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