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. Author manuscript; available in PMC: 2021 Jul 4.
Published in final edited form as: Nat Struct Mol Biol. 2021 Jan 4;28(2):152–161. doi: 10.1038/s41594-020-00539-5

Extended Data Fig. 2. Transcriptional changes during neural differentiation of control and CTCF-depleted mES cells.

Extended Data Fig. 2

a, Gene expression profiles of pluripotent marker genes (Pou5f1, Sox2, Nanog) and examples of induction failure gene upon CTCF loss that is important for nervous system development (Neurog1, Neurod4, Vcan, Pax6, Tubb3 (Tuj1), Rbfox3 (NeuN)) in control and CTCF-depleted cells during differentiation from ESC to NPC and 2 days after washing out of auxin in NPCs.

b, Gene expression profiles of Pcdhga and Hoxc gene clusters during multiple days of auxin treatment in ESCs and during differentiation from ESC to NPC in control and CTCF-depleted cells followed by washing out auxin in NPCs.

c, Transcriptional changes between control ESCs and NPCs (day 4). Differentially up-regulated and down-regulated genes are plotted in red and blue, respectively (fold change > 2, FDR < 0.05).

d, Top two enriched GO terms of the sets of differentially expressed genes upon CTCF loss are shown along with p values (Fisher’s exact test).