The CCA-adding enzyme adds CCA to the 3'' ends of transfer RNAs (tRNAs), a critical step in tRNA biogenesis that generates the amino acid attachment site. We found that the CCA-adding enzyme plays a key role in tRNA quality control by selectively marking unstable tRNAs and tRNA-like small RNAs for degradation. Instead of adding CCA to the 3'' ends of these transcripts, CCA-adding enzymes from all three kingdoms of life add CCACCA. Here, we report deep sequencing analysis of the 3'' ends of tRNA-Ser-CGA and tRNA-Ser-UGA from S. cerevisiae strains and show that hypomodified mature tRNAs are subjected to CCACCA (or poly(A) addition) as part of a rapid tRNA decay pathway in vivo. We conjecture that CCACCA addtion is a universal mechanism for controlling tRNA levels and preventing errors in translation. Overall design: 121 samples analyzed in total, representing time courses of 10 different yeast strains; Biological replicates for each time point are included
tRNAs marked with CCACCA are targeted for degradation.
Cell line, Subject
View SamplesGene expression microarrays have made a profound impact in biomedical research. The diversity of platforms and analytical methods has made comparison of data from multiple platforms very challenging. In this study, we describe a framework for comparisons across platforms and laboratories. We have attempted to include nearly all the available commercial and in house platforms. Using probe sequences matched at the exon level improved consistency of measurements across the different microarray platforms compared to annotation-based matches. Generally, consistency was good for highly expressed genes, and variable for genes with lower expression values as confirmed by QRT-PCR. Concordance of measurements was higher between laboratories on the same platform than across platforms. We demonstrate that, after stringent pre-processing, commercial arrays were more consistent than in-house arrays, and by most measures, one-dye platforms were more consistent than two-dye platforms.
A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies.
No sample metadata fields
View SamplesGene expression microarrays have made a profound impact in biomedical research. The diversity of platforms and analytical methods has made comparison of data from multiple platforms very challenging. In this study, we describe a framework for comparisons across platforms and laboratories. We have attempted to include nearly all the available commercial and in-house platforms. Using probe sequences matched at the exon level improved consistency of measurements across the different microarray platforms compared to annotation-based matches. Generally, consistency was good for highly expressed genes, and variable for genes with lower expression values as confirmed by QRT-PCR. Concordance of measurements was higher between laboratories on the same platform than across platforms. We demonstrate that, after stringent pre-processing, commercial arrays were more consistent than in-house arrays, and by most measures, one-dye platforms were more consistent than two-dye platforms.
A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies.
No sample metadata fields
View SamplesThe purpose of this experiment was to identify genes responding differently to a 24 h low red to far red ratio (R:FR) treatment in plants grown at 16 and 22 degrees
Light-quality regulation of freezing tolerance in Arabidopsis thaliana.
Age
View SamplesMotivation: RNA-seq is replacing microarrays as the primary tool for gene expression studies. Many RNA-seq studies have used insufficient biological replicates, resulting in low statistical power and inefficient use of sequencing resources. Results: We show the explicit trade-off between more biological replicates and deeper sequencing in increasing power to detect differentially expressed (DE) genes. In the human cell line MCF-7, adding more sequencing depth after 10M reads gives diminishing returns on power to detect DE genes, while adding biological replicates improves power significantly regardless of sequencing depth. We also propose a cost-effectiveness metric for guiding the design of large scale RNA-seq DE studies. Our analysis showed that sequencing less reads and perform more biological replication is an effective strategy to increase power and accuracy in large scale differential expression RNA-seq studies, and provided new insights into efficient experiment design of RNA-seq studies Overall design: Treatment (10nM E2 treatment for 24h) and control MCF7 cells are both replicated 7 times, and collected for mRNA-seq. Reads are then subsampled for statistical analysis.
RNA-seq differential expression studies: more sequence or more replication?
No sample metadata fields
View SamplesIn the present study, we hypothesized that C/EBPa (CCAAT/enhancer-binding protein alpha) plays a role in cell regeneration in response to bronchiolar epithelial cell injury. C/EBPa mediated ciliated cell regeneration after naphthalene bronchiolar epithelial cell injury in vivo. Furthermore, we demonstrated that C/EBPa regulates protease/anti-protease balance after lung injury, and intratracheal treatment with anti-protease (BPTI) restored ciliated cell regeneration after naphthalene injury in CebpaD/D mice.
CCAAT/enhancer binding protein-α regulates the protease/antiprotease balance required for bronchiolar epithelium regeneration.
Specimen part, Treatment
View SamplesEwg differentially regulated genes in 16-18 h Drosophila embryos. The experiment contains expression measurements from wild type, ewg l1 protein null allele and ewg l1 elavEWG (elavEWG rescue construct expressing a ewg cDNA from the elav promoter) mutants.
Erect wing regulates synaptic growth in Drosophila by integration of multiple signaling pathways.
Age
View SamplesGrowth plate chondrocytes were isolated from the distal metacarpus of young dairy cattle (all under 10 mo of age), the chondrocytes were released from the extracellular matrix by digestion with Collagenase P for 4 hours, and the various zones of the growth plate were separated by density centrifugation. The least-dense Hypertrophic Zone (HZ) cells were compared to the most-dense Reserve Zone (RZ) cells. 6 pairs of HZ vs RZ were compared by microarray.
SCF, BDNF, and Gas6 are regulators of growth plate chondrocyte proliferation and differentiation.
Sex, Specimen part
View SamplesThe expression of a very large number of genes changes as male germ cells pass through differentiation into spermatids and then sperm. Much of this transcriptional programme requires the activity of the meiotic arrest genes.
The RNA export factor, Nxt1, is required for tissue specific transcriptional regulation.
Specimen part
View SamplesThis experiment was a time course performed over 24 hours to look at the effects on gene expression of exposure to low red:far-red ratio light in Arabidopsis thaliana plants. In this way genes involved in the shade avoidance response might be identified. This experiment was designed for gene identification only and containes no replicates,genes identified were verified by quantitative PCR for publication.
Gating of the rapid shade-avoidance response by the circadian clock in plants.
Specimen part, Disease, Disease stage, Subject
View Samples