The tomato small RNA database contains all tomato small RNAs collected from the following samples (Spet. 2013):

sample ID	organism	cultivar	tissue	link	study
S0371	Solanum lycopersicum	Heinz 1706	leaf	Link
S0372	Solanum lycopersicum	Heinz 1706	flower	Link
S0373	Solanum lycopersicum	Heinz 1706	fruit	Link
S0707	Solanum lycopersicum	MicroTom	closed bud before flower blooming	GSM452712	Mohorianu et al. (2011) Plant J
S0708	Solanum lycopersicum	MicroTom	flower, open	GSM452713
S0709	Solanum lycopersicum	MicroTom	fruit, 1mm to 3mm in diameter	GSM452714
S0710	Solanum lycopersicum	MicroTom	fruit, 5mm to 7mm in diameter	GSM452715
S0711	Solanum lycopersicum	MicroTom	fruit, 11mm to 14mm in diameter	GSM452716
S0712	Solanum lycopersicum	MicroTom	fruit, mature green	GSM452717
S0713	Solanum lycopersicum	MicroTom	fruit, breaker stage	GSM452718
S0714	Solanum lycopersicum	MicroTom	fruit, 3 days post breake	GSM452719
S0715	Solanum lycopersicum	MicroTom	fruit, 5 days post breaker	GSM452720
S0716	Solanum lycopersicum	MicroTom	fruit, 7 days post breaker	GSM452721
S0717	Solanum lycopersicum	M82	seedlings, two-week-old, replicate1	GSM577998	Shivaprasad et al. (2012) EMBO J
S0718	Solanum lycopersicum	M82	seedlings, two-week-old, replicate2	GSM577999
S0719	Solanum pennellii	LA716	seedlings, two-week-old, replicate1	GSM578000
S0720	Solanum pennellii	LA716	seedlings, two-week-old, replicate2	GSM578001
S0721	Solanum lycopersicum x S. pennellii	M82 x LA716 (F1)	seedlings, two-week-old, replicate1	GSM578002
S0722	Solanum lycopersicum x S. pennellii	M82 x LA716 (F1)	seedlings, two-week-old, replicate2	GSM578003
S0723	Solanum lycopersicum x S. pennellii	M82 x LA716 (F2)	seedlings, two-week-old, replicate1	GSM578004
S0724	Solanum lycopersicum x S. pennellii	M82 x LA716 (F2)	seedlings, two-week-old, replicate2	GSM578005
S0725	Solanum lycopersicum x S. pennellii	M82 x LA716 (F2)	seedlings, two-week-old, replicate3	GSM578006
S0726	Solanum lycopersicum	IL1-1	seedlings, two-week-old	GSM578007
S0727	Solanum lycopersicum	IL2-5	seedlings, two-week-old	GSM578008
S0728	Solanum lycopersicum	IL8-1-1	seedlings, two-week-old	GSM578009
S0729	Solanum lycopersicum	IL8-1D	seedlings, two-week-old	GSM578010
S0730	Solanum lycopersicum	IL8-1-3	seedlings, two-week-old	GSM578011
S0731	Solanum lycopersicum	IL8-2	seedlings, two-week-old	GSM578012
S0732	Solanum lycopersicum	IL8-2-1	seedlings, two-week-old	GSM578013
S0733	Solanum lycopersicum	IL8-3	seedlings, two-week-old	GSM578014
S0734	Solanum lycopersicum	IL8-3-1	seedlings, two-week-old	GSM578015
S0735	Solanum lycopersicum	Sunny	leaf, TSWV-infected	SRX328502
S0736	Solanum lycopersicum	Ailsa Craig	fruit, immature (17 days after anthesis)	SRX099432	Zhong et al. (2013) Nature Biotech
S0737	Solanum lycopersicum	Ailsa Craig	fruit, mature green (39 days after anthesis)	SRX099433
S0738	Solanum lycopersicum	Ailsa Craig	fruit, breaker (42 days after anthesis)	SRX099433
S0739	Solanum lycopersicum	Ailsa Craig	fruit, red ripe (52 days after anthesis)	SRX099432

The small RNA datasets were combined by removing redundancies (same sequences, same lengths, and same directions). Small RNAs derived from rRNA and tRNA were discarded. sRNAs with transcripts per million (TPM) >=50 in at least one sample and with length of 19-24 nt were included in the miRNA identification. These sRNAs were aligned to the tomato genome sequence and the flanking sequences (200bp to each side) of sRNAs with no more than 20 unique genome hits were extracted and folded with the RNAfold program. The structures were then checked with miRcheck to identify potential miRNA candidates. miRNA candidates were then compared to miRBase to identify conserved miRNA candidates (up to two mismatches). The miRNA targets (ITAG predicted cDNAs, v2.3) were identified using the target prediction tool developed and implemented in the database.