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[CHIP-seq] QA-ChIP-seq,放在这里,我也不知道干嘛的

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发表于 2017-5-17 15:07:35 | 显示全部楼层 |阅读模式
其实我是想说些什么的,但是忘记了。
O(∩_∩)O哈哈~
The DNA binding proteins most frequently investigated in this way
are transcription factors (for example, p53 or NFκB),
chromatin-modifying enzymes (for example, p300, histone deacetylases),
modifed histones interacting with genomic DNA (for example, histone 3 trimethylated on lysine 4), and
components of the basal transcriptional machinery (for example, RNA polymerase II).


Te DNA sequence motif that is recognized by the binding protein can be computed;
the precise regulatory sites in the genome for any transcription factor can be identifed;
the direct downstream targets of any transcription factor can be determined;
the clustering of transcription-regulatory proteins at specifc DNA sites can be assessed

Roughly speaking, ChIP-seq has three key steps that determine its success.
Te frst and most crucial is antibody selection;
the second is the actual sequencing, which is subject to several possible biases; and
the third is the algorithmic analysis, including mapping and peak-calling.


If the amount of material is not a limiting factor (for example, when it comes from a tissue culture) the amount of DNA used for library preparation is about 10 to 15 ng.
When material is limited, which is often the case with primary cell or tissue samples, smaller starting amounts of DNA have to be used.

However, one should keep in mind the biases that can give rise to differences between the libraries.
Tese include differences in DNA fragmentation protocol, time of cross-linking, the sequencing platform, and the software and parameters used in mapping.


The primary functions of chromatin are
1) to package DNA into a more compact, denser shape,
2) to reinforce the DNA macromolecule to allow mitosis,
3) to prevent DNA damage, and
4) to control gene expression and DNA replication.
The primary protein components of chromatin are histones that compact the DNA.
Chromatin is only found in eukaryotic cells (cells with defined nuclei).





上一篇:markdown 我还可以理解,但是 LaTeX 怎么看都是反人类的设计~
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