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 | Â | Â | Â | Â | Â |
nuclear coding genes (3' biased)2 | 8,058 | 11 | Â | 88,638 | 39.12% |
nuclear non-coding genes | 22 | 20 | Â | 440 | 0.19% |
apicoplast organellar genome (nt) | 34,997 | Â | 25 | 1,400 | 0.62% |
mitochondrial organellar genome (nt) | 6,071 | Â | 25 | 243 | 0.11% |
all exons (chr Ib only)3 | 1,080 | 6 | Â | 6,480 | 2.86% |
all introns (chr Ib only) | 1,080 | 5 | Â | 5,400 | 2.38% |
antisense probes (opposite CDS; chr Ib only) | 227 | 20 | Â | 4,540 | 2.00% |
Gene Discovery | Â | Â | Â | Â | Â |
ESTs without predicted gene models (nt) | 830,867 | Â | 35 | 23,739 | 10.48% |
ORFs with BLASTX or TBLASTN hits (nt) | 1,263,357 | Â | 35 | 36,096 | 15.93% |
Expression Profiling (host species) | Â | Â | Â | Â | Â |
human (immune response & housekeeping)4 | 301 | 11 | Â | 3,311 | 1.46% |
mouse (immune response & housekeeping)4 | 291 | 11 | Â | 3,201 | 1.41% |
cat (housekeeping genes) | 12 | Â | 30 | 360 | 0.16% |
Genotyping | Â | Â | Â | Â | Â |
T. gondii genetic markers | 228 | 40 | Â | 9,120 | 4.02% |
SNPs inferred from T. gondii ESTs, etc | 3,490 | 4 | Â | 13,960 | 6.16% |
P. falciparum genetic markers | 1,985 | 4 | Â | 7,940 | 3.50% |
Other Analyses | Â | Â | Â | Â | Â |
SFP discovery on 24 selected genes5 | 23,110 | Â | 2 | 11,555 | 5.10% |
promoters (for ChIP) on 12 selected genes6 | 12,000 | Â | 10 | 1,200 | 0.53% |
Controls | Â | Â | Â | Â | Â |
commonly used transgene reporters7 | 39 | 11 | Â | 429 | 0.19% |
human & mouse normalization probes | Â | Â | Â | 2,200 | 0.97% |
yeast (housekeeping & spike-in probes) | Â | Â | Â | 839 | 0.37% |
mismatch probes (genes on chr 1b) | 227 | 11 | Â | 2,497 | 1.10% |
surrogate mismatch (background) probes | Â | Â | Â | 3,000 | 1.32% |
Total | Â | Â | Â | 226,588 | 100.00% |