GEO series

Identification of immune reconstitution and hematopoiesis restoration in bone marrow of multiple myeloma patients with high-dose melphalan following auto-HSCT by scRNA-seq

GSE304661 Homo sapiens (human) Single-cell RNA-seq 9 samples Submitted 2026/03/18 Platform GPL34284

At a glance

Single-cell RNA-seq · human · 9 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Homo sapiens (human)
Topic: Multiple myelomaThis series is part of our curated briefing on it.
Samples: 9 samples: 9 samples, each with a distinct title — no replicated groupsGroups are read from the sample names, not from the paper. Check the list below.
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper: Identification of immune reconstitution and hematopoiesis restoration by scRNA-seq in bone marrow of multiple myeloma patients treated with high-dose melphalan following auto-HSCTCancer biology & medicine · 2026

Summary (written by the submitters)

Multiple myeloma (MM) is a hematologic malignancy characterized by the clonal expansion of plasma cells in the bone marrow (BM). The high-dose chemotherapy following autologous hematopoietic stem cell transplantation (auto-HSCT) is a mainstay therapy for MM. However, effect of therapy on reconstitution of both immune and hematopoietic stem and progenitor cell (HSPCs) in BM of MM patients is pooly understood.

Read the full summary ↓

In this study, we investigated the significance of that using single-cell RNA sequencing (scRNA-seq). The scRNA-seq data of bone marrow mononuclear cells (BMMCs) from three MM patients with high-dose melphalan following auto-HSCT were integrated these data with scRNA-seq profiles from three newly diagnosed MM patients and three healthy donors. Our data showed that the malignant plasma cells in BM were strongly reduced to 0.09% in the MM group with therapy relative to 22.03% in control MM group. Notably, the proportions of pre-B cells, T cells, natural killer (NK) cells, and HSPCs were significantly elevated to 0.97%, 61.01%, 10.81% and 2.32% in BM of MM groupwith therapy relative to 0.10%, 27.34%, 7.17% and 0.46% in control MM group, indicating a robust reconstitution of both immune and HSPCs. The transcriptional landscape of HSPCs demonstrated functional restoration, with the enrichment of pathways involved in immune activation and multilineage differentiation. Pseudotime analysis revealed the distinct plasma cell trajectories and a notable downregulation of the unfolded protein response (UPR) pathway following by the treatment. Our findings provide a new insight into the comprehensive understanding of single-cell atlas in BM of MM by the therapy.

Published in

Identification of immune reconstitution and hematopoiesis restoration by scRNA-seq in bone marrow of multiple myeloma patients treated with high-dose melphalan following auto-HSCT

Li Q, Wang Y, Yuan H et al. · Cancer biology & medicine 2026 · PMID 41766112 · doi:10.20892/j.issn.2095-3941.2025.0585

This dataset

Open GSE304661 in finder → Find more human RNA-seq datasets → Multiple myeloma landscape →

Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE304661_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1302215 and SRA study SRP607115. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41766112) ↗

Study design

9 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 9 sample titles: 9 distinct titles with little repetition. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

GSM9154923 BMMCs from MM patient 1, high-dose melphalan following auto-HSCT, RNA, rep1
GSM9154924 BMMCs from MM patient 2, high-dose melphalan following auto-HSCT, RNA, rep2
GSM9154925 BMMCs from MM patient 3, high-dose melphalan following auto-HSCT, RNA, rep3
GSM9154926 BMMCs from MM patient 1, high-dose melphalan following auto-HSCT, BCR, rep1
GSM9154927 BMMCs from MM patient 2, high-dose melphalan following auto-HSCT, BCR, rep2
GSM9154928 BMMCs from MM patient 3, high-dose melphalan following auto-HSCT, BCR, rep3
GSM9154929 BMMCs from MM patient 1, high-dose melphalan following auto-HSCT, TCR, rep1
GSM9154930 BMMCs from MM patient 2, high-dose melphalan following auto-HSCT, TCR, rep2
GSM9154931 BMMCs from MM patient 3, high-dose melphalan following auto-HSCT, TCR, rep3

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