Arabidopsis thaliana
ENA first public
2024-09-30
INSDC center name
Biology Centre CAS
INSDC status
public
Submitter Id
S-M_3
air temperature regimen
22 °C 16hrs (light)/20°C 8 hrs (dark)
biological status
wild-type
collection date
2017
common name
thale cress
estimated size
119100000
genotype
WT (Col-0)
geographic location (country and/or sea)
Czechia
geographic location (latitude)
missing: lab stock
geographic location (longitude)
missing: lab stock
growth facility
growth chamber
isolation and growth condition
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 7 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.
light regimen
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)
mineral nutrient regimen
1/2 strength Murashige-Skoog (Duchefa M0222)
pH regimen
5.8
plant developmental stage
7d-seedling
plant growth medium
cultivation medium: 1/2 Murashige-Skoog + 5 mM MES + 0.8% (w/v) plant agar + 1% (w/v) sucrose
plant structure
cell
plant treatment
1% (w/v) sucrose
ploidy
diploid
sample material processing
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 name
S-M_3
scientific_name
Arabidopsis thaliana