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In addition to confirming the expression of known markers by comparing our microarray data to previously documented findings, we verified transcript accumulation of selected factors with qRT-PCR.
A predicted RNA structure is reported as transcribed if its overlap with an experimentally verified transcript is larger than 50%.
qRT-PCR analysis of a subset of DEGs further verified transcript expression levels as revealed by transcriptome comparison from raw RNA-seq data.
In several instances, our experimentally verified transcript assemblies overlapped multiple Twinscan or EuGene predictions, such as neighboring genes At.chr4.2.13 and At.chr4.2.14.
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Within 48 hours after every focus group, audio recordings were transcribed verbatim, and we verified transcripts against the original recording to ensure transcription accuracy.
Once verified, transcripts were imported into a data analysis software package, NVivo Version 10 (QRS International, Doncaster, Australia).
The sequences of the predicted and/or verified transcripts of Arabidopsis thaliana, Populus trichocarpa and Ricinus communis were downloaded or determined from the genomic sequences.
In our studies, we divided the 4,792 verified transcripts [ 5, 30] into four significant groups by k-means clustering, based on the stable nucleosome map with a window of ~1600 bp surrounding the TSS.
The sequences of experimentally verified transcripts with known protein products of one-to-one human-mouse orthologous genes, based on the Ensembl release 54 http://www.ensembl.org, were retrieved through BioMart [ 35].
These observations emphasize the need for a concise computational analysis of non-coding RNAs in yeast, and for a comparison of those elements with verified transcripts of recent large-scale experiments.
We used qPCR to independently verify transcript levels of Wnt genes identified by the PCR array.
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