Table 1.

Repeat-associated miRNAs from OsAGO1s-enriched, OsDCLs-dependent datasets.

MIRNA	Enriched sequencea	Abundance (TP10M)b	Positionc	Size (nt)	Repeat class/familyi	Matching repeat	DCL dependency
MIR435	TATCCGGTATTGGAGTTGAGG	1268.1	Mature	21	DNA/MULE-MuDR	Mermiteh	DCL1
	TTATCCGGTATTGGAGTTGA	323.4	Mature	20			DCL1/4
MIR1850	CCAAATTCCCAACTTTTCATC	87.1	Star	21	DNA	Unique	DCL3
	TTAGTTCACATCAATCTTCCT	107.8	Otherd	21			DCL4
MIR1862d,e	TTTGTTTATTTTGGGACGGAG	27.7	Othere	21h	DNA/TcMar-Stowaway	Stowaway47	DCL4
MIR1867	TAGGACAGAGGGAGTAGATGT	25.4	Otherf	21h	DNA/CMC-EnSpm	EnSpm-11	DCL1
	TTTTTCTAGGACAGAGGGAGT	125.1	Otherg	21h			DCL1/4
MIR1868	TACTTCCTCGTTTTCCGTAAA	48.6	Star	21h	DNA/PIF-Harbinger	Wanderer	DCL3
MIR1884b	TATGACGCTGTTGACTTTT	7.7	Otherd	19h	DNA/TcMar-Stowaway	Stowaway2	DCL1/3
	TATGACGCTGTTGACTTTTAGA	62.3	Otherd	22h			DCL1
	TATGACGCTGTTGACTTTTA	160.7	Otherd	20h			DCL3
	TATGACGCTGTTGACTTTTAG	1515.7	Otherd	21h			DCL3/4
MIR2872	TTCGGTTTGTAGAATACCATC	23.1	Star	21	LTR/Gypsy	SZ-42_LTR	DCL1

^aEnriched sequences for each miRNA precursor in the pooled AGO1 datasets. Datasets include GSE18251 (Wu et al. 2009), GSE20748 (Wu et al. 2010), and GSE22763 (Song et al. 2012);

^bThe normalized abundance (transcript per ten million, TP10M) in the pooled AGO1 datasets;

^cMapping positions of each sequence on miRNA hairpin (mature: ±2nt of mature miRNA; star: ±2nt of miRNA*; other: any position other than mature and star);

^d5' end of these species were +4 nt off comparing to annotated mature miRNAs in miRBase;

^e5' end of these species were +6 nt off comparing to annotated mature miRNAs in miRBase;

^f5' end of these species were +9 nt off comparing to annotated mature miRNAs in miRBase;

^g5' end of these species were +3 nt off comparing to annotated mature miRNAs in miRBase;

^hAnnotated mature miRNAs in miRBase are 24-nt long;

ⁱDNA, DNA transposons; TcM-Stowaway: parallel homologous groups Tourist class Mariner and Stowaway MITES; LTR, long terminal repeat retrotransposons.