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Flashcards in Technology Deck (52):
1

similarities of DNA and RNA microarrays

both end with DNA microarray

2

DNA microarray

do for entire genome

3

RNA microarray

only target those genes
purify RNA
make cDNA

4

aCGH (array comparative genomic hybridization)

saw huge differences and compared reference to genome to another genome

5

Genome wide technologies

DNA/RNA microarrays
aCGH
NGS (next generation sequencing)

6

applications of DNA microarrays

- gene transcription measurement
- SNP/CNV
- chromatin immune precipitation
- clinical diagnostics

7

uses glass surface with probes with a specific nucleotide sequence to anneal to DNA

DNA microarrays

8

hybridization based technology

denature so cDNA can find probe and bid firm
wash DNA not attached

9

how many unique features do DNA microarrays have?

2.1-3 million

10

uses DNA with chromophore

DNA microarrays

11

how many different probes are there for each gene in DNA microarrays?

22

12

southern blot

dna

13

northern blot

rna

14

western blot

protein
most common

15

two microarray platforms

spotted arrays
affymetrix

16

uses 2 colors and glass

spotted arrays

17

1 or more color to compare 2 samples against each other

affymetrix

18

which is more common?

spotted array or affymetrix

affymetrix

19

what do spotted arrays contain?

oligonucleotides 50-70mer

20

What are samples labeled with in spotted arrays?

CY5 (red)
CY3 (green)

21

samples loaded and mixed and hybridized simultaneously to a single slide

spotted array

22

oligonucleotides to detect genes

anneal to certain area of gene
multiple areas

23

what percent of genome is expressed in oligonucleotides?

2%

24

what is RNA used to measure?

gene transcription

25

what is DNA used to measure?

CNV or SNP difference between genomes

26

what do aCGH measure?

congenital abnormalities
cancer

27

how many oligonucleotides are used in aCGH?

>1 probe per kb genome wide in human

28

what is the length of oligonucleotides used in aCGH?

25-100 bp

29

t/s arrays function well for high copy number sequences

false

30

is the control or cancer labeled green?

control

31

is the control or cancer labeled red?

cancer

32

what color is shown if cancer and control are expressed in both?

yellow

33

what length do affymetrix use of oligo?

25 mer length

34

how many different olives are there for each gene in affymetrix?

22

35

single sample goes on a single array located in cartridge

affymetrix

36

illumina SNP genotyping

know difference between normal or WT allele
SNP extension

37

what is exon sequencing?

next generation sequencing

38

sanger sequencing

DNA sequencing

39

capillary dna sequencers

whole genome project

40

next generation DNA sequencing

multiple applications
the reality of whole genome sequencing at a reasonable cost

41

have a piece of DNA you want to sequence and need multiple copies of this part of DNA

sanger sequencing

42

separation b electrophoresis, fluorescent tags

sanger sequencing

43

what terminate the reaction in sanger sequencing

dNTPs
ddNTPs

44

sanger sequencing outcome

dozens of gels
label with p52

45

deep sequencing outcome

one run
5 days

46

How how does it take to analyze the DNA in whole genome sequencing?

2 months/2 days

47

what company was formed for NGS?

454

48

sequencing in 454 company

emulsion PCR
pyrosequencing

49

single molecule PCR in microsphere compartments

emulsion PCR

50

chemiluminescent detection of pyrophosphate

pyrosequencing

51

use sedimentation and fragmentation with oil in water emulsion

emulsion pcr

52

what do you add in emulsion pcr

micro beads