Functional Genomics

Question 1

What do functional genomics experiments do?

Answer 1

Describes gene functions and interactions

Question 2

What are the steps for using microarrays?

Answer 2

• extract RNA
• microarray is a glass/silicone plate where molecules can be bound to it
• RNA converted to cDNA bcs it is more stable than DNA.
• fluorescent labels added, RNA and chip are added and bound.

Question 3

How does illumia sequencing work?

Answer 3

an adaptor binds to slide surface containing our DNA and adds one base pair each time to gnerate a fluorescent signal.

Question 4

How does RNA sequencing work?

Answer 4

1. use extra cellular RNA
2. get rid of the ribosomal RNA by Poly-A selection using a magnet
3. fragment the RNA by heating it
4. turn fragments of mRNA by copied of DNA through reverse transcription to give the first stand of DNA
5. mRNA is degraded and another replication occurs to give ds cDNA to make the sequencing library
6. the sequencing adapters are bound to cDNA

Question 5

What are the steps for ChIP-seq?

Answer 5

1. cross-link proteins to DNA
2. isolated DNA and shear
3. immunoprecipitate protein of intrest
4. reverse cross-linking
5. purify DNA
6. sequence

Question 6

What is the role of ATAC-sequence?

Answer 6

tells you the openness of the DNA

Question 7

What does ATAC-sequence rely on to work?

Answer 7

transposase Tn5

Question 8

What does Bisulphite sequencing/treatment determine?

Answer 8

determines the methylation state of DNA

Question 9

In regards to Bisulphite sequencing/treatment. how can we tell if DNA is/isn’t methylated?

Answer 9

• methylated cytosine = doesn’t turn into thymine
• unmethylated cytosine = turns into thymine