Additional data: Longitudinal single-cell multiomic atlas of high-risk neuroblastoma reveals chemotherapy-induced tumor microenvironment rewiring
Authors/Creators
- 1. University of Pennsylvania
-
2.
Children's Hospital of Philadelphia
Description
This repository provides additional data for the manuscript titled "Longitudinal single-cell multiomic atlas of high-risk neuroblastoma reveals chemotherapy-induced tumor microenvironment rewiring", currently under revision at Nature Genetics. The primary data cohort has been deposited in the HTAN data portal. This repository includes processed 10x Xenium spatial transcriptomic data for six TH-MYCN mice (three chemotherapy-treated and three treatment-naive) as well as processed scRNA-seq data for CHLA15 and CHLA20 neuroblastoma (NBL) cells. The scRNA-seq data includes mono-cultured, co-cultured cells with THP-1 macrophages, and co-culture cells treated with Afatinib/CRM197.
Notes
Detailed description for each data file:
In vitro scRNA-seq data
- seurat_deMULTIplex2_CHLA15.rds, seurat_deMULTIplex2_CHLA20.rds: seurat objects for all cells in mono- and co-culture experiments involving CHLA15 and CHLA20 cell lines, respectively.
- seurat_deMULTIplex2_CHLA15_malignant.rds,seurat_deMULTIplex2_CHLA20)malignant.rds: seurat objects for all malignant cells in mono- and co-culture experiments involving CHLA15 and CHLA20 cell lines, respectively.
In vivo Xenium spatial transcriptomic data
- nbl_xenium_anndata_final.h5ad: Anndata object with cell type annotated for Xenium spatial transcriptomic data on TH-MYCN mice.
- label_transfer_xenium_neuroblast_rpca.csv: Neuroblast cell state annotation in Xenium data by Seurat label transfer pipeline using rpca integration.
- label_transfer_xenium_macrophage_rpca.csv: Macrophage subset annotation in Xenium data by Seurat label transfer pipeline using rpca integration.
Files
label_transfer_xenium_macrophage_rpca.csv
Files
(3.8 GB)
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md5:b396438418b06c9813efc13169774850
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md5:8c2f1962ac3700978a44e3adf51934e1
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md5:cd2d8b46af7531a33ee0c087b34b024a
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2.5 GB | Download |
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md5:5cb48ef6b19fae93f3340adeacd15193
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240.9 MB | Download |
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md5:8a1d6f80ebcf3f0e68cd077c1fb09eba
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364.0 MB | Download |
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md5:6fa09c0419243a6aa68cd960a7cd1fa9
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166.7 MB | Download |
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md5:3d6b16eef53aff0640da51649e10b8d9
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121.1 MB | Download |
Additional details
Dates
- Submitted
-
2024-12-02