Data and code for Brun et al. - Seed metabolites headstart haustoriogenesis and potentiate aggressiveness of parasitic weeds

Data, codes, and final outputs for the research article Brun et al., "Seed metabolites headstart haustoriogenesis and potentiate aggressiveness of parasitic weeds", containing raw data tables and R scripts for bioassays, RNAseq read mapping data and analysis code, MS raw files from LC-MS analysis, annotation details, as well as post-processing information as follows: 1) Directory "Bioassays" : contains all raw data are available as Excel spreadhseet. The R scripts are organized per Figure panel or supplementary figure for easy processing. 2) Directory "LC-MS" - Annotation : contains the four main files used as supplementary data S7-S10 - Post-processing : contains the two abundance files from each kinetic analysis and the R script to generate the final heatmap. - RAW MS files - Conditioning_raw_files : all *.raw MS files pertaining to LC-MS quantification of exudome of P. ramosa seeds undergoing conditioning for 1, 4, 7, and 14 days (in five biological replicates each), and a series of 6 blank replicates corresponding to autoclaved distilled water supplemented with 0.1% PPM - Haustoriogenesis_raw_files: all *.raw MS files pertaining to LC-MS quantification of exudome of P. ramosa conditioned and washed seeds stimulated with rac-GR24 for 0 (t_0_*), 3 (t_1_*), 6 (t_2_*), and 12 (t_3_*) days (in five biological replicates each), and a series of 5 blank replicates corresponding to autoclaved distilled water supplemented with 0.1% PPM. 3) Directory "RNASeq" - Conditioning - Assembly & Annotation Trinity.filtered.estscan.vsearch.rmdup.fasta = reference transcriptome assembly encompassing all 15 samples of P. ramosa seeds collected over the first 24 hours of conditioning. Trinity.filtered.estscan.vsearch.rmdup.fasta.transdecoder.pep = translated assembly using Transdecoder Trinotate_annotation_report.xls = Full transcriptome annotation report as output by Trinotate trinotate_report_gene_ontology_with_parents.xls = GO strings per transcriptome unigene as output by Trinotate - Count data rsem_matrix.gene.* = count, TPM, and TMM matrices in gene mode (the one used for the DEG analysis) rsem_matrix.isoform.* = count, TPM, and TMM matrices in isoform mode - DEG analysis conditioning_RNAseq_clustering+enrichment.R = the full R script to cluster kinetic RNAseq data and perform enrichment analyses. *.RData = intermediate RData files for lazy loading Fig*.R and fig*.R = R scripts to generate the corresponding figures. The remaining files are in/outfiles necessary for either script to execute. - Haustoriogenesis - Assembly & Annotation Trinity.filtered.estscan.vsearch.rmdup.fasta = reference transcriptome assembly encompassing all 42 samples of P. ramosa washed and unwashed seeds treated with rac-GR24 for 0 to 144 hours. Trinity.filtered.estscan.vsearch.rmdup.fasta.transdecoder.pep = translated assembly using Transdecoder Trinotate_annotation_report.xls = Full transcriptome annotation report as output by Trinotate trinotate_report_gene_ontology_with_parents.xls = GO strings per transcriptome unigene as output by Trinotate - Count data rsem_matrix.gene.* = count, TPM, and TMM matrices in gene mode (the one used for the DEG analysis) rsem_matrix.isoform.* = count, TPM, and TMM matrices in isoform mode - DEG analysis haustoriogenesis_RNAseq_clustering+enrichment.R = the full R script to cluster kinetic RNAseq data and perform enrichment analyses. *.RData = intermediate RData files for lazy loading Fig*.R and fig*.R = R scripts to generate the corresponding figures. The remaining files are in/outfiles necessary for either script to execute.