Modulation of enhacer networks during differentiation of human ESCs in to ADE

This dataset is part of ERC funded HumEn project (http://www.hum-en.eu/). This dataset reletes to standardization of genome wide DNase 1 hypersensitivity methods in the differentiation system developed in HumEn project.Methods: HUES4 human ESCs carrying a PDX1::eGFP knock-in transcriptional reporter (1) was maintained in DEF-CS system, with over 95% of SSEA3/4 double-positive cells as analysed by flow cytometry. These cells were differentiated to ADE cells and subsequently expanded in VFG culture, according to the protocol established by Cheng et al., 2012 (2). CXCR4/KIT double-positive endoderm cells from transient ADE population (day 5) and from passage 3 VFG culture (one month) were sorted by Fluorescence Activated Cell Sorting (FACS). 50000 sorted endoderm and hESC cells were subjected to ATAC-seq libraries preparation using Nextera DNA library preparation kit from Illumina (cat no; FC-121-1030) using a slight modification of protocol published by Buenrostro et al. 2015 (3).1. Ameri J, Borup R, Prawiro C, Ramond C, Schachter KA, Scharfmann R, et al. Efficient Generation of Glucose-Responsive Beta Cells from Isolated GP2(+) Human Pancreatic Progenitors. Cell reports. 2017;19(1):36-49.2. Cheng X, Ying L, Lu L, Galvao AM, Mills JA, Lin HC, et al. Self-renewing endodermal progenitor lines generated from human pluripotent stem cells. Cell stem cell. 2012;10(4):371-84.3. Buenrostro, Jason et al. “ATAC-Seq: A Method for Assaying Chromatin Accessibility Genome-Wide.” Current protocols in molecular biology / edited by Frederick M. Ausubel ... [et al.] 109 (2015): 21.29.1–21.29.9. PMC. Web. 28 Dec. 2017.