GEO series

Bulk RNA-seq analysis of murine and human TCF3-fusion B-ALL cells

GSE303755 Homo sapiens (human) Single-cell RNA-seq 15 samples Submitted 2025/10/03 Platform GPL20795Platform GPL21273

At a glance

Single-cell RNA-seq · human · 15 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Homo sapiens (human)
Topic: Acute lymphoblastic leukemiaThis series is part of our curated briefing on it.
Samples: 15 samples: 5 conditions, mostly in triplicateGroups 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 TCF3::HLF fusion protein defines a subtype of incurable B cell acute lymphoblastic leukemia (B-ALL). Here, we identified self-reinforcing IL-1b networks in TCF3::HLF B-ALL cells using a newly-established mouse model that fully recapitulates human TCF3::HLF B-ALL, including osteolysis. We found significant upregulation of several inflammatory cytokines, including IL1B, IL6 and IFNG in the B-ALL mice.

Read the full summary ↓

Deletion of IL1B or IL1R1 strongly inhibited the growth of the human TCF3::HLF B-ALL cells, reduced the expression of RANKL and ameliorated the destruction of bone in the transplanted mice. Genetic and epigenetic analyses identified a previously unknown regulatory region of the IL1B gene locus, where TCF3::HLF directly binds. Importantly, single cell RNA-seq profiling of TCF3::HLF B-ALL patients revealed a dramatic upregulation of IL1B at relapse compared to the time of diagnosis. These findings suggest a critical role of TCF3::HLF-IL-1b axis for the progression of TCF3::HLF B-ALL.

This dataset

Open GSE303755 in finder → Find more RNA-seq datasets → Acute lymphoblastic leukemia 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 GSE303755_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 PRJNA1297615 and SRA study SRP603940. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

5 conditions, mostly in triplicate

WT mouse Pro-B cells ×3 PBX1 B-ALL cells ×3 HLF B-ALL cells ×3 YCUB2 cells, sg_Control ×3 YCUB2 cells, sg_IL1B ×3

Supports a between-group comparison across 15 samples.

How we read this: 5 replicated groups read from 15 sample titles; they account for 15 of them. 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

GSM9135249 WT mouse Pro-B cells_Rep1 WT mouse Pro-B cells
GSM9135250 WT mouse Pro-B cells_Rep2 WT mouse Pro-B cells
GSM9135251 WT mouse Pro-B cells_Rep3 WT mouse Pro-B cells
GSM9135252 murine TCF3::PBX1 B-ALL cells_Rep1 PBX1 B-ALL cells
GSM9135253 murine TCF3::PBX1 B-ALL cells_Rep2 PBX1 B-ALL cells
GSM9135254 murine TCF3::PBX1 B-ALL cells_Rep3 PBX1 B-ALL cells
GSM9135255 murine TCF3::HLF B-ALL cells_Rep1 HLF B-ALL cells
GSM9135256 murine TCF3::HLF B-ALL cells_Rep2 HLF B-ALL cells
GSM9135257 murine TCF3::HLF B-ALL cells_Rep3 HLF B-ALL cells
GSM9135258 YCUB2 cells, sg_Control_Rep1 YCUB2 cells, sg_Control
GSM9135259 YCUB2 cells, sg_Control_Rep2 YCUB2 cells, sg_Control
GSM9135260 YCUB2 cells, sg_Control_Rep3 YCUB2 cells, sg_Control
GSM9135261 YCUB2 cells, sg_IL1B_Rep1 YCUB2 cells, sg_IL1B
GSM9135262 YCUB2 cells, sg_IL1B_Rep2 YCUB2 cells, sg_IL1B
GSM9135263 YCUB2 cells, sg_IL1B_Rep3 YCUB2 cells, sg_IL1B

More Acute lymphoblastic leukemia datasets

GSE115656 Alternative splicing analysis of pediatric B-cell acute lymphoblastic leukemia compared to normal bone marrow derived pro-B cells 38 samples same disease briefing
GSE13425 Expression data from ALL patients included in the set used to construct a classification signature (COALL cohort) 190 samples same disease briefing
GSE12995 Expression data for diagnosis acute lymphoblastic leukemia samples 175 samples same disease briefing
GSE193713 Genome-wide maps of chromatin state for histone modifications and chromatin remodeling factors in WT and PHF6-KO conditions in Jurkat T-ALL cells. 20 samples same disease briefing
GSE18198 Expression profile of human T-ALL cell lines treated with DMSO or SAHM1 12 samples same disease briefing
GSE160298 The chromatin accessibility landscape of T-Cell Acute Lymphoblastic Leukemia 80 samples same disease briefing
GSE154675 PHF6 Interacts with LMO2 During Normal Haematopoiesis and in Leukaemia and Regulates the Level of Gene Expression and Genome Integrity 41 samples same disease briefing
GSE279594 BCR::ABL1-induced enhancer reprogramming uncovers hypersensitivity of Ph+B-ALL cells to enhancer-targeting drugs [RNA-Seq] 52 samples shares b-all, rna-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.