HTAPP_Designing gene panels for neuroblastoma targeted spatial transcriptomics assays v1
Year: 2021
Type: preprint
Abstract: To generate a comprehensive atlas characterizing neuroblastoma for the Human Tumor Atlas Pilot Project (HTAPP), we profiled tumor samples using molecular (single-cell/nucleus RNA-sequencing) and spatial transcriptomics and proteomics profiling technologies. Some of the spatial technologies used employ targeted approaches requiring pre-selection of a specific set of genes or proteins to be profiled. Designing targeted panels requires careful consideration in terms of the genes/probes or antibodies selected in order to identify the different cell types and programs in the tumor microenvironment and to gain biological/mechanistic insights. This document briefly describes our approach to designing a ~300-gene panel for HTAPP’s MERFISH profiling of neuroblastoma samples.
Authors: Timothy R Blosser, Orr Ashenberg, Anand Patel, Natalie Collins, Michael Dyer, Bruce Johnson, Xiaowei Zhuang, Orit Rozenblatt-Rosen, Aviv Regev
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W4255392631