Data from Lunardon et al. (2020)

Citation

If you make use of these data and/or this website, please cite: Lunardon et al. (2020) Genome Research https://doi.org/10.1101/gr.256750.119

People

• Michael J. Axtell, Ph.D.

  Principal Investigator

  Project management, web development, software development
  [email protected]

• Matthew Jones-Rhoades, Ph.D.

  Co-Principal Investigator

  Undergraduate education and mentoring
  [email protected]

• Alice Lunardon, Ph.D.

  Postdoctoral researcher

  Lead scientist; Data analysis and processing; supervision of students
  [email protected]

• Nathan Johnson

  Ph.D. Candidate

  Software development and testing
  [email protected]

• Emily Hagerott

  Undergraduate Researcher

  Small RNA-seq of spinach, carrot
  [email protected]

• Tamia Phifer

  Undergraduate Researcher

  Small RNA-seq of Cuscuta
  [email protected]

• Seth Polydore, Ph.D.

  Ph.D. student (degree earned Fall 2018!)

  Preparation of Arabidopsis thaliana annotations
  [email protected]

• Ceyda Coruh, Ph.D.

  Postdoctoral Researcher

  Small RNA-seq of maize
  [email protected]

Software

All of the analyses and web applications are built with open-source software, for which we are very grateful. Here is a listing of the packages used with citations / urls:

• samtools Tools for storing and manipulating sequence alignments in the SAM / BAM formats : Li et al., 2009. Bioinformatics. doi: 10.1093/bioinformatics/btp352
• bowtie : A high-performance aligner optimized for short reads : Langmead et al., 2009. Genome Biology. doi: 10.1186/gb-2009-10-3-r25
• ViennaRNA : A suite of programs for assessment and prediction of RNA secondary structure : Lorenz et al., 2011. Algorithms for Molecular Biology. doi: 10.1186/1748-7188-6-26
• bedtools : Tools for genome arithmetic : Quinlan and Hall, 2010. Bioinformatics. doi: 10.1093/bioinformatics/btq033
• deepTools : Tools for processing and analyzing genomic datasets : Ramirez et al., 2016. Nucleic Acids Research. doi: 10.1093/nar/gkw257
• cutadapt : A tool for rapid adapter trimming of RNA-seq data : Martin, 2011. EMBnet.journal. doi: 10.14806/ej.17.1.200
• JBrowse : An AJAX-powered genome browser : Skinner et al., 2009. Genome Research. doi: 10.1101/gr.094607.109
• jbplugin-smallrna : A JBrowse plugin for visualization of small RNA-seq BAM files : Hofmeister and Schmitz, 2018. Bioinformatics. doi: 10.1186/s12859-018-2160-z
• multibigwig : A jbrowse plugin for viewing multiple bigwig datasets in a single track
• BLAST : The basic local alignment search tool : Altschul et al. 1990. J. Mol. Biol. doi: 10.1016/S0022-2836(05)80360-2
• R : The open-source statistical computing environment
• Apache : Open-source web server
• MariaDB : Open-source MySQL database server

And of course we've made use of our own open-soruce tools, namely:

• ShortStack : Alignment and annotation of small RNAs : Johnson et al. 2016. G3. doi: 10.1534/g3.116.030452
• strucVis : Visualization of small RNA-seq depth over a predicted RNA secondary structure.

Data

Although some of the sRNA-seq was generated by our labs, most came from public repositories like GEO and SRA. We thank the countless scientists who've made their sRNA-seq data publicly available. We also relied entirely on publicly available genome assemblies for all of the plants analyzed, and thank everyone involved in those genome projects as well