Metadata record for the manuscript: FOXA1 and adaptive response determinants to HER2 targeted therapy in TBCRC 036

Summary This metadata record provides details of the data supporting the claims of the related manuscript: “FOXA1 and adaptive response determinants to HER2 targeted therapy in TBCRC 036”. The related study aimed to determine the global alterations in gene enhancers and transcriptional changes to identify factors involved in the adaptive response to HER2 inhibition. In parallel, it analysed the in vivo human adaptive molecular responses to HER2 targeting in a window-of-opportunity clinical trial using both RNAseq and a chemical proteomics method (MIB/MS) to assess the functional kinome. Type of data: mass spectrometry proteomics data; normalised patient RNA sequencing data; cell line RNA sequencing data; cell line ChIPseq data Subject of data: Homo sapiens; Eukaryotic cell lines Recruitment: Eligible women included those with newly diagnosed Stage I-IV HER2+ breast cancer scheduled to undergo definitive surgery (either lumpectomy or mastectomy). Stage I-IIIc patients could not be candidates for a therapeutic neoadjuvant treatment. Study subjects provided informed written consent that included details of the nontherapeutic nature of the trial. Trial registration number: https://clinicaltrials.gov/ct2/show/NCT01875666 Data access The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier https://identifiers.org/pride.project:PXD021865. Normalized patient RNAseq data (https://identifiers.org/geo:GSE161743), cell line RNAseq (https://identifiers.org/geo:GSE160001 and https://identifiers.org/geo:GSE160001), and cell line ChIPseq (https://identifiers.org/geo:GSE160667) are all part of the SuperSeries https://identifiers.org/geo:GSE160670 available through the Gene Expression Omnibus. Processed and normalized data are provided as supplemental materials associated with the article on the journal website, and also attached to this data record in the Excel spreadsheets called Supplementary Data 1-10 and the PDF called Supplementary material file.PDF. Accompanying Supplementary Information and Supplementary Data files contain relevant data used to produce the included figures and are available with this article. A detailed list of which data files underlie which figures and tables in the related article is included in the file ‘Angus_et_al_2021_underlying_data_files_list.xlsx’, which is shared with this data record. The data supporting Figure 3c is in the GraphPad Prism file called ‘siGrowth’, which is not shared publicly as it is in a non-open format, but it can be made available upon reasonable request to the corresponding author. Corresponding author(s) for this study Gary L. Johnson, PhD, Department of Pharmacology, 4079 Genetic Medicine Building, University of North Carolina School of Medicine, Chapel Hill, NC 27599. Email: [e-mail]. Phone: [phone]. Study approval Approved by the UNC Office of Human Research Ethics and conducted in accordance with the Declaration of Helsinki. IRB# 13-1826本元数据记录详述了支撑相关论文《FOXA1与TBCRC 036中HER2靶向治疗的适应性反应决定因素》研究结论的实验数据。本研究旨在明确基因增强子的全局改变及转录组变化，以鉴定参与HER2靶向抑制适应性反应的相关因子。与此同时，本研究通过一项机会窗临床试验，采用RNA测序（RNAseq）与化学蛋白质组学方法（MIB/MS）评估功能激酶组，分析了人体内针对HER2靶向治疗的适应性分子反应。数据类型：质谱蛋白质组学数据；标准化患者RNA测序数据；细胞系RNA测序数据；细胞系染色质免疫沉淀测序（ChIPseq）数据。数据研究对象：智人（Homo sapiens）；真核细胞系。招募标准：纳入的合格女性受试者为新诊断为I-IV期HER2阳性乳腺癌且计划接受根治性手术（乳房肿块切除术或乳房切除术）的患者。I-IIIc期患者不得接受治疗性新辅助治疗。研究受试者已签署书面知情同意书，其中明确载明本试验为非治疗性研究。试验注册号：https://clinicaltrials.gov/ct2/show/NCT01875666。数据获取：质谱蛋白质组学数据已通过PRIDE合作数据库提交至蛋白质组交换联盟（ProteomeXchange Consortium），数据集标识符为https://identifiers.org/pride.project:PXD021865。标准化患者RNA测序数据（https://identifiers.org/geo:GSE161743）、细胞系RNA测序数据（https://identifiers.org/geo:GSE160001与https://identifiers.org/geo:GSE160001）以及细胞系染色质免疫沉淀测序（ChIPseq）数据（https://identifiers.org/geo:GSE160667）均属于超级数据集（SuperSeries）https://identifiers.org/geo:GSE160670，可通过基因表达综合数据库（Gene Expression Omnibus）获取。经处理与标准化的数据以补充材料形式发表于期刊官网，同时以Excel表格（命名为Supplementary Data 1-10）与PDF文件（命名为Supplementary material file.PDF）附于本数据记录中。配套的补充信息与补充数据文件包含了用于生成论文配图的相关原始数据，可随本文一同获取。文件‘Angus_et_al_2021_underlying_data_files_list.xlsx’中详细列出了相关论文各图表与表格对应的原始数据文件，本数据记录已附带该文件。支撑图3c的数据位于GraphPad Prism格式文件‘siGrowth’中，因该文件采用非开放格式，暂未公开，但若向通讯作者提出合理请求，可予以提供。本研究的通讯作者为Gary L. Johnson博士，就职于北卡罗来纳大学医学院药理学系，遗传医学大楼4079室，教堂山市，北卡罗来纳州27599。电子邮箱：[e-mail]；联系电话：919-843-3106。研究伦理审批：本研究已通过北卡罗来纳大学人类研究伦理办公室审批，严格按照《赫尔辛基宣言》开展相关研究。伦理审查编号：IRB# 13-1826