investigating genetic regulation at genome scale 1 Flashcards
what are the parameters of Illumina sequencing
you run many miniaturaised sequencing reactions for different DNA fragments in parallel. you generate short sequence reads.
name 2 Illumina bench top sequencing
MiSeq and NextSeq
name 2 production sequencing
HiSeq and NovaSeq
describe the outline of DNA seq
DNA digested by DNAse. moslty cut at nucleosome free regions. sequenced from cut ends. results aligned with genome. peaks present where reads align to DNAse hypersensitive sites.
what does the location of hypersensitive sites tell us
where the transcription factors are binding
which method needs fewer cells than DNA seq
ATAC-seq
what does chromatin immuno-precipitation sequencing do
protein is cross linked and NDA sheared. protein specific antibody is added. immunoprecipitated and complexes are purified. cross links are reversed and DNA purified for sequencing. then mapped to genome.
what is binding site co occurrence analysis
TFs sometimes function in groups so bind to same or nearby sites as a mutlicomplex.
what is H3K4Me1
enhancers
what is H3K4Me3
active promoters
what are H3K27Me3
repressed genes
what are H3K27ac
active enhancers
what does RNA seq do
measure the gene expression
what is TAL1 locus
a key blood transcription factor
does TAL1 increase in intermediate cell types
yes
