title: NimbleGen Plasmodium falciparum 385K tiling expression array [2007-05-16_Pfal_DS_Tiling; gene-level]
status: Public on Jul 01 2014
contact.city: Seattle
contact.first: Robert
contact.middle: D
contact.last: Morrison
contact.email: bob.morrison@cidresearch.org
contact.state: WA
contact.address: 307 Westlake Ave N
contact.country: USA
contact.institute: Center for Infectious Disease Research
organism: Plasmodium falciparum
description: NimbleGen design name:  2007-05-16_Pfal_DS_Tiling
  NimbleGen design ID: 5713
  
  A high coverage expression design tiling the entire genome of P.falciparum (PlasmoDB v5.2),  with 386,222 perfect match probes (probe length 50-75bp, spaced every 60-85bp along genome).  The design includes random GC and other control probes.
  The Platform data table reflects a complete remapping of the original probe sequences to the recent genomic resequencing and reannotation of P. falciparum by GeneDB (Mar 1, 2013,  PlasmoDB version 9.2).  The original .ndf and .pos files are linked below as supplementary files.
  
  native array description file: 2007-05-16_Pfal_DS_Tiling.ndf
  native array description file: 2007-05-16_Pfal_DS_Tiling.pos
  native array description file: 2007-05-16_Pfal_DS_Tiling.ProbeMap.txt
  
  2007-05-16_Pfal_DS_Tiling.ProbeMap.txt contains the following columns;
  
  PROBE_ID: unique identifier for each probe on the array, identical to PROBE_ID in the original .ndf file
  SEQ_ID: chromosome identifier of the remapped probe location, in new GeneDB/PlasmoDB notation
  POSITION: starting coordinate (base 1) of remapped probe location on the chromosome's forward strand
  END: ending coordinate (base 1) of remapped probe location on the chromosome's forward strand
  MATCH: Blast match result from best alignment of original probe sequence to the new re-sequenced genome
  E_VALUE: Blast E value from best alignment of original probe sequence to the new re-sequenced genome
  GENE_ID: gene identifier of the annotation locus the probe falls inside of.  Intergenic spaces between genes are assinged a unique numbered identifier containing the flag '(ng)'
  EXON_ID: gene identifier of the coding exon the probe falls inside of.  Probes landing outside of coding exons will have a blank ExonID.  All probes with the same ExonID are averaged to get a single gene expression value.
manufacture_protocol: High-density DNA array prepared with Maskless Array Synthesizer (MAS) technology. See manufacturer's website at http://www.nimblegen.com/.