2. ChIP有哪些应用？
答：近年来由于该技术不断的发展和完善，其应用范围已经从研究目的蛋白与已知靶序列间的相互作用，发展到研究目的蛋白与整个基因组的未知序列的相互作用；从研究一个目的蛋白与DNA的相互作用，发展到研究两个蛋白与DNA共同结合的相互作用；从研究启动子区域的组蛋白的修饰，发展到研究结合在DNA序列上的蛋白复合物。
3. ChIP技术的原理？
答：生理状态下把细胞内的DNA与蛋白质交联在一起，通过超声或酶处理将染色质切为小片段后，利用抗原抗体的特异性识别反应，将与目的蛋白相结合的DNA片段沉淀下来。染色质免疫沉淀技术一般包括细胞固定，染色质断裂，染色质免疫沉淀，交联反应的逆转，DNA的纯化，以及DNA的鉴定。因为ChIP实验涉及的步骤多，结果的重复性较低，所以对ChIP实验过程的每一步都应设计相应的对照，而且对结果的分析也需要有一定的经验。
4. 做ChIP试验，必须做甲醛固定么？
答：不一定，视样品及试验方案而定。做甲醛固定的为X-ChIP，而不需要固定的为N-ChIP。甲醛能有效的使蛋白质-蛋白质，蛋白质-DNA，蛋白质-RNA交联，形成生物复合体，防止细胞内组分的重新分布。甲醛的交联反应是完全可逆的，便于在后续步骤中对DNA和蛋白质进行分析。甲醛的交联反应可被加入的甘氨酸终止。
5. 为什么必须将DNA切碎至少于1000bp大小（大约3个核小体~400-500bp）?
答：为确保ChIP实验有良好精度。若您的平均片段长度大于1000bp，您将会分离获得包含您目标序列的DNA，但所要研究的蛋白会离您目标序列有700个核苷酸的距离。
6. 为什么使用鲑鱼精子DNA来封闭琼脂糖珠子？为什么我的样品中鲑鱼精子DNA不会发生PCR反应？ 答：鲑鱼精子用于降低降低染色质DNA与琼脂糖珠子的非特异性结合。实验者不太可能对鲑鱼组织做ChIP实验，所以此DNA不会因交叉杂交而被PCR引物扩增。
7. 引物最佳设计是什么样的？
答：引物长度应为24个核苷酸，应含有50%GC碱基对，Tm值为60°C。不要扩增大于600-800个核苷酸的序列。不必考虑基因组内不独一序列。
8. 您推荐下如何从琼脂糖（或琼脂糖凝胶）中洗脱抗体-蛋白-DNA复合物，用来做re-ChIP试验？
答：在ChIP分析试剂盒内可找到洗脱缓冲液，用它洗脱复合物。对于re-ChIP，有必要
添加蛋白酶抑制剂到免疫沉淀洗液和洗脱缓冲液，及第二轮实验用的稀释缓冲液。请确定所有溶液处于低温，蛋白质不会因此而在收集第一次免疫沉淀的复合物或第二次免疫沉淀时降解。
9. 蛋白A琼脂糖能被用于小鼠IgM?
答:蛋白质A不能与小鼠IgM结合。可以考虑用一个桥接抗体连接。
10. 在做ChIP之前，有办法纯化细胞核么？
答:在细胞与甲醛交联后，细胞核可通过“溶胀缓冲液”培育及剪刀细胞均质器（douncehomogenization）制备（至少10倍体积）。
溶胀缓冲液：
25M Hepes, pH 7.8 1.5mM MgCl2 10mM KCl 0.1% NP-40 1mM DTT 0.5mM PMSF 蛋白酶抑制剂混合剂
然后按照protocol在SDS裂解液中裂解 11. ChIP超声波的最佳条件？
答:1. 确定裂解物在冰上放置了至少10分钟。不要震荡或者摇晃裂解物，避免有气饱（气泡产生）。超声波仪会替你做这些。
2．脉冲应在~10秒（与体积一致）。
3. 样品量小于400uL间隔应大于1分钟，在EP管中的更大体积间隔大于3分钟。
4. 避免泡沫。请确定超声探头靠近液体底部（不能让探头碰到管壁）。
5．若发现泡沫，立即停止超声，置于冰上。旋转EP管以去除泡沫，继续超声。 6. 在按“开始”键之前将探头置于液体中。
12. 客户能只用哺乳动物细胞的细胞核而不是整个细胞么？
答:是，实际上比起全细胞，细胞核更好。我们用全细胞裂解物，因为它更简便，通常也能
得到好结果。此页有一些相关信息：
http://www.epigenome-noe.net/researchtools/protocol.php?protid=10
13. 我是否可以改变逆转交联的时间和温度? 答：并不推荐少于4个小时的逆转交联.但是,可以将样本在65度过夜逆转交联.需要注意的是,样品不能干掉。
14. 做组蛋白ChIP时, 什么时候不需要交联? 答：nativeChIP中,Histone H3 and Histone H4 都不需要交联反应,因为它们本身来说和DNA结合的非常紧密.组蛋白H2A和H2B并不是紧密联接,但是在nativeChIP中依然可以不需要交联反应。
15. 什么是inputDNA? Output DNA?
答：从染色质 上获得的未做过IP的已经被逆转交联的DNA.它是检查PCR是否有效的对照。OutputDNA是来自每次IP实验的DNA.
其实就是genomicDNA. 在ChIP实验中,sonication 或酶解后,样本取部分不做IP,直接逆转交联.它的最主要的作用就是检查PCR系统是否work.通常情况下,在该条道中,都可以看到条带的.如果没有,说明PCR系统不work。
16. 通过改善交联是否能提高ChIP的enrichment?
答：Notlikely.Formaldehyde is a very reactive dipolar compound in whichthe carbon atom acts as a nucleophilic center for amino and imino groups ofamino acids (Lys, Arg, and His) and of DNA (primarily A and C), leading to theformation of a Schiff base. This intermediate can further react with a secondamino group, resulting in the final DNA–protein complex 1-3. Your protein, orthe protein-DNA complex, also crosslink with other proteins and lipids, via thesame mechanism,. Increasing formaldehyde concentration and/or the incubationtime may adversely affect immunoprecipitation. It is recommended that youoptimize other parts of the protocol for improvement.
17. 如何来量化经IP后的DNA?
答：DNApurified from ChIP experiments can be quantitated by PCR, providing theamplifying oligos meet specific criteria. Oligos should be 24 mers, with a GCcontent of 50% (+/- 4) and a Tm of 60.0C (+/- 2.0). You must be certain
thatthe PCR reactions are within the linear range of amplification. Generally ittakes time to achieve this. Too much input DNA will affect your results, so setup several tubes for each experiment to optimize the input DNA. Generally, thisis about 1/25th to 1/100th for yeast, approximately 1/10 for mammalian cells,but depends on the amount of antibody and input chromatin. Also, do not usemore than 20 cycles, making sure that dNTP's always remain in excess. Also,include each reaction a control primer (to compare your experimental bandagainst-make sure the sizes are sufficiently different to allow properseparation-75 base pairs is usually OK) set to a region of the genome thatshould not change throughout your experimental conditions. Also PCR frompurified input DNA (no ChIP) and include no antibody control PCR's as well. PCRproducts should be no more than 500 base pairs and should span the area ofinterest (where you think you will see changes in acetylation or methylation ofhistones). All PCR products should be run on 7-8% acrylamide gels and stainedwith SYBR Green 1 (Molecular Probes) at a dilution of 1:10,000 (in 1XTris-borate-EDTA buffer, pH 7.5) for 30 minutes-no destaining is required.Quantitation is carried out subsequent to scanning of the gel on a MolecularDynamics Storm 840 or 860 in Blue fluorescence mode with PMT voltage at 900with ImageQuant software. This has distinct advantages over ethidium bromidestaining. SYBR Green is much more sensitive, and illumination of ethidiumstained gels can vary across the gel based on the quality of UV bulbs in yourin your light box. For further info, see Strahl-Bolsinger et al. (1997) GenesDev. 11: 83-93. A radioactive quantitation method is described in Suka et al(2001) Molec. Cell, 8: 473-479.
18. 为什么ChIP试验需要用经验证的抗体？
答：抗原抗体之间的结合是通过抗体特异性的识别抗原表位并结合的，有的抗体识别的抗原表位比较小，不容易暴露，在ChIP实验中容易被DNA包裹，从而使抗体无法结合，因此用来做ChIP的抗体一般是需要经过chip实验验证的，商业化的抗体都应该是验证过的。
19. 如何确保在最大功率下超声裂解不起泡
答：1.Use the volume of SDS lysis buffer you choose, cool on ice
2. Startsonication with increasing power until foaming occurs.
3. Lower thepower a little. This is the power you can use (for instance, if it startsfoaming at 40%, then 35% should be OK).
4. Cool theabove vial and sonicate for one pulse. Touch the vial without glove and itshould not be hot (warm is OK), otherwise shorten the time (10-15 seconds aregenerally used).
5. Preparecells in lysis buffer and sonicate for 3, 6, 9 (or whatever
you prefer) pulsesand check DNA on gel. Other things to watch out:
Load ~1 x 10^5 cell equivalent (This is <0.7 ugDNA)/Lane. Make sure you digested all the RNA (The big smiley band) Load non-sonicated DNA in one lane.
20. 什么是reChIP技术？
答：ChIPreChIP是在第一次ChIP的基础上不解交联，而继续进行另一个目的蛋白的免疫沉淀，从而得到与两种目的蛋白都结合的DNA序列。值得注意的是，因为 通过两次免疫沉淀富集的DNA量比较少，所以在分析时通常要把多次免疫沉淀的DNA浓缩后再进行
操作。
21. Protein L与ProteinA, Protein G的区别
答：ProteinL is an immunoglobulin-binding protein that originates from the
bacteriaPeptostreptococcus magnus. Unlike Protein A and Protein G, which bind primarilythrough Fc regions (i.e., heavy chain) of immunoglobilins, Protein L binds Igsthrough interactions with the light chains. Since no part of the heavy chain isinvolved in the binding interaction, Protein L binds a wider range of Igclasses than Protein A or G. Protein L binds to representatives of all classesof Ig, including IgG, IgM, IgA, IgE and IgD. Single chain variable fragments(ScFv) and Fab fragments also bind to Protein L. Fromhttp://www.piercenet.com/Objects ... ctFamilyID=01010323
Despite this wide-ranging binding capability with respect toIg classes, Protein L is not a universal immunoglobilin-binding protein.Binding of Protein L to immunoglobulins is restricted to those containing kappalight chains (i.e., k chain of the VL domain).1 In humans and mice, kappa (k)light chains predominate. The remaining immunoglobulins have lambda (l) lightchains. Furthermore, Protein L is effective in binding only certain subtypes ofkappa light chains. For example, it binds human VkI, VkIII and VkIV subtypesbut does not bind the VkII subtype. Binding of mouse immunoglobulins isrestricted to those having VkI light chains.
22. 关于酶切DNA片段，Micrococcal Nuclease Enzyme是什么？
答：Itpreferentially digests single-stranded DNA and AT or AU-rich regions but isalso active against RNA and double-stranded DNA (all sequences are ultimatelycleavable). Products of digestion are nucleic acid fragments containing 3'phosphate termini. Exhaustive digestion with excess enzyme yields mono- anddinucleotides. The enzyme requires calcium ions for activity and is easilyinactivated by EDTA or EGTA.
Application. 1. Removal of nucleic acids, especiallysingle-stranded DNA or