fer_Control_RiboSeq_2
Solanum lycopersicum
Protocols: Root tissues were harvested from wild-type and fer tomato seedlings under control and salt-treated conditions. For each condition, roots from biologically independent seedlings were collected after 5 days of treatment, immediately frozen in liquid nitrogen, and stored at low temperature until ribosome profiling library preparation. Three biological replicates were collected for each genotype-by-treatment group. Wild-type tomato (Solanum lycopersicum cv. Condine Red) and the CRISPR/Cas9-generated fer mutant line in the cv. Condine Red background were grown in a greenhouse under controlled conditions with a 16 h light/8 h dark photoperiod at 30°C during the light period and 25°C during the dark period. Plants were maintained in 1/4-strength Hoagland's medium before treatment. At 3–4 weeks after sowing, tomato seedlings were divided into control and salt-treatment groups. Salt-treated plants were subjected to a progressive salt treatment culminating in 150 mM NaCl. Control plants were maintained in 1/4-strength Hoagland's medium. Root tissues were harvested after 5 days of salt treatment from each group. Ribosome profiling libraries were prepared from tomato root tissue lysates. Clarified lysates were digested with RNase I and DNase I to generate ribosome-protected fragments (RPFs). Ribosome-associated fractions were recovered using MicroSpin S-400 columns. RPFs were then extracted, followed by rRNA depletion and RNA cleanup. For matched RNA-seq libraries, total RNA was extracted from tomato roots using the RNAprep Pure Plant Kit (DP419; Tiangen Biotech, Shanghai, China) according to the manufacturer's instructions. Ribosome profiling libraries were constructed using a modified Ribo-seq workflow. Purified ribosome-protected fragments were subjected to 5′ phosphorylation with T4 polynucleotide kinase, sequential ligation to 3′ and 5′ adaptors, reverse transcription, and PCR amplification for 12 cycles. The final libraries were size selected by PAGE, and fragments of approximately 140 bp were recovered for sequencing.
ENA first public
2026-06-26
INSDC center name
Department of Horticulture, Zhejiang University
INSDC status
public
Submitter Id
E-MTAB-17159:fer_Control_RiboSeq_2
age
3
broker name
ArrayExpress
collection date
not collected
common name
tomato
cultivar
Condine Red
developmental stage
seedling development stage
genotype
fer
geographic location (country and/or sea)
not collected
isolate
not applicable
organism part
root
sample name
E-MTAB-17159:fer_Control_RiboSeq_2
scientific_name
Solanum lycopersicum
stimulus
control