I'm using TCGA data set to analysis the expression of miRNA in cancers. They used Illumina HiSeq to sequence the micorRNAs. now the question for me is that, they sequenced all miRNAs (miRNA precursores, mature miRNA, miRNA stem loop ), or they just isolated mature miRAN from Gel electrophoresis and sequenced it ? because I cheecked some of the IDs of miRNAs at TCGA data set via miRBase database, some of them seems to belong to miRNA precursore or miRNA stem loop.
Also I looked at the META data file of miRNA at TCGA, they describe like this:
Ligation of linkers and reverse transcription of small RNAs PCR with sequencing primers, size fractionation Sequencing on Illumina GAIIx Alignment of reads to reference genome Read counts per mirna isoform Normalized expression per mirna gene SDRF Files