{"doi":"10.17504/protocols.io.bw86phze","title":"HTAPP_Designing gene panels for neuroblastoma targeted spatial transcriptomics assays v1","abstract":"<p>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. </p>","journal":null,"year":2021,"id":10873,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.1075,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-08-09","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":2691,"name":"Orr Ashenberg","orcid":"0000-0002-7802-8834","position":1,"is_corresponding":false},{"id":55229,"name":"Anand G. Patel","orcid":"0000-0002-1438-8275","position":2,"is_corresponding":false},{"id":88762,"name":"Natalie Collins","orcid":null,"position":3,"is_corresponding":false},{"id":3627,"name":"Xiaowei Zhuang","orcid":"0000-0002-6034-7853","position":6,"is_corresponding":false},{"id":2697,"name":"Orit Rozenblatt–Rosen","orcid":"0000-0001-6313-3570","position":7,"is_corresponding":false},{"id":29633,"name":"Prisca Liberali","orcid":"0000-0003-0695-6081","position":8,"is_corresponding":false},{"id":88764,"name":"Natalie J. Collins","orcid":"0000-0001-9950-0192","position":9,"is_corresponding":false},{"id":55259,"name":"Michael A. Dyer","orcid":"0000-0003-4027-4850","position":10,"is_corresponding":false},{"id":5601,"name":"Bruce E. Johnson","orcid":"0000-0002-5252-3677","position":11,"is_corresponding":false},{"id":3735,"name":"Orit Rozenblatt‐Rosen","orcid":null,"position":12,"is_corresponding":false},{"id":56739,"name":"Timothy R. Blosser","orcid":"0000-0002-7739-922X","position":0,"is_corresponding":true}],"reference_count":0,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}