Standard NextSeq 500 paired-end Sequencing; Capture-C upon optogenetic depletion of the cofactor Chip in Drosophila melanogaster embryos at 2-4h after egg-laying
Capture-C upon optogenetic depletion of the cofactor Chip in Drosophila melanogaster embryos at 2-4h after egg-laying
All fly lines were maintained in a standard cornmeal-agar medium and grown at 25°C. ; The collections were aged at 25°C to the corresponding time window (2-3h, 2-4 h, 6-7h, 6-8 h, 10-12 h), and exposed to blue light for the indicated durations (as stated in the results).  Embryos were fixed in 1.8% formaldehyde for 15 minutes, with the exception of ChIP-seq and CUT&Tag using the rabbit anti-Chip antibody and guinea pig anti-CBP antibody, where 3% formaldehyde for 30 min was used. ; Extraction was performed as described in Bonn et al. 2012 (doi: 10.1038/ng.1064). ; After permeabilization of 25mio nuclei, DNA was digested with DpnII and ligated with T4 DNA ligase. After decrosslinking and PCI purification, the DNA was sheared and library prep including indexing of the samples using NEBNext Ultra II DNA library Kit for Illumina was performed. Samples were pooled and capture was performed using Twist Target Enrichment protocol.