A single-cell atlas characterizes dysregulation of the bone marrow immune microenvironment associated with outcomes in multiple myeloma

The MMRF VLAB is fully accessible and online. We recommend users access data through the MMRF VLAB resource to ensure they have access to the most up-to-date objects and clinical information. See below: ACCESS TO ADDITIONAL CLINICAL METADATA AND ORIGINAL FASTQ FILES: All the single-cell raw data, and clinical information used for this analysis, is available at MMRF’s VLAB shared resource (https://mmrfvirtuallab.org) under controlled access to protect patient genetic and clinical information. Access can be requested by filling the VLAB data access request form on the MMRF VLAB website. This form will require basic information such as name, email address, organization, a statement of intended use, and the types of data to be accessed. Senior investigators may apply for access, but must be permanent employees of their institution at a level equivalent to a tenure-track professor. Senior investigators meeting this criteria may nominate members of their immediate team for access. Once a form is submitted, the MMRF data access committee will review the form and respond within one business week from time of submission. If access to the requested data is granted, a temporary link to login and access the dataset will be provided with a one week expiry time under a data transfer agreement that will protect the identities of patients involved in the study. The MMRF VLAB will contain both the processed Seurat object for the original discovery cohort and the combined discovery and validation cohorts, along with the clinical metadata used for samples in the Immune Atlas study. The original unprocessed fastq.gz files for all samples in the Immune Atlas study will also be available. =========== This repository contains R Seurat objects associated with our study titled "A single-cell atlas characterizes dysregulation of the bone marrow immune microenvironment associated with outcomes in multiple myeloma" (https://doi.org/10.1038/s43018-025-01072-4), and our follow-up study focused on longitudinal analysis titled "Longitudinal profiling of tumor and immune compartments uncovers mechanisms of dysregulation and predictors of response in multiple myeloma." A shiny app is available through the MMRF to explore some of the single-cell RNA sequencing data online without downloading the dataset: https://myelomaimmuneatlas.themmrf.org. This repository contains two Seurat objects stored in .rds files containing processed single-cell RNA sequencing data from the original ‘Discovery’ cohort of the MMRF Immune Atlas study, along with an additional ‘Discovery + Validation’ cohort, as described in the original publication. These .rds files contain Seurat v4 objects with basic cell type annotation and qc metadata. Specific file contents will be detailed below. A copy of the ‘Cell Annotation Dictionary’ is also included, which contains additional details on the individual annotated clusters in the Immune Atlas dataset. Information on how to request additional metadata about these samples and accessing the original fastq files will be detailed at the end of this description