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By fluorescence-activated cell sorting (FACS) purification and RNA sequencing analysis of D-cells, we identified which stimuli are associated with the expression of matching G protein-coupled receptors (GPCRs).
We decided, therefore, to proceed to analyze different hematopoietic precursors simultaneously (ERY, MKC, MYELO and MONO) with the leading hypothesis that increased expression of a cell-context-enriched microRNA is believed to result in at least partial decreased expression of matching target mRNAs.
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Hence, all data were expressed as an n-fold difference in relation to the expression of matched controls (sham).
Hence, all data that are expressed as an n-fold difference are related to the expression of matched controls.
We performed next-generation RNA sequencing (RNA-seq) and determined expression of matched hemizygous and homozgyous genes to avoid comparing expression of X chromosomes to autosomal genes directly.
For differential expression of matched gels, protein spots whose intensities were either increased or decreased two-fold or greater were marked and then confirmed by manual inspection of all relevant 2D gel, not only those included in the matchsets, to ensure consistency.
We found decreasing correlation between probes and the expression patterns of matching off-target transcripts as the match edit distance between the probe and transcript is increased.
The expression profiles of matching gene loci with at least 100 bp overlap and ≥ 98% sequence identity were selected and then interrogated against our DGE dataset.
Gene and miRNA expression data sets of matching normal samples from GBM, KIRC, and OvCa were also extracted from the TCGA database.
Secondly, we analyze how comparable the gene expression profiles of matched FF and FFPE samples are.
A multivariate analysis of expression data of matched spots was conducted for all classes and evaluated by principal component analysis (PCA).
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