organism: Arabidopsis thaliana
description: Protocols: Whole seedlings were harvested. 2-3 g Col-Sf2 seedling tissue was collected. Bleach sterilized seeds were sown on 1xMS agar plates and stratified for 48 h at 4 °C. Seedlings were grown at 21 °C and 16 h long day conditions. For vernalization, seedlings after 4 weeks of cold treatment were transferred back to 21 °C long day conditions for 7 more days. Nuclei were isolated, resuspended in 250 µl 1.2 x buffer B (Roche) and treated with 0.2% (w/v) SDS. 3C analysis was performed similar as previously described with adaptations to A. thaliana (Hövel et al., 2012; Louwers et al., 2009b) using BglII. To obtain 4C samples, DNA was digested with 50 U NlaIII (NEB, 5U/µl) and re-ligated for circularization in a 2 ml volume. 100 ng of re-ligated, precipitated DNA served as template in each inverse PCR to produce 4C libraries.
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2020-01-03T15:59:17Z
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2019-02-01T11:03:23Z
attributes.tag: External Id
attributes.value: SAMEA5314118
attributes.tag: INSDC center name
attributes.value: Institute of Plant Genetics, Polish Academy of Sciences
attributes.tag: INSDC first public
attributes.value: 2020-01-03T15:59:17Z
attributes.tag: INSDC last update
attributes.value: 2019-02-01T11:03:23Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-7629:Sample B 3
attributes.tag: age
attributes.value: 4
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: common name
attributes.value: thale cress
attributes.tag: cultivar
attributes.value: Col-Sf2
attributes.tag: developmental stage
attributes.value: seedling
attributes.tag: genotype
attributes.value: wild type
attributes.tag: organism part
attributes.value: whole organism
attributes.tag: sample name
attributes.value: E-MTAB-7629:Sample B 3
attributes.tag: scientific_name
attributes.value: Arabidopsis thaliana
attributes.tag: stimulus
attributes.value: Vernalized