Ch. 20 Flashcards
ChiP steps
1- Proteins are fixed to DNA, 2- shear DNA into fragments, 3- immunoprecipitation with antibodies, 4- protein and antibody release from chromatin (reverse crosslink), 5- sequence is recovered from a pool of associated DNA
Contig assembly
overlap of restriction enzyme digest pattern- DNA marker or other known sequence can be used to determine clone order to assemble a contig
What are the two approaches to whole genomic sequencing?
map based approach and whole genome shotgun sequencing
describe the map based approach for whole genomic sequencing
it uses detailed genetic and physical maps to identify the least number of clones to cover the genome, and then sequences and assembles the smaller number of clones
describe the whole genome shotgun sequencing
shear genome itno small pieces and clone; sequence millions of clones; and then assemble all those sequences
Human genome first drafted in
2000
Describe eukaryotic genomes
they are very repetitive
Roughly 2% of the human genome is _________
protein coding
Most genomic variation is in
single nucleotide polymorphisms
the genome wide association study uses…
pedigrees and linkage using SNP haplotypes to identify disease loci
What are single nucleotide polymorphisms
a site in the genome where individual members of a species differ in a single base pair
haplotypes
a specific set of linked genetic varients or alleles on a single chromosome
Manhattan plot
showing genomic regions associated with a trait
Synteny
colinearity between related genomes; the genomes are descended from a common ancestor
transgenic organisms
a way to analyze gene function; add DNA sequences of interest to the genome of an organism that normally lacks such sequences and then we can observe the effect of the introduced sequence on the organism’s phenotype
CRISPR-Cas9
can be used to target specific locations in the genome to introduce changes
DNA fingerprinting
we can use variations in the genome to identify a person; short tandem repeats or microsatellites are known places of variation (people vary in the number of copies of repeats that they possess at each of these loci)
Combined DNA index system
FBI system of STR loci to identify people and solve crimes
