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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.