Tomato gene explorer

A Shiny application to explore RNA-seq results from processed (= gene counts) data coming from mRNA-seq data.

Data provenance (ITAG2.4)

Genome references

Genomic references can be found on Zenodo Link.

Genome assembly and annotation ITAG2.4 were used:

• Genome FASTA: S_lycopersicum_chromosomes.2.50.fa.gz
• Genome annotation: ITAG2.4_gene_models.gtf

Snakemake pipeline

To get the scaled gene counts, the v0.3.8 release of the snakemake_rnaseq pipeline was used:

• Link GitHub
• Link Zenodo

Dataset 01: 20 cultivated and wild tomato accessions

mRNA-seq files (5 parts):

• Part 1
• Part 2
• Part 3
• Part 4
• Part 5

Dataset 02: cultivated and wild tomato tissues

mRNA-seq files: Zenodo link

Samples S31 to S48 were used.

Dataset 03: S. lyc Elite x S. hab PI127826 F2 lines

mRNA-seq files (two parts):

• Parents and F1 (2017): Zenodo link
• F2 (2019): Zenodo link

Dataset 04: MYC1 knock-out and knock-down mutants

mRNA-seq files Zenodo link