GEO series

RNA-seq of sorted murine long-term hematopoietic stem cells segmented on CUX1 levels with and without CUX1 knockdown

GSE274033 Mus musculus (mouse) RNA-seq (gene expression) 35 samples Submitted 2025/08/01 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 35 samples

What it is: RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism: Mus musculus (mouse)
Samples: 35 samples: 35 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)

Hematopoietic stem cells (HSCs) possess properties of both self-renewal and multipotent differentiation; however, the regulation of these opposing properties remains elusive. Using a novel reporter mouse, we demonstrate the dose-dependent role of the transcription factor, CUX1, in HSC fate. As CUX1 levels naturally rise, HSCs gradually lose repopulating capacity.

Read the full summary ↓

CUX1 knockdown reverses this process and reverts HSCs to an earlier cell state—restoring the transcriptome, chromatin accessibility, repopulating capacity, and self-renewal ability of HSCs with normally low CUX1 levels. In the absence of CUX1, endogenous retroelements (EREs) are aberrantly expressed, leading to a cell-intrinsic inflammatory response, which contributes to CUX1-dependent HSC activity. Likewise, loss of the transcription factor IRF1 attenuates CUX1-mediated HSC reprogramming. This mechanism could be relevant to leukemogenesis as acute myeloid leukemias with CUX1 deletions upregulate EREs and the interferon response. Our findings attribute CUX1 and innate immune activation to the complex molecular underpinnings of HSC fate decisions.

This dataset

Open GSE274033 in finder → Find more mouse RNA-seq datasets →

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 GSE274033_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1144496 and SRA study SRP524690. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

35 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 35 sample titles: 35 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

GSM8442177 CUX1Dim Replicate A
GSM8442178 CUX1Int Replicate A
GSM8442179 CUX1Bright Replicate A
GSM8442180 CUX1Dim Replicate B
GSM8442181 CUX1Int Replicate B
GSM8442182 CUX1Bright Replicate B
GSM8442183 CUX1Dim Replicate C
GSM8442184 CUX1Int Replicate C
GSM8442185 CUX1Bright Replicate C
GSM8442186 CUX1Dim Replicate D
GSM8442187 CUX1Int Replicate D
GSM8442188 CUX1Bright Replicate D
GSM8442189 CUX1Dim shControl Replicate A
GSM8442190 CUX1Int shControl Replicate A
GSM8442191 CUX1Bright shControl Replicate A
GSM8442192 CUX1Dim shCUX1 Replicate A
GSM8442193 CUX1Int shCUX1 Replicate A
GSM8442194 CUX1Bright shCUX1 Replicate A
GSM8442195 CUX1Int shControl Replicate B
GSM8442196 CUX1Bright shControl Replicate B
GSM8442197 CUX1Dim shCUX1 Replicate B
GSM8442198 CUX1Int shCUX1 Replicate B
GSM8442199 CUX1Bright shCUX1 Replicate B
GSM8442200 CUX1Dim shControl Replicate C
GSM8442201 CUX1Int shControl Replicate C
GSM8442202 CUX1Bright shControl Replicate C
GSM8442203 CUX1Dim shCUX1 Replicate C
GSM8442204 CUX1Int shCUX1 Replicate C
GSM8442205 CUX1Bright shCUX1 Replicate C
GSM8442206 CUX1Dim shControl Replicate D
GSM8442207 CUX1Int shControl Replicate D
GSM8442208 CUX1Bright shControl Replicate D
GSM8442209 CUX1Dim shCUX1 Replicate D
GSM8442210 CUX1Int shCUX1 Replicate D
GSM8442211 CUX1Bright shCUX1 Replicate D

Datasets on a similar topic

GSE338821 RNA profiles of hematopoietic stem cells before and after long-term culture [RNA-Seq] 24 samples shares hematopoietic, long-term, rna-seq
GSE222941 Endomucin marks quiescent long-term multi-lineage repopulating hematopoietic stem cells and is essential for their transendothelial migration [RNA-seq: wildtype_EMCN] 11 samples shares hematopoietic, long-term, rna-seq
GSE266586 RNA-seq in murine LSKs after Cux1 and/or Ezh2 loss, in the presence or absence of the DNA damaging agent N-ethyl-N-nitrosourea 39 samples shares cux1, rna-seq
GSE274544 Single cell profiling reveals three endothelial to hematopoietic transitions with divergent isoform expression landscapes [scRNA-Seq] 1494 samples shares hematopoietic, rna-seq
GSE265909 yHSC and oHSC scRNAseq with oHSC AThi ATlo Index Sorting. Assessing the transcriptional changes associated with autophagy engagement in old hematopoietic stem cells at single cell resolution. [scRNA-Seq] 563 samples shares hematopoietic, rna-seq
GSE266509 A Bcl11a-driven mechanism maintaining hematopoietic stem cell functionality gives rise to dysfunction during aging [RNA-Seq] 52 samples shares hematopoietic, rna-seq
GSE306744 Pre-division TCF1 downregulation determines long-term effector and memory CD8 T cell fates [RNA-Seq] 31 samples shares long-term, rna-seq
GSE276137 The ac4C acetyltransferase Nat10 promotes RNA stability to support hematopoietic stem cell fate [RNA-seq-32D] 24 samples shares hematopoietic, rna-seq

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.