Project description:Two different early developmental stages of gilthead sea bream: i) larvae at 24 hours post-hatching ( Stage 1), and ii) larvae at 96 hours post-hatching (Stage 4), were used for gene expression analysis. For each stage, total RNA was extracted from five (5) independent biological replicates, each consisting of pools of approximately 40-50 larvae. Based on SAM analysis, 1518 genes were differentially expressed between the two stages with a FDR (False Discovery Rate) of 0.0. In this study, we analyzed the gene expression profiles of two early developmental stages of gilthead sea bream using Agilent-016251 Sparus aurata Oligo Microarray platform (10 arrays, no replicate) based on single-colour detection (Cyanine-3 only). Microarrays are scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides are scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software creates a unique ID for each pair of XDR scans and saves it to both scan image files. Feature Extraction 9.5 uses XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal .
Project description:Agilent custom-made 8x60k 60-mer oligonucleotide microarray slides were used, covering unique sequences (21,093 annotated sequences and 4,299 unannotated sequences) of Sparus aurata transcriptomic data obtained from assembling of reads deposited in the NCBI SRA database corresponding to BioProject ID PRJNA391557, together with controls (8 transcripts of Sparus aurata plus Agilent controls). Two probes per sequence were used (in sense orientation for annotated sequences).
Project description:A gilthead sea bream (Sparus aurata) microarray platform was developed to identify brain gene expression profiles in response to environmental concentrations of human pharmaceuticals.
