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In vivo CRISPR screening identifies SAGA complex members as a key regulators of hematopoiesis [RNA]

GSE312282 Mus musculus (mouse) RNA-seq (gene expression) 56 samples Submitted 2025/12/02 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 56 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
56 samples: 15 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
In vivo CRISPR screening identifies SAGA complex members as key regulators of hematopoiesisNature communications · 2026
Summary (written by the submitters)
The biological mechanisms that sustain the vast blood production required for healthy life remain incompletely understood. To search for novel regulators of hematopoiesis, we performed a genome-wide in vivo hematopoietic stem and progenitor cell (HSPC)-based CRISPR knockout screen for regulators of hematopoiesis. We discovered SAGA complex members, including Tada2b and Taf5l, as key regulators of hematopoiesis.
Read the full summary ↓
Loss of Tada2b or Taf5l strongly inhibited hematopoiesis in vivo, causing a buildup of immature hematopoietic cells in the bone marrow. The SAGA complex deposits histone H3 lysine 9 acetylation (H3K9ac) and removes histone H2B ubiquitination (H2Bub). Loss of Tada2b led to reductions in H3K9ac levels and altered H2Bub enrichment in HSPCs, implicating disruption of SAGA complex activity. This was associated with upregulation of interferon pathway genes, reduced mitochondrial activity, and increased megakaryocyte progenitor cell commitment. Loss of these factors also enhanced the cell outgrowth and the interferon pathway in an in vivo human myelodysplastic syndrome cell line model. In summary, this study has identified the SAGA complex as an important regulator of hematopoiesis.
Published in
In vivo CRISPR screening identifies SAGA complex members as key regulators of hematopoiesis
Shankar A, Olender L, Hsu I et al. · Nature communications 2026 · PMID 41577693 · doi:10.1038/s41467-026-68465-6
This dataset
Open GSE312282 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 GSE312282_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 PRJNA1372767 and SRA study SRP650833. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41577693) ↗
Study design
15 conditions, mostly in triplicate
DMSO_2days ×4 GSK699_2days ×4 Tada2b_KO ×4 AAVS1 ×3 Tada2b_OE ×3 Tada2b_g3 ×3 inVivo_mm_Rosa26_sgRNA ×3 inVivo_mm_Tada2b_SgRNA1 ×3 +20 more

Supports a between-group comparison across 43 samples.

How we read this: 15 replicated groups read from 56 sample titles; they account for 43 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

+ 16 more — browse all 56 samples with per-sample file links →

Datasets on a similar topic

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