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Utilizing this data set and the process described in Materials and Methods, the gene content of each segment described in Chin et al. was identified.
To explore the process of PGC derivation in vitro using these two methods, the gene expression dynamics of GFP-positive cells from days 4 to 8 in the attachment culture technique (Att+) and days 2 to 4 in the EB method (EB+) were analyzed by Quantitative RT-PCR (Q-PCR) (Fig. 3).
However, in these methods the gene expression data matrices for test samples from one experiment are not compared to the control samples from another experiment.
To test for categories with more eQTLs than expected by chance (~1 eQTL every 10 genes, see Methods), the gene functional classification assigned by the Gene Ontology Consortium was used [ 28].
Although a low proportion of common genes were reported by both methods, the gene list from association rule in ALL > AML and those from t-test have a strong agreement in pathway analysis.
For both methods, the gene ontology (GO) term analysis was very similar and included enrichment for ribosome components, translation initiation and elongation factors, protein targeting/sorting genes (co-translational process, and post-translational translocation), and RNA metabolism genes (Tables S2, S3, S4).
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The two different constructs were delivered using two different methods; the gene-gun and the Biojector, which both are needle-free devices.
However, to allow comparison with other methods, the genes were rank ordered using the FDR values, and the desired numbers of genes were then selected for further analysis.
The difference in results obtained using the oligonucleotide based methods and the gene based methods suggest that the genomic properties reflected by the respective methods represent different perspectives.
Three methods including the phylogenetic profiles method, the gene neighbors method and the gene fusion method were adapted to construct the genome context networks [20].
Using this method, the gene is disrupted and expression of genes downstream of the disrupted gene is driven from the erythromycin promotor.
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