title: [Sorgh-WTa520972F] Affymetrix Whole-transcriptome Sorghum Array
status: Public on Dec 31 2013
contact.city: Chicago
contact.first: Nadia
contact.last: Shakoor
contact.state: Illinois
contact.address: 10 South LaSalle Street, Suite 2100
contact.country: USA
contact.institute: Chromatin, Inc.
organism: Sorghum bicolor
  Saccharum hybrid cultivar
  Zea mays subsp. mays
description: The genechip contains 1,026,373 probes covering 149,182 exons (27,577 genes) across the Sorghum bicolor nuclear, chloroplast and mitochondrial genomes.  Specific probesets were also included for putative non-coding RNAs that may play a role in gene regulation (e.g., microRNAs), and confirmed functional small RNAs in related species (corn and sugarcane) were also included in our array design.
  The Sb01gnnnnn.n ids represent the Ensembl Transcript ids. The FRnnnn, M-sbi-miR, zma-MIRnnn, etc. are probes for small RNAs from Sorghum bicolor as well as non-Sorghum bicolor organisms (sbi=sorghum bicolor, zma=maize, ssp=sugarcane).  These were included in our microarray design as add-on probes, in case there are researchers that are interested in the expression of small RNAs.
  Briefly, the PMRD sequences (zma-MIR437f, M-sbi-miR)  were obtained at the plant microRNA database http://bioinformatics.cau.edu.cn/PMRD/.  fRNAdb (FRnnnn) sequences were obtained at the functional noncoding RNA sequence database http://www.ncrna.org/frnadb/.
manufacture_protocol: see manufacturer's web site