Human Tumor Atlas Pilot Project: single-cell/nucleus RNA-seq atlas of neuroblastoma

Dyer Lab

Dyer Lab

Oct 13, 2021

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The data presented in this website were generated as part of a multi-institutional collaboration between St. Jude Children's Research Hospital, Dana Farber Cancer Institute and Broad Institute of MIT and Harvard. A patient cohort of 55 neuroblastoma samples were collected to generate 13 single-cell RNA-seq datasets (from fresh tissue) and 43 single-nucleus RNA-seq datasets (from frozen tissue). Single-cell suspensions were generated using papain dissociation (Slyper et al, Nat Medicine 2020) and single-nucleus suspensions were generated using a Tween-based buffer (Slyper et al, Nat Medicine 2020). All samples were processed using the 10x Genomics 3' Gene Expression platform. After sequencing, cell count matrices were generated using Cell Ranger followed by artifact removal using CellBender (Fleming SJ et al, BioRxiv 2019). Datasets were then combined using LIGER (Welch JD et al Cell 2019). In total, we present 530,055 cell/nuclei.

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