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I am familiar that the RedFly database provides annotations for 1,458 sites in the genome of Drosophila melanogaster subject to cleavage by DNase I. It seems the vast majority of those annotations come from the original FlyReg database originally reported in 2005, which merged with RedFly early on. I have looked, but not found any additional sources of annotations of the Drosophila genome of DNase cleavage sites. I wanted to ask, to be sure, if there are no additional studies / experiments which record DNase annotations in the Drosophila genome outside of the ones recorded by RedFly.

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I think that DNAse-seq is no longer the favored assay for chromatin accessibility.

These days, I believe ATAC-seq is favored, or even single-cell variants of ATAC-seq. (links to drosophila papers)

I can't comment on a general Drosophila regulatory database beyond what you already know about, beyond what's obvious via google (here, here).

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  • $\begingroup$ Very useful answer but are you sure it's no longer favored? 2021: "DNase I is still the reagent of choice for TF footprinting, which can determine the location of TF binding sites due to the protection of the site by the TF itself." doi.org/10.1038/s43586-020-00008-9 $\endgroup$
    – arara
    Dec 11, 2022 at 21:46
  • $\begingroup$ @arara interesting, I don't have access to the review unfortunately so it's hard for me to evaluate. I suspect that there is a subtle distinction between "TF binding sites" and "chromatin accessibility". Chromatin accessibility is a rather more generic phenomenon. What I would bet is that ATAC-seq is more common these days in large part because it's easier methodologically. But I could readily accept that DNAseI is a more diagnostic, less biased reagent at the single molecule level (or for e.g. one locus probed on a Southern blot). But I'm also not an expert in the field! $\endgroup$ Dec 13, 2022 at 20:06

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