In a rRNA cleanup procedure for RNA-seq, use of glycogen(10mg/ml) was mentioned for purification of rRNA-depleted sample by ethanol precipitation. In routine practice we don't use glycogen in ethanol precipitation. Can anyone tell me the role of glycogen here?
Glycogen is a polymer which is used to trap the nucleic acids (DNA, rRNA,RNA...). In ethanol Glycogen is in soluble so it forms polymer structure and traps the nucleic acids and forms pellet with nucleic acids trapped during the centrifugation...
It's glycogen, not glycerol. It is used to stabilize the RNA.
Ramesh here explained the mechanism of this stabilization. I can say from my practical experience that the yield of RNA extraction is more when I use glycogen. Also, glycogen makes your RNA pellet visible and it's easier to control that you didn't touch the pellet during the supernatant withdrawing.
Saad Jan Yes you can use glycogen its quite helpful. It helps to co precipitate DNA and if visibility is an issue due to low quantity of the DNA in your sample, you can use GlcoBlue which imparts a blue color to the pellet during ethanol precipitation.
as for the concentration of glycoblue that should be used during the protocol is 50 ug/mL.
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