2nd generation of Schmidtea med. array, incporporating more recent view of transcriptome. Contains new probes and some probes from smed_v1. Arrays of this design have barcodes that begin with 16033226 or 2533226. 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.
The array was designed in 2011 using ArrayOligoSelector (Bozdech et al. 2003) and any available sequence that might represent a flatworm transcript as a design target. The Accession String column contains legacy information about the source of each sequence. The "supported" and "unsupported? entries denote Maker gene predictions (Canterel et al., 2008; Robb et al.,2008) with or without EST support, respectively. The "blythe", "blythe_rajewski", and "rajewski" entries denote sequences from Martin Blythe (Blythe et al., 2010) or Nikolaus Rajewsky (Adamidi et al., 2011) obtained prior to publication. Entries marked "contigs", "smed_20110214", or "sanchez" denote sequences or assemblies curated in the Sanchez lab. For ids ending in 1 or 3 sets of digits separated by an underscore, the last set of digits represents the distance between the 3' end of design target and the 70-mer oligo probe.
Adamidi C, Wang Y, Gruen D, Mastrobuoni G, You X, Tolle D, Dodt M,Mackowiak SD, Gogol-Doering A, Oenal P, Rybak A, Ross E, Sanchez Alvarado A, Kempa S, Dieterich C, Rajewsky N, Chen W. (2011) De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics. Genome Res. 2011 21(7):1193-200. PMID: 21536722
Bozdech Z, Zhu J, Joachimiak MP, Cohen FE, Pulliam B, DeRisi JL. (2003). Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. Genome Biol. 4(2):R9.PMID: 12620119
Blythe MJ, Kao D, Malla S, Rowsell J, Wilson R, Evans D, Jowett J, Hall A, Lemay V, Lam S, Aboobaker AA. (2010) A dual platform approach to transcript discovery for the planarian Schmidtea mediterranea to establish RNAseq for stem cell and regeneration biology. PLoS One. 2010 5(12):e15617. PMID: 21179477
Cantarel BL, Korf I, Robb SM, Parra G, Ross E, et al. (2008) MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res 18: 188-196. PMID: 18025269
Robb SM, Ross E, Sanchez Alvarado A (2008) SmedGD: the Schmidtea mediterranea genome database. Nucleic Acids Res 36: D599-606. PMID: 17881371
Less...
More...