In my opinion, the best workflow is:

1) extract RNA

2) check it by gel electrophoresis immediately

3) store RNA in -80°C waiting for the results

4) cDNA synthesis and re-store RNA in -80°C immediately

5) store cDNA at -20°C

DNA can be stored and used every time but RNA  stored on -80 C and used freshly its better because cDNA is more stable then RNA

I normally synthesize the cDNA immediately after RNA extraction. Because cDNA is more stable.

DNA can be stored for as long as you want without much compromise in the quality.  However, RNA is more tricky and must be stored at -80C in small aliquots.  That way you avoid repeated freeze and thaw cycles which degrade RNA. I do suggest running an agarose gel to see the integrity of the RNA before proceeding to synthesize cDNA.  In general, the cDNA yield is good if the RNA has been properly stored and not subjected to repeated freeze-thaw cycles.  Of course the best option would be to do the cDNA synthesis together with RNA extraction.  Alternatively, if you are amplifying cDNA by PCR, the cDNA synthesis and DNA amplification could be done in the same procedure.  All the best!

RNA must be immediately kept in the -80C freezer in small aliquots. Despite DNA being more stable, it can also be degraded in a short period of time (mainly if you have bias composition). In some instances, it can happen in a short period of time. I usually keep a "voucher" aliquot of the DNA and another aliquot for "daily use". That prevents that freeze/thaw cycles degrade your entire sample. Alternatively, you can add RNAstable or DNAstable to your samples. My experience with DNAstable showed that high molecular weight can be preserved for a longer time.

In my opinion, the best workflow is:

1) extract RNA

2) check it by gel electrophoresis immediately

3) store RNA in -80°C waiting for the results

4) cDNA synthesis and re-store RNA in -80°C immediately

5) store cDNA at -20°C

I've used poor quality RNA (lots of RNA degradation products seen on MOPS gel; virtually no 28 or 18s rRNA) before to make cDNA. I still managed to amplify GAPDH RNA and even viral RNA, but I agree with Giulia; the faster you deal with fresh RNA the better the results will be, but I would not freeze thaw it so often. I'd run the gel and make cDNA while its running and freeze the rest of the RNA @ -80°C. DNA is much more stable so if you can RT your RNA quickly your cDNA should be fine.

DNA is much more stable than RNA and the problem with contamination for RNA as we know is higher. If you keep it on - 70 C it will keep integral, but I agree with the previous answer that if you intend to use it many times, better split into many vials and use one at a time.

Aliquoting and keeping them in -80 is fine. freeze thawing the same aliquote I can say wont work after several times the results might become confusing or even contrary

I think the best is to proceed immediately with cDNA synthesis after RNA extraction. The cDNA can then either be used directly for your experiments or stored for a few time until used. Clearly, the cDNA is more stable during storage than is the RNA. In my experience, I could observe that the RNA concentrations were different the samples were re-measured some months later.  

From my experience keeping in -80 is fine for a long time. 

And what about other chemicals, which you used?

I agree with Mohamed.  Using a fresh DNA or RNA sample is always a best option for experiment. Making aliquots of RNA or cDNA samples and proper storage as mentioned in above answers is also preferred. While thawing you can thaw on ice.

Regards,

Regarding your last question: I also lost my DNA stored at -20°C once - not freeze-thawed, in aliquots. I think this was due to contamination with DNase or so. I changed water and after the next DNA extraction my aliquots were fine for longer time.

Anyway, fresh is better.

Freeze-thaw cycles are the killer, as the other already mentioned.

For RNA there are even some commericals out like RNAlater. But check carful the papers around such things, they might effect downstream application.

Best regards

Giulia has provided ideal stragy to handle RNA

I think It is better to use fresh DNA/RNA in experiment.

Dear Mahboubah,

For RNA, repeated  thawing and freezing will adversely affect the integrity of your RNA. therefore its recommended to test the RNA immediately after extraction on the gel, prepare your cDNA as soon as possible then store it. For DNA, its more stable than RNA. For both DNA and RNA you can prepare aliquots and save them in -20 C for short-term or at -80 C for long term storage. overall, its always recommended to use fresh extraction whenever possible.

Yes, For cDNA preparation fresh RNA are PREFERABLE

Yes, particularly in case of RNA fresh samples are preferable in comparison to DNA due to integrity concern in case of RNA.

I think that it's better to extract RNA and retrotranscribe it the same day. I usually extract RNA, verify its integrity on polyacrilammide gel (or Bioanalyser) and then I immediately synthetize the corresponding cDNA. I also store RNA at -80 preparing different aliquots of the same sample trying to avoid repetitive thawing and freezing that  affect the integrity of the RNA.

Its always better to use fresh DNA or RNA samples for PCR or RTPCR. Storage, repetitive freezing and thawing may affect the integrity of the samples as nucleases are present in the environment and cause degradation partially or completely. Fresh samples are always better for quantitaion experiments

I agree with Mohamed according to RNA. cDNA is not more stable than RNA. I keep it at 20°C, but use no longer than during 6 months for PCR.

DNA is more stable than RNA, RNases are ubiquitous. Its better to prepare cDNA immideatly.  If stored DNA has some contamination it wont givegood band in electrophoresis

I don't have much experience with DNA, but I know RNA is very unstable. It is best to work with it as soon as you extract it. Freezing and thawing can cause your sample to break down, leading to unclear electrophoresis results. If you have to freeze it, try to aliquot out the amount you will need for each experiment first, so you don't have to repetitively freeze and thaw the whole sample each time you need a little bit. 

If you are worried about RNA stability, people store RNA in alcohol at -80 and precipitate and dry before use. As long as it is stored with out possibility of RNAse contamination, its should be fine.

Let me discuss you the problem i faced when RNA was thrown out of the -80 by someone unknowingly. The amount of RNA was reduced after 6hours by 400 units less than as it was initially. So immidiately prepare cDNA. Try to reduce freeze thaw...