All MPSS was performed essentially as described by Brenner et al. (Nat Biotechnol. 2000 18:630). The specific modifications to the method for the MPSS sequencing of small RNAs are described in the paper Lu et al. (Science 2005, 309:1567) .
Data processing
To determine the normalized abundance value for each signature in the library, we separately merged 2-step runs and 3-step runs to create a raw abundance count for each stepper. The average total number of signatures sequenced in all 2-step or for all 3-step runs was calculated within the library. The normalized abundance is the raw abundance count divided by the average total number of signatures for both of the steppers in the library, multiplied by 250,000 to obtain a "transcripts per quarter million" or TPQ value. For each signature, only one normalized value is used - either the 2-step or 3-step normalized value, selected based on the higher of the sum of the 2-step or 3-step data across all libraries. The numbers in the VALUE column represent the expression level of the corresponding signatures in the SNU libraries. More details are available in Meyers et al. (2004, Genome Research 14:1641).