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For Affymetrix gene expression microarray experiments, approximately 5,000 10,000 purified primary hematopoietic cells were sorted directly into 350 μl of RLT buffer containing 3.5 μl of β-mercaptoethanol (RNeasy micro kit, Qiagen).
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It is generally assumed that the log intensities (or expression levels) in a microarray experiment are approximately normally distributed.
Between the two independent (microarray and QPCR) experiments, approximately 70% (15) of the genes assessed show strong correlation (r2 = 0.8, p<0.0001) in direction and magnitude of regulation by UAG (Figure S1).
BayMiR analysis was conducted on 1,539 human miRNAs and the expression levels of 13,303 genes measured on 5,372 microarray experiments and predicts that approximately 60% of miRNA-mRNA duplexes with matched conserved targets sites have detectable down-regulation signal on gene expression.
P-values are associated with scores by comparing them to an empirical probability distribution derived from 1009 microarray experiments, which was found to be approximately log normal.
By re-analyzing subsets of our data that represented the scale of replication more commonly found in microarray experiments (4 replicates), we showed that approximately half of the transcriptional changes that we detected could not be observed with the small-scale experiments.
Interestingly, roughly one third of the genes that were downregulated more than 2-fold in one or both CATMA microarray experiments cluster in a genomic region of approximately 84 kb upstream of RLK902.
Ovine microarray experiments were performed using the Affymetrix Bovine Expression Array (representing approximately 23,000 transcripts).
All microarray experiments were conducted using the minimal information about a microarray experiment (MIAME) guidelines.
Although microarray experiments were performed using only two replicates, correlations within groups were very high (approximately 97% for both symptomatic and controls).
The equitoxic doses that led to approximately 50% prolongation in doubling time as compared to untreated cells were chosen for the microarray experiments.
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