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BAM Telemetry Files on TCGA Sequence Data in dbGaP report identifies TCGA sequence data that is available from the dbGaP database.
The State of Whole Genome/Exome/RNA sequencing: 9-2011
WGS.WES.RNAseq_September.2011v2.pptx
The NCBI SRA: An Evaluation
Some interesting comments from the "tree of life" blog http://phylogenomics.blogspot.com/2011/02/though-i-generally-love-ncbi.html
3 general problems
1) Difficult to upload and download data
2) Limited search functionality
3) The data model (study/experiment/sample/run) is not intuitive and often does not make sense
DNAnexus SRA: An Evaluation
Same data model as NCBI and therfore the same problem in evaluating the linearity between a study and its data
Slightly better search capabilities than NCBI