Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing
Summary
We identify a profoundly remodelled TME in targeted therapy resistant (RTT) tumours. We provide bulk transcriptomic data of targeted therapy naive (NTT) and RTT tumours of 3 murine models. Additionally, we provide low-input sequencing of CD103+ dendritic cells and T cells from NTT and RTT Braf/Pten tumours. We identified that in RTT cell lines the MAPK pathway is reactivated and provide SLAM-seq data to determine transcriptional targets of MAPK pathway inhibition in NTT and RTT cell lines. We also provide ATAC-Seq data of NTT and RTT cell lines sorted from tumors of the Braf/Pten melanoma model.
Overall design
RNA-Seq, SMART-seq and Quant-seq of bulk tumors in vivo, sorted tumor cells and sorted CD45 + cells seperately. RNA-Seq and Quant-seq of NTT and RTT cell lines in vitro ± IFNy. Smart-seq of sorted CD11c+ CD103+ DCs from tumors, Smart-seq of sorted CD3+ CD8+ T cells from tumours. SLAM-Seq of targeted therapy naïve and RAFi resistant Braf/Pten melanoma ± MEKi. ATAC-Seq of NTT and RTT cell lines sorted from Braf/Pten melanoma tumors.
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