Plant Secondary Phased siRNA Database

small RNA libraries

Species	reference	Sample	Cleaned reads	Matched reads	Distinct reads	Matched distinct read	Data source
Eudicot
Populus trichocarpa	Genome Transcriptome	Leaves	3499435	1643146	1335178	706169	udel.edu
		Xylem	3649082	1846758	2048338	1133574	udel.edu
		Mechanically treated xylem	2122892	722665	950348	388955	udel.edu
Citrus sinensis	Genome Transcriptome	Leaves	3082032	1722868	1614670	902238	udel.edu
		Flower	2612979	1206575	1489530	676695	udel.edu
		Fruit	2215692	1073748	1027204	539346	udel.edu
Arabidopsis lyrata	Genome Transcriptome	Flowers (stage1-12), replicate 1	4498159	3483402	1599150	1599141	GSM518430
		Flowers (stage1-12), replicate 2	3934017	3063299	1339392	1339386	GSM518431
		Leaves	3747830	3127429	856513	856511	GSM518429
Arabidopsis thaliana	Genome Transcriptome	aerial bolting	3628042	3379583	730552	730521	GSM518432
Carica papaya	Genome Transcriptome	Leaves	3820445	1974866	1968208	1089162	udel.edu
		Flower	3865797	1779088	2145990	1127258	udel.edu
		Leaves inoculated with ringspot virus	3204306	1177743	1217047	632386	udel.edu
Vitis vinifera	Genome Transcriptome	Leaves	2971603	1695097	823291	417668	udel.edu
		Flower	1686208	816428	620254	317831	udel.edu
		Fruit	1431197	612443	530705	240594	udel.edu
Nicotiana tabacum	Genome Transcriptome	Leaves	2326484	440345	1558803	417611	udel.edu
		Flower	4068724	682101	2930127	748631	udel.edu
		Pod	1525359	257383	995716	244556	udel.edu
Solanum tuberosum	Genome Transcriptome	Leaves	3774694	1674311	1991254	802003	udel.edu
		Flower	4183920	1738773	2331999	956111	udel.edu
		Stolon	3511180	1284511	1861588	739728	udel.edu
Solanum lycopersicum	Genome Transcriptome	Leaves	4130263	2852221	1493928	1085053	udel.edu
		Flower	4361332	2817928	2109755	1522007	udel.edu
		Fruit	4334932	2731643	2172623	1628762	udel.edu
Mimulus guttatus	Genome Transcriptome	Leaves	2948811	2023306	499954	200731	udel.edu
		Flower	3788230	2434158	2071391	1421861	udel.edu
		Root	3866276	1809745	2059471	1074556	udel.edu
Monocot
Musa acuminata	Genome Transcriptome	Leaves	2746122	896150	975425	224084	udel.edu
		Flower	3617237	918804	1561483	392400	udel.edu
		Fruit	4527226	1029742	2492949	625850	udel.edu
Oryza sativa L. ssp. indica	Genome Transcriptome	93-11 shoot	3496537	1607274	1799476	1227233	GSM489088
Oryza sativa L. ssp. japonica	Genome Transcriptome	Nipponbare shoot	3561149	1719110	1984553	1356286	GSM489087
Oryza rufipogon	Genome Transcriptome	Leaves	12116270	3969802	6130962	1382025	GSM960649
		Root	6090929	1691857	3630108	1039481	GSM960650
		Seed	10782959	3966358	5781973	1724101	GSM960651
Panicum virgatum	Genome Transcriptome	Leaves	2491730	1184975	870444	502544	udel.edu
		Flower	2822611	1352766	1911780	1233960	udel.edu
		Drought-treated leaves	1741344	732720	649745	348792	udel.edu
Setaria italica	Genome Transcriptome	Leaves	3007115	1544507	836849	519943	udel.edu
		Flower	5053097	3561932	2321739	1806750	udel.edu
		Root	3468075	1706269	1063438	726523	udel.edu
Zea mays	Genome Transcriptome	Leaves	3085701	1496133	1181833	776492	udel.edu
		Female inflorescence (Ears)	4394339	2353397	2569994	1933950	udel.edu
		Male inflorescence (Tassels)	4081366	2326810	2441621	1928062	udel.edu
Sorghum bicolor	Genome Transcriptome	Leaves	2573286	1303266	728125	321320	udel.edu
		Flower	3973760	2564772	1544749	973924	udel.edu
		Young panicle in early grain fill	3494555	2096174	1276810	826598	udel.edu
basal angiosperm
Amborella trichopoda	Genome Transcriptome	Leaves	3793655	2543541	1557524	971938	udel.edu
Gymnosperm
Cycas rumphii	Transcriptome	Leaves	2820155	152193*	817883	17723*	udel.edu
		Female cone	2851241	81015*	888293	12614*	udel.edu
		Male cone	4481064	120612*	1375549	19559*	udel.edu
Ginkgo biloba	Transcriptome	Leaves	3024449	143705*	702737	34506*	udel.edu
		Female cone	2910746	122191*	658666	23802*	udel.edu
		Male cone	2773329	119213*	597520	31845*	udel.edu
moss
Physcomitrella patens	Genome Transcriptome	Protonemata	120199	39382	72553	20241	GSM115095
		Protonemata and young gametophores	191952	98629	74115	38359	GSM115096
		Gamteophores and sporophytes	217692	108678	69541	30623	GSM115097
Green algae
Volvox carteri	Genome Transcriptome	Control	13456382	8148715	1115476	408629	udel.edu
		Sulfate starvation	13930076	8608931	1117792	426961	udel.edu
		Phosphate starvation	13545039	8305919	838469	307744	udel.edu
Chlamydomonas reinhardtii	Genome Transcriptome	Control	13135855	6035176	498802	97020	udel.edu
		Phosphate starvation	13836178	6159765	495612	124653	udel.edu
		Sulfate starvation	14671497	4802365	677615	293760	udel.edu

* small RNAs were only aligned to transcriptome