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We used RNA-seq data of colon cancer patients and compared expression values from control and paracancerous and cancer tissue.
The primary differential expression (DE) analysis was done using EdgeR and compared expression values of the unique miRNAs as determined by miRDeep2 normalization (Additional file 5).
Probe-sets that had > 0 MM between species were filtered before conducting statistical analyses that directly compared expression values between axolotl and tiger salamander larvae (see below).
We then compared expression values obtained at time 0 in the culture medium against those obtained after 2 or 6 hours of internalization.
For RNA-seq libraries produced by previous studies (Brawand et al., 2011), we compared expression values with in-house data and examined CV to ensure that the downloaded data contained no instrumental or sampling errors (Fig. S25).
To ascertain that species misassignment and potential biases in read loss does not cause S expression values to lose accuracy, we mixed pairs of human and mouse samples in silico and compared expression values before and after mixing the samples and using S (Fig. 1e, f), with good correlation.
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β-actin mRNA expression was used to normalize and compare expression values for genes of interest.
These transcriptomes were then used to compare expression values between the rat and human cell lines.
The logarithmic fold-change (logFC) comparing expression values during infection with the common reference was calculated.
β-Actin mRNA expression levels were used to normalise and compare expression values for the genes of interest.
Genomic DNA contamination was assessed by comparing expression values for splice-junction spanning and intergenic TFCP2 assays.
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