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The calculation of the mean fluorescence intensity levels revealed that different ranges of transcript abundance are present in both experimental setups.
We believe many of these diverse phenotypes are caused by effects on the populations of a wide range of transcripts, either through transcriptional regulation or mRNA stability.
On the basis of the phenotypes of the mutant and overexpressors (complemented lines), it is highly likely that MpSIG1 is involved in the transcription of a wide range of transcripts and that its function overlaps with and/or is complemented by those of other sigma factors.
Due to its flexibility and the declining cost of massively parallel sequencing, NGS-based RNA-seq is becoming an increasingly attractive tool to investigate the full range of transcripts and to reveal the complex landscape and dynamics of the transcriptome.
This criterion should be evaluated for a broad range of transcripts.
To explore the broadest range of transcripts, Affymetrix extended probes were imported, yielding transcripts of which 112,207 have annotation with 50,601 at the gene or mRNA-level.
This suggested the possibility that use of the expression array platform may have failed to identify the complete range of transcripts associated with HRG-induced gene regulation.
Thus, our analysis revealed that independent tiling array analysis may have failed to identify the complete range of transcripts associated with HRG-induced gene regulation.
The RNA tagging conditions were thoroughly optimized and compared to previous methods by using a biochemical oligonucleotide tagging assay and RACE PCRs on a range of transcripts.
The present report focuses on the implementation and validation of the protocol; its sensitivity as compared to previous methods is shown by RACE PCR on a range of transcripts.
This technology has been expanded into RNAi libraries encompassing reagents that target a wide range of transcripts, allowing the role of multiple genes in a cellular process to be assessed in an unbiased fashion [4], [5].
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