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The left front pugmarks of these TSs were always smaller in size than the right front tracks of the same TSs.
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If multiple sequences pointing to the same TSS were obtained it is more likely that they represented authentic TSSs rather than random mRNA degradation products.
Expression levels as measured by total RNAseq of primary transcripts (those containing the same TSS) of genes found to have altered promoter usage between MCF10A and MCF7.
Expression levels as measured by polysomal RNAseq of primary transcripts (those containing the same TSS) of genes found to have altered promoter usage between MCF10A and MCF7 cells.
In a previously generated transgenic line not discussed here, where the nanos promoter was also driving expression of DsRed, we detected transcripts in 0- to 1-hr embryo by 5′ RACE, three of four clones showed the same TSS as found above, and one had a TSS that started 6 bp upstream.
However, the EPD dataset (Additional file 1) has been cleared of redundant promoters that shared the same TSS.
We found that the promoter sets specific to each σ-factor overlap extensively, and a large number of promoters bound by multiple σ-factor share the same TSS.
We decided to simply assume that transcripts with the same initial exon arose from the same TSS and that transcripts with different initial exons arose from different TSSs.
We found that 25 out of 124 miRNAs with the same TSSs as upstream genes were intronic miRNAs (Supplementary Table 1), which means these miRNAs had the same regulatory region as host genes.
We divided this set of transcripts into groups that use the same TSSs, and counted the number of transcripts in which the exon was included, and the number of transcripts in which the exon was excluded in each TSS group.
TSSs from different conditions with very close positions were regarded as the same TSSs using 10 nt sliding window.
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