DOI: 10.5281/zenodo.4268081
title: Small RNA-seq data from leaf trichomes, stem trichomes, bald stems and leaf primordiums from different tomato genetic backgrounds

description: <strong>Description</strong> Various tissues of cultivated and wild tomato genotypes were harvested. Trichomes are stem trichomes (isolated from the stem of tomatoes). <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>Small RNA-Seq</strong> Small RNA-Seq libraries were generated from the &lt;200 nt RNA fraction according to the manufacturers’ protocols using the Small RNA-Seq Library Prep Kit (Lexogen). 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. Pik is an introgression line containing a fragment of chromosome 1 from <em>S. habrochaites</em> PI127826 into a MicroTom genetic background. <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>Pooled samples</strong> Some samples corresponding to the same tomato genotype and tissue were pooled altogether and are also available in fastq format. <pre><code class="language-markdown">| species | genotype | pool_of | tissue | file | reads | |--------------|------------|---------------|----------------|----------|----------| | habrochaites | PI127826 | S01, S02, S03 | trichomes | PI127826.fastq.gz | 16,539,495 | | lycopersicum | Moneymaker | S04, S05, S06 | trichomes | Moneymaker.fastq.gz | 11,539,748 | | habrochaites | LYC4 | S07, S08, S25 | trichomes | LYC4.fastq.gz | 15,980,718 | | lycopersicum | LA4024 | S10, S11, S12 | trichomes | LA4024.fastq.gz | 13,888,953 | | habrochaites | LA1777 | S13, S14, S15 | trichomes | LA1777.fastq.gz | 14,136,265 | | pennellii | LA0716 | S19, S20, S21 | trichomes | LA0716.fastq.gz | 14,045,182 |</code></pre>