SAS_defense_transcriptome

Please download data from following places:

For mapping reads

• raw fastq files: chunmei@whitney:~/RNAseq/trimmed
• Arabidopsis thaliana cDNA reference sequences: chunmei@whitney:~/RNAseq/reference/TAIR10_cdna_20110103_representative_gene_model_updated

For differential gene expression analysis

• Saved edgeR dge object ("dge.Rdata"): ~/Box/Chunmei_Myc_Paper/manuscripts/output/dge.Rdata
• Arabidopsis thaliana gene annotationta: chunmei@whitney:~/RNAseq/output/gene.description.Rdata

explanation of DEG file names

Please find DEG files under DEGs_with_descritipn folder (KN; where the description has been added in the script?). Or should I use DEGs files under "figure_and_tables"? If so, we need to replace "DEGs_with_description" into "figure_and_tables" in all scripts used.

DEG files in "/Box/Chunmei_Myc_Paper/manuscripts/output/DEGs_with_description", "/Box/Chunmei_Myc_Paper/manuscripts/output/figures_and_tables", and "~/Box/Chunmei_Myc_Paper/manuscripts/Figures and tables" are the same, I added the detailed description of each DEG files at the end of the manuscipt. Because I might move the DEG files generated with out saving the scipts to other folders and also might rename the file not through R, I don't think there is description in the script.

RNAseq data was splitted by time points (1h or 49h).

• Interaction model (gt*trt) RNAseq data analysis.Rmd

  • DEgenes.Col.1h.rH.csv: Col, 1h, shade responsive genes (reference is H).
  • DEgenes.Col.49h.4H.csv: Col, 49h, shade responsive genes (reference is H)
  • DEgenes.myc234.1h.rCol.rH.csv: myc234, 1h, (double coefficients, c("gtmyc234", "gtmyc234:trtL") )

• subsetted by genotype further?

  • DEgenes.myc234.1h.rH.csv: myc234, 1h, (KN, what is the difference between "DEgenes.myc234.1h.rCol.rH.csv" and "DEgenes.myc234.1h.rH.csv"? )

"DEgenes.myc234.1h.rCol.rH.csv" was generated by using Col or Col under H as reference, "DEgenes.myc234.1h.rH.csv" was generated by using the genotype itself myc234 under H as reference.

GO term over-representation analysis (GOseq_analysis_CL.Rmd)

• Arabidopsis thaliana GOslim

GO term heatmap (GOseq_heatmap2.Rmd)

gene clustering (DE_genes_heatmap_scale_center_f.Rmd)

Schweizer (2013) myc234 transcriptome data reanalized (2013_data_reanalized.Rmd)

Detailed analysis of PIFtargets and myc234 misregulated genes (MYC234_PIF4target.Rmd, .md, .html, MYC234_PIF4target_files) (by Kazu)

Differentially expressed genes overlap between different conditions (101218differentially expressed genes.Rmd)

All output files are stoerd in output folder not included in this repository.

|-input

|-output

|-SAS_defense_transcriptome (this repository)