This may be a crazy simple question but one I am not sure about.
Last year we did some RNA-Seq to identify any off-target effects for a therapeutic. This was a fairly simple experimental design involving three pseudo-biological replicates of an untreated control and two treatment doses. We looked for genes that were DE between the untreated and treated samples to see if there were any potential off-target effects.
This year we are determining the effect of the therapeutic in patients using RNA-Seq. Initially, we want to compare the untreated patient data with a control to estimate the baseline disease phenotype. One option is to re-submit the same control sample from our previous experiment for sequencing. However, this would obviously take up space on the run and we'd rather use that space for deeper sequencing of our patient samples.
So my question is, are we safe to re-use the previous control RNA-Seq data from last year? The new patient data will be processed in the same way (STAR alignment, RSEM quantification, DE using EdgeR) and would be generated in the same way (same library prep, sequencing platform, read length). I am just concerned that last year's control data may harbour bias due to not being prepared and run at the same time as this year's patient samples.
Incidentally, we will also submit a different control sample as part of this year's RNA-Seq run, but re-using last year's control data in addition should help us get a better idea of what is going on in our patients.
Any advice would be very gratefully received. Many thanks in advance.