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Fold changes were calculated for each transcripts between 3 weeks stored and heat-killed samples and 3 weeks stored positive controls (non heat-killed).
The differential genes for each transcripts were subjected to 2 by 2 Chi-square test.
Because we have not got the full-length form for each transcripts, we can not estimate the proportion of our results that would be affected by NMD.
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Each dot represents the mean spacer count for each transcript, n = 4 independent biological samples.
Reads overlapping exonic SNP positions were identified, and HTSeq was used to count these SNP-containing reads for each transcript.
For each transcript under examination and each sample, cDNA was PCR-analyzed in technical triplicate, against absolute standards, and average results calculated.
Each dot represents the mean spacer count for each transcript, horizontal black bars are mean genome-aligning spacer count ± s.e.m., n = 10 independent biological samples.
For the Bristol and Hawaiian RNA-seq data, we calculated a distance score between the mismatch 0 and mismatch 1 read counts for each transcript.
Expression quantification included correction for sequence-specific biases and fragment-level GC biases to generate counts per million for each transcript scaled up to library size.
TMM-normalized "transcripts per million transcripts" (TPM) for each transcript were calculated, and differentially expressed transcripts were identified using edgeR56, all as implemented in the Trinity package version 2.1.157.
To detect stress response transcripts from all RAP transcripts and unannotated transcripts, statistical analysis by G test was conducted between two stages of stress treatments for each transcript.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com