Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Genomics > Microarrays > Flashcards

Microarrays Flashcards

1
Q

What is a microarray?

A

An ordered assembly of nucleic acids immobilised on a solid support

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What is usually the solid support in microarrays?

A

The solid support is usually glass

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What is transcriptomics and what does it allow?

A

Study of transcription and their functions

Allows to classify samples

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What is there in microarrays for gene expression?

A

Lots of copies of the same probe in a spot

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What does each spot in microarrays for gene expression give?

A

Each spot gives the relative expression for one transcript

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What do microarrays for gene expression detect?

A

Detect all known transcripts in one sample

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

When we scan the solid support in microarrays, what do we end up with?

A

We end up with red, green and yellow spots

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What does each spot represent?

A

Represents one SNP

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Whats involved in expression profiling workflow?

A

-Sample–>RNA extraction–>Labelling–>Hybridisation of labelled sample to array–>Detect a signal–>Data analysis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What needs to be done once you have collected raw data?

A

Microdata analysis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Steps involved in microdata analysis

A

Normilisation–>Hierarchial clustering–>Gene filtering–>Statistical test–>Generate gene list–>Biological interpretation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What is clustering?

A

A technique that organises data with similar patterns into classes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What is an alternative way of displaying similarities between samples?

A

Alternative ways are dendrograms

-Distant samples are less similar

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What is also used in clustering?

A

Heat maps

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Why do we use data repositories?

A
  • Microarray experiments aren’t cheap, so this maximises utility
  • Can share data
  • Easier to compare results
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Techniques to predict cancer recurrence

A 
Mamma print:
-Uses microarrays
-70 genes are observed
Oncotype DX:
-qRT-PCR used
-21 genes are observed
Mammostrat:
-Immunohistochemistry used
-5 proteins observed
Prosigna gene signature:
-58 genes observed
-Direct digital barcode used
17
Q

What do can we do in RT-PCR?

A

-Do PCR on cDNA and look whether things are expressed or not

18
Q

How can we make RT-PCR quantitative?

A

We can make it quantitative by counting the number of copies of amplified DNA present

19
Q

What is the Ct value and what does it stand for?

A

Stands for threshold cycle

Is a value to compare across all experiments and is fluorescence at 225 copies of the transcript

20
Q

Relation between cDNA and Ct value

A

The higher the amount of cDNA, the lower the Ct value

21
Q

How can you count the number of amplified molecules present?

A
  • Include a dye in PCR reaction mix that fluoresces when its incorporated in the PCR product
  • Or label a probe in the PCR that only fluoresces when its incorporated in the PCR product
22
Q

Why do we use qPCR?

A
  • Used to independently confirm differences in RNA levels between samples
  • Probe binding is noisy and differences can be detected that aren’t real, especially when differences are small
23
Q

What is a more accurate measure of RNA transcript abundance?State an advantage and disadvantage

A

RNA-seq

  • Data more reproducible
  • But its expensive
24
Q

Why is GWAS possible and how?

A

GWAS only possible because we can genotype large number of SNPs in large number of subjects

  • Possible by using microarrays that hybridise with genomic DNA adjacent to SNPs
  • SNP then extended by one base that is fluorescently labelled and detected using a HD scanner
25
Q

What is a spot?

A

Its lots of copies of the same single stranded oligonucleotide
-A probe essentially

26
Q

What is each probe for?

A

Each probe is for genotyping one SNP

27
Q

What is each probe designed to do?

A

Designed to hybridise with one SNP

28
Q

What are copy number variants?

A

Sequences which are greater than 1kb that have different copy numbers in different people

Range in size and can see repeats or absentees.

29
Q

Structural variants of copy number variants

A
  • Arise due to:
  • Deletion
  • Insertion
  • Inversion
30
Q

Steps involved in Array-CGM

A
  1. Patient DNA taken and labelled green with fluroesence and control labelled red
  2. Control and patient DNA are mixed and hybridised to array of DNA fragment
31
Q

What do red and green areas show in array CGM?

A

Show difference between normal and patient DNA

Genomics (19 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions