835) were generated. Keywords: parallel sample
2003-10-22 | GSE761 | GEO
Project description:ABSTRACT: Inorganic arsenic is a carcinogen and its ingestion in foods such as rice presents a significant risk to human health. Plants chemically reduce arsenate to arsenite. Using genome-wide association (GWA) mapping of loci controlling natural variation in arsenic accumulation in Arabidopsis thaliana allowed us to identify the arsenate reductase required for this reduction, which we named High Arsenic Content1 (HAC1). Complementation verified the identity of HAC1, and expression in Escherichia coli lacking a functional arsenate reductase confirmed the arsenate reductase activity of HAC1. The HAC1 protein accumulates in the epidermis, the outer cell layer of the root, and also in the pericycle cells surrounding the central vascular tissue. Plants lacking HAC1 lose their ability to efflux arsenite from roots, leading to both increased transport of arsenic into the central vascular tissue and on into the shoot. HAC1 therefore functions to reduce arsenate to arsenite in the outer cell layer of the root, facilitating efflux of arsenic as arsenite back into the soil to limit its accumulation in the root and transport to the shoot. Arsenate reduction by HAC1 in the pericycle may play a role in limiting arsenic loading into the xylem. Loss of HAC1 encoded arsenic reduction leads to a significant increase in arsenic accumulation in shoots causing an increased sensitivity to arsenate toxicity. We also confirmed the previous observation that the ACR2 arsenate reductase in A. thaliana plays no detectable role in arsenic metabolism. Further, ACR2 does not interact epistatically with HAC1, since arsenic metabolism in the acr2 hac1 double mutant is disrupted in an identical manner to that described for the hac1 single mutant. Our identification of HAC1 and its associated natural variation provides an important new resource for the development of low arsenic containing food stuffs such as rice.
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Project description:Transcriptional profiling of Control and hac1 deletion mutant in ER stress condition on P. angusta DL1 strain. WT+ER stress vs. hac1 deletion mutant+ER stress. Six-condition experiment: Control+ER stress (TM 30, 60, 120min; DTT 30, 60, 120min) vs. hac1 deletion mutant+ER stress condition (TM 30, 60, 120min; DTT 30, 60, 120min) in P. angusta DL1 strain. Independently grown and harvested. Dye-swapping.
2015-07-22 | E-GEOD-68217 | biostudies-arrayexpress