Petra Bleeker Research Group
Published October 19, 2020 | Version v4
Dataset Restricted

Small RNA-seq data from leaf, stem trichomes, bald stems and leaf primordiums from different tomato genetic backgrounds

Authors/Creators

  • 1. University of Amsterdam, SILS

Description

Description

Various tissues of cultivated and wild tomato genotypes were harvested.

Trichomes are stem trichomes (isolated from the stem of tomatoes).

RNA isolation

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 (>200 nt and <200 nt) using the miRNeasy Mini kit (Qiagen). For the >200 nt RNA an on-column treatment was included using the RNase-free DNase set (Qiagen).

Small RNA-Seq

Small RNA-Seq libraries were generated from the <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).

 

The list of samples is available in the sample_list.csv file.

  • 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 S. habrochaites PI127826 into a MicroTom genetic background. 

 

Pooled samples

Some samples corresponding to the same tomato genotype and tissue were pooled altogether and are also available in fastq format.

| 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  |

 

Files

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Please contact Petra Bleeker (P.M.Bleeker@uva.nl) or Marc Galland (m.galland@uva.nl) to request access to this dataset.

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