title: GSM7830719: VIP3-GFP, rep1; Arabidopsis thaliana; ChIP-Seq
library_construction_protocol: H2B and H2Bub ChIP-Rx were conducted in parallel using the same two biological replicates of 7-day-old WT and elf7-3 seedlings grown under standard conditions. For each biological replicate, two immunoprecipitations (IP) were performed using an anti-H2Bub antibody (MM-0029-P, Medimabs) and one using an anti-H2B (ab1790, abcam). 100 µg of Arabidopsis chromatin mixed with 3 µg of Drosophila chromatin was used for each IP. DNA eluted from the two technical replicates of H2Bub IP was pooled before library preparation. Library preparation and sequencing were carried out by the CRG Genomics Core Facility (Barcelona, Spain). Flag-ELF7 and GFP-VIP3 ChIP-seq was performed using 7-day-old seedlings and an anti-Flag M2 antibody (F1804, Sigma). We used double in vitro crosslinking using 1.5 mM ethylene glycol bis (succinimidyl succinate) for 20 min and then with 1% formaldehyde for 10 min at room temperature. Library preparation and sequencing were carried out by the CRG Genomics Core Facility (Barcelona, Spain). ChIP-seq for RNAPII was done using the anti-NRPB1 antibody (active motif, Clone: 4H8) using similar growth conditions and protocol than for H2Bub profiling without Drosophila cells spike-in. Library preparation and sequencing were carried out by the Epigenomics platform at IPS2 (Paris, France). Libraries were prepared using commercial kits as follows: GFP-VIP3, H2B and H2Bub with NEBNext® Ultra DNA Library Prep for Illumina® kit, PolII with NEBNext® Ultra II DNA Library Prep for Illumina® kit, and Flag-ELF7 with Ovation Ultralow System V2.