Human Tumor Atlas Network Consortium
The visualizer here houses single-cell/nucleus transcriptomic data generated from the Human Tumor Atlas Pilot Project neuroblastoma workgroup. Tissue from 55 neuroblastoma tumors were were obtained from either Dana Farber Cancer Institute or St. Jude Children’s Research Hospital. The samples underwent processing using protocols described in Slyper et al, Nat Med 2020. The integrated dataset browser allows a user to browse through the combined across all of processed samples. To see individual samples, please click on the single-sample dataset corresponding to the dataset of interest. For questions, please contact Dr. Anand Patel at anand.patel2@stjude.org.
About
The datasets contained within this community were generated as part of the neuroblastoma working group of the Human Tumor Atlas Pilot Project (HTAPP). HTAPP is a part of the Human Tumor Atlas Network consortium HTAN. The data was generated as a collaboration between Dana Farber Cancer Institute, Broad Institute and St. Jude Children's Research Hospital. In total, 55 patient tumors underwent transcriptomic analysis using single-cell RNA-sequencing (for fresh tissue) or single-nucleus RNA-sequencing (for frozen issue). Protocols for tissue handling and processing were described in a Nature Medicine resource article and detailed protocols are available through protocols.io dx.doi.org/10.17504/protocols.io.98ah9se and https://dx.doi.org/10.17504/protocols.io.bhbcj2iw.
Each individual sample has a viewer that enables the user to see the cell state annotation process, which occurred in 4 stages. Additionally, inferred copy number variation plots, using inferCNV, using the immune and endothelial cells as reference observations are available for inspection. Finally, a combined dataset that includes all 55 samples integrated using LIGER is available. Users can input genes to visualize expression patterns and generate violin plots comparing expression to unsupervised clusters or clinicopathologic covariates.
Contact Us
For questions, please contact Dr. Anand Patel anand.patel2@stjude.org or Dr. Michael Dyer Michael.dyer@stjude.org.