Code and resources for Tomato Root Atlas

Title: Novelty, conservation, and repurposing of gene function in root cell type development

Authors: Kaisa Kajala, Mona Gouran, Lidor Shaar-Moshe, G. Alex Mason, Joel Rodriguez-Medina, Dorota Kawa, Germain Pauluzzi, Mauricio Reynoso, Alex Canto-Pastor, Concepcion Manzano, Vincent Lau, Mariana A. S. Artur, Donnelly A. West, Sharon B. Gray, Alexander T. Borowsky, Bryshal P. Moore, Andrew I. Yao, Kevin W. Morimoto, Marko Bajic, Elide Formentin, Niba Nirmal, Alan Rodriguez, Asher Pasha, Roger B. Deal, Daniel Kliebenstein, Torgeir R. Hvidsten, Nicholas J. Provart, Neelima Sinha, Daniel E. Runcie, Julia Bailey-Serres, Siobhan M. Brady

Journal: TBC

Abstract:

TBC

• Obtaining RNA-seq read counts: Trimming, Kallisto and STAR
• Relative differential expression: Roku
• Co-expression network analysis: WGCNA
• ATAC-aseq analysis
• Motif enrichment
• Ontology enrichment
• Orthology maps
• Detecting constitutively expressed genes
• Differential expression: limma-voom

These detailed bench protocols describe the methods as carried out in the Tomato Root Atlas paper.

• TRAP purification of translating ribosomes
• RNA-seq library preparation from TRAP
• INTACT isolation of nuclei
• ATAC-seq library preparation from INTACT

• Pairwise comparison of ATAC cut-counts between cell types

• [Data on GEO]
• [eFP browser]

• Flowchart for identification and annotation of ATAC-seq data. Data analysis overview for methods used for identification of replicate transposase hypersensitive sites.

  

• Unique cell type network construction pipeline. Data analysis overview for methods used to construct inferred cell type-unique regulatory networks.

  

• Pipeline of cross-species analysis. An overview of the pipeline and methods used for exploring the conservation of homologous cell types and tissues among tomato, Arabidopsis, and rice.