I am PhD student and struggeling with one question: is there any possibility to compare RNAseq data of own experiments (i will compare two macrophage subsets or better one subset in inflammatory conditions to the same in steady state condititions) to already published datasets? I mean: Can I get raw data (readcounts of mRNA seq, already normalized, of clearly defined macrophage subsets) somewhere and then: Can I compare them to my own data??? (I already looked at GEO and immgen.org, but don´t really understand if I can just take this data out of there...)
Although the other answers in this thread are technically correct, they entirely miss the point of the question (or answer it only partially).
Can I get raw data somewhere and then:
Yes, as pointed out you can find raw data online from other experiments.
Can I compare them to my own data???
But here starts trouble. What comparison do you want to do? If you want to compare your "treatment" samples to publicly available "control" samples, you are going to have a bad time. This analysis is invalid because you have no idea what you are comparing. You might think you are comparing treatment vs control, or mutated vs wildtype, but in fact, it's perfectly possible that you are comparing library prep A with library prep B, or lab C vs lab D, or RNA-extraction method E vs F. You have no idea about all the possible confounders/interactors.
Obvious example: if your data is generated using polyT beads and the other library is generated using ribo-depletion, you are going to see a lot of irrelevant stuff.
If you have done a comparison in which a treatment group is compared to controls, and you want to see if a similar study (with their own treatment and controls) found the same results, then that's valid because you are doing a meta-analysis and not comparing across experiments.
I believe you could go to either GEO, ENA or SRA and search for transcriptomics data for your desired cell type. The specific substets/condtions should also be described otherwise you can find it in the associated publications.
After that you can download them and analyse the same way you'd analyse your data.
