DOI: 10.5281/zenodo.4249358
title: Messenger RNA-seq data from leaves, stem trichomes, bald stems and leaf primordia from different tomato genetic backgrounds

description: <strong>RNA isolation</strong> To isolate RNA, plant tissues were flash frozen in liquid nitrogen immediately after harvesting and stored at −80°C prior to RNA extraction. Frozen pellets were grounded by using a mortar and pestle before immersion in QIAzol Lysis Reagent (Qiagen). RNA was isolated and purified into two separate fractions (&gt;200 nt and &lt;200 nt) using the miRNeasy Mini kit (Qiagen). For the &gt;200 nt RNA an on-column treatment was included using the RNase-free DNase set (Qiagen). <strong>mRNA sequencing protocol</strong> A poly-A enrichment was performed on the &gt;200 nt RNA fraction using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs). RNA-Seq libraries were generated according to the manufacturers’ protocols using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina (Unique Dual Index Primer Pairs) (New England BioLabs). The size distribution of the libraries with indexed adapters was assessed using a 2200 TapeStation System with Agilent D1000 ScreenTapes (Agilent Technologies). The libraries were quantified on a QuantStudio 3 Real-Time PCR System (Thermo Fisher Scientific) using the NEBNext Library Quant Kit for Illumina (New England BioLabs) according to the instructions of the manufacturer. The libraries were clustered and sequenced (75 bp) on a NextSeq 550 Sequencing System (Illumina) using a NextSeq 500/550 High Output Kit v2.5 (75 Cycles) (Illumina). <strong>List of samples</strong> Myc-1 stands for a knock-out mutant of the MYC1 gene (Solyc08g005050). The line full name is MS5-4. <pre><code class="language-markdown">| tube | accession | tissue | sample | small RNA | mRNA | researcher | |------|------------|------------------|--------|-----------|------|------------| | SQ1 | PI127826 | trichomes | 1 | 1 | 0 | Michelle | | SQ2 | PI127826 | trichomes | 2 | 1 | 0 | Michelle | | SQ3 | PI127826 | trichomes | 3 | 1 | 0 | Michelle | | SQ4 | Moneymaker | trichomes | 4 | 1 | 0 | Michelle | | SQ5 | Moneymaker | trichomes | 5 | 1 | 0 | Michelle | | SQ6 | Moneymaker | trichomes | 6 | 1 | 0 | Michelle | | SQ7 | LYC4 | trichomes | 1 | 1 | 0 | Michelle | | SQ8 | LYC4 | trichomes | 2 | 1 | 0 | Michelle | | SQ9 | PIK | trichomes | 3 | 1 | 1 | Rodrigo | | SQ10 | LA4024 | trichomes | 1 | 1 | 0 | Michelle | | SQ11 | LA4024 | trichomes | 2 | 1 | 0 | Michelle | | SQ12 | LA4024 | trichomes | 3 | 1 | 0 | Michelle | | SQ13 | LA1777 | trichomes | 1 | 1 | 0 | Michelle | | SQ14 | LA1777 | trichomes | 2 | 1 | 0 | Michelle | | SQ15 | LA1777 | trichomes | 3 | 1 | 0 | Michelle | | SQ16 | MicroTom | trichomes | 1 | 1 | 1 | Rodrigo | | SQ17 | MicroTom | trichomes | 2 | 1 | 1 | Rodrigo | | SQ18 | MicroTom | trichomes | 3 | 1 | 1 | Rodrigo | | SQ19 | LA0716 | trichomes | 1 | 1 | 0 | Michelle | | SQ20 | LA0716 | trichomes | 2 | 1 | 0 | Michelle | | SQ21 | LA0716 | trichomes | 3 | 1 | 0 | Michelle | | SQ22 | Myc-1 | trichomes | 1 | 1 | 1 | Michelle | | SQ23 | Myc-1 | trichomes | 2 | 1 | 1 | Michelle | | SQ24 | Myc-1 | trichomes | 3 | 1 | 1 | Michelle | | SQ25 | LYC4 | trichomes | 4 | 1 | 0 | Michelle | | SQ26 | Myc-1 | leaf | 1 | 1 | 1 | Michelle | | SQ27 | Myc-1 | bald stem | 1 | 1 | 1 | Michelle | | SQ28 | Moneymaker | leaf primordium | 1 | 1 | 1 | Michelle | | SQ29 | PI127826 | leaf primordium | 1 | 1 | 1 | Michelle | | SQ30 | LA0716 | leaf primordium | 1 | 1 | 1 | Michelle | | SQ31 | Moneymaker | bald stem | 4 | 1 | 1 | Michelle | | SQ32 | Moneymaker | bald stem | 5 | 1 | 1 | Michelle | | SQ33 | Moneymaker | bald stem | 6 | 1 | 1 | Michelle | | SQ34 | PI127826 | bald stem | 1 | 1 | 1 | Michelle | | SQ35 | PI127826 | bald stem | 2 | 1 | 1 | Michelle | | SQ36 | PI127826 | bald stem | 3 | 1 | 1 | Michelle | | SQ37 | LA0716 | bald stem | 1 | 1 | 1 | Michelle | | SQ38 | LA0716 | bald stem | 2 | 1 | 1 | Michelle | | SQ39 | LA0716 | bald stem | 3 | 1 | 1 | Michelle | | SQ40 | Moneymaker | leaf | 1 | 1 | 1 | Michelle | | SQ41 | Moneymaker | leaf | 1+2 | 1 | 1 | Michelle | | SQ42 | Moneymaker | leaf | 2 | 1 | 1 | Michelle | | SQ43 | PI127826 | leaf | 1 | 1 | 1 | Michelle | | SQ44 | PI127826 | leaf | 2 | 1 | 1 | Michelle | | SQ45 | PI127826 | leaf | 3 | 1 | 1 | Michelle | | SQ46 | LA0716 | leaf | 1 | 1 | 1 | Michelle | | SQ47 | LA0716 | leaf | 2 | 1 | 1 | Michelle | | SQ48 | LA0716 | leaf | 3 | 1 | 1 | Michelle | | SQ49 | PIK | trichomes | 1 | 1 | 1 | Rodrigo | | SQ50 | PIK | trichomes | 2 | 1 | 1 | Rodrigo |</code></pre> <strong>Processed data</strong> <strong>Samples S28 to S48 </strong> Provenance: run from the snakemake_rnaseq pipeline v0.3.1 available from GitHub and Zenodo: <strong>Scaled counts:</strong> `S28_to_S48_scaled_counts.tsv<strong>`. </strong>A file with DESeq2 normalised counts wiith tab-separated values. Useful for visualisations (heatmaps, PCA) <em>NOT</em> for differential expression analysis. <strong>Raw counts:</strong> `S28_to_S48_raw_counts.tsv<strong>`. </strong>A file with the raw counts that can be used for differential expression analysis with DESeq2.