ChIP-seq of Arabidopsis: ZT0_Input_Replicate1
Briefly, 2 grams of aerial rosette tissues from ~3-week-old A. thaliana (Col-0) were crosslinked in 1% formaldehyde, and the chromatin fractions were isolated and purified. Antibodies against H3K4me3 (Abcam; Ab8580) or H3K9ac (Abcam; Ab10812) were added to the chromatin extracts (with a 1:1000 dilution) and incubated overnight at 4C with gentle rotation. Immunoprecipitated DNA was extracted using Protein A/G Magnetic Beads. Immunoprecipitated DNA (IP-DNA) and input DNA (without IP but with incubation of beads) were subjected to reverse cross-linking and purified using QIAquick PCR Purification Kit. Libraries with three biological replicates were constructed from IP DNA and non-IP DNA using NEBNext Ultra II DNA Library Prep Kit for Illumina.