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

PARE-Seq / degradome dataset

Obtained from 10µg of total RNA isolated from stem trichomes of cultivated (S. lycopersicum) and wild relatives of tomato (Solanum section Lycopersicon). 

Degradome sequencing (sequencing of 5' end of uncapped mRNAs --> to find the site of microRNA cleavage).
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' uncapped end of the mRNA. 

Sample description
Stem trichomes total RNA from several individual plants of the "20 accessions" (see table of genotypes below). See lab book - Marc Galland lab book #4 (2017): pages 61-69 + 73-75.

Protocol used
Qiagen RNeasy Plant Mini Kit (Cat No./ID: 74904).
DNAse treatment by Vertis. 
Minimal amount of 10µg of total RNA per sample.

Sequencing at Vertis Biotech AG (Germany)
See Doc_VB1745_Galland.pdf and Doc_VB1745_2_Galland.pdf together with the two SeqData08.08.2017.pdf and SeqData08.

The sequencing run has generated a total of 20 fastq files: 

1. Moneymaker_C32_S3_R1_001.fastqc.gz
2. LA0407_S10_R1_001.fastq.gz
3. LA0716_S29_R1_001.fastq.gz
4. LA1278_S27_R1_001.fastq.gz
5. LA1364_S8_R1_001.fastq.gz
6. LA1401_S5_R1_001.fastq.gz
7. LA1578_S26_R1_001.fastq.gz
8. LA1718_S4_R1_001.fastq.gz
9. LA1777_S7_R1_001.fastq.gz
10. LA1840_S6_R1_001.fastq.gz
11. LA1954_S28_R1_001.fastq.gz
12. LA2133_S9_R1_001.fastq.gz
13. LA2172_S11_R1_001.fastq.gz
14. LA2386_S21_R1_001.fastq.gz
15. LA2695_S20_R1_001.fastq.gz
16. LA4024_S26_R1_001.fastq.gz
17. LA0735_LYC140_S24_R1_001.fastq.gz
18. PI134418_LYC38_S23_R1_001.fastq.gz
19. LYC4_S25_R1_001.fastq.gz
20. PI127826_S22_R1_001.fastq.gz

Table of genotypes used

| 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        |

Reference:

German et al., Nature Protocols 2009 4(3):356-62)