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(i) Define a realistic set of transcripts as a 'transcript pool' and define a subset of the transcript pool as the 'truly expressed set'. (ii) Assign an expression value to each element of the truly expressed set and simulate RNA-seq reads accordingly.
The gene-associated repeats predicted to play a role in gene regulation in the first part of this study are not among this more highly expressed set. Figure 6 shows the expression levels of the single, particularly highly expressed individual repeats in placenta, myoblast, and lung fibroblast.
Microarray gene expression analysis was done to compare the differentially expressed set of mRNAs from the mutant diminuendo mouse and a wild type (WT) control.
It was as if I had permission to be more fully expressed, set boundaries and be assertive rather than remain the starry eyed idealist who was like a dishrag at times.
Fifteen maternally expressed SET domain genes were identified by WISH analyses (Figure S6 and Table 2).
We identified 1501 gene models from the differentially expressed set with a transcriptomic sequence coverage of 23 or higher.
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These studies typically focused on a single phenotype and identified significant differentially expressed sets of genes across multiple datasets.
Bold values are the common expressed sets in both 489 and pra backgrounds.
These differentially expressed sets were used as input to the DAVID tool using the default parameters recommended by the developers.
The upregulated and downregulated gene sets between EPH-4 EV-50 and shGR-19, as well as both differentially expressed sets together, were used for network analysis.
Differentially expressed sets of genes were obtained from the GeneCards database (12) containing 830 different embryonic tissues based on manual curation (28).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com