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Single-cell RNA-seq of out-of-thaw bone marrow-derived mesenchymal stromal cells (BM-MSCs)

GSE338608 Homo sapiens Expression profiling by high throughput sequencing 7 samples Submitted 2026/07/14 Platform GPL18573
Summary
Human mesenchymal stromal cells (MSCs) used in cell therapy are frequently administered directly out of thaw, yet the single-cell transcriptomic landscape of out-of-thaw MSC products is poorly defined. Here, cryopreserved bone marrow-derived MSCs from six healthy donors (seven lots) were characterized immediately after thawing using droplet-based single-cell RNA-sequencing on the Illumina-Bio-Rad ddSEQ platform. After SureCell-based UMI counting and knee filtering, profiles were analyzed with SC3 and Seurat. Donor-level clusters were identified that differ in immune-signaling, cell-surface, cell-cycle and metabolic gene programs, with low within-sample heterogeneity; cell-cycle status emerged as a major axis of inter-donor variation. Only the bone marrow samples are included in this submission.
Published in
Single-cell RNA-seq of out-of-thaw mesenchymal stromal cells shows tissue-of-origin differences and inter-donor cell-cycle variations
Medrano-Trochez C, Chatterjee P, Pradhan P et al. · Stem cell research & therapy 2021 · PMID 34736534 · doi:10.1186/s13287-021-02627-9
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Direct links to NCBI, no account and no request form: the whole study as GSE338608_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 7 samples. Raw sequencing reads are also available from ENA.

Also filed as BioProject PRJNA1495244 and SRA study SRP717988. Searching any of these in the dataset finder brings you back here.

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