For the published MeDIP dataset [ 40], the microarray design used was similar to our design so we were able to construct a 1-1 mapping between over half of the probes across our respective designs.
The microarray design used in this study, contained probes for 74 VSGs, 70 atypical VSGs, and 46 VSGs that were unclassified on VSGdb [ 33]; 21 sub-telomeric ESAGs, 104 chromosome-internal ESAGs and GRESAGs, as well as 17 ESAGs from three T. brucei strain 427 ESs (no T. brucei strain 927 ESs have been annotated to date).
All the strains of Group II C. botulinum listed in Table 3 were tested on a second microarray designed using probes to published ha cluster genes or orfX cluster genes.
To deconvolute shRNA representation in the T = 4 weeks vs. T = 0 cell pools, gel-purified PCR products were differentially labeled and co-hybridized (using manufacturer protocols) to a custom Agilent microarray designed (using Agilent eArray software) to include probes complementary to shRNA hairpin sequences.
The data and the microarray designs used to generate the data have been deposited in NCBI's Gene Expression Omnibus [22] and are accessible through GEO Series accession number GSE19413 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi acc=GSE19413).nih.gov/geo/query/acc.cgi acc=GSE19413
Transcriptional responses in PT and S salmon lice were investigated using custom 15 K oligonucleotide microarrays designed using the above sequence resources.
Samples were added to full-genome zebrafish microarrays designed using the Zv7 genome assembly and containing 385,000 probes at approximately 12 probes for each of 37,157 genes (071105_Zv7_EXPR; NimbleGen, Inc).
The microarray experimental design used in this study provided direct comparisons to identify differentially expressed genes due to SE infection (infection or non-infection) or genetic differences (line A or B).
Microarray array design used in this article can be found at the Array-Express arrayexpress under accession number A-MEXP-244 and A-MEXP-249 and experiment data under accession E-MEXP-418.
A custom microRNA microarray was designed using eArray (Agilent Technologies) comprising of 2371 different probes for 851 human microRNAs (Agilent Human miRNA microarray V3, Sanger Database V12).
