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Starting with normal and cancer intact cells as well as the preparation of the DNA microarray chip, explain in detail how the typical DNA microarray experiment will be performed in order to identify differentially expressed genes. What are the types of probes that can be used for this experiment, and how are they different? Explain how the data will be interpreted.

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Sixta Kovacek
Sixta KovacekLv2
18 Apr 2018

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Related questions

BIOTECHNOLOGY!!!

1. A DNA microarray is used to quantify mRNA levels. Why is itcalled DNA microarray then, instead of RNA microarray?

2. What is the advantage of DNA microarrays over other methodsto study gene transcription?

3. In this particular experiment, what was the objective of theDNA microarray experiment?

4. In part 3 (isolate mRNA), how were mRNAs separated from tRNAsand rRNAs? What were on the beads? What unique property of mRNAsenabled its separation from tRNAs and rRNAs?

5. In part 4 (make labeled DNA copy), briefly describe howlabeled cDNAs were generated. Practice using technical terms thatyou’ve encountered in your professor’s highly informative lectures.Describe the primers and enzymes that were used. Explain the reasonfor the choice of primer/s. Explain what the “special enzyme”does.

6. Parts 5 and 6. What do the colors red, yellow, and greenrepresent? What do the dark spots mean?

7. Part 7. If you’re a researcher developing a drug to shut offgenes that are expressed mostly in cancer cells, will you try toturn off genes that showed up green, red, or yellow? 8. Give tworeasons or examples as to why DNA microarray experiments don’talways identify all genes that have “gone bad”. Answers arementioned in the interactive.

lex A is an E. coli gene whose product regulates thetranscription of certain target

genes that are located at different positions in the bacterialchromosome.

Identified target genes appear to be involved in DNA repair andrecombination.

Under normal conditions, the LexA protein binds near andrepresses

transcription of target genes; however, when the cellexperiences significant

DNA damage caused by environmental mutagens, the LexA proteinis

inactivated and transcription of the target genes occurs. Yourresearch objective

is to identify all of the target genes repressed by the LexAprotein. (Assume that

you have access to a DNA microarray consisting of sequencesrepresenting each

of the genes in the E. coli genome.) As the starting point foryour work, you

isolate a lexA mutant strain that produces no functional LexAprotein.

a) Briefly describe an experiment that uses a functionalgenomics approach to identify all

of the LexA target genes.

b) Give the basic steps of the experiment and show how it

would allow you to achieve your objective

Please answer the following multiple-part question regarding probe synthesis and nucleic acid hybridization:

a) You would like to determine how many genes are expressed in the normal hepatocytes (liver parenchymal cells) of a healthy person and the hepatocytes of an alcoholic. Which of the following blots would you utilize and how many hybridization experiments you must perform to complete the experiment?

A. A Sothern blot (membrane-based)/two

B. A Northern blot (membrane-based)/one

C. A microarray/two

D. A gene chip/one

b) Of the two genes, one has a sequence of 5’CCCAUUUGG3’ and another has the sequence 5’CCCAAUUGG3’. You want to distinguish the two genes by Southern blot hybridization. Which of the following parameters you may not have to control?

A. The membrane to be used (nylon membrane versus PVDF membrane)

B. Detergent (i.e. SDS) concentration in the hybridization buffer

C. Presence of non-specific DNA in the hybridization buffer

D. Temperature of the hybridization buffer

c) Solid-phase hybridization is different from solution hybridization because of all these, except______.

A. the former uses probes, the later do not

B. the later may use enzymes, the former don’t

C. the former uses membrane, the later don’t

D. the former immobilize nucleic acids, the later don’t

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