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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 performance of ChIP-seq was then compared to the alternative protein–DNA interaction methods of ChIP-PCR and ChIP-chip. [17] Nucleosome Architecture of Promoters: Using ChIP-seq, it was determined that Yeast genes seem to have a minimal nucleosome-free promoter region of 150bp in which RNA polymerase can initiate transcription. [18]
The costs per megabyte were estimated at $12,400 to encode data and $220 for retrieval. However, it was noted that the exponential decrease in DNA synthesis and sequencing costs, if it continues into the future, should make the technology cost-effective for long-term data storage by 2023. [20]
The term was coined by The Economist [3] and is named after author Rob Carlson. [1]Carlson curves illustrate the rapid (in some cases above exponential growth) decreases in cost, and increases in performance, of a variety of technologies, including DNA sequencing, DNA synthesis and a range of physical and computational tools used in protein production and in determining protein structures.
The ChIA-PET method combines ChIP-based methods, [2] and Chromosome conformation capture (3C) based methods, [3] to extend the capabilities of both approaches. ChIP-Sequencing (ChIP-Seq) is a popular method used to identify transciption factor binding sites (TFBS) while 3C has been used to identify long-range chromatin interactions.
Wilbanks and colleagues [3] is a survey of the ChIP-seq peak callers, and Bailey et al. [4] is a description of practical guidelines for peak calling in ChIP-seq data. Peak calling may be conducted on transcriptome/exome as well to RNA epigenome sequencing data from MeRIPseq [ 5 ] or m6Aseq [ 6 ] for detection of post-transcriptional RNA ...
Introduced in 2007, ChIP sequencing (ChIP-seq) is a technology that uses chromatin immunoprecipitation to crosslink the proteins of interest to the DNA but then instead of using a micro-array, it uses the more accurate, higher throughput method of sequencing to localize interaction points. [13]
The cost of acquiring a pH-mediated sequencer at time of launch was priced at around $50,000 USD, excluding sample preparation equipment and a server for data analysis. [8] [11] [15] The cost per run is also significantly lower than that of alternative automated sequencing methods, at roughly $1,000. [8] [12]