GEO .h5 data access
In addition to the assembled data provided in the scRNA-seq and CITE-seq Downloads page, we have deposited the demultiplexed, per-sample Cell Ranger output .h5 files in the Gene Expression Omnibus (GEO) for public access.
These .h5 files for PBMC data can be found on GEO at accession ID GSE309595.
Files related to the BMMC data can be found on GEO at accession ID GSE309593.
These files can be read into analysis packages using functions designed for reading 10x Genomics Cell Ranger .h5 files.
Raw data in dbGaP
Raw scRNA-seq data was generated using a 3' reverse transcription method, and therefore includes subject-derived single nucleotide polymorphisms. To comply with personally identifiable information protection standards, raw data in FASTQ format is available in dbGaP for controlled access at accession phs004383.v1.p1.
Additional code and results in Zenodo
Additional files, analysis code, and results can be obtained from the Zenodo repository:
Chander, A. (2026). Multiple myeloma and therapy reshape the bone marrow niche to durably constrain immune reconstitution and vaccine responsiveness. In Cell Press Blue (Version 1.0.0) [Computer software]. Zenodo. https://doi.org/10.5281/zenodo.21283102