GEO series
Clonal evolution permits outgrowth of chemoresistant LMPP-like early progenitors in relapsed NPM1c AML [scRNA-Seq]
GSE296649
Homo sapiens (human)
Single-cell RNA-seq
58 samples
Submitted 2026/05/01
Platform GPL18573Platform GPL24676
At a glance
Single-cell RNA-seq · human · 58 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
- Acute myeloid leukemiaThis series is part of our curated briefing on it.
- Samples
- 58 samples: 58 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.
Summary (written by the submitters)
The most recurrent acute myeloid leukemia (AML) driver in adult patients is a DNA frameshift insertion in the Nucleophosmin 1 (NPM1) gene. This mutation causes a translocation of the coding protein from the nucleus to the cytoplasm (NPM1c). We have generated paired single-cell multi-omics profiles for ~205,000 bone marrow cells collected from NPM1c AML patients at diagnosis and relapse.
Read the full summary ↓
Detailed single-cell clonal analysis unveiled the evolution, expansion, and concomitant phenotypic changes of pathogenic AML (sub)clones. Blasts with an internal tandem duplication in the FLT3 gene (FLT3-ITD+ blasts) were often lowly abundant at diagnosis but expanded drastically at relapse at the expense of other blasts. Intriguingly, genetically identical FLT3-ITD+ blasts switched from granulocyte-monocyte progenitor-like at diagnosis toward more immature lympho-myeloid primed progenitor (LMPP)-like blasts at relapse. Our data shows that clonal evolution and the accumulation of a FLT3-ITD, is a key evolutionary event that alters AML blast plasticity with minimal changes in the blast phenotype. Increased plasticity favors the specific selection and expansion of FLT3-ITD+ blasts, which adopt a unique LMPP-like phenotype. The overriding transition between diagnosis and relapse suggests that therapeutic interventions (against proliferating cells) could license or accelerate this shift, highlighting the need for a tailored drug composition to target relapsed NPM1c AML.
This dataset
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.
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 GSE296649_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1260444 and SRA study SRP583861. Searching any of these in the dataset finder brings you back here.
Study design
58 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 58 sample titles: 58 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
- GSM8974195 NPM1 patient 01, diagnosis sample [Illumina NovaSeq 6000]
- GSM8974196 NPM1 patient 01, relapse sample [Illumina NovaSeq 6000]
- GSM8974197 NPM1 patient 02+03, diagnosis+relapse sample replicate 1 [Illumina NovaSeq 6000]
- GSM8974198 NPM1 patient 02+03, diagnosis+relapse sample replicate 2 [Illumina NovaSeq 6000]
- GSM8974199 NPM1 patient 02+03, diagnosis+relapse sample replicate 3 [Illumina NovaSeq 6000]
- GSM8974200 NPM1 patient 02+03, diagnosis+relapse sample replicate 4 [Illumina NovaSeq 6000]
- GSM8974201 NPM1 patient 04+05, diagnosis+relapse sample replicate 1 [Illumina NovaSeq 6000]
- GSM8974202 NPM1 patient 04+05, diagnosis+relapse sample replicate 2 [Illumina NovaSeq 6000]
- GSM8974203 NPM1 patient 04+05, diagnosis+relapse sample replicate 3 [Illumina NovaSeq 6000]
- GSM8974204 NPM1 patient 04+05, diagnosis+relapse sample replicate 4 [Illumina NovaSeq 6000]
- GSM8974205 NPM1 patient 06+07, diagnosis+relapse sample replicate 1 [Illumina NovaSeq 6000]
- GSM8974206 NPM1 patient 06+07, diagnosis+relapse sample replicate 2 [Illumina NovaSeq 6000]
- GSM8974207 NPM1 patient 06+07, diagnosis+relapse sample replicate 3 [Illumina NovaSeq 6000]
- GSM8974208 NPM1 patient 06+07, diagnosis+relapse sample replicate 4 [Illumina NovaSeq 6000]
- GSM8974209 NPM1 patient 08+09, diagnosis+relapse sample replicate 1 [Illumina NovaSeq 6000]
- GSM8974210 NPM1 patient 08+09, diagnosis+relapse sample replicate 2 [Illumina NovaSeq 6000]
- GSM8974211 NPM1 patient 08+09, diagnosis+relapse sample replicate 3 [Illumina NovaSeq 6000]
- GSM8974212 NPM1 patient 08+09, diagnosis+relapse sample replicate 4 [Illumina NovaSeq 6000]
- GSM8974213 NPM1 patient 10, diagnosis+relapse sample replicate 1 [Illumina NovaSeq 6000]
- GSM8974214 NPM1 patient 10, diagnosis+relapse sample replicate 2 [Illumina NovaSeq 6000]
- GSM8974215 NPM1 patient 01, diagnosis sample [Illumina Nextseq 500 ]
- GSM8974216 NPM1 patient 01, relapse sample [Illumina Nextseq 500 ]
- GSM8974217 NPM1 patient 02+03, diagnosis+relapse sample replicate 1 [Illumina Nextseq 500 ]
- GSM8974218 NPM1 patient 02+03, diagnosis+relapse sample replicate 2 [Illumina Nextseq 500 ]
- GSM8974219 NPM1 patient 02+03, diagnosis+relapse sample replicate 3 [Illumina Nextseq 500 ]
- GSM8974220 NPM1 patient 02+03, diagnosis+relapse sample replicate 4 [Illumina Nextseq 500 ]
- GSM8974221 NPM1 patient 04+05, diagnosis+relapse sample replicate 1 [Illumina Nextseq 500 ]
- GSM8974222 NPM1 patient 04+05, diagnosis+relapse sample replicate 2 [Illumina Nextseq 500 ]
- GSM8974223 NPM1 patient 04+05, diagnosis+relapse sample replicate 3 [Illumina Nextseq 500 ]
- GSM8974224 NPM1 patient 04+05, diagnosis+relapse sample replicate 4 [Illumina Nextseq 500 ]
- GSM8974225 NPM1 patient 06+07, diagnosis+relapse sample replicate 1 [Illumina Nextseq 500 ]
- GSM8974226 NPM1 patient 06+07, diagnosis+relapse sample replicate 2 [Illumina Nextseq 500 ]
- GSM8974227 NPM1 patient 06+07, diagnosis+relapse sample replicate 3 [Illumina Nextseq 500 ]
- GSM8974228 NPM1 patient 06+07, diagnosis+relapse sample replicate 4 [Illumina Nextseq 500 ]
- GSM8974229 NPM1 patient 08+09, diagnosis+relapse sample replicate 1 [Illumina Nextseq 500 ]
- GSM8974230 NPM1 patient 08+09, diagnosis+relapse sample replicate 2 [Illumina Nextseq 500 ]
- GSM8974231 NPM1 patient 08+09, diagnosis+relapse sample replicate 3 [Illumina Nextseq 500 ]
- GSM8974232 NPM1 patient 08+09, diagnosis+relapse sample replicate 4 [Illumina Nextseq 500 ]
- GSM8974233 NPM1 patient 10, diagnosis+relapse sample replicate 1 [Illumina Nextseq 500 ]
- GSM8974234 NPM1 patient 10, diagnosis+relapse sample replicate 2 [Illumina Nextseq 500 ]
+ 18 more — browse all 58 samples with per-sample file links →
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- GSE270894 Molecular Characterization of Chemoresistant Cell Populations Improves Risk Stratification and Therapy Response Prediction in Pediatric AML [pAML Patients scRNA-seq] 20 samples shares aml, chemoresistant, scrna-seq
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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.