title: CBCB Listeria monocytogenes 385K v1.0
status: Public on Jul 30 2009
contact.city: College Park
contact.first: Adam
contact.last: Phillippy
contact.email: amp@umiacs.umd.edu
contact.state: MD
contact.address: Biomolecular Sciences Building #296, University of Maryland
contact.department: Center for Bioinformatics and Computational Biology
contact.country: USA
contact.institute: University of Maryland
organism: Listeria monocytogenes
  Listeria monocytogenes EGD-e
  Listeria monocytogenes serotype 4b str. F2365
  Listeria monocytogenes serotype 1/2a str. F6854
  Listeria monocytogenes serotype 4b str. H7858
  Listeria monocytogenes FSL F2-515
  Listeria monocytogenes FSL J1-194
  Listeria monocytogenes FSL J1-175
  Listeria monocytogenes FSL J1-208
  Listeria monocytogenes FSL J2-003
  Listeria monocytogenes FSL J2-071
  Listeria monocytogenes FSL J2-064
  Listeria monocytogenes FSL N1-017
  Listeria monocytogenes FSL N3-165
  Listeria monocytogenes FSL R2-503
  Listeria monocytogenes F6900
  Listeria monocytogenes J0161
  Listeria monocytogenes J2818
  Listeria monocytogenes LO28
  Listeria monocytogenes 10403S
  Listeria monocytogenes HPB2262
description: This array is a Listeria monocytogenes pan-genome tiling array covering the full genomes of 20 L. monocytogenes strains. Each probe on the array may target multiple strains. Each probe may contain either zero or one mismatch to its intended genomic targets. The whole genomes of all 20 strains are tiled at an average depth of coverage of 2.65x, and the 50-mer probes are offset on average 21 bp from one another. The tiled strains by GenBank TaxID are: 265669, 267409, 267410, 393116, 393117, 393118, 393119, 393120, 393122, 393123, 393124, 393125, 393128, 393130, 393131, 393132, 393133, 401650, 393121, 169963.
  IMPORTANT: The genomic positions in the data table only represent the position on a single genome. The supplementary files contain the mapping of probes to pan-genomic positions. The columns in the supplementary "probe_mapping" file are:
  ID_REF: Probe ID. Each probe can appear in multiple rows depending on how many genomes it targets.
  GI_RANGE: Sequence GenBank GI and probe mapping location.
  RANGE_STRAND: Strand on the GI sequence the probe maps to.
  MISMATCH: Number of mismatches between probe and genomic sequence, 0 or 1.
manufacture_protocol: Nimblegen 385k CGH HD2 Array: http://www.nimblegen.com/products/lit/cgh_hd2_datasheet_2008_04_07.pdf
  Nimblegen Protocols: http://www.nimblegen.com/products/lit/cgh_userguide_v5p1.pdf