Probes/TargetsDNA Arrays

...Probes: are the tethered nucleic acids with known sequence,

– the DNA on the chip,

...Target: is the free nucleic acid sample whose identity/abundance is being detected,

– the labeled nucleic acid that is washed over the chip.

Figure 1d

Figure 1a, DNA Chip Figure 1b, DNA Microarray

Probe?

Target?

Oligos

Yeast Transcripts Under Two Conditions.

Probe? cDNAs

Signal to Noise, Data?

• Establish noise levels,

• Detect single colors alone to determine expression yes/no questions.

• Compare ratios of red to green to establish relative expression levels.

Hybridization Detection

…fluorescent images are read by an optical scanner, and intensities are compared using algorithms to differentiate artifacts.

Figure 2

Fig. 3

Figure 4

Figure 5

Figure 6

Probe?

Target?

Adult retina cDNA library wt mice?

cDNA libraries from Crx+/+ and Crx-/-10 day postnatal mice.

Control #1

...one cDNA library,

...split, 1/2 Cy3, 1/2 Cy5,

... + 1/1 correlation between signals.

Control #2

...one brain polyA-mRNA,

...two reverse transcriptases,

...one labeled with Cy3, one with Cy5,

... + 1/1 correlation between signals.

Replicates #1 and #2

... targets Crx+/+ and Crx-/-10 day postnatal mice.,

...two reverse transcriptases,

...one labeled with Cy3, one with Cy5,

... + 1/1 correlation between signals.

Replicate #1

... targets Crx+/+ and Crx-/- 10 day postnatal mice,

... some points fall off of the + 1/1 regression.

...high on the Cy5 side.

Table #1

Figure #3

• Northern Blot,– RNA on substrate,– probed with “hot DNA”.

Table #2

What does this mean?

Does it really?

Figure #4

Probe?

Target (a.)?

Adult retina cDNA library wt mice?

adult mouse retinaprenatal mouse retina

Target (b.)?

adult retinaadult brain

Figure #5

• (a) spot 501, (b) spot 140, (c) calcium channel (Crx+/+), (d) (c) calcium channel (Crx-/-).

Figure #6