2024-02-29
ENA first public
ERC000011
ENA-CHECKLIST
SAMEA111458882
External Id
agroparistech
INSDC center name
2022-10-12T16:15:51Z
INSDC last update
public
INSDC status
ERS13552918
SRA accession
E-MTAB-12284:ire1dm_dmso_shoot_rep5
Submitter Id
14
day
age
ArrayExpress
broker name
thale cress
common name
Col-0
cultivar
Protocols: Shoot and root samples were seperated using a scalpel. Seedlings were grown in vitro on plates in growth chamber (16h light/8h dark, average light intensity: 1500 lux). Seeds were directly stratified on growth medium (equivalent halh MS + 1% sucrose) for \" days at 4°C, in the dark. Medium was supplemented with either DMSO (0.01% final concentration, control condition) or tunicamycin (final concentration: 100ng/mL, treatment conditions). Total RNA were extracted using the RNeasy Plant Mini kit (#74904, QIAGEN) following manufacturer's instructions. Five µg of total RNA were then treated with Dnase I (RNase-free, EN0525, Fisher, Thermoscientific). DNase I was heat inactivated and treated RNA were precipitated using lithium chloride. Quality of chosen RNA samples to be sequenced was checked using bioanalyzer. RNA samples prepared from shoots displayed RIN values ranging from 6.7 to 7.3 and a ratio RNA 28S/RNA 18S ranging from 1.5 to 1.7. RNA samples prepared from roots displayed RIN values ranging from 7.7 to 10 and a ratio RNA 28S/RNA 18S ranging from 1.7 to 2.1. 1. Take a certain amount of total RNA samples, and use oligo dT beads to enrich mRNA with poly A tail; 2. mRNA molecules were fragmented into small pieces; 3. The fragmented mRNA was synthesized into first strand cDNA using random primers; 4. The second strand cDNA was synthesized with dUTP instead of dTTP; 5. The synthesized cDNA was subjected to end-repair and 3' adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments; 6. Digest the U-labeled second-strand template with Uracil-DNA-Glycosylase (UDG) and perform PCR amplification; 7. Library quality control; 8. Library circularization; 9. The library was amplified to make DNA nanoball (DNB);
description
plant embryo true leaf formation stage
developmental stage
ire1a ire1b mutant
genotype
Sample 20
individual
not applicable
isolate
Arabidopsis thaliana
organism
Arabidopsis thaliana
organism
shoot
organism part
Arabidopsis thaliana
scientific_name
ire1dm_dmso_shoot_rep5
title