title: Agilent-017743 Physcomitrella patens agilent microarrays
status: Public on Jul 29 2013
contact.city: Sheffield
contact.first: Martin-Timothy
contact.last: O'Donoghue
contact.address: Western Bank
contact.department: Department of Animal and Plant Sciences
contact.country: United Kingdom
contact.institute: University of Sheffield
organism: Physcomitrium patens
manufacture_protocol: Microarrays were manufactured according to Agilent protocols. The Physcomitrella array was designed to maximize genome coverage.  The transcripts from the JGI assembly version 1.1 were used (see http://genome.jgi-psf.org/physcomitrella/physcomitrella.download.ftp.html) as input.  There are 35,939 filtered transcripts (combination of predicted models and based on EST evidence) identified from the genome assembly.  The annotations can be downloaded from the JGI web site.  Of the ~36K transcripts probes were designed for 31K; the remaining 4K are either redundant (>99% identical) or composed of low-complexity (simple repeats, poly Q, etc.; probably not real transcripts as they do not produce a meaningful translation) sequences so no high quality probes can be designed.  The array format of the Physcomitrella patens array is a 4 x 44K, and the actual number of user defined probes is 41,384 (the other probes are used for QC). Therefore, the manufacturer repeated a subset of 31K (picked at random) to fill out the 41, 384 probe real estate. This microarray was commissioned by the Ralph Quatrano group (Washingtom University) and they gave us permission to use this microarray in our study.