A stromal cell-neutrophil axis promotes tumor-supportive bone marrow inflammation in newly diagnosed and treated myeloma

Published: 1 November 2023| Version 2 | DOI: 10.17632/sm7fvt8hsg.2
Contributors:
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Description

Cellranger output files (after soupx) and .RDS integrated datasets of single-cell RNA sequencing from: - the bone marrow myeloid compartment of newly diagnosed and treated individuals with multiple myeloma, as well as non-cancer controls - the bone marrow non-hematopoietic compartment of treated individuals with multiple myeloma, and previously published non-cancer controls

Files

Steps to reproduce

Important notices Regarding .RDS files of datasets: Files are integrated datasets of newly diagnosed or treated MM patients with controls. Datasets have been pre-split into progenitors, monocytes/macrophages and neutrophils. Metadata tags are: source (MM vs. control), patient, and if applicable, treatment. Regarding Cellranger output files: These are divided over two zip-files 1) Myeloid.zip; this folder contains subfolders per patient as mentioned in the paper (see supplementary tables for patient characteristics). Within the subfolders are the filtered_feature_bc_matrix output directories for the myeloid dataset, after processing with soupx. Progenitors, monocytes or neutrophils can be subsetted using barcodes and a script that are shared on our Github page (https://github.com/MyelomaRotterdam). 2) Nonhematopoietic.zip; this folder contains subfolders per patient as mentioned in the paper (see supplementary tables for patient characteristics). Within the subfolders are the filtered_feature_bc_matrix output directories for the non-hematopoietic dataset after soupx pre-processing. However, sorted stromal cells were supplemented with hematopoietic cells to improve recovery. Stromal cells can be subsetted using barcodes and a script that are shared on our Github page (https://github.com/MyelomaRotterdam). With any questions please contact us at t.cupedo@erasmusmc.nl

Institutions

Erasmus MC

Categories

Multiple Myeloma, Neutrophil, Bone Marrow Stromal Cell, Single-Cell RNA Sequencing

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