description: Protocols: Plants were harvested directly after the 4 h treatment. 2 g of leaves were put in a 50 ml plastic tube and filled up with 30 ml pre-cooled crosslinking buffer containing 1 % formaldehyde. The tubes were put in a desiccator and vacuum was applied for 10 min. Crosslinking was stopped by adding 0.125 M glycine and vacuum infiltration for another 5 min. After that, leaves were washed twice with cooled water and dried on paper towels. Collected material was frozen in liquid nitrogen and stored at -80 °C. Plants were grown for 4 weeks under short day (10 h light/14 h dark and 20 °C/16 °C, respectively). The relative humidity during the day and night was 50 %. Four-week-old plants were transferred at 11 am (5 h after turning on the light) for 4 h either to dark (0 µE, 22 °C) or low light (100-130 µE, 22 °C). Leaves were ground to fine powder with mortar and pistil in liquid nitrogen. 1.3 g of material was transferred into a 50 ml plastic tube and mixed with 20 ml extraction buffer. The suspension was incubated for 15-20 min at 4 °C on a rotation platform, followed by centrifugation at 4°C and 2800 g for 20 min. After that, the supernatant was removed and the pellet was suspended in 3 ml NRBT buffer. After nuclei isolation and sonication by Covaris E220 Evolution, DNA was quantified with a NanoDrop. The immunoprecipitation was performed using an anti-H3K9ac antibody, followed by reverse crosslinking at 0.2 M NaCl end concentration and phenol-chloroform DNA extraction. Size selection of fragmented DNA was performed using AMPure XP beads (Beckman Coulter). Library preparation was done by IGA Technology Services (https://igatechnology.com/) using the Ovation® Ultralow V2 DNA-Seq Library Preparation Kit (NuGEN, Redwood City, CA) and following the manufacturer's instructions.
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2021-03-01T12:17:01Z
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2020-07-03T21:15:57Z
attributes.tag: External Id
attributes.value: SAMEA7039507
attributes.tag: INSDC center name
attributes.value: Institute of Biochemical Plant Pathology Helmholtz Zentrum Munchen Deutsches Forschungszentrum fur Gesundheit und Umwelt (GmbH)
attributes.tag: INSDC first public
attributes.value: 2021-03-01T12:17:01Z
attributes.tag: INSDC last update
attributes.value: 2020-07-03T21:15:57Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-9299:Sample 11
attributes.tag: age
attributes.value: 4
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: common name
attributes.value: thale cress
attributes.tag: developmental stage
attributes.value: rosette growth stage
attributes.tag: ecotype
attributes.value: Columbia
attributes.tag: genotype
attributes.value: hda6
attributes.tag: organism part
attributes.value: rosette leaf
attributes.tag: replicate
attributes.value: 2
attributes.tag: sample name
attributes.value: E-MTAB-9299:Sample 11
attributes.tag: scientific_name
attributes.value: Arabidopsis thaliana
attributes.tag: stimulus
attributes.value: continuous dark (no light) regimen