2024-04-24
ENA first public
ERC000011
ENA-CHECKLIST
SAMEA113564433
External Id
Plant-Environment Signaling Group, Dept. of Biology, Faculty of Science, Utrecht University, The Netherlands
INSDC center name
2023-05-30T16:15:59Z
INSDC last update
public
INSDC status
ERS15560581
SRA accession
E-MTAB-13023:Sab-FR-R-4
Submitter Id
6
day
age
ArrayExpress
broker name
Asian cultivated rice
common name
Sabharaj
cultivar
Protocols: At harvesting, tissue was snap frozen in liquid nitrogen and stored at -80 °C. All plants were grown in the greenhouse facilities of the Botanical Gardens, Utrecht University, in The Netherlands, in summer and autumn of 2021 (Supplemental Figure 1 A). Temperatures were set to 30 °C during the day and 25 °C during the night and a 12 h photoperiod from 8 am to 8 pm, with automatic watering keeping the soil saturated. Pots were arranged at 10 cm distance. For control group (WL) the light intensity was min 400 µmol m-2 s-1 of sunlight and artificial light (Valoya, Model Rx400 500mA 5730, Spectrum AP673L) switching on if sunlight flux rate dropped below 400 ɥmol m-2 s-1. For supplemental FR during photoperiod (WL+FR), the treatment group received in addition to the WL background, FR from LEDs (Valoya FR). Light intensity in PPFD range was the same between the control and treatment group. PFD was approx 400 µmol photons m–2 s–1 in control and 900 µmol photons m–2 s–1 (where approximately 500 ɥmol m-2 s-1 FR light was added (Supplemental Figure 1 B, C) in WL+FR. R:FR ratio was approximately 0.2. For end-of-day FR (EoD FR) treatment, control and treated group received the same light during photoperiod. EoD FR group received 10 minutes after the end of photoperiod (set to 8 pm) a 15-minute pulse of FR light (60-80 µmol m-2 s-1 FR light). To prevent transmission of FR to the control group, a black plastic screen was put up between treatment groups. Harvested tissue was ground with a Retsch grinder. From tissue powder, RNA was isolated using the Qiagen RNeasy kit with on-column DNAse treatment and quality was checked with the Bioanalyzer, before sequencing. RNA quality was checked with the Agilent Fragment Analyzer 5300 system using the RNA Kit (15nt) (Cat. DNF-471-1000). And RNA quantity was measured with the Invitrogen™ Qubit ™ Fluorometer using the Qubit RNA HS Assay Kit (Cat. Q32855). 100ng of total RNA was used to prepare TruSeq Stranded mRNA libraries (Cat. 20020594) following the manufacturers protocol. With custom 384 xGen UDI-UMI adapters from IDT. After the library preparation libraries were checked with the Fragment Analyzer system dsDNA 910 Reagent Kit (35-1500bp) (Cat. DNF-910-K1000) and with Qubit dsDNA HS Assay Kit (Cat. Q32854). Sample libraries were pooled equimolar.
description
seedling development stage
developmental stage
wild type genotype
genotype
not applicable
isolate
Oryza sativa
organism
Oryza sativa
organism
shoot
organism part
Oryza sativa
scientific_name
supplementary far red light
stimulus
Sab-FR-R-4
title