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We have analyzed 43 Arabidopsis thaliana microarray experiments, encompassing 857 hybridization samples, performed in a variety of experimental conditions in 37 different labs (Table 1).
The Rice Expression Profile Database (RiceXPro) (http://ricexpro.dna.affrc.go.jp/index.html) is a repository of gene expression data derived from microarray experiments encompassing the entire life cycle of the rice plant from the germination, seedling, tillering, stem elongation, panicle initiation, booting, heading, flowering, and ripening stages.
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Total RNA from wt and ashh2-1 young flowers and buds was used in a microarray experiment encompassing oligonucleotides representing ∼27 000 unique genes aimed at identifying target genes for ASHH2 (see Materials and Methods) (Figure 6A).
The Gene expression database contains 9 972 862 baseline gene expression values from microarray and RNA-Seq experiments, encompassing 140 different control, non-diseased mouse and human tissue types.
The model plant species Arabidopsis thaliana is ideal for studying global transcriptional responses since there are thousands of publicly available full-genome microarray experiments that encompass a broad range of experimental conditions including different developmental stages, stress, chemical and hormone treatments and mutants.
Putting together published [ 5, 25, 32] and unpublished microarray experiments (NCBI Gene Expression Omnibus database accessions: GSE18149, GSE33176, GSE41014 and GSE53636), we collected 48 gene expression experiments encompassing 23 different conditions and/or mutant strains for the 3571 genes on the R. capsulatus microarrays.
We used 48 gene expression experiments encompassing 23 different conditions and/or mutant strains for the 3571 genes on the R. capsulatus microarrays to construct a gene co-expression network using WGCNA.
The microarray experiments revealed more than two hundred genes that were unusually active in the placentas of the women suffering from preeclampsia.
Detailed information of rice microarray experiments available in ROAD.
Microarray expression profiles are inherently noisy and many different sources of variation exist in microarray experiments.
One advantage of microarray experiments is that, at the outset, microarray experiments need not be hypothesis driven.
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