Journal: BMC Genomics

Article Title: Prepartum body condition score and plane of nutrition affect the hepatic transcriptome during the transition period in grazing dairy cows

doi: 10.1186/s12864-016-3191-3

Figure Lengend Snippet: Correlation between qPCR and microarray expression fold change results. Upregulated genes are highlighted in red , while downregulated genes are in green . Black circles represent genes validated for the comparison B4F125vsB4F75, while white circles represent genes validated for the comparisons B5F125vsB5F75

Article Snippet: Liver samples were obtained at −7, 7, and 28 d relative to parturition and subsequent RNA was hybridized to the Agilent 44 K Bovine (V2) Microarray chip.

Techniques: Microarray, Expressing

Journal: The Journal of Reproduction and Development

Article Title: Epigenetic analysis of bovine parthenogenetic embryonic fibroblasts

doi: 10.1262/jrd.2017-040

Figure Lengend Snippet: Scatterplot of the microarray data. Genes expressed only in bovine embryonic fibroblasts (BEFs) but not in bovine parthenogenetic embryonic fibroblasts (BpEFs) are candidates for bovine paternally expressed genes (PEGs).

Article Snippet: The RNA samples were then sent to the Chemicals Evaluation and Research Institute (Tokyo, Japan), and Agilent Bovine DNA Microarray 44K (G2519F#23647) v2.0 (Agilent Technologies, Santa Clara, CA, USA) was used for the microarray analysis.

Techniques: Microarray

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