GEO series

RNA-seq of V-SZV derived aNS cells with siRNA mediated depletion of Pbx1, Tcf3 and Tcf4

GSE248755 Mus musculus (mouse) RNA-seq (gene expression) 21 samples Submitted 2024/09/16 Platform GPL30172

At a glance

RNA-seq (gene expression) · mouse · 21 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: 21 samples: 7 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.
Paper: Integrated multi-omics analysis of PBX1 in mouse adult neural stem- and progenitor cells identifies a transcriptional module that functionally links PBX1 to TCF3/4Nucleic acids research · 2024

Summary (written by the submitters)

Developmental transcription factors act in networks, but how these networks achieve cell- and tissue specificity is still poorly understood. Here we explored pre-B cell leukemia homeobox 1 (PBX1) in adult neurogenesis combining genomic, transcriptomic, and proteomic approaches. ChIP-Seq analysis uncovered PBX1 binding to a wide range of different sites.

Read the full summary ↓

Integration of PBX1 ChIP-seq with ATAC-seq data predicted interaction partners, which were subsequently validated by mass spectrometry. Spatial transcriptomics revealed distinct temporal expression dynamics of Pbx1 and interacting factors. Among these were class I bHLH proteins TCF3, TCF4 and TCF12. RNA-seq upon Pbx1, Tcf3 and Tcf4 knockdown identified proliferation- and differentiation associated genes as shared targets. Neuronal differentiation was reduced upon depletion of either factor, suggesting functional cooperation between PBX1 and TCF3/4. Notably, while physiological PBX1-TCF interactions have not yet been described, chromosomal translocation resulting in genomic TCF3::PBX1 fusion characterizes a subtype of acute lymphoblastic leukemia. Introducing Pbx1 into Nalm6 cells, a pre-B cell line expressing TCF3 but lacking PBX1, upregulated leukemogenic genes including BLK and NOTCH3, arguing that functional PBX1-TCF cooperation likely extends to hematopoietic contexts. Our study hence uncovers a PBX1-TCF module orchestrating the balance between progenitor cell proliferation and differentiation in adult neurogenesis with implications for leukemia etiology.

Published in

Integrated multi-omics analysis of PBX1 in mouse adult neural stem- and progenitor cells identifies a transcriptional module that functionally links PBX1 to TCF3/4

Laub V, Nan E, Elias L et al. · Nucleic acids research 2024 · PMID 39377397 · doi:10.1093/nar/gkae864

This dataset

Open GSE248755 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 GSE248755_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 PRJNA1045712 and SRA study SRP474486. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39377397) ↗

Study design

7 conditions, mostly in triplicate

RNA-seq_aNS_Pbx1-ctrl ×3 RNA-seq_aNS_Pbx1-kd ×3 RNA-seq_aNS_Tcf3-ctrl ×3 RNA-seq_aNS_Tcf3-kd ×3 RNA-seq_aNS_Tcf4-ctrl ×3 RNA-seq_aNS_Tcf4-kd ×3 RNA-seq_aNS_WT ×3

Supports a between-group comparison across 21 samples.

How we read this: 7 replicated groups read from 21 sample titles; they account for 21 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

GSM7919530 RNA-seq_aNS_Pbx1-ctrl_rep1 RNA-seq_aNS_Pbx1-ctrl
GSM7919531 RNA-seq_aNS_Pbx1-ctrl_rep2 RNA-seq_aNS_Pbx1-ctrl
GSM7919532 RNA-seq_aNS_Pbx1-ctrl_rep3 RNA-seq_aNS_Pbx1-ctrl
GSM7919533 RNA-seq_aNS_Pbx1-kd_rep1 RNA-seq_aNS_Pbx1-kd
GSM7919534 RNA-seq_aNS_Pbx1-kd_rep2 RNA-seq_aNS_Pbx1-kd
GSM7919535 RNA-seq_aNS_Pbx1-kd_rep3 RNA-seq_aNS_Pbx1-kd
GSM7919536 RNA-seq_aNS_Tcf3-ctrl_rep1 RNA-seq_aNS_Tcf3-ctrl
GSM7919537 RNA-seq_aNS_Tcf3-ctrl_rep2 RNA-seq_aNS_Tcf3-ctrl
GSM7919538 RNA-seq_aNS_Tcf3-ctrl_rep3 RNA-seq_aNS_Tcf3-ctrl
GSM7919539 RNA-seq_aNS_Tcf3-kd_rep1 RNA-seq_aNS_Tcf3-kd
GSM7919540 RNA-seq_aNS_Tcf3-kd_rep2 RNA-seq_aNS_Tcf3-kd
GSM7919541 RNA-seq_aNS_Tcf3-kd_rep3 RNA-seq_aNS_Tcf3-kd
GSM7919542 RNA-seq_aNS_Tcf4-ctrl_rep1 RNA-seq_aNS_Tcf4-ctrl
GSM7919543 RNA-seq_aNS_Tcf4-ctrl_rep2 RNA-seq_aNS_Tcf4-ctrl
GSM7919544 RNA-seq_aNS_Tcf4-ctrl_rep3 RNA-seq_aNS_Tcf4-ctrl
GSM7919545 RNA-seq_aNS_Tcf4-kd_rep1 RNA-seq_aNS_Tcf4-kd
GSM7919546 RNA-seq_aNS_Tcf4-kd_rep2 RNA-seq_aNS_Tcf4-kd
GSM7919547 RNA-seq_aNS_Tcf4-kd_rep3 RNA-seq_aNS_Tcf4-kd
GSM7919548 RNA-seq_aNS_WT_rep1 RNA-seq_aNS_WT
GSM7919549 RNA-seq_aNS_WT_rep2 RNA-seq_aNS_WT
GSM7919550 RNA-seq_aNS_WT_rep3 RNA-seq_aNS_WT

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GSE233940 Dynamic evolution of TCF3-PBX1 leukemias at the single-cell level under chemotherapy pressure [scRNA-seq] 15 samples shares pbx1, tcf3, rna-seq
GSE233937 Dynamic evolution of TCF3-PBX1 leukemias at the single-cell level under chemotherapy pressure [Bulk RNA-seq] 12 samples shares pbx1, tcf3, rna-seq
GSE233941 Dynamic evolution of TCF3-PBX1 leukemias at the single-cell level under chemotherapy pressure 27 samples shares pbx1, tcf3
GSE286961 Deep learning identifies Pbx1 as a network hub of hematopoietic stem cell aging [Pbx1 RNA-seq] 12 samples shares pbx1, rna-seq
GSE286957 Deep learning identifies Pbx1 as a network hub of hematopoietic stem cell aging [26hr RNA-seq] 8 samples shares pbx1, rna-seq
GSE277737 Phf23 regulates embryonic neurogenesis by increasing the level of H3K27ac of Tcf4 [RNA-seq] 8 samples shares tcf4, rna-seq
GSE286966 Deep learning identifies Pbx1 as a network hub of hematopoietic stem cell aging [scRNA-seq] 8 samples shares pbx1, rna-seq
GSE244709 Astrocyte allocation during brain development is controlled by Tcf4-mediated fate restriction 20 samples shares tcf4, mediated

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