I´ve tried to check my total RNA i isolated from whole tissue. Nanodrop ratio was ok. I´ve loaded the total RNA on a normal agarose gel (1%, 2ul Eth-Br, 130V, 30min). I saw the smear i didn´t whanted to see... within this smear two fade bands i think of to be the bands i was hoping for.
Now i have some quenstions:
- I´ve already amplified a 500bp fragment from the cDNA made of this smeary RNA. The product sizes i whant to detect later in qPCR are 80-110bp. Is it possible that the RNA is partially degradadet but still could be used for qPCR?
- is loading the cDNA made from RNA on a gel is leading to the same two bands?
- Can i assume that if one sample from an extraction-charge is smeared, all other samples from this charge will be smeared too?
Thanks for every advice you can give me!!