title: NimbleGen Pseudomonas putida  KT2440 12x135k
status: Public on Dec 22 2013
contact.city: Kgs Lyngby
contact.first: Gamze
contact.last: Gulez
contact.email: gamzegulez@gmail.com
contact.address: Miljoevej 113
contact.department: Environmental Engineering
contact.country: Denmark
contact.institute: Technical University of Denmark
organism: Pseudomonas putida KT2440
description: Custom 12x135k expression and tiling design for Pseudomonas putida KT2440 genome (AE015451) and plasmid pWW0 (AJ344068)
  The expression probes were selected as follows:   Sequence and annotation for both accession numbers were downloaded from NCBI on January 18th, 2012. 5350 CDS features were extracted from AE015451 and 140 CDS features were extracted from AJ344068. The sequence IDs (SEQ_ID) for the AJ344068 include PWW0.   45-60mer probes were selected from the entire length of the 5490 CDS sequences. 6 probes were selected for 5440 sequences. 50 sequences share all 6 probes with another sequence and are represented on the array by exemplars. All 32640 expression probes were added to container EXPRESSION.      The tiling probes were selected as follows:   Probes were selected for AE015451 and AJ344068 using a median probe spacing of 1 probe starting every 58 base pairs (interval=43, window=15). Unique probes were used (mm=1). Every other probe was reverse complemented to generate reverse strand probes. 52434 forward strand probes were added to container FORWARD. 52434 reverse strand probes were added to container REVERSE.       The remainder of the array was filled with randomly generated probes of comparable length and composition.
  120123_Pput_LG_til_exp_HX12.ncd
  120123_Pput_LG_til_exp.ndf
  120123_Pput_LG_til_exp_HX12
manufacture_protocol: Array prepared using Maskless Array Synthesizer (MAS). For more information  www.nimblegen.com