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ChIP-sequencing, also known as ChIP-seq, is a method used to analyze protein interactions with DNA. ChIP-seq combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. It can be used to map global binding sites precisely for any protein of interest.
The cost and accessibility of ChIP-seq is a major disadvantage, which has led to the more predominant use of ChIP-chip in laboratories across the world. [2] This photo compares the efficacy of the two experimental techniques, ChIP-seq and ChIP-chip. Table 1 Advantages and disadvantages of NChIP and XChIP
The cost of the DNA microarrays is often a limiting factor to whether a laboratory should proceed with a ChIP-on-chip experiment. Another limitation is the size of DNA fragments that can be achieved. Most ChIP-on-chip protocols utilize sonication as a method of breaking up DNA into small pieces.
The ideal size of DNA fragments for the sequencing library depends on the sequencing platform that will be used. [4] [16] DNA can first be sheared to fragments around 300–500 bp long using sonication. [4] [16] [17] Fragments of this size are suitable for high-throughput sequencing.
The cost of sequencing a human genome is dropping rapidly, due to the continual development of new, faster, cheaper DNA sequencing technologies such as "next-generation DNA sequencing". The National Human Genome Research Institute, an arm of the U.S. National Institutes of Health , has reported that the cost to sequence a whole human-sized ...
Other chip-based methods such as comparative genomic hybridization can detect genomic gains or deletions leading to LOH. SNP arrays, however, have an additional advantage of being able to detect copy-neutral LOH (also called uniparental disomy or gene conversion). Copy-neutral LOH is a form of allelic imbalance.
This has enabled a drastic increase in available sequence data and fundamentally changed genome sequencing approaches in the biomedical sciences. [9] Newly emerging NGS technologies and instruments have further contributed to a significant decrease in the cost of sequencing nearing the mark of $1000 per genome sequencing. [10] [11]
Sequencing technology platforms commonly used for RNA-Seq [77] [78] Platform Commercial release Typical read length Maximum throughput per run Single read accuracy RNA-Seq runs deposited in the NCBI SRA (Oct 2016) [79] 454 Life Sciences: 2005 700 bp 0.7 Gbp 99.9% 3548 Illumina: 2006 50–300 bp 900 Gbp 99.9% 362903 SOLiD: 2008 50 bp 320 Gbp 99. ...