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It turns out inference for the considered example becomes increasingly more difficult, the more transcripts are expressed (Fig. 3B).
More transcripts are upregulated between the gastrula and planula than downregulated, and a comparatively lower number of transcripts significantly change between planula and polyp.
To the contrary, the majority of MeCP2-bound promoters are actively expressed (9) and more transcripts are upregulated by increasing Mecp2 genetic dosage than downregulated (10).
As more samples are added, more transcripts are correctly predicted, and both ISP and Cuffmerge achieve similar improvements of sensitivity on six samples.
As more RNA-Seq samples are added, more transcripts are merged by Cuffmerge, and this number reaches 150 , 000(over 100% growth) when all seven samples are included.
One of the possible issues responsible for this is the normalization because in normalized libraries more transcripts are represented and thus the probability of being sequenced is lower for each transcript than in case of non-normalized library.
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Of these, three times more transcripts were up-regulated than down-regulated.
Many more transcripts were anti- correlated to qP, and gene set enrichment analysis (GSEA) revealed that those were involved in cell cycle progression, transcription, mRNA processing, translation and protein folding.
More transcripts were inversely correlated than positively correlated (23 versus 12).
For 215 genes, two or more transcripts were covered by the newly defined transcript-specific probe sets with a minimal probe set size of 1 (Table 2).
Overall, more transcripts were present in in vitro activated and FBR CD68+ cells (47.1% and 45% from a total of 31099 probe sets) as compared to freshly isolated CD68+ cells (40.4%).
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CEO of Professional Science Editing for Scientists @ prosciediting.com