The context for this question can be found in this paper by Lara-Astiaso et al. Here, to study H3K4 trimethylation in various cell types, they
- sort cells
- sonicate chromatin
- immobilize chromatin on Dynabeads with anti-H3 antibody
- index chromatin (barcode)
- pool samples
- perform H3K4me3 ChIP
I am interested in the purpose of step 3 and how that contributes to step 4. What could be the purpose of essentially adding another IP step?
The Supplementary Materials (where all the methodology is described) mentions that "magnet based bead capture was used to efficiently add, wash and remove the different master mixes used in the indexing process." I'm somewhat confused as to how this adds efficiency, as I thought barcoding prior to sequencing is typically performed as a ligation step without selection (they perform the H3K4me3 ChIP after the indexing step anyway, so why select for histone H3 chromatin first?).