Download - Probes/Targets DNA Arrays
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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.
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Figure 1d
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Figure 1a, DNA Chip Figure 1b, DNA Microarray
Probe?
Target?
Oligos
Yeast Transcripts Under Two Conditions.
Probe? cDNAs
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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.
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Hybridization Detection
…fluorescent images are read by an optical scanner, and intensities are compared using algorithms to differentiate artifacts.
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Figure 2
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Fig. 3
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Figure 4
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Figure 5
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Figure 6
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Probe?
Target?
Adult retina cDNA library wt mice?
cDNA libraries from Crx+/+ and Crx-/-10 day postnatal mice.
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Control #1
...one cDNA library,
...split, 1/2 Cy3, 1/2 Cy5,
... + 1/1 correlation between signals.
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Control #2
...one brain polyA-mRNA,
...two reverse transcriptases,
...one labeled with Cy3, one with Cy5,
... + 1/1 correlation between signals.
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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.
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Replicate #1
... targets Crx+/+ and Crx-/- 10 day postnatal mice,
... some points fall off of the + 1/1 regression.
...high on the Cy5 side.
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Table #1
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Figure #3
• Northern Blot,– RNA on substrate,– probed with “hot DNA”.
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Table #2
What does this mean?
Does it really?
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Figure #4
Probe?
Target (a.)?
Adult retina cDNA library wt mice?
adult mouse retinaprenatal mouse retina
Target (b.)?
adult retinaadult brain
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Figure #5
• (a) spot 501, (b) spot 140, (c) calcium channel (Crx+/+), (d) (c) calcium channel (Crx-/-).
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Figure #6