Stem trichome PARE-Seq (degradome) data from the 20 accessions

<p><strong>PARE-Seq / degradome dataset</strong></p> <p>Obtained from 10&micro;g of total RNA isolated from stem trichomes of cultivated (S. lycopersicum) and wild relatives of tomato (Solanum section Lycopersicon).&nbsp;</p> <p>Degradome sequencing (sequencing of 5&#39; end of uncapped mRNAs --&gt; to find the site of microRNA cleavage).<br> Degradome sequencing is also called PARE-Seq (see German et al., Nature Protocols 2009 4(3):356-62). Here, Vertis Biotech AG used a slightly modified protocol that generates 75nt reads from the 5&#39; uncapped end of the mRNA.&nbsp;</p> <p><strong>Sample description</strong><br> Stem trichomes total RNA from several individual plants of the &quot;20 accessions&quot; (see table of genotypes below). See lab book - Marc Galland lab book #4 (2017): pages 61-69 + 73-75.</p> <p><strong>Protocol used</strong><br> Qiagen RNeasy Plant Mini Kit (Cat No./ID: 74904).<br> DNAse treatment by Vertis.&nbsp;<br> Minimal amount of 10&micro;g of total RNA per sample.</p> <p><strong>Sequencing at Vertis Biotech AG (Germany)</strong><br> See Doc_VB1745_Galland.pdf and Doc_VB1745_2_Galland.pdf together with the two SeqData08.08.2017.pdf and SeqData08.</p> <p>The sequencing run has generated a total of 20 fastq files:&nbsp;</p> <ol> <li>Moneymaker_C32_S3_R1_001.fastqc.gz</li> <li>LA0407_S10_R1_001.fastq.gz</li> <li>LA0716_S29_R1_001.fastq.gz</li> <li>LA1278_S27_R1_001.fastq.gz</li> <li>LA1364_S8_R1_001.fastq.gz</li> <li>LA1401_S5_R1_001.fastq.gz</li> <li>LA1578_S26_R1_001.fastq.gz</li> <li>LA1718_S4_R1_001.fastq.gz</li> <li>LA1777_S7_R1_001.fastq.gz</li> <li>LA1840_S6_R1_001.fastq.gz</li> <li>LA1954_S28_R1_001.fastq.gz</li> <li>LA2133_S9_R1_001.fastq.gz</li> <li>LA2172_S11_R1_001.fastq.gz</li> <li>LA2386_S21_R1_001.fastq.gz</li> <li>LA2695_S20_R1_001.fastq.gz</li> <li>LA4024_S26_R1_001.fastq.gz</li> <li>LA0735_LYC140_S24_R1_001.fastq.gz</li> <li>PI134418_LYC38_S23_R1_001.fastq.gz</li> <li>LYC4_S25_R1_001.fastq.gz</li> <li>PI127826_S22_R1_001.fastq.gz</li> </ol> <p><strong>Table of genotypes used</strong></p> <pre><code class="language-markdown">| accession | species | accession nr | synonym | origin | |------------|--------------------------------|--------------|---------|-------------| | LA2172 | S. arcanum | TR0009 | - | Peru | | LA1401* | S. cheesmaniae f. minor | EA00652 | - | Ecuador | | LA1840 | S. chmielewskii | - | - | unknown | | LA2695 | S. chmielewskii | EA00759 | - | Peru | | LA0407 | S. habrochaites f. glabratum | EA00558 | - | Ecuador | | LA1777 | S. habrochaites f. hirsutum | EA00703 | - | Peru | | PI134418 | S. habrochaites f. glabratum | TR00015 | LYC38 | unknown | | LYC4 | S. habrochaites f. hirsutum | TR00017 | - | unknown | | LA1718 | S. habrochaites f. glabratum | EA00699 | LYC4934 | Peru | | PI127826 | S. habrochaites f. hirsutum | - | - | Peru | | LA1364 | S. huaylasense | TR00030 | - | Peru | | Moneymaker | S. lycopersicum | - | C32 | Netherlands | | LA4024 | S. lycopersicum | TA209 | - | unknown | | LA2133 | S. neorickii/L. parviflorum | EA00729 | - | Peru | | LA0735 | S. neorickii | TR00025 | LYC140 | unknown | | LA0716 | S. pennellii | EA00585 | - | Peru | | LA1278 | S. peruvianum/pimpinellifolium | TR00005 | - | unknown | | LA1954 | S. peruvianum | EA00713 | - | Peru | | LA1578 | S. pimpinellifolium | EA00674 | - | Peru |</code></pre> <p>&nbsp;</p> <p><strong>Reference:</strong></p> <p>German et al., Nature Protocols 2009 4(3):356-62)</p>