NeoLetExe clinical trial single-cell RNA-seq, scTCR-seq, scBCR-seq and cis-regulatory elements mapping

We performed single cell RNA sequencing, single cell T cell receptor and B cell receptor sequencing on breast tumor biopsies collected from patient of the NeoLetExe clinical trial at 3 time points of neoadjuvant therapy with aromatase inhibitors. The NeoLetExe study is a randomized open-label clinical trial aimed at evaluating the effects of sequential aromatase inhibition in postmenopausal women with ER-positive, HER-2 negative locally advanced breast cancer (stages T3-T4 and/or N2-3, including larger T2 tumors). Fresh tumor biopsies were dissociated at the single cell level which when then processed using the 10x Genomics Chromium platform, using the Single-Cell 5′ RNA-seq method along with single cell BCR and TCR-seq. The target was 7,500 to 10,000 cells per well, with libraries prepared using Gel Bead, Multiplex, and Chip Kits, following the manufacturer’s guidelines. Sequencing was performed on NovaSeq6000. We used SCAFE v1.0.065 to identify TSSs and map transcriptionally active regulatory elements.

• Type: RNASeq
• Archive: European Genome-phenome Archive (EGA)