We take as an example recent published reports on microarray experiments that were designed to identify retinoic acid responsive genes.
The design and analysis of ChIP-microarray (also called ChIP-chip) experiments differ significantly from the conventions used for more traditional microarray experiments that measure relative transcript levels.
Using a collection of 1152 neuronally relevant cDNAs, this report describes simple modifications in experimental design of radioactive microarray experiments that, (1) improves reproducibility; (2) allows recovery from a failed experiment and; (3) provides a type of replicate data set with no requirement for additional arrays, no additional probe labelings, and little extra cost.
The importance of DegS/U was further underscored in two microarray experiments that independently demonstrated a total of 135 transcriptional units regulated either directly or indirectly by this two-component system [10], [11].
This means explicitly that we do not use time series data from, e.g., DNA microarray experiments that would allow to test statistically for periodic behavior or appearance of genes.
We followed up a surprising observation that a large number of mitochondrial transcripts are detectable in microarray experiments that used poly(A -specific RNA -specificnd that these tRNAscriprobesels and significanthatenhanced aftheseeatranscriptt.
First, we identify suitable microarray experiments that derive gene sets related to ovary activation.
We assess the results in the context of microarray experiments that were performed earlier.
Not surprisingly, we found that different EPv cutoffs should be used for the different microarray experiments that we examined.
GER directed the microarray experiments that were meta-analyzed, helped interpret the results, and reviewed the manuscript.
In this study, we screened hundreds of expression microarray experiments that were reported in the GEO and involved genes that were knocked down using siRNA or shRNA.
