characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2023-01-31T00:19:44Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2023-01-31T00:19:44Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA110473501
characteristics.characteristic: External Id
characteristics.text: Wageningen University and Research
characteristics.characteristic: INSDC center name
characteristics.text: 2023-01-31T00:19:44Z
characteristics.characteristic: INSDC first public
characteristics.text: 2023-01-31T00:19:44Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS12571193
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-12044:Sample 26
characteristics.characteristic: Submitter Id
characteristics.text: 20
characteristics.unit: day
characteristics.characteristic: age
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: tomato
characteristics.characteristic: common name
characteristics.text: RF008
characteristics.characteristic: cultivar
characteristics.text: Protocols: Upon inoculation with M. incognita, the locations of the root-tips in the infected and uninfected plants were marked on the plates. At the moment of collection (1, 2, 3, 4, 7, and 10 days post inoculation) this allowed for harvesting similar tissue in the mock-infected plants when compared to the infected plants. Approximately 50-90 galls per genotype per timepoint were dissected and kept in liquid nitrogen / -80°C storage until the moment RNA was isolated. Tomato, Solanum lycopersicum (accessions RF004, RF005, RF008, RF022, RF023, RF029, RF032, RF036, RF041, and RF096) seeds were incubated for three days in tap water at 4°C in the dark. Seeds were sterilized by washing with 70% (v/v) ethanol and subsequently with bleach 2.5% (v/v). Then, seeds were washed in sterile tap water and transferred to plates with MS20 medium and kept at 24°C in 16h light/8h dark. Seedlings were transferred to a fresh MS20 plate, one plant per plate. Infection was done with 10-days old seedlings. After addition of 120 J2s, plates were kept in the dark for two days to allow infection. Thereafter plates were again kept in a 16h light/8h dark regime. RNA was using a Maxwell® 16 AS2000 instrument with a Maxwell® 16 LEV Plant RNA Kit (both Promega Corporation, Madison, WI, USA) following the manufacturer’s instructions. RNA samples were stored at -80 ℃ until further use. After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA. Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. The suitable fragments are size-selected for the PCR amplification as templates.
characteristics.characteristic: description
characteristics.text: plant structure development stage
characteristics.characteristic: developmental stage
characteristics.text: wild type genotype
characteristics.characteristic: genotype
characteristics.text: long day length regimen
characteristics.characteristic: growth condition
characteristics.text: mixed pool of 50 to 90 galls
characteristics.characteristic: individual
characteristics.text: Meloidogyne incognita
characteristics.characteristic: infect
characteristics.text: Solanum lycopersicum
characteristics.characteristic: organism
characteristics.text: Solanum lycopersicum
characteristics.characteristic: organism
characteristics.text: root
characteristics.characteristic: organism part
characteristics.text: Solanum lycopersicum
characteristics.characteristic: scientific_name
characteristics.text: Sample 26
characteristics.characteristic: title