I would like to get all the sequencing data for a specific organism and/or experiment type from ArrayExpress. I looked into REST queries here, and built the following request:
If I get the accession number from each experiment, I can get a table summarizing the samples:
However, the fields don't have fixed names. I need to get either the SRR and SRX identifiers, or the ERR one, in order to reach the SRA files or fastq files:
I would also like to do it from GEO, but then I need the GSE & GSM identifiers from the experiments, and I can't find them reliably either. This page seems useful but it doesn't say how to construct a query from scratch.
Overall, I'm completely lost by all the different types of identifiers and their connections...