Experiment vs. assay vs. run vs. sample

Question

[julie_dddd]

Hi,

I'm very new to bioinformatics and try to grasp the basic concepts. In my course notes I encounter terms as "experiment", "runs", "assays", "samples", ... and I have the expression they can be used interchangeably. However, I would like to know the difference & when to use what. Ideally, can this be explained with an example. Also, what accession numbers to use: ERX (experiment), ERR (run) , ERS (sample) for fastq files and why?

Thank you so much in advance.

Answer 1

[Jeremy Leipzig]

this is pretty confusing. in NCBI terms, a layman's translation would be something like:

study - all the work done to learn something
experiment - one approach to learning something, like an RNA-Seq experiment
biosample  - an actual physical thing like a tissue sample
sample - an extraction from that biosample like an aliquot of RNA
run - something that was run on the sample that will usually produce one or more files