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Based on the silkworm genome-wide microarray dataset http://silkworm.swu.edu.cn/microarray[ 24], expressions of BmCOEs in multiple tissues on the day three of the fifth instar were surveyed.
We used a publicly available microarray dataset (http://www.ncbi.nlm.nih.gov/geo/, accession number GSE9954; see also Thorrez et al., 2008) that we generated via Affymetrix mRNA expression analysis using 430 2.0 arrays.
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GEO microarray datasets (http://www.ncbi.nlm.nih.gov/geo/) included in this study were GSE12891 [ 12] and GSE10856 [ 13] (the sources of the microarray data were summarized in Additional file 1: Table S1).
Common target mRNAs were subjected to functional enrichment analysis using CapitalBio Molecule Annotation System V4.0 and compared to abnormally expressed mRNA profiles from microarray datasets (MAS, http://bioinfo.capitalbio.com/mas3/).
The Gene Expression Omnibus (GEO) accession number for the microarray dataset is GSE21942 (http://www.ncbi.nlm.nih.gov/geo/).nih.gov/geo/
We next made use of the publically available Versteeg microarray gene expression dataset http://r2.amc.nl, which contained both gene expression levels and patient prognosis.
The complete microarray dataset is available at http://smd.stanford.edu/cgi-bin/publication/viewPublication.pl?pub_no484.
The entire microarray dataset is available at http://www.ncbi.nlm.nih.gov/geo/(GSE20431).
The complete MIAME-compliant microarray dataset is available on GEO (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi acc=GSE41571).nih.gov/geo/query/acc.cgi acc=GSE41571
Raw CEL files from the microarray dataset GSE3189 were downloaded from GEO (http://www.ncbi.nlm.nih.gov).nih.gov
In order to assess the reliability of our findings, we exploited the E-GEOD-16011 microarray dataset downloaded from the ArrayExpress archive (https://www.ebi.ac.uk/arrayexpress/) and RNA-seq data from NCBI SRA study SRP027383 including brain tumor samples with an histological classification comparable to the ones in the GDS1962 dataset.
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