Experimental procedures for non-coding sRNA identification. (a) Sample preparation for deep sequencing with GS FLX: Sample 1 is enriched for primary transcripts. Treatment 1: Terminator Phosphate Dependent Exonuclease (TPE) was used to eliminate processed transcripts. Treatment 2: Tobacco Acid Pyrophosphatase (TAP) was used to eliminate pyrophosphates from primary transcripts. Sample 2 is enriched for processed transcripts. (b) Sample preparation for deep sequencing with Genome Analyzer II. (c) Sample labeling and hybridization for microarray-based screening. (d) Sample preparation for Affymetrix Symbiosis Chip-based screening.