Fig. 3: Deletion analysis of endogenous cis-regulatory regions in the BAC RP24-78D24 region.

Confocal images showing GFP-MYC endogenous fluorescence and DAPI in control Myc^GFP/GFP cells cultured in SR + LIF (a), SR + LIF+2i (a´), and N2B27 + F/A (a´´). Myc^GFP/GFP ES cells with heterozygous deletion of sub-cluster A (b, b´´), homozygous deletion of sub-cluster B (c, c´´), homozygous deletion of sub-cluster C (d, d´´) and heterozygous deletion of Sub-cluster D (e, e´´) and WT Myc^+/+ ES cells (f, f´´) cultured in the same 3 conditions. Scale bar = 30 microns. N = 3 clones for each genotype. g, g´´ Graphs showing the normalized median intensity of 3 clones for each genetic condition with 2 biological replicates for each clone. g´ 3 independent clones for all conditions except for the GFP condition in which 5 independent clones were used. The number of cells quantified per clone/replicate is available from the source data provided. GFP-MYC levels in SR + LIF and N2B27 + F/A conditions were analyzed by flow cytometry (g, g´´) and by confocal imaging in SR + LIF+2i condition (g´). Each dot represents the median of an individual clone/biological replicate and bars indicate the mean ± standard deviation of all clones/replicate in each condition. The number of cells quantified per clone/biological replicate is available from the Source Data in Figshare. One-way ANOVA with Dunnett’s correction; ns: P-value > 0,05; **P-value < 0,01, ***P-value < 0,001, ****P-value < 0,0001. h Violin plots with median and quartiles show GFP-MYC intensity in control Myc^GFP/GFP and sub-cluster C KO cell populations cultured in three conditions, as indicated. The number of cells analyzed is shown below the graphs. Mann–Whitney test, two-sided; ****P-value < 0,0001. Source data for all graphs are available from the Source Data file and raw data from Figshare (see “Data availability” section).