Table 1 List of databases for plant small RNA research

TAIR (the Arabidopsis information resource)

www.arabidopsis.org/

Genomic information database of Arabidopsis

(Huala et al., 2001)

RGAP (rice genome annotation project)

rice.plantbiology.msu.edu/

Genomic information database of rice

(Kawahara et al., 2013)

RAP-DB (the rice annotation project database)

rapdb.dna.affrc.go.jp/

(Ohyanagi et al., 2006)

Phytozome

phytozome.jgi.doe.gov/pz/portal.html

Genomic information of diverse plant species

(Goodstein et al., 2012)

miRBase (the microRNA database)

www.mirbase.org/

MicroRNA database of diverse organisms

(Griffiths-Jones et al., 2006)

PLncDB (plant long non-coding RNA database)

chualab.rockefeller.edu/gbrowse2/homepage.html

Long non-coding RNA database of Arabidopsis

(Jin et al., 2013)

PNRD (a plant non-coding RNA database)

(structuralbiology.cau.edu.cn/PNRD)

non-coding RNA database of diverse plant species

(Yi et al., 2015)

GEO (gene expression omnibus)

www.ncbi.nlm.nih.gov/geo/

Public repositories for next-generation sequence data

(Edgar et al., 2002)

SRA (sequence read archive)

www.ncbi.nlm.nih.gov/sra/

(Kodama et al., 2012)

DDBJ (DNA Data Bank of Japan) Sequence Read Archive

trace.ddbj.nig.ac.jp/dra/index_e.html

(Kaminuma et al., 2010)

Next-Gen Sequence Databases

mpss.danforthcenter.org/index.php

Public repositories for plant next-generation sequence data

(Nakano et al., 2006)

ASRP (Arabidopsis small RNA project)

asrp.danforthcenter.org/

(Gustafson et al., 2005)

CSRDB (cereal small RNAs database)

sundarlab.ucdavis.edu/smrnas/

(Johnson et al., 2007)

PlantNATsDB (plant natural antisense transcripts database)

bis.zju.edu.cn/pnatdb/

Database of plant natural antisense transcripts

(Chen et al., 2012)

mirEX (Arabidopsis pri-miRNA expression atlas)

www.combio.pl/mirex1/

Databases containing expression data of plant microRNA precursors

(Bielewicz et al., 2012)

PmiRKB (plant microRNA knowledge base)

bis.zju.edu.cn/pmirkb/

(Meng et al., 2011a)

AVT (AtGenExpress visualization tool)

jsp.weigelworld.org/expviz/expviz.jsp

Arabidopsis gene expression databases with user-friendly interface

(Kilian et al., 2007; Goda et al., 2008)

Arabidopsis eFP Browser

bar.utoronto.ca/efp_arabidopsis/cgi-bin/efpWeb.cgi

(Winter et al., 2007)

PceRBase (plant ceRNA database)

bis.zju.edu.cn/pcernadb/index.jsp

Database of plant competing endogenous RNAs

(Yuan et al., 2017)

Arabidopsis epigenome maps

neomorph.salk.edu/epigenome/epigenome.html

Arabidopsis epigenome maps

(Lister et al., 2008)

The SIGnAL Arabidopsis Methylome Mapping Tool

signal.salk.edu/cgi-bin/methylome

(Zhang et al., 2006)

UCSC Genome Browser on Arabidopsis thaliana (2004)

epigenomics.mcdb.ucla.edu/cgi-bin/hgTracks?clade = plant&org = A. + thaliana

(Zhang et al., 2006; Zhang et al., 2007)

UCSC Genome Browser on Arabidopsis thaliana (2009)

genomes.mcdb.ucla.edu/cgi-bin/hgTracks?db = araTha2

(Stroud et al., 2013)

Rice epigenome maps

(plantgenomics.biology.yale.edu)

Rice epigenome maps

(Li et al., 2008)

Plant Methylome DB

epigenome.genetics.uga.edu/PlantMethylome/

Database including epigenome data of 40 wild type plant species

(presented by the Schmitz lab at the University of Georgia)