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Flashcards in MCB Lecture 24 ENCODE Deck (21)
0

What does ENCODE stand for?

Encyclopaedia of DNA elements

1

When did ENCODE occur?

1990-2003

2

What is Celera and what effect did it have on ENCODE

This is a private company that started its own project.
This accelerated the completion of the public project ENCODE

3

What were the goals of ENCODE?

1. Complete sequence
2. Identify all genes
3. Physical and genetic map
4. Detailed annotation

4

What is important about Sanger sequencing?

This was used to carry out the ENCODE project

5

Describe the process of Sanger sequencing

1. Single stranded DNA, primers, DNA pol, dNTP and ddNTP are combined
2. The DNA pol elongates the complimentary DNA strand
3. Every so often, a ddNTP will be added in, and no more nucleotides may be added because there is no hydroxyl group on the 3' carbon
4. This creates DNA fragments of many different lengths
5. The fragments are run on a gel that resolves down to differences of one nucleotide
6a. Read manually 6b. Automated reading

6

What was the important technical advance with Sanger sequencing that allowed the ENCODE project to occur?

Automated sequencing

7

Describe the change in cost of Sanger sequencing over the years

Reduced in cost
Before: $1 per base
Now: thousands

8

How many bases can Sanger sequencing do per run?

800-1000

9

What are 5 new generation sequencing techniques?

Illumina
454
Ion torrent
ChIP seq
RNA seq

10

Describe Illumina

Imaging detects different colours associated with the different nucleotides

11

Describe 454 sequencing

Fluoretic chambers containing DNA
Detect the length of nucleotides added

12

Describe Ion torrent sequencing

When a nucleotide is added, a proton is given off
This is detected by a very sensitive pH monitor

13

Describe ChIP Seq

Sonic action of the DNA to break it up
Specific proteins bound to DNA are selected out
The protein is degraded.
We now have DNA that is associated with a certain protein
Sequence this DNA

This allows us to determine activity of different bits of DNA at different points in time in different tissues

14

Describe RNA seq

RNAs synthesised from DNA are sequenced

This tells us about transcribed regions in different tissues at different times

15

When did the next generation techniques arise?

After the end of the ENCODE project, 2003

16

What is good about the next generation sequencing techniques

Cheaper
Faster
Quicker

17

Describe 3 cases of personal genomics

Michael Schnyder
Watson
23 and me

18

What do the cancer sequencing projects intent to do?

Sequence many cancers to identify mutations that cause cancer
Also, what sort of mutations they are, how they arose

19

What are some issues to do with the ENCODE project?

A raw sequence is difficult to interpret

What about function?

We don't need the entire sequence to identify disease linked mutations

20

What did the ENCODE achieve in terms of functional characterisation of the genome?

Which functions are aimed to be characterised? (4)

They were able to characterise the function of 80% of DNA regions

1. Transcription factors
2. Histone modification
3. Regions of transcription
4. Chromatin structure

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