bovine whole-genome gene expression microarray  (Agilent technologies)

Journal: BMC Genomics

Article Title: A mRNA landscape of bovine embryos after standard and MAPK-inhibited culture conditions: a comparative analysis

doi: 10.1186/s12864-015-1448-x

Figure Lengend Snippet: Microarray set-up and sample validation. RNA from morula ( A , purple), blastocyst ( B , green), trophectoderm ( C , blue) and inner cell mass ( D , orange) was hybridized on microarrays. A common reference sample composed of blastocysts was hybridized with each sample in duplicate in balanced dye-swap ( E , arrows indicate an array and the used fluorescent label; Cy3: green; Cy5: red). The heat map ( F ) illustrates pairwise clustering of microarray sample replicates. Yellow colour represents over-expressed probes and blue colour represents under-expressed probes as indicated by the colour legend (B = blastocyst; ICM = inner cell mass; M = morula; TE = trophectoderm). Representative pictures of immunofluorescent labelling of dissected ICM ( G ) and TE ( H ) for GATA6 (green) and CDX2 (red); double GATA6-CDX2 nuclei appear yellow. Nuclear staining by DAPI (blue). A 2D principal component analysis plot ( I ) with sample position indicating clustering of trophectoderm (blue), blastocyst (green), inner cell mass (orange) and morula (purple) replicates.

Article Snippet: Microarrays used were bovine whole genome gene expression microarrays V2 (Agilent Technologies) representing 43,653 Bos taurus 60-mer oligos in a 4x44K layout. cDNA synthesis, cRNA double amplification, labelling, quantification, quality control and fragmentation were performed with an automated system (Caliper Life Sciences NV/SA, Teralfene, Belgium), starting with 10–20 ng total RNA from each sample, all as previously described in detail [ , ].

Techniques: Microarray, Staining