Bulk data dumps for each species are available via http here.
The data are in 'long format' tables with the columns: 'dataset', 'gene', 'count'. Long tables are prefered for loading into databases as compared to wide matrix format. STAR counts have the prefix 'se.tsv.bz2' while kallisto estimated counts have the 'ke.tsv.bz2' prefix.
QC metrics are also available in long table format with the columns 'dataset','QC metric type', 'QC metric result'.
Corresponding metadata can be obtained here via http here. The files with the ".tsv" suffix are obtained from SRA and describe each run. The files with the ".tsv.cut" are a reduced metadata, which just contains the corresponding accession numbers and QC summary.
Data for studies with more than 4 runs are packaged as zip files and available here.