Genes expressed at very low levels (read counts < 10 across all six libraries) were not used in analysis of differential gene expression.
In summary, analysis of transcripts around HMS2 and BAT2 supports (i) an overlapping, reciprocally related and temporally segregated, sense antisense pair (SAP) at HMS2, (ii) reciprocally expressed sense transcripts at HMS2 and BAT2, and (iii) low-level read-through di-cistronic transcripts (HMS2 BAT2 and SUT650 RPS4A).
DOI: http://dx.doi.org/10.7554/eLife.03635.010 A number of different methods revealed heterogeneity at both the 5′ and 3′ ends of the HMS2 and SUT650 transcripts and longer RNA species (C1 and C2) on the HMS2 sense strand extending through the coding region of BAT2 and beyond, consistent with low-level read-through transcripts initiating at the HMS2 promoter.
The festival's planners decided to keep the music "at a low level today," read a sign posted at the entrance.
We observed a low level of reads along the length of each chromosome and sequence enrichment (relative to input) at ∼8200 regions across the fer-1 genome.
Our mapped RNA-Seq reads and DESeq analysis suggested a moderate approximately 11-fold de-repression (padj =3.20E-25) of SPO74 in the mutant strains compared to the low level of reads seen in wild type strains.
The clinical use of these drugs to suppress nonsense mutations is precluded because of toxicity of these drugs at high dose, required for a low level of read through of premature nonsense codons.
However, our existing RNAseq data corresponding to the HITS-CLIP experiments shown in Figures 4 and 5 are polyA-selected and therefore, given the low level of reads mapping to introns, it is not suitable for intronic HITS-CLIP normalization.
For example, the data show very low levels of reads for nifHDK and other nif operons at 0, 6, and 12 hours after nitrogen step-down (when heterocysts are not yet fully formed).
In the untreated library, low levels of reads were distributed throughout the transcribed regions with no peaks generally observed at the 5′ ends of annotated genes.
