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. Author manuscript; available in PMC: 2020 Sep 30.
Published in final edited form as: Nat Cell Biol. 2020 Mar 30;22(4):380–388. doi: 10.1038/s41556-020-0494-z

Extended Data Fig. 4. H3K9me3 μChIP-Seq signal using standard FPKM normalization.

Extended Data Fig. 4

(a) 2D-histogram comparing H3K9me3 signal in wild type MII oocytes replicate 1 (X-axis) to that of previously published MII oocyte H3K9me3 (Y-axis) quantified within 24,402 non-redundant gene bodies (blue) and 12,133 bdH3K4me3 (orange) of each type of loci. Values are FPKM normalized, and represent average signal at each locus independent of its size. Pearson’s correlation coefficients(r) are shown for each subset of loci.

(b) Heat maps of published H3K9me3 μChIP-seq signal in Kdm4a+/+ MII oocytes at bdH3K4me3 (left) and entire genes (right), ordered and visualized as in Figure 2 b, c.

(c) Illustration of changes in read distribution for H3K9me3 towards covering bdH3K4me3 areas previously devoid of the mark, resulting in signal dispersion and lowering read densities at canonically enriched areas such as gene bodies.

(d) Line graphs of averaged H3K9me3 μChIP-Seq signal in Kdm4a+/+ (blue) and Kdm4a-/- (red) MII oocytes at bdH3K4me3 (left) and surrounding loci as well as non-redundant UCSC genes (right), using two different normalization strategies: standard FPKM (upper row) and FPKM followed by scaling of Kdm4a-/- signal to Kdm4a+/+ samples based on 5000 gene bodies with the highest H3K9me3 signal in each sample.

(e) Heat maps of averaged H3K9me3 μChIP-Seq signal in Kdm4a+/+ (blue) and Kdm4a-/- (red) MII oocytes at bdH3K4me3 (left) and surrounding loci as well as non-redundant UCSC genes (right) ordered and visualized as in Figure 2, using two different normalization strategies as described above in (d). Statistical source data are provided in source data extended data fig. 4.