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To eliminate all other small non-coding RNAs, clean tags from each sample were annotated as tRNAs, rRNAs, scRNAs, snRNAs, and snoRNAs.
Nimblegen scan pair files (635 nm and 532 nm) for each sample were annotated against hg18 and enriched regions were detected using a two-way ANOVA between an affected twin and their unaffected co-twin.
Cases were subdivided according to the three major histotypes (papillary, follicular and anaplastic) and the modal number, the total number of chromosome aberrations, and all breakpoints in each sample were annotated.
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The transcriptome-wide binding sites from each sample are annotated with genomic elements, which are summarized using pie charts.
In two cases, the samples were annotated as male but clustered within the females; these are likely mis-annotations.
An additional 30 of the genes with higher expression in the neo aortic samples were annotated to Wnt receptor signaling pathway, which was the term ranked in third place by MGSA.
Firstly, the SNPs/InDels detected in the samples were annotated.
The samples were annotated with an anonymous but traceable barcode.
Of the 98 cores stained, 81 breast cancer samples were annotated for patient survival data.
And, the samples were annotated by 33 SMD categories which describe the experimental context of microarray samples.
All tumor samples were annotated with available clinical information in a manner that protected the patient identity.
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CEO of Professional Science Editing for Scientists @ prosciediting.com