SOX transcription factors direct TCF-independent Wnt/beta-catenin transcription

We report ChIP-Seq experiments to profile the genomic binding dynamics of ß-catenin, SOX17, SOX2 and TCF/LEF TFs in definitive endoderm and neuromesodermal progenitor cells and RNA-Seq/ATAC-Seq experiments for transcriptomic and chromatin profiling of these cell types. Overall design: ChIP-Seq, RNA-Seq and ATAC-Seq experiments were performed every 24hrs during DE specification in WT and SOX17KO cells. ChIP-Seq, RNA-Seq and ATAC-Seq was performed in NMP cells after Day 3 of differentiation in WT and SOX2KD conditions. ChIP-Seq and RNA-Seq experiments were performed at day 3 of DE specification in WT and SOX17KO iPSCs or in HEK293T cells.

本研究报道了染色质免疫共沉淀测序（ChIP-Seq）实验，用于解析β-连环蛋白（β-catenin）、SOX17、SOX2及TCF/LEF转录因子在定型内胚层与神经中胚层祖细胞中的基因组结合动态；同时配套开展了RNA测序（RNA-Seq）与转座酶可及性测序（ATAC-Seq）实验，以对上述细胞类型进行转录组学与染色质图谱分析。整体实验设计：在野生型（WT）与SOX17基因敲除（SOX17KO）细胞的定型内胚层分化过程中，每24小时开展一次ChIP-Seq、RNA-Seq及ATAC-Seq实验；在野生型与SOX2基因敲低（SOX2KD）条件下的神经中胚层祖细胞中，于其分化第3天后完成上述三类测序实验；在野生型与SOX17KO诱导多能干细胞（iPSCs）的定型内胚层分化第3天，或在HEK293T细胞中，开展了ChIP-Seq与RNA-Seq实验。