2024-09-30
ENA first public
ERC000037
ENA-CHECKLIST
Biology Centre CAS
INSDC center name
public
INSDC status
ERS21101718
SRA accession
csS-H_3
Submitter Id
22 °C 16hrs (light)/20°C 8 hrs (dark)
air temperature regimen
mutant
biological status
2017
collection date
thale cress
common name
119100000
estimated size
clf-29 swn-3 (Col-0)
genotype
Czechia
geographic location (country and/or sea)
missing: lab stock
DD
geographic location (latitude)
missing: lab stock
DD
geographic location (longitude)
growth chamber
growth facility
Seeds were surface sterilised by 70% and 100 % ethanol series, placed on Petri dishes with cultivation medium and stratified over 2 nights at 4°C, dark. Growth was at LD conditions: 110-120 µmol m-2 s-1, 16hrs light/8 hrs dark, 22 °C during light/20 °C during dark. Seedlisng were grown for 9 days before harvest. Separated shoots and roots were collected by seedling dissection, and the same seedling pool was used as the corresponding shoot and root sample for RNA-seq and ChIP-seq. Replicates 1, 2, and 3 were harvested at zeitgeber time (ZT) 4 – 7, ZT 7 – 10 and ZT 10 – 13, resp.
isolation and growth condition
long-day conditions (110-120 µmol m-2 s-1, 16hrs light/8 hrs dark, light source: OSRAM FQ 54W/840 HO CONSTANT LUMILUX Cool White)
light regimen
1/2 strength Murashige-Skoog (Duchefa M0222)
mineral nutrient regimen
Arabidopsis thaliana
organism
5.8
pH regimen
9d-seedling
plant developmental stage
cultivation medium: 1/2 Murashige-Skoog + 5 mM MES + 0.8% (w/v) plant agar + 1% (w/v) sucrose + 10μM DCMU
plant growth medium
cell
plant structure
1% (w/v) sucrose + 10μM DCMU
plant treatment
diploid
ploidy
RNA-seq: sample (tissue pool ~ 200 seedlings) was collected into RNAlater (Thermo, ct. no. AM7020) and flash frozen in liquid nitrogen for RNA extraction. Total RNA was extracted using MagMAX™ Plant RNA Isolation Kit (Thermo, cat.no. A33784). polyA-mRNA was enriched using NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB, cat. No. E7490) and Illumina sequencing libraries were prepared using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB, cat. No. E7770)
sample material processing
Arabidopsis thaliana
scientific_name
clf swn_9d_shoot_heterotrophic_rep3
title