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All of the following are advantages of array-CGH except? - CORRECT ANSWER: The
use of metaphase chromosomes.
DAPI is a _______ counterstain. - CORRECT ANSWER: Blue.
Formamide is used in the FISH procedure for which of the following purposes? -
CORRECT ANSWER: To lower the DNA melting point.
How do we artificially age FISH slides less than 2 weeks old? - CORRECT ANSWER:
2xSSC (pH 7.0) at 37 degrees C for 30mins, and dehydration in 70%, 85%, and 100%
ethanol at 2mins each at room temp.
How do we co-denature? - CORRECT ANSWER: Place probe on slide, add coverslip,
seal with rubber cement and place in hybrite.
How do we conduct aCGH testing? - CORRECT ANSWER: Extract DNA, label sample
with Cy5 (red) and reference with Cy3 (green), and co-hybridize on slide.
How do we denature slides? - CORRECT ANSWER: 72 degrees C for 2mins in 70%
formamide/2xSSC (pH 7.0).
How do we denature the probe? - CORRECT ANSWER: 72 degrees C for 5mins before
use, then place on ice.
, How do we interpret a gain or loss in aCGH? - CORRECT ANSWER: When the log2 is
ratio is greater than 1 there is a gain, and when the log2 ratio is less than -1 there is a
loss.
How do we pretreat chromosome preps? - CORRECT ANSWER: Typically with
methanol/acetic acid treatment, but if cytoplasm persists then we can use an acid wash
or proteinase K.
How do we pretreat non-chromosome preps? - CORRECT ANSWER: 1:1 glacial acetic
acid/methanol for 2mins in one jar and 1:1 glacial acetic acid/methanol for 5mins in
another jar.
How do we store FISH slides? - CORRECT ANSWER: -20 degrees C for up to 6
months or -80 degrees C for up to a year.
How do we validate probes? - CORRECT ANSWER: By probing metaphases from both
known positive and negative samples, and analyzing at least 5 metaphases per sample.
How do we wash slides? - CORRECT ANSWER: 2mins at 72 degrees C in various
concentrations of SSC (0.25 to 2x)
How do you correct cross hybridization and high background? - CORRECT ANSWER:
Increase stringency when re probing.
How does BAC array compare to oligo array? - CORRECT ANSWER: BAC array has
lower resolution and lower probe specificity.
How long does hybridization in aCGH last? - CORRECT ANSWER: 8-48hrs
How many interphase cells need to be scored in FISH analysis? - CORRECT ANSWER:
200-500 cells.