A comprehensive online database for exploring ~20,000 public Arabidopsis RNA-Seq libraries

Application of Next Generating Sequencing (NGS) technology in transcriptome profiling has greatly improved our understanding of transcriptional regulation at genome-wide scale in the last decade, and tens of thousands of RNA-sequencing (RNA-seq) libraries have been produced by the research community. However, accessing such huge amount of RNA-seq data poses a big challenge for groups that lack dedicated bioinformatic personnel or expensive computational resources. Here, we introduce the Arabidopsis RNA-seq database (ARS), a free, web-accessible, and user-friendly to quickly explore expression level of any gene in 20,000+ publicly available Arabidopsis RNA-seq libraries.

[1]  Tom H. Pringle,et al.  The human genome browser at UCSC. , 2002, Genome research.

[2]  Craig S. Pikaard,et al.  An ARGONAUTE4-Containing Nuclear Processing Center Colocalized with Cajal Bodies in Arabidopsis thaliana , 2006, Cell.

[3]  S. Jacobsen,et al.  The Arabidopsis Chromatin-Modifying Nuclear siRNA Pathway Involves a Nucleolar RNA Processing Center , 2006, Cell.

[4]  Kan Nobuta,et al.  Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA , 2005, Nucleic Acids Res..

[5]  N. Fedoroff,et al.  Dynamic Regulation of ARGONAUTE4 within Multiple Nuclear Bodies in Arabidopsis thaliana , 2008, PLoS genetics.

[6]  R. Lister,et al.  Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis , 2008, Cell.

[7]  I. Henderson,et al.  Tandem repeats upstream of the Arabidopsis endogene SDC recruit non-CG DNA methylation and initiate siRNA spreading. , 2008, Genes & development.

[8]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[9]  Rasko Leinonen,et al.  The sequence read archive: explosive growth of sequencing data , 2011, Nucleic Acids Res..

[10]  Sean R. Davis,et al.  NCBI GEO: archive for functional genomics data sets—update , 2012, Nucleic Acids Res..

[11]  Steven L Salzberg,et al.  HISAT: a fast spliced aligner with low memory requirements , 2015, Nature Methods.

[12]  S. Salzberg,et al.  StringTie enables improved reconstruction of a transcriptome from RNA-seq reads , 2015, Nature Biotechnology.

[13]  She Chen,et al.  The Arabidopsis acetylated histone-binding protein BRAT1 forms a complex with BRP1 and prevents transcriptional silencing , 2016, Nature Communications.

[14]  M. Matzke,et al.  Identification of Coilin Mutants in a Screen for Enhanced Expression of an Alternatively Spliced GFP Reporter Gene in Arabidopsis thaliana , 2016, Genetics.

[15]  James T. Robinson,et al.  Variant Review with the Integrative Genomics Viewer. , 2017, Cancer research.

[16]  Erik S. Ferlanti,et al.  ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology[OPEN] , 2017, Plant Cell.

[17]  F. Thibaud-Nissen,et al.  Araport11: a complete reannotation of the Arabidopsis thaliana reference genome , 2016, bioRxiv.

[18]  Sebastian Proost,et al.  CoNekT: an open-source framework for comparative genomic and transcriptomic network analyses , 2018, bioRxiv.

[19]  Brian D. Gregory,et al.  EPIC-CoGe: managing and analyzing genomic data , 2018, Bioinform..

[20]  Thomas M. Keane,et al.  The European Nucleotide Archive in 2018 , 2018, Nucleic Acids Res..

[21]  Osamu Ogasawara,et al.  DDBJ update: the Genomic Expression Archive (GEA) for functional genomics data , 2018, Nucleic Acids Res..

[22]  Sequence Alignment Map , 2020, Definitions.