Flashcards in Technology Deck (52):
similarities of DNA and RNA microarrays
both end with DNA microarray
do for entire genome
only target those genes
aCGH (array comparative genomic hybridization)
saw huge differences and compared reference to genome to another genome
Genome wide technologies
NGS (next generation sequencing)
applications of DNA microarrays
- gene transcription measurement
- chromatin immune precipitation
- clinical diagnostics
uses glass surface with probes with a specific nucleotide sequence to anneal to DNA
hybridization based technology
denature so cDNA can find probe and bid firm
wash DNA not attached
how many unique features do DNA microarrays have?
uses DNA with chromophore
how many different probes are there for each gene in DNA microarrays?
two microarray platforms
uses 2 colors and glass
1 or more color to compare 2 samples against each other
which is more common?
spotted array or affymetrix
what do spotted arrays contain?
What are samples labeled with in spotted arrays?
samples loaded and mixed and hybridized simultaneously to a single slide
oligonucleotides to detect genes
anneal to certain area of gene
what percent of genome is expressed in oligonucleotides?
what is RNA used to measure?
what is DNA used to measure?
CNV or SNP difference between genomes
what do aCGH measure?
how many oligonucleotides are used in aCGH?
>1 probe per kb genome wide in human
what is the length of oligonucleotides used in aCGH?
t/s arrays function well for high copy number sequences
is the control or cancer labeled green?
is the control or cancer labeled red?
what color is shown if cancer and control are expressed in both?
what length do affymetrix use of oligo?
25 mer length
how many different olives are there for each gene in affymetrix?
single sample goes on a single array located in cartridge
illumina SNP genotyping
know difference between normal or WT allele
what is exon sequencing?
next generation sequencing
capillary dna sequencers
whole genome project
next generation DNA sequencing
the reality of whole genome sequencing at a reasonable cost
have a piece of DNA you want to sequence and need multiple copies of this part of DNA
separation b electrophoresis, fluorescent tags
what terminate the reaction in sanger sequencing
sanger sequencing outcome
dozens of gels
label with p52
deep sequencing outcome
How how does it take to analyze the DNA in whole genome sequencing?
2 months/2 days
what company was formed for NGS?
sequencing in 454 company
single molecule PCR in microsphere compartments
chemiluminescent detection of pyrophosphate
use sedimentation and fragmentation with oil in water emulsion