Bioinformatics resources for deciphering the biogenesis and action pathways of plant small RNAs

Yu, Dongliang; Ma, Xiaoxia; Zuo, Ziwei; Shao, Weishan; Wang, Huizhong; Meng, Yijun

doi:10.1186/s12284-017-0177-y

Rice

Table 3 List of sequencing data for plant small RNA research

From: Bioinformatics resources for deciphering the biogenesis and action pathways of plant small RNAs

Data type	Species	Dataset ID		Description^a	Reference
RNA-seq	Arabidopsis (Col-0)	GSE57215	GSM1377353	dcl234 rep1	(Li et al., 2015)
			GSM1377354	dcl234 rep2
			GSM1377355	dcl234 rep3
			GSM1377356	dcl234 nrpd1 rep1
			GSM1377357	dcl234 nrpd1 rep2
			GSM1377358	dcl234 nrpd1 rep3
			GSM1377359	dcl234 DSN
			GSM1377360	dcl234 nrpd1 DSN
			GSM1377361	dcl234 rdr2 DSN
			GSM1377362	dcl234 PolyA+ rep1
			GSM1377363	dcl234 PolyA+ rep2
			GSM1377364	dcl234 nrpd1 PolyA+ rep1
			GSM1377365	dcl234 nrpd1 PolyA+ rep2
			GSM1377366	dcl234 PolyA- rep1
			GSM1377367	dcl234 PolyA- rep2
			GSM1377368	dcl234 nrpd1 PolyA- rep1
			GSM1377369	dcl234 nrpd1 PolyA- rep2
	Rice	GSE50778	GSM1229044	Nipponbare	(Wei et al., 2014)
			GSM1229045	Nipponbare dcl3a RNAi-1
			GSM1229046	Nipponbare dcl3a RNAi-3
DsRNA-seq	Arabidopsis	GSE23439	GSM575243	WT 1 × ribominus	(Zheng et al., 2010)
			GSM575244	WT 2 × ribominus
			GSM575245	rdr6
		GSE57215	GSM1377347	dcl234 unopened flower buds rep1	(Li et al., 2015)
			GSM1377348	dcl234 unopened flower buds rep2
			GSM1377349	dcl234 unopened flower buds rep3
			GSM1377350	dcl234 nrpd1 unopened flower buds rep1
			GSM1377351	dcl234 nrpd1 unopened flower buds rep2
			GSM1377352	dcl234 nrpd1 unopened flower buds rep3
Degradome-seq	Arabidopsis (Col-0)	GSE77549	GSM2054358	WT 11-day-old seedlings	(Hou et al., 2016)
			GSM2054359	WT inflorescences
			GSM2253889	WT inflorescences rep1
			GSM2253892	WT inflorescences rep2
			GSM2253890	rdr6 inflorescences rep1
			GSM2253893	rdr6 inflorescences rep2
			GSM2253891	ago7 inflorescences rep1
			GSM2253894	ago7 inflorescences rep2
		GSE52342	GSM1263708	WT inflorescences	(Creasey et al., 2014)
			GSM1263709	ddm1-2 inflorescences
			GSM1263710	rdr6–15 inflorescences
			GSM1263711	ddm1–2 rdr6–15 inflorescences
		GSE47121	GSM1145327	Flower buds rep1	(Willmann et al., 2014)
		GSE47121	GSM1145328	Flower buds rep2	(Willmann et al., 2014)
		GSE11007	GSM278333	Inflorescences, dT primed	(Addo-Quaye et al., 2008)
			GSM278334	Inflorescences, dT primed
			GSM278335	Inflorescences, random primed
			GSM278370	Seedlings, random primed
		GSE11094	GSM280226	WT inflorescences	(German et al., 2008)
		GSE11094	GSM280227	xrn4 inflorescences	(German et al., 2008)
		GSE55151	GSM1330569	Young leaves	(Thatcher et al., 2015)
			GSM1330570	Mature leaves
			GSM1330571	Early senescence leaves rep 1
			GSM1330573	Early senescence leaves rep 2
			GSM1330572	Late senescence leaves rep 1
			GSM1330574	Late senescence leaves rep 2
		GSE11070	GSM284751	WT Flowers rep1	(Gregory et al., 2008)
		GSE11070	GSM284752	ein5-6 flowers rep1	(Gregory et al., 2008)
		GSE71913	GSM1847333	Unopened flower buds, abh1–1	(Yu et al., 2016b)
			GSM1847334	Unopened flower buds, abh1–8
			GSM1939001	Leaves, treated with translation inhibitor CHX rep1
			GSM1939002	Leaves, treated with translation inhibitor CHX rep2
		GSE66224	GSM1617433	Immature inflorescences rep1	(Vandivier et al., 2015)
		GSE66224	GSM1617434	Immature inflorescences rep2	(Vandivier et al., 2015)
	Rice	GSE42467	GSM1040649	Young panicles of ZH11 (japonica) at high temperature
		GSE66610	GSM1626143	Nipponbare Leaves	(Baldrich et al., 2015)
		GSE66610	GSM1626145	Nipponbare Leaves	(Baldrich et al., 2015)
		GSE62334	GSM1525457	Nipponbare leaves
		GSE17398	GSM434596	Nipponbare seedlings	(Li et al., 2010)
		GSE19050	GSM476257	93-11 (indica) young inflorescences	(Zhou et al., 2010)
		GSE18251	GSM455938	Nipponbare seedlings	(Wu et al., 2009)
		GSE18251	GSM455939	Nipponbare inflorescences	(Wu et al., 2009)
SRNA-seq	Arabidopsis (Col-0)	GSE57215	GSM1377370	WT rep1	(Li et al., 2015)
			GSM1377371	WT rep2
			GSM1377372	nrpd1 rep1
			GSM1377373	nrpd1 rep2
			GSM1377374	dcl3 rep1
			GSM1377375	dcl3 rep2
			GSM1377376	rdr2 rep1
			GSM1377377	rdr2 rep2
			GSM1377378	dcl234 rep1
			GSM1377379	dcl234 rep2
			GSM1377380	dcl234 nrpd1 rep1
			GSM1377381	dcl234 nrpd1 rep2
		GSE23439	GSM575246	WT	(Zheng et al., 2010)
		GSE23439	GSM575247	rdr6	(Zheng et al., 2010)
		GSE14695	GSM366868	Whole aerials	(Fahlgren et al., 2009)
			GSM366869	Whole aerials dcl1–7
			GSM366870	Whole aerials dcl2–1dcl3-1dcl4–2
		GSE44622	GSM1087973	WT, flowers rep1	(Jeong et al., 2013)
			GSM1087974	WT, flowers rep2
			GSM1087975	dcl1–7, flowers rep 1
			GSM1087976	dcl1–7, flowers rep 2
			GSM1087977	dcl234, flowers rep 1
			GSM1087978	dcl234, flowers rep 2
			GSM1087979	rdr2, flowers rep 1
			GSM1087980	rdr2, flowers rep 2
		GSE35562	GSM1178880	WT flowers, rep1	(Zhai et al., 2013)
			GSM1178881	WT flowers, rep2
			GSM1178882	WT flowers, rep3
			GSM1178883	hen1–8 flowers, rep1
			GSM1178884	hen1–8 flowers, rep2
			GSM1178885	hen1–8 flowers, rep3
		GSE26161	GSM642337	sRNAs cloned from total RNA	(Zhang et al., 2011)
		GSE26161	GSM642338	sRNAs cloned from AGO2	(Zhang et al., 2011)
		GSE28591	GSM707678	WT, flowers	(Wang et al., 2011)
			GSM707679	WT, leaves
			GSM707680	WT, roots
			GSM707681	WT, seedlings
			GSM707682	AGO1-associated sRNAs, flowers
			GSM707683	AGO1-associated sRNAs, leaves
			GSM707684	AGO1-associated sRNAs, roots
			GSM707685	AGO1-associated sRNAs, seedlings
			GSM707686	AGO4-associated sRNAs, flowers
			GSM707687	AGO4-associated sRNAs, leaves
			GSM707688	AGO4-associated sRNAs, roots
			GSM707689	AGO4-associated sRNAs, seedlings
		GSE39885	GSM980695	sRNAs cloned from total RNA	(Zhu et al., 2011)
		GSE39885	GSM980697	sRNAs cloned from AGO10	(Zhu et al., 2011)
		GSE16545	GSM415783	sRNAs cloned from total RNA, flowers	(Havecker et al., 2010)
			GSM415784	sRNAs cloned from total RNA, flowers
			GSM415785	sRNAs cloned from total RNA, flowers
			GSM415791	sRNAs cloned from AGO9, flowers
			GSM415792	sRNAs cloned from AGO9, flowers
		GSE10036	GSM253622	sRNAs cloned from AGO1	(Mi et al., 2008)
			GSM253623	sRNAs cloned from AGO2
			GSM253624	sRNAs cloned from AGO4
			GSM253625	sRNAs cloned from AGO5
		GSE12037	GSM304282	sRNAs cloned from total RNA (AGO2 mock)	(Montgomery et al., 2008)
			GSM304283	sRNAs cloned from AGO2
			GSM304284	sRNAs cloned from total RNA (AGO7 mock)
			GSM304285	sRNAs cloned from AGO7
	Rice	GSE20748	GSM520640	Nipponbare WT seedlings	(Wu et al., 2010)
			GSM520639	Nipponbare rdr2 seedlings
			GSM520637	Nipponbare dcl1 seedlings
			GSM520638	Nipponbare dcl3 seedlings
GSE26405		GSM648139	ZH11 (japonica) high temperature panicles	(Song et al., 2012b)
		GSM648140	ZH11 (japonica) rdr6 high temperature panicles
		GSM648141	ZH11 (japonica) low temperature panicles
		GSM648142	ZH11 (japonica) rdr6 low temperature panicles
GSE22763		GSM562942	93–11 (indica) WT seedlings	(Song et al., 2012a)
		GSM562944	93-11 (indica) dcl4–1 seedlings
		GSM562943	93–11 (indica) WT panicles
		GSM562945	93–11 (indica) dcl4–1 panicles
GSE35562		GSM913524	Dongjin hen1–3, leaves	(Zhai et al., 2013)
GSE35562		GSM913525	Dongjin WT, leaves	(Zhai et al., 2013)
GSE50778		GSM1229047	Nipponbare WT	(Wei et al., 2014)
		GSM1229048	Nipponbare dcl3a, RNAi-1
		GSM1229049	Nipponbare dcl3a, RNAi-3
GSE32973		GSM816687	Nipponbare seedlings rep1	(Jeong et al., 2011)
		GSM816688	Nipponbare seedlings rep2
		GSM816689	Nipponbare seedlings rep3
		GSM816700	Nipponbare seedlings dcl1 RNAi rep1–1
		GSM816701	Nipponbare seedlings dcl1 RNAi rep1–2
		GSM816702	Nipponbare seedlings dcl1 RNAi rep2–1
		GSM816703	Nipponbare seedlings dcl1 RNAi rep2–2
		GSM816730	Nipponbare panicles rep1–1
		GSM816731	Nipponbare panicles rep1–2
		GSM816732	Nipponbare panicles rep2
		GSM816745	Nipponbare panicles dcl1 RNAi rep1–1
		GSM816746	Nipponbare panicles dcl1 RNAi rep1–2
		GSM816747	Nipponbare panicles dcl1 RNAi rep2–1
		GSM816748	Nipponbare panicles dcl1 RNAi rep2–2
GSE20748		GSM520640	Nipponbare seedlings, sRNAs cloned from total RNA	(Wu et al., 2010)
		GSM520634	Nipponbare seedlings, sRNAs cloned from AGO4a
		GSM520635	Nipponbare seedlings, sRNAs cloned from AGO4b
		GSM520636	Nipponbare seedlings, sRNAs cloned from AGO16
GSE18250		GSM455962	Nipponbare seedlings, sRNAs cloned from AGO1a	(Wu et al., 2009)
		GSM455963	Nipponbare seedlings, sRNAs cloned from AGO1b
		GSM455964	Nipponbare seedlings, sRNAs cloned from AGO1c
PRJNA273330		SRX847816	Nippbare sRNAs cloned from AGO1a Rep1
		SRX847817	Nippbare sRNAs cloned from AGO1a Rep2
		SRX847818	Nippbare sRNAs cloned from AGO1b Rep1
		SRX847819	Nippbare sRNAs cloned from AGO1b Rep2
		SRX847820	Nippbare sRNAs cloned from AGO18 Rep1
		SRX847821	Nippbare sRNAs cloned from AGO18 Rep2
DRP000161		DRX000196	sRNA-IP in WT (Nipponbare)	(Komiya et al., 2014)
		DRX000197	sRNA-IP in mel1 (Nipponbare)
		DRX000198	Total sRNA in WT (Nipponbare)
		DRX000199	Total sRNA in mel1 (Nipponbare)

^aPlease see detailed descriptions of the datasets in the related references

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