About Next-Gen Sequence Databases

About Our Databases

Our new UC Davis websites:  Meyers Lab   Databases & Tools

The database and the web pages that you see were produced by the Meyers lab at the UC Davis Genome Center. These data are freely available, but we ask that you cite this web page or related publications; most libraries have been published as part of specific papers, but the best general citation for the website is Nakano et al. (2019) Plant Physiology. We would also like to know that you have found our data to be useful, so please if you use data from this page. Please note, however, that the availability of this data and information does not constitute scientific publication; we request that you respect our right to publish on the complete data sets.

Listed below are the different data sets that we have generated and the sites that we have developed for accessing these data.

Available Databases

SBS Databases

	Organism	small RNA DBs	scRNA-seq DBs	RNA-seq DBs	PARE DBs	nanoPARE DBs	mRNA DGE DBs	MethylC-seq DBs	ChIP DBs
	Aegilops tauschii	tauschii_sRNA   tauschii_sRNA2		tauschii_RNAseq
	Amborella trichopoda	amborel_sRNA			amborel_pare
	Ananas comosus	pineapple_sRNA   pineapple_sRNA2		pineapple_RNAseq
	Aquilegia coerulea	columbine_sRNA		columbine_RNAseq
	Arabidopsis thaliana	at_sRNA   at_sRNA2   at_sRNA3   at_sRNA4   at_sRNA5   at_sRNA_classy   at_sRNA_EV   at_sRNA_FBW   at_sRNA_hen1   at_sRNA_oxy   at_sRNA_RNase   at_sRNA_threshold		at_RNAseq   at_RNAseq2   at_RNAseq_DST   at_RNAseq_polysome   at_RNAseq_RNase   at_RNAseq_URT1   at_RNAseq_xrn4	at_pare   at_pare_EXO   at_pare_FBW   at_pare_oxy   at_pare_RNase   at_pare_threshold   at_pare_xrn4	at_nanoPARE		AT_met
	Asparagus officinalis	asparagus_sRNA		asparagus_RNAseq	asparagus_pare
	Avena sativa	oat_sRNA_evo		oat_RNAseq_evo		oat_nanoPARE_evo
	Brachypodium distachyon	brachy_sRNA   brachy_sRNA_evo		brachy_RNAseq   brachy_RNAseq_evo	brachy_pare	brachy_nanoPARE_evo
	Brassica rapa	brassica_sRNA
	Capsicum annuum	pepper_sRNA_SOL		pepper_RNAseq_SOL
	Carica papaya	papaya_sRNA
	Citrus sinensis	orange_sRNA
	Clostridium acetobutylicum			clos_RNAseq
	Coffea canephora	coffee_sRNA_ufla		coffee_RNAseq_ufla	coffee_pare_ufla
	Erythranthe guttata				mimulus_pare
	Erythranthe lewisii	mimulus_sRNA
	Fragaria vesca	strwbry_sRNA			strwbry_pare
	Gallus gallus	gga_sRNA			gga_pare
	Glycine max	soy_sRNA   soy_sRNA_dcl2   soy_sRNA_seed   soy_sRNA_USB   soy_sRNA_USB2		soy_RNAseq   soy_RNAseq_USB	soy_pare   soy_pare_USB			SOY_met_USB
	Hordeum vulgare	barley_sRNA_anther   barley_sRNA_evo   barley_sRNA_laval		barley_RNAseq   barley_RNAseq_anther   barley_RNAseq_evo   barley_RNAseq_laval	barley_pare   barley_pare_laval	barley_nanoPARE_evo
	Lactuca sativa	lettuce_sRNA			lettuce_pare
	Lemna gibba	lemna_sRNA
	Linum usitatissimum			flax_RNAseq
	Litchi chinensis	litchi_sRNA			litchi_pare
	Magnaporthe oryzae	mg_sRNA		mg_RNAseq
	Malus domestica	apple_sRNA
	Manihot esculenta	cassava_sRNA
	Medicago truncatula	mt_sRNA   mt_sRNA2		mt_RNAseq_miRNAox	mt_pare   mt_pare_miRNAox
	Musa acuminata	banana_sRNA
	Nicotiana benthamiana	nbenthi_sRNA_SOL			nbenthi_pare_SOL
	Nicotiana tabacum	tobacco_sRNA_CP   tobacco_sRNA_SOL			tobacco_pare_SOL
	Oryza brachyantha	obrachy_sRNA			obrachy_pare
	Oryza glaberrima	rice_glab_sRNA		rice_glab_RNAseq
	Oryza punctata	opunctata_sRNA			opunctata_pare
	Oryza sativa	rice_sRNA   rice_sRNA2   rice_sRNA3   rice_sRNA4   rice_sRNA5   rice_sRNA_ago1d   rice_sRNA_dclCrispr   rice_sRNA_drt   rice_sRNA_flr   rice_sRNA_KAanther   rice_sRNA_m6a   rice_sRNA_sub		rice_RNAseq   rice_RNAseq_ago1d   rice_RNAseq_anther   rice_RNAseq_drt   rice_RNAseq_KAanther   rice_RNAseq_sub	rice_pare   rice_pare_ago1d   rice_pare_drt		rice_dge	RICE_met	rice_chip
	Petunia axillaris	petunia_ax_sRNA
	Petunia inflata	petunia_sRNA
	Phalaenopsis equestris	orchid_sRNA
	Phaseolus vulgaris	commonbean_sRNA
	Phoenix dactylifera	datepalm_sRNA
	Phyllostachys edulis	bamboo_sRNA
	Populus trichocarpa	poplar_sRNA
	Prunus persica	peach_sRNA
	Raddia distichophylla	raddiadi_sRNA_evo		raddiadi_RNAseq_evo		raddiadi_nanoPARE_evo
	Rosa chinensis			rose_RNAseq
	Secale cereale	rye_sRNA_evo		rye_RNAseq_evo		rye_nanoPARE_evo
	Setaria viridis	setaria_sRNA
	Solanum lycopersicum	tomato_sRNA   tomato_sRNA_SOL
	Solanum melongena	eggplant_sRNA_SOL
	Solanum tuberosum	potato_sRNA   potato_sRNA_atlas			potato_pare
	Sorghum bicolor	sorghum_sRNA   sorghum_sRNA_purdue		sorghum_RNAseq_purdue	sorghum_pare
	Spirodela polyrhiza	spirodela_sRNA			spirodela_pare
	Streptochaeta angustifolia	streptochaeta_sRNA		streptochaeta_RNAseq	streptochaeta_pare
	Triticum aestivum	wheat_sRNA   wheat_sRNA_anther   wheat_sRNA_evo   wheat_sRNA_JIC		wheat_RNAseq   wheat_RNAseq_anther   wheat_RNAseq_evo	wheat_pare	wheat_nanoPARE_evo
	Triticum turgidum	durumwheat_sRNA_dcl5   durumwheat_sRNA_dcl5_2   durumwheat_sRNA_evo		durumwheat_RNAseq_dcl5   durumwheat_RNAseq_evo		durumwheat_nanoPARE_dcl5   durumwheat_nanoPARE_evo
	Ustilago maydis			ustilago_RNAseq
	Vitis vinifera	grape_sRNA_atlas   grape_sRNA_GxE
	Zea mays	maize_sRNA   maize_sRNA2   maize_sRNA3   maize_sRNA4   maize_sRNA_dcl5   maize_sRNA_embryo   maize_sRNA_MAGO   maize_sRNA_phas	maize_scRNA_singleProtoplast	maize_RNAseq   maize_RNAseq2   maize_RNAseq3   maize_RNAseq4   maize_RNAseq_dcl5   maize_RNAseq_phas   maize_RNAseq_phas2   maize_RNAseq_protoplast	maize_pare
	Zostera marina	zostera_sRNA

MPSS Databases

	Organism	small RNA & mRNA DGE DBs	mRNA DGE DBs
The data in these databases are from an obsolete technology.
	Arabidopsis thaliana	link
	Magnaporthe oryzae		link
	Oryza sativa	link	link
	Vitis vinifera		link