Next generation transcriptomics: a practical approach

Question 1

What’s the difference between transcriptomics and exomics?

Answer 1

Transcriptomics: All RNA is assayed.

Exomics: All exons are assayed.

Question 2

Why can’t you find new transcripts using microarrays?

Answer 2

The probes which are anchored to each well derive from known sequences.

Question 3

In short, describe RNAseq.

Answer 3

1. Purify RNA
2. Fragment RNA
3. Generate cDNA
4. Add adapters to cDNA
5. Paired-end reads are generated.

Question 4

Watch the video on RNAseq.

Answer 4

Do it feller.

Question 5

When doing RNAseq, what result do you want to attain (raw data)?

Answer 5

You want to find the relative molar concentration of RNA in the cell.

In order to find the absolute numbers, you need to add standards.

Question 6

What does “differential gene expression” mean?

Answer 6

The differential gene expression is the change in gene transcription.

False positives are tended to by the boneferoni method: You find the p-value required for any amount of false positives (ex 0.05).

Question 7

What’s the gene onthology?

Answer 7

The egene ontology (GO) describes our knowledge of a gene with regards to:
1. Function
2. Molecular activity

ex: gene X and Y are grouped together because they both participlate in TCA cycle.

Question 8

What’s one major benefit of RNAseq compared to microarrays?

Answer 8

RNAseq can be used to find novel sequences (you sequence RNA pair-endedly).

Question 9

Can you find allele-specific expression using RNAseq?

Answer 9

Yes. You sequence all the thangs.