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We benchmarked the rRNA depletion-based sequencing with a specific analysis of the cytoplasmic and nuclear transcriptome fractions, suggesting that the large majority of the intronic reads correspond to unprocessed nuclear transcripts rather than to independent transcriptional units.
This transcript seems unusually long, but a global analysis (ENCODE project) has previously suggested that such long-distance transcription products are present in primary nuclear transcripts [18].
Evidently, global analyses of cytoplasmic RNA transcripts appear more likely to reflect the patterns of protein biosynthesis at any particular time, whereas analyses of nuclear transcripts appear more likely to track the process of transcription.
In summary we identified four cellular processes likely altered by CUG repeat RNA: gene transcription, cell adhesion, programmed cell death and export of nuclear transcripts.
In order to ensure that final unigenes covered only S. sulcatum nuclear transcripts, we BLASTed contigs to databases consisting of Oxytricha trifallax mitochrondrial genome and bacterial genomes because Strombidium is closely related to Oxytricha.
Exclusion of 5'phosphorylated transcripts by Terminator nuclease would help to differentiate between nuclear transcripts and polyadenylated transcripts of mitochondrial origin.
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TTF-1 is a nuclear transcript factor that is expressed in epithelial cells of the lung and thyroid.
We must, however, be careful in our interpretation of cordycepin effects, because cordycepin has been shown to inhibit polyadenylation in some systems [19], and because we could only use a nuclear transcript to confirm the efficiency of the cordycepin treatment.
Collection of GenBank accession numbers for all new plastid genome and individual nuclear transcript sequences reported in this study.
These two polymorphisms have been studied extensively because they could alter the nuclear transcript factors which mediate the insulin response.
The stem-loop region of a long primary nuclear transcript (called miR precursor or pre-miR) is processed into 21-nucleotide RNAs by a multistep process involving the activity of DCL1 [ 4, 5], HEN1 and HYL1 proteins [ 6, 7].
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