In the last issue, I talked about the chip vs RNA-seq which is good (please point me), but many students may find that there are many kinds of gene chips on the market. I don't know where to start? Come to 818 today to pick tips on gene chips. One sentence - look at the purpose of the study.
First give you two words in science:
Gene expression: The chip that detects the gene expression is generally designed for all transcripts of a certain gene. After the algorithm for each probe signal, the expression level of the whole gene is obtained, and the often heard expression profile chip belongs to This one.
Transcript expression: Design probes for different transcripts of each gene. In addition to analyzing the amount of gene expression, the expression level of each transcript can be analyzed separately (that can be used to study the variable splicing of large heat). . According to Xiaobian, the only thing that can do this is Affymetrix's HTA (a new generation called Clariom) series of chips.
So what are the options when doing specific research?
Option 1: Do you want to find a mechanism or find a target for research?
The mechanism is simply to find the signal pathway for change. At present, the signal pathways we study are basically composed of coding genes. Therefore, when selecting a chip, only the gene expression profile is needed.
Option 2: Find the target, is it the coding gene, or is it non-coding?
The coding gene is the same as above. The previous article also mentioned that the coding gene has always been the mainstream of research, so the price of the chip is relatively low, and the price/performance ratio is very high.
However, the hotspot of the article can also be chased after it, maybe it will become the star (CNS) with the same paragraph. Non-coding, according to the research object, is mainly divided into two kinds of miRNA, lncRNA. Because of the short fragment, miRNAs have a special probe design method, often independent of a chip. And lncRNA, because its mechanism ultimately comes down to the regulation of the expression of the coding gene, so manufacturers like Affymetrix put it and the coding RNA on a chip, you can get two at a time, you can also study Their expression and control relationship with each other is very convenient.
Notes on lncRNA research:
Human, large mouse and other model organisms, the coding genes have been basically found, so the genes detected by different manufacturers' chips are almost the same, that is, more than 20,000. However, LncRNA is relatively new. After a hot spot in recent years, it has a big outbreak and many new lncRNA molecules have been discovered. Therefore, when selecting a chip, a very important issue is the design of the probe and the source of the annotation. The database is not new. If it is still a lncRNA chip a few years ago, it may miss a lot of interesting things.
The skill points for chip selection, are you getting it?
Long press and pay attention
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