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Table 1 Microarray Design1.

From: A novel multifunctional oligonucleotide microarray for Toxoplasma gondii

Application (for T. gondii unless otherwise indicated) # of features probes/feature Tiling density total # probes % of chip
Expression Profiling      
nuclear coding genes (3' biased)2 8,058 11   88,638 39.12%
nuclear non-coding genes 22 20   440 0.19%
apicoplast organellar genome (nt) 34,997   25 1,400 0.62%
mitochondrial organellar genome (nt) 6,071   25 243 0.11%
all exons (chr Ib only)3 1,080 6   6,480 2.86%
all introns (chr Ib only) 1,080 5   5,400 2.38%
antisense probes (opposite CDS; chr Ib only) 227 20   4,540 2.00%
Gene Discovery      
ESTs without predicted gene models (nt) 830,867   35 23,739 10.48%
ORFs with BLASTX or TBLASTN hits (nt) 1,263,357   35 36,096 15.93%
Expression Profiling (host species)      
human (immune response & housekeeping)4 301 11   3,311 1.46%
mouse (immune response & housekeeping)4 291 11   3,201 1.41%
cat (housekeeping genes) 12   30 360 0.16%
Genotyping      
T. gondii genetic markers 228 40   9,120 4.02%
SNPs inferred from T. gondii ESTs, etc 3,490 4   13,960 6.16%
P. falciparum genetic markers 1,985 4   7,940 3.50%
Other Analyses      
SFP discovery on 24 selected genes5 23,110   2 11,555 5.10%
promoters (for ChIP) on 12 selected genes6 12,000   10 1,200 0.53%
Controls      
commonly used transgene reporters7 39 11   429 0.19%
human & mouse normalization probes     2,200 0.97%
yeast (housekeeping & spike-in probes)     839 0.37%
mismatch probes (genes on chr 1b) 227 11   2,497 1.10%
surrogate mismatch (background) probes     3,000 1.32%
Total     226,588 100.00%
  1. 1 See http://ancillary.toxodb.org/docs/Array-Tutorial.html for a detailed description, including probe sequences.
  2. 2 A small minority of the 7,793 genes are represented by more than 1 probeset, differing in the degree to which they cross hybridize, while even fewer don't have named probesets of their own as they are interragated by probesets for other genes.
  3. 3 Non-terminal exons only (terminal exons are interrogated as part of 3'-biased profiling).
  4. 4 See http://ancillary.toxodb.org/docs/HostResponse.htm for details.
  5. 5 CDS for AMA1, B1, BSR4/R, GRA3/6/7, MIC2, ROP1/16, SAG1/2/3/4, SRS1/2/9; introns from ATUB, BTUB, BAG1, UPRT. See http://ancillary.toxodb.org/docs/SNPDiscovery.htm for details.
  6. 6 BAG1, BTUB, LDH1, LDH2, SAG1, SAG2, SAG2C, DHFR-TS, MIC2, GRA1, OWP1, OWP2; see http://ancillary.toxodb.org/docs/ChIP.htm.
  7. 7 For selectable drug-resistance markers, enzyme and fluorescent protein reporters, etc; see http://ancillary.toxodb.org/docs/TransgeneReporters.seq.