DOI: 10.6084/m9.figshare.14376746.v1
title: Metadata record for the manuscript: FOXA1 and adaptive response determinants to HER2 targeted therapy in TBCRC 036

description: <b>Summary</b><br>

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 <i>in vivo</i> 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: <i>Homo sapiens</i>; 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

 

<b>Data
access</b>

The mass
spectrometry proteomics data have been deposited to the ProteomeXchange
Consortium via the <i>PRIDE</i> 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 <i>Gene Expression
Omnibus</i>.

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.

 

<b>Corresponding author(s) for this study</b>

Gary
L. Johnson, PhD, Department of Pharmacology, 4079 Genetic Medicine Building, University
of North Carolina School of Medicine, Chapel Hill, NC 27599. Email: glj@med.unc.edu.
Phone: 919-843-3106.

<br>
<b>Study approval </b>

Approved
by the UNC Office of Human Research Ethics and conducted in accordance with the
Declaration of Helsinki. IRB# 13-1826