title: HPI-AG KSHV 15k v. 3.0
status: Public on Jun 06 2010
contact.city: Hamburg
contact.first: Thomas
contact.last: Guenther
contact.email: thomas.guenther@hpi.uni-hamburg.de
contact.address: Martinistr.52
contact.department: Mechanisms of Antiviral Defense
contact.country: Germany
contact.institute: Heinrich-Pette-Institut
organism: Human gammaherpesvirus 8
manufacture_protocol: Custom high-resolution KSHV microarrays were designed by shifting a sequence window of 60 nt. across both strands of the prototypic type P KSHV sequence (NC_009333) and the terminal repeat unit (KSU86666). Probes with a length between 45 and 60 nucleotides were selected from these windows such that their melting temperature was close to the optimal Tm of  80°C. To also ensure complete coverage of type M KSHV strains, the resulting probesets were aligned to the type M reference sequence (genbank accession NC_003409) and additional probes were designed in an identical manner for all regions which were not already covered by the original probeset. The length of all probes was subsequently adjusted to 60 nucleotides using sequences from a common linker (ATAACCGACGCCTAA), and each probe was synthesized in duplicate on Agilent 8x15k custom microarrays. For normalization purposes, the array also contains probesets which were generated in an identical manner to cover the adenovirus type 5 genome (AY339865) as well as the pCR2.1 plasmid (Invitrogen).