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I am working on an RNA-Seq project, and I am aware that some researchers use housekeeping genes as a method of normalization. My project has several different tissues, and I was wondering if housekeeping gene expression is generally invariant across tissue type?

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  • $\begingroup$ There is no such thing as a universal housekeeping gene. $\endgroup$ – MattDMo Sep 23 '16 at 16:10
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My experience is: Yes they can vary quite a lot (according to differences in the genetic profile of the cells) and you have to test this. As a primer I can recommend reading the articles listed below. These are mostly looking into this in the context of realtime PCR, but this should be valid for RNAseq as well. For some applications it is also a good idea to use more than one gene for normalization.

References:

  1. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes.
  2. Selection of housekeeping genes for gene expression studies in human reticulocytes using real-time PCR
  3. Reference Genes / Housekeeping Genes
  4. Gene Ontology Based Housekeeping Gene Selection for RNA-seq Normalization
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