Eif3k/WT polysome loading and transcript levels
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
SUBMITTER: Albrecht von Arnim
PROVIDER: E-GEOD-28224 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:To understand the contribution of the k subunit of eukaryotic transcription factor 3 (eif3k) to the translation of specific mRNAs, we compared the polysome loading states and overall transcript levels of wild type Arabidopsis and the eif3k T-DNA insertion mutant by Affymetrix arrays. We analyzed the polysome loading states of wild type Arabidopsis and the eif3k mutant using the Arabidopsis Affymetrix ATH1 array. Data from 3 biological replicates were collected.
2011-03-29 | E-GEOD-28223 | biostudies-arrayexpress
Project description:To understand the contribution of the k subunit of eukaryotic transcription factor 3 (eif3k) to the translation of specific mRNAs, we compared the polysome loading states and overall transcript levels of wild type Arabidopsis and the eif3k T-DNA insertion mutant by Affymetrix arrays. We analyzed the transcript levels of wild type Arabidopsis and the eif3k mutant using the Arabidopsis Affymetrix ATH1 array. Data from 3 biological replicates were collected.
2011-03-29 | E-GEOD-28222 | biostudies-arrayexpress
Project description:To understand the contribution of the RPL24B protein, a component of the large 60S ribosomal subunit, to the translation of specific mRNAs, we compared the ribosome occupancy of mRNAs in wild type Arabidopsis and the rpl24b/stv1-1 T-DNA insertion mutant. RNA was fractionated using sucrose gradients into polysomal and nonpolysomal RNAs. We also determined overall total transcript levels. We used Affymetrix ATH1 microarrays. Each plant sample was analyzed for the mRNA abundance in total mRNA, polysomal mRNA, and nonpolysomal mRNA. Three biological replicates were collected. The rpl24b mutant was compared with wild type.
2014-01-01 | E-GEOD-51474 | biostudies-arrayexpress
Project description:To understand the contribution of the poly(A)binding protein to the translation of specific mRNAs, we compared the ribosome occupancy of mRNAs in wild type Arabidopsis and pab2 pab8 double mutant seedlings. The mutants continue to express the PAB4 paralog of PABP. RNA was fractionated using sucrose gradients into polysomal and nonpolysomal RNAs. We also determined overall total transcript levels. We used Affymetrix ATH1 microarrays. Each plant sample was analyzed for the mRNA abundance in total mRNA (T), polysomal mRNA (PL), and nonpolysomal mRNA (NP). Four biological replicates were collected for polysomes and three for total RNA. The pab2 pab8 double mutant was compared with wild type.
2014-01-01 | E-GEOD-51480 | biostudies-arrayexpress
Project description:Type 2 diabetes (T2D) is the most common form of diabetes in humans and is closely associated with dyslipidemia and obesity that magnifies the mortality and morbidity related to T2D. The TALLYHO/JngJ (TH) mouse is a polygenic model for T2D characterized by obesity, hyperinsulinemia, impaired glucose uptake and tolerance, hyperlipidemia, and hyperglycemia. To determine the genetic factors that contribute to these T2D related characteristics in TH mice, we interbred TH mice with C57BL/6J (B6) mice. The parental, F1, and F2 mice were phenotyped at 8, 12, 16, 20, and 24 weeks of age for 4-hour fasting plasma triglyceride, cholesterol, insulin, and glucose levels, as well as body weights. Fat pad and carcass weights were measured at 24 weeks after sacrificing the mice. The F2 mice were genotyped genome-wide for 68 markers. Of 393 genotyped F2 mice, 16 were chosen from the extremes of the triglyceride distribution (8 high and 8 low), and liver, pancreas, muscle and adipose tissue were measured for gene expression. Gene expression quantitative trait locus (eQTL) analysis aided in selection of candidates underlying hyperlipidemia, diabetes and obesity QTLs. We identified several genetic loci that affected quantitative variation in plasma lipid and glucose levels and obesity traits. 16 (8 high and 8 low) out of 393 F2 mice were chosen from the extremes of the triglyceride distribution, excluding overtly diabetic mice, and liver, pancreas, muscle and adipose tissue were measured for gene expression. In addition to data from the 64 microarrays on the 16 mice, a supplemental file with phenotypes and marker genotypes is provided for all mice as a supplementary file on the Series record (below). Mouse identification numbers are included to connect the data files.
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Project description:Hepatitis C Virus protein NS5A was found to upregulate assembly of cap binding initiation complex eIF4F in Huh7.5 cells. NS5A also was found to associate with translation machinery. To understand consequences of NS5A mediation in host translation, we analyzed mRNA associated with polysome fractions of NS5A expressing Huh7.5 cells and compared them with the corresponding fractions from control cells. Agilent-027114 Genotypic Technology designed Custom Human Whole Genome 8x60k Microarray
2014-05-01 | E-GEOD-46273 | biostudies-arrayexpress
Project description:The mechanistic target of rapamycin, (mTOR) kinase plays a pivotal role in controlling critical cellular growth and survival pathways, and its aberrant induction is implicated in cancer pathogenesis. Therefore, suppression of active mTOR signaling has been of great interest to researchers; several mTOR inhibitors have been discovered to date. Ethanol (EtOH), similar to pharmacologic mTOR inhibitors, has been shown to suppress the mTOR signaling pathway, though in a non-catalytic manner. Despite population studies showing that the consumption of EtOH has a protective effect against hematological malignancies, the mechanisms behind EtOHM-bM-^@M-^Ys modulation of mTOR activity in cells and its downstream consequences are largely unknown. Here we evaluated the effects of EtOH on the mTOR pathway, in comparison to the active-site mTOR inhibitor INK128, and compared translatome analysis of their downstream effects in diffuse large B-cell lymphoma (DLBCL). SUDHL-2 and SUDHL-4 diffuse large B-cell lymphoma (DLBCL) cell lines (ATCC) were cultured in RPMI Medium 1640 (Gibco BRL) supplemented with 10% fetal bovine serum (FBS) at 37M-BM-0C in 5% CO2. EtOH-treated cells were cultured in sealed flasks to maintain EtOH concentrations, 20mM in the culture medium, water was added to EtOH control wells. INK128-treated cells were treated with INK128 at 40nM (Selleckchem) dissolved in dimethyl sulfoxide (DMSO) or 0.01% DMSO was added for the control wells. To create polysomal fractions, cells were lysed in cytoplasmic lysis buffer (5mM Tris, 2.5mM MgCl2, 1.5mM KCl, 1% Triton X-100, 0.5% Sodium Deoxycholate and 2 mM DTT), loaded on 10 - 50% linear sucrose gradients and fractionated. The RNA in each fraction was monitored by optical density measurement (A254) and eleven fractions were collected with a fraction collector (Brandel). The RNA from each fraction was isolated by Trizol (Invitrogen) and used for RT-qPCR analysis. RNA from high molecular weight polysomal fractions, with actively translated mRNAs (fractions 9 - 11) were pooled and used for microarray analysis. RNA was isolated using Qiagen RNeasy protocols and quality and quantity were checked with an Agilent 2100 Bio-Analyzer using RNA 6000 Nano chips. Labeling and amplification were done with the standard Illumina protocol and the biotin-labeled cRNA was hybridized to Illumina's HumanHT-12 V4.0 Expression BeadChip. The arrays were washed, blocked and the biotin-labeled cRNA was detected by staining with streptavidin-Cy3.
2015-03-03 | E-GEOD-62790 | biostudies-arrayexpress
Project description:Circadian control of gene expression has been established in plants at the transcriptional level, but relatively little is known about circadian control of translation. We used polysome profiling to characterize regulation of transcription and translation over a 24-hour diurnal cycle in Arabidopsis, both in wild type and in plants with a disrupted clock due to constitutive overexpression of the CIRCADIAN CLOCK ASSOCIATED 1 gene (CCA1-ox, AGI AT2G46830). 10 day-old wild type and CCA1-ox (described in Cell. 1998 Jun 26;93(7):1207-17) Arabidopsis seedlings were harvested at 6am (Zeitgeber time ZT0), 12pm (ZT6), 6pm (ZT12), and 12am (ZT18), with 3 replicates for each time and genotype.
2015-02-01 | E-GEOD-61896 | biostudies-arrayexpress
Project description:Circadian control of gene expression has been established in plants at the transcriptional level, but relatively little is known about circadian control of translation. We used polysome profiling to characterize regulation of transcription and translation over a 24-hour diurnal cycle in Arabidopsis, both in wild type and in plants with a disrupted clock due to constitutive overexpression of the CIRCADIAN CLOCK ASSOCIATED 1 gene (CCA1-ox, AGI AT2G46830). 10 day-old wild type and CCA1-ox (described in Cell. 1998 Jun 26;93(7):1207-17) Arabidopsis seedlings were harvested at 6am (Zeitgeber time ZT0), 12pm (ZT6), 6pm (ZT12), and 12am (ZT18), with 3 replicates for each time and genotype.
2015-02-01 | E-GEOD-61895 | biostudies-arrayexpress
Project description:Circadian control of gene expression has been established in plants at the transcriptional level, but relatively little is known about circadian control of translation. We used polysome profiling to characterize regulation of transcription and translation over a 24-hour diurnal cycle in Arabidopsis, both in wild type and in plants with a disrupted clock due to constitutive overexpression of the CIRCADIAN CLOCK ASSOCIATED 1 gene (CCA1-ox, AGI AT2G46830). 10 day-old wild type and CCA1-ox (described in Cell. 1998 Jun 26;93(7):1207-17) Arabidopsis seedlings were harvested at 6am (Zeitgeber time ZT0), 12pm (ZT6), 6pm (ZT12), and 12am (ZT18), with 3 replicates for each time and genotype.
2015-02-01 | E-GEOD-61898 | biostudies-arrayexpress