BCH5413 Exam 3 Assessment Test Tested
A+ Questions and Answers Verified
Solutions Latest Update 2026/2027
Question:
delta-delta Ct method.
Answer:
[delta-Ct(treated sample)] - [delta-Ct(control sample)]
Question:
delta-Ct.
Answer:
Ct(gene) - Ct(endogenous control)
Question:
RT-PCR: semi-quantitative v. quantitative.
Answer:
Semi- quantitative
- "regular"
Quantitative
- graphing the RT-PCR
- is a form of analysis of data
Question:
Measuring changes in gene expression
- using RT-PCR v. Northern blot.
Answer:
,Northern blot
- in example, took up to 2 months
RT-PCR
- in example, took up to 2 days
Question:
Microarray analysis
- allows you to....
Answer:
measure amounts of a nucleic acid species, not one at a time on a Northern blot or RT-PCR, but
every expressed gene in a cell at one time
Question:
Two different microarray's.
Answer:
cDNA and oligonucleotide
Question:
Microarrays: RNA isolation
- RNA must be....
Answer:
- RNA must be high quality, free of
DNA/contamination (A260/280 ratio; should be above 1.5)
Question:
Microarrays: RNA isolation
- techniques.
Answer:
Clontech column-based
- start with sample
- homogenize, centrifuge, filter
- wash column and collect purified RNA
,Invitrogen TRizol reagent
- homogenize sample in TRizole
- phase separation
- RNA precipitation
- wash and solubilize RNA
- degrade any genomic DNA that came through purification steps
Question:
cDNA Microarrays
- steps.
Answer:
- glass slide arrays are usually probed with
fluorescent cDNA
- by using two different color dyes (red and green), each RNA serves
as its own control
- if the spot is red, one probe is more abundant
- if the spot is green, the other probe is more abundant
- if the spot is yellow, then the two probes are equally abundant
Microarrays:
Question:
cDNA Microarrays
- colored dyes and steps.
Answer:
- cDNA reverse transcribed from
mRNA and labeled with a fluorescent dye
- the control sample without serum has green dye
- treated sample with serum has red dye
- both were mixed and incubated with microarray
- microarray washed
- fluorescence measured on chip
Question:
, cDNA Microarrays
- if a spot is green, expression is...
- if a spot is red, expression is....
Answer:
- if a spot is green,
expression of that gene decreases in cells after serum addition
- if a spot is red, expression of that gene increases in cells after
serum addition
Question:
cDNA Microarrays
- what each colored dye means.
Answer:
- Red = gene expression
increased
- Green = gene expression decreased
- Yellow = no change (expression equal)
- Blue/Black = low to no expression
Question:
Oligonucleotide Microarrays: Affymetrix GeneChip
- what is it/how it works.
Answer:
- short oligonucleotides are
synthesized on a silicon chip, using the same kind of photolithography process used to make
microprocessors
- About 15-20 match and mismatch oligos are made for each gene to
be probed; each oligo is 20nt in length
Question:
Labeling your target for GeneChip/oligonucleotide analysis
- steps.
Answer:
A+ Questions and Answers Verified
Solutions Latest Update 2026/2027
Question:
delta-delta Ct method.
Answer:
[delta-Ct(treated sample)] - [delta-Ct(control sample)]
Question:
delta-Ct.
Answer:
Ct(gene) - Ct(endogenous control)
Question:
RT-PCR: semi-quantitative v. quantitative.
Answer:
Semi- quantitative
- "regular"
Quantitative
- graphing the RT-PCR
- is a form of analysis of data
Question:
Measuring changes in gene expression
- using RT-PCR v. Northern blot.
Answer:
,Northern blot
- in example, took up to 2 months
RT-PCR
- in example, took up to 2 days
Question:
Microarray analysis
- allows you to....
Answer:
measure amounts of a nucleic acid species, not one at a time on a Northern blot or RT-PCR, but
every expressed gene in a cell at one time
Question:
Two different microarray's.
Answer:
cDNA and oligonucleotide
Question:
Microarrays: RNA isolation
- RNA must be....
Answer:
- RNA must be high quality, free of
DNA/contamination (A260/280 ratio; should be above 1.5)
Question:
Microarrays: RNA isolation
- techniques.
Answer:
Clontech column-based
- start with sample
- homogenize, centrifuge, filter
- wash column and collect purified RNA
,Invitrogen TRizol reagent
- homogenize sample in TRizole
- phase separation
- RNA precipitation
- wash and solubilize RNA
- degrade any genomic DNA that came through purification steps
Question:
cDNA Microarrays
- steps.
Answer:
- glass slide arrays are usually probed with
fluorescent cDNA
- by using two different color dyes (red and green), each RNA serves
as its own control
- if the spot is red, one probe is more abundant
- if the spot is green, the other probe is more abundant
- if the spot is yellow, then the two probes are equally abundant
Microarrays:
Question:
cDNA Microarrays
- colored dyes and steps.
Answer:
- cDNA reverse transcribed from
mRNA and labeled with a fluorescent dye
- the control sample without serum has green dye
- treated sample with serum has red dye
- both were mixed and incubated with microarray
- microarray washed
- fluorescence measured on chip
Question:
, cDNA Microarrays
- if a spot is green, expression is...
- if a spot is red, expression is....
Answer:
- if a spot is green,
expression of that gene decreases in cells after serum addition
- if a spot is red, expression of that gene increases in cells after
serum addition
Question:
cDNA Microarrays
- what each colored dye means.
Answer:
- Red = gene expression
increased
- Green = gene expression decreased
- Yellow = no change (expression equal)
- Blue/Black = low to no expression
Question:
Oligonucleotide Microarrays: Affymetrix GeneChip
- what is it/how it works.
Answer:
- short oligonucleotides are
synthesized on a silicon chip, using the same kind of photolithography process used to make
microprocessors
- About 15-20 match and mismatch oligos are made for each gene to
be probed; each oligo is 20nt in length
Question:
Labeling your target for GeneChip/oligonucleotide analysis
- steps.
Answer:
