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biochem exam 6 > Technology > Flashcards

Technology Flashcards

1
Q

similarities of DNA and RNA microarrays

A

both end with DNA microarray

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2
Q

DNA microarray

A

do for entire genome

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3
Q

RNA microarray

A

only target those genes
purify RNA
make cDNA

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4
Q

aCGH (array comparative genomic hybridization)

A

saw huge differences and compared reference to genome to another genome

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5
Q

Genome wide technologies

A

DNA/RNA microarrays
aCGH
NGS (next generation sequencing)

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6
Q

applications of DNA microarrays

A
  • gene transcription measurement
  • SNP/CNV
  • chromatin immune precipitation
  • clinical diagnostics
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7
Q

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

A

DNA microarrays

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8
Q

hybridization based technology

A

denature so cDNA can find probe and bid firm

wash DNA not attached

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9
Q

how many unique features do DNA microarrays have?

A

2.1-3 million

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10
Q

uses DNA with chromophore

A

DNA microarrays

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11
Q

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

A

22

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12
Q

southern blot

A

dna

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13
Q

northern blot

A

rna

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14
Q

western blot

A

protein

most common

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15
Q

two microarray platforms

A

spotted arrays

affymetrix

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16
Q

uses 2 colors and glass

A

spotted arrays

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17
Q

1 or more color to compare 2 samples against each other

A

affymetrix

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18
Q

which is more common?

spotted array or affymetrix

A

affymetrix

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19
Q

what do spotted arrays contain?

A

oligonucleotides 50-70mer

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20
Q

What are samples labeled with in spotted arrays?

A

CY5 (red)

CY3 (green)

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21
Q

samples loaded and mixed and hybridized simultaneously to a single slide

A

spotted array

22
Q

oligonucleotides to detect genes

A

anneal to certain area of gene

multiple areas

23
Q

what percent of genome is expressed in oligonucleotides?

A

2%

24
Q

what is RNA used to measure?

A

gene transcription

25
Q

what is DNA used to measure?

A

CNV or SNP difference between genomes

26
Q

what do aCGH measure?

A

congenital abnormalities

cancer

27
Q

how many oligonucleotides are used in aCGH?

A

> 1 probe per kb genome wide in human

28
Q

what is the length of oligonucleotides used in aCGH?

A

25-100 bp

29
Q

t/s arrays function well for high copy number sequences

A

false

30
Q

is the control or cancer labeled green?

A

control

31
Q

is the control or cancer labeled red?

A

cancer

32
Q

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

A

yellow

33
Q

what length do affymetrix use of oligo?

A

25 mer length

34
Q

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

A

22

35
Q

single sample goes on a single array located in cartridge

A

affymetrix

36
Q

illumina SNP genotyping

A

know difference between normal or WT allele

SNP extension

37
Q

what is exon sequencing?

A

next generation sequencing

38
Q

sanger sequencing

A

DNA sequencing

39
Q

capillary dna sequencers

A

whole genome project

40
Q

next generation DNA sequencing

A

multiple applications

the reality of whole genome sequencing at a reasonable cost

41
Q

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

A

sanger sequencing

42
Q

separation b electrophoresis, fluorescent tags

A

sanger sequencing

43
Q

what terminate the reaction in sanger sequencing

A

dNTPs

ddNTPs

44
Q

sanger sequencing outcome

A

dozens of gels

label with p52

45
Q

deep sequencing outcome

A

one run

5 days

46
Q

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

A

2 months/2 days

47
Q

what company was formed for NGS?

A

454

48
Q

sequencing in 454 company

A

emulsion PCR

pyrosequencing

49
Q

single molecule PCR in microsphere compartments

A

emulsion PCR

50
Q

chemiluminescent detection of pyrophosphate

A

pyrosequencing

51
Q

use sedimentation and fragmentation with oil in water emulsion

A

emulsion pcr

52
Q

what do you add in emulsion pcr

A

micro beads

biochem exam 6 (3 decks)

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