ATAC-seq profiling of pancreatic endoderm derived from expanding ventral foregut progenitors

This dataset is part of ERC funded HumEn project (http://www.hum-en.eu/). This dataset relates to standardization of genome wide DNase 1 hypersensitivity methods in the differentiation system developed in HumEn project. Overall design: 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.

本数据集隶属于欧洲研究理事会（European Research Council, ERC）资助的HumEn项目（http://www.hum-en.eu/）。本数据集聚焦于HumEn项目所开发的分化系统中，全基因组DNase I超敏检测方法的标准化工作。

整体实验设计：
实验方法：携带PDX1::eGFP敲入转录报告基因的人胚胎干细胞系HUES4（1）在DEF-CS培养体系中传代培养，经流式细胞术检测，其阶段特异性胚胎抗原3/4（Stage-Specific Embryonic Antigen 3/4, SSEA3/4）双阳性细胞占比超过95%。按照Cheng等人2012年建立的实验方案（2），将上述细胞诱导分化为前内胚层（Anterior Definitive Endoderm, ADE）细胞，随后在VFG培养体系中进行扩增。通过荧光激活细胞分选术（Fluorescence Activated Cell Sorting, FACS），分别分选得到瞬时前内胚层群体（诱导第5天）以及VFG培养体系第3代（培养1个月）的CXCR4与KIT双阳性内胚层细胞。取50000个分选得到的内胚层细胞及人胚胎干细胞，采用因美纳（Illumina）公司的Nextera DNA文库制备试剂盒（货号：FC-121-1030），并对Buenrostro等人2015年发表的实验方案进行小幅修改，进行转座酶可及性测序（Assay for Transposase-Accessible Chromatin using sequencing, ATAC-seq）文库构建（3）。

参考文献：
1. Ameri J, Borup R, Prawiro C, Ramond C, Schachter KA, Scharfmann R, 等. 从分离的GP2阳性人胰腺祖细胞高效制备葡萄糖响应性β细胞. 细胞报告. 2017;19(1):36-49.
2. Cheng X, Ying L, Lu L, Galvao AM, Mills JA, Lin HC, 等. 从人多能干细胞构建可自我更新的内胚层祖细胞系. 细胞干细胞. 2012;10(4):371-84.
3. Buenrostro, Jason 等. ATAC-seq：全基因组染色质可及性检测方法. 分子生物学当前实验方案 / 主编Frederick M. Ausubel 等. 109 (2015): 21.29.1–21.29.9. PubMed Central（PMC）. 网络发布. 2017年12月28日.