定义

Chip-Seq: CHromatin Immunoprecipitation combined with high-throughput sequenceing. It identifies the locations in the genome bound by the proteins.

原理

glue all proteins to DNA -> cut up DNA -> bind proteins of interest with antibodies -> isolate antibodies -> unglue and wash away proteins (only DNA and histones left) -> apply to all of the chromosomes in the cell

Then just like RNAseq, prepare sequencing library by adding adapters, PCR amplification -> check library concentration -> sequence -> filter garbage sequence -> alignment

Ultimately, get a long list of genomic coordinates(chromosome x, position 123-456) for all the reads(usually 50-100 million reads). Then use reads to create a genome browser track.

Control track: made by taking some of the input chromatin from the original ChIP-seq experiments. WIthout using an antibody to enrich for any particular protein, ungluing all of the proteins and wash off. sequencing -> aligning

The control track uses some of the same input chromatin for the ChIP-seq experiment but doesn't try to enrich for any particular protein binding.

why use control track?

Then we could compare peaks for the same protein in different cell types. Or if we didn't know the specific DNA sequence that the green thing bound to, we could guess that is a motif found in all of the peaks.