title: [FDA-LMON_expr] Affymetrix  Listeria GeneChip
status: Public on Apr 16 2014
contact.city: Laurel
contact.first: Atin
contact.last: Datta
contact.email: atin.datta@fda.hhs.gov
contact.state: MD
contact.address: 8301 Muirkirk Rd
contact.department: CFSAN/DVA
contact.country: USA
contact.institute: FDA
organism: Listeria monocytogenes
description: PMID 22457724
  As this microarray includes sequences are from 24 different genomes, each design location refers a genome location.
  For example, "Lm FSL F2-515" is sequence from L. monocytogenes strain FSL F2-515 and ID indicates the name of the probe set for the corresponding locus/ORF. Description is the basic annotation, though some may have been updated since the array was designed.
  The SPOT_ID refers to the ORF/locus_ID or intergenic region (denoted by an IG at the start) examined.
  All of the 24 genome sequences were pulled from NCBI. The locus tags for sequences from 15 genomes {CLIP81459 (eg. Lm4b_00380), HCC23, EGD-e (eg. LMHCC_0003), F2365 (eg. LMOf2365_0022), FSL J1-194 (eg. LMBG_01616), FSL J2-071 (eg. LMFG_01366), FSL N3-165 (eg. LMIG_00640), FSL R2-503 (eg. LMJG_02388), FSL R2-561 (eg. LMKG_00998), F6900 (eg. LMMG_03051), F6854 (eg. LMOf6854_0326), H7858 (eg. LMOh7858_0217), J2818 (LMPG_02290), 10403S (LMRG_00152), and HPB2262 (eg. LMSG_00007)} work readily in the GenBank system.
  The remaining genomes were sequenced at the Broad Institute and the data can be found at http://www.broadinstitute.org/annotation/genome/listeria_group/MultiHome.html. For three of them, the annotation is searchable best at the Broad using the locus tags. They are FSL N1-017 (eg. LMHG_00112 which is now LMHG_10112), Finland 1988 (eg. LML_00218) and J0161 (eg. LMOG_00878). These annotations have been changed in some cases as the Broad Institute has updated some of their data.
  Indeed, for these 18 genomes some of the annotations may have changed as sequencing was completed or otherwise modified by the sequencing facility since the microarray was originally designed. For this reason, we've provided GenBank accession numbers along with the corresponding nucleotide base locations, formatted as described below.
  However, six of the genomes (FSL F2-515, FSL J1-175, FSL J1-208, FSL J2-003, FSL J2-064 and LO28) haven't been annotated by the Broad Institute. We performed an auto-annotation on those sequences and assigned locus tags based on the first four letters of their accession numbers.
  The sequences for these targets can be identified as follows. For example, AARI_0004, we've provided the GenBank accession number for the strain AARI02000001 followed by ':4318-5304' (eg. AARI02000001:4318-5304). These latter numbers indicate the nucleotide sequence location corresponding to the ORF for which the probe sets were designed.
  Finally, some of the strains had closed genome sequences which were used to identify intergenic regions. These loci are indicated by an "IG" in front of the strain's standard call letters. For example, an intergenic region from L. monocytogenes F2365 is IGLMOf2365_0003. The sequences for these loci can be identified as with the previous group. In the example IGLMOf2365_0003 can be found using AE017262:3014-3120 to look up the AE017262 accession and nucleotides 3014-3120.
manufacture_protocol: Affymetrix builds the oligonucleotides in situ via photolithography. The Listeria expression/genotyping microarray was designed to represent 64,539 annotated gene sequences from 24 sequenced strains of L. monocytogenes. The expression array consists of 253,361 25-mer oligonucleotides that represent a total of 18,630 probe sets including 45 AFFY controls, 4,481 intergenic regions and 14,104 genes. Each probe set contains approximately 28 oligonucleotide probes; up to 14 perfect match (PM) probes and 14 mismatch probes (MM). Mismatch probes are identical to the perfect match probe with the exception of a one nucleotide (nt) mismatch located at the 13th (middle) position of the oligo nucleotide sequence.