Chip assembly with public ESTs and 454 runs from Verjo Lab
Please note that Schistosoma mansoni is not a model organism, thus the gene information used in databases and literatures consists in Smp_XXXXXX to protein coding genes as in Ensembl database http://metazoa.ensembl.org/Schistosoma_mansoni/Info/Index
The custom designed microarray contains 60-mer probes, of which 4,854 are Agilent control probes and 176,026 non-control probes designed to detect Schistosoma mansoni expressed transcripts. All publicly available transcript information for S. mansoni were used in the design of probes, namely 260,035 ESTs available in dbEST database (downloaded in 2010), high-throughput RNA-seq sequences from 454 Roche sequencing obtained in our laboratory (doi:10.1016/j.exppara.2011.06.010) and gene predictions from the Wellcome Trust Sanger Institute. We annotated the probes with the latest S. mansoni gene predictions from genome version ASM23792v2 available in the Ensembl Metazoa database, allowing the identification of unique probes to 9,255 Smp genes and probes to 9,079 transcripts eventually generated from the genomic strand opposite to Smp genes, noting that the Agilent cRNA labeling technology is strand specific.
Arrays of this design have barcodes that begin with 16033004 or 2533004.
Orientation: Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.
The ID column represents the Agilent Feature Extraction feature number.
Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).
To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.
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