Myeloid-biased HSC require Semaphorin 4A from the bone marrow niche for self-renewal under stress and life-long persistence
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 10 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Mus musculus (mouse)
- Samples
- 10 samples: 4 × Sema4aKO_myHSC vs 4 × WT_myHSC vs 2 × WT_lyHSCGroups 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
- Niche-derived Semaphorin 4A safeguards functional identity of myeloid-biased hematopoietic stem cellsNature aging · 2025
Read the full summary ↓
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE281145_RAW.tar (it can run to tens of gigabytes).
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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA1182374 and SRA study SRP543355. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 10 samples.
How we read this: 3 replicated groups read from 10 sample titles; they account for 10 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.
- GSM8611683 Sema4aKO_myHSC_1 Sema4aKO_myHSC
- GSM8611684 Sema4aKO_myHSC_2 Sema4aKO_myHSC
- GSM8611685 Sema4aKO_myHSC_3 Sema4aKO_myHSC
- GSM8611686 Sema4aKO_myHSC_4 Sema4aKO_myHSC
- GSM8611687 WT_myHSC_1 WT_myHSC
- GSM8611688 WT_myHSC_2 WT_myHSC
- GSM8611689 WT_myHSC_3 WT_myHSC
- GSM8611690 WT_myHSC_4 WT_myHSC
- GSM8611691 WT_lyHSC_1 WT_lyHSC
- GSM8611692 WT_lyHSC_2 WT_lyHSC
- GSE301680 MLL3 and MLL4 redundantly license HSC self-renewal and myeloid identity while opposing B-cell priming, independently of COMPASS enzymatic functions [ChIP II] 6 samples shares hsc, self-renewal
- GSE301672 MLL3 and MLL4 redundantly license HSC self-renewal and myeloid identity while opposing B-cell priming, independently of COMPASS enzymatic functions [ChIP-seq I] 5 samples shares hsc, self-renewal
- GSE301675 MLL3 and MLL4 redundantly license HSC self-renewal and myeloid identity while opposing B-cell priming, independently of COMPASS enzymatic functions [scATAC] 4 samples shares hsc, self-renewal
- GSE204933 Age-associated chromatin reorganization drives overexpression of a novel Btaf1 variant regulating HSC self-renewal and MkP differentiation in male mice 82 samples shares hsc, self-renewal
- GSE166518 Small Nucleolar RNAs in the Dlk1-Gtl2 Imprinting Locus Maintains LT-HSC Self-renewal by Regulation of rRNA Modification and Translation 19 samples shares hsc, self-renewal
- GSE236765 RNA sequencing of LT-HSCs in the bone marrow from WT and Trim47-/- mice untreated or treated with 5-FU for 10 days 12 samples shares hsc, marrow
- GSE233828 RNA sequencing of Mmrn1-high LT-HSCs and Mmrn1-low LT-HSCs from murine bone marrow 6 samples shares hsc, marrow
- GSE237748 Phosphatase, Mg2+/Mn2+ Dependent 1B (Ppm1b) regulates the self-renewal of HSCs through the Wnt/β-catenin pathway 6 samples shares hsc, self-renewal
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.