title: Plant Viroid Detection Microarray
status: Public on Dec 31 2013
contact.city: Beijing
contact.first: Yongjiang
contact.last: Zhang
contact.email: zhangyjpvi@yeah.net
contact.country: China
contact.institute: Chinese Academy of Inspection and Quarantine
organism: Hostuviroid
  Pospiviroid
  Cocadviroid
  Apscaviroid
  Coleviroid
  Avsunviroid
  Pelamoviroid
  Elaviroid
description: This microarray platform is designed to detect plant viroids infection at the genus level. It is able to detect a wide spectrum of all the 8 reported viroid genera, including 37 known plant viroid species.
manufacture_protocol: Microarrays were synthesized using 40-mer probes on 75-mm×25-mm glass slides using the SmartArrayer system. All probes were spotted in triplicate on the microarray. Several control probes were used to monitor the performance of the microarray. (i) The 5' amino-linker oligonucleotide (5'-TTTTTTTTTTTTTTTCTCATGCCCATGCCGATGC-3') was a random sequence which did not hybridize with any viroid sequences. The targeting sequence of this probe was mixed with the samples before hybridization. This probe was used as a positive control (PC) monitoring the probe hybridization efficiency. (ii) The internal control (HEX) was spotted on the microarray to monitor the probes linking to the chips. It was a 5' Hex-linker oligonucleotide (5'-GTCACATGCGATGGATCGAGCTCCTTTATCATCGTTCCCACCTTAATGCA-3').(iii) The spotting buffer was used as the negative control (NC). Spotted slides were air dried for 10 min and then fixed by UV exposure at 240mJ/cm2. After being incubated in a 0.5% sodium dodecyl sulfate solution at 60oC for an hour, slides were rinsed in 100 mM Tris (pH 8.0) for 5 min, and kept moist at 4oC for use.