GEO series
Metabolic control of innate immune activation in TET2-mutant clonal hematopoiesis [ChIP-seq]
GSE309775
Homo sapiens (human)
ChIP-seq / ATAC-seq (genome binding and open chromatin)
44 samples
Submitted 2026/01/15
Platform GPL19057Platform GPL18573
At a glance
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 44 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
- Homo sapiens (human)
- Samples
- 44 samples: 42 distinct titles, 2 of them repeatedGroups 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
- Metabolic control of innate immune activation in TET2-mutant clonal hematopoiesisCell chemical biology · 2026
Summary (written by the submitters)
TET2 mutations drive inflammation in clonal hematopoiesis of indeterminate potential (CHIP), but the mechanism by which TET2 inactivation leads to inflammation is not understood. Here, we used in vivo genome-wide genetic perturbations in primary wildtype (WT) or Tet2 knockout (KO) Cas9+ hematopoietic stem-progenitor cells (HSPCs) in a model of zymosan peritonitis to elucidate the basis of Tet2 KO inflammation.
Read the full summary ↓
We found that Tet2 restrains O-linked N-acetylglucosamine (O-GlcNAc) glycosyltransferase (Ogt), a Tet2 binding partner and metabolic sensor that integrates nutrient availability. Tet2 loss disrupts this Tet2-Ogt interaction, and dysregulated Ogt facilitates widespread H3K4 trimethylation including lipid-related gene loci and inflammatory lipid droplet formation. We identified ATP citrate lyase (Acly) as a critical node for lipid accumulation, inflammation, and myeloid expansion in Tet2 deficiency. In summary, we reveal that Tet2 serves as a negative regulator of the nutrient sensor Ogt, and that Tet2 inactivation leads to aberrant lipid droplet formation and inflammation.
Published in
Kim PG, Hergott CB, Miller AP et al.
· Cell chemical biology 2026
· PMID 41672066
· doi:10.1016/j.chembiol.2026.01.006
This dataset
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.
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 GSE309775_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1363152 and SRA study SRP644306. Searching any of these in the dataset finder brings you back here.
Study design
42 distinct titles, 2 of them repeated
Tet2 KO BMDMs treated with glucose, 55mM, 24 … ×2
WT BMDMs treated with glucose, 55mM, 24 hrs; … ×2
Supports a case/control comparison: 9 samples read as cases, 13 as controls.
How we read this: Read from 44 sample titles: 42 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
- GSM9278838 WT U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 0.1ng/ml, IP: H3K4me3
- GSM9278839 WT U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 1ng/ml, IP: H3K4me3
- GSM9278840 WT U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 100ng/ml, IP: H3K4me3
- GSM9278841 TET2KO U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 0.1ng/ml, IP: H3K4me3
- GSM9278842 TET2KO U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 1ng/ml, IP: H3K4me3
- GSM9278843 TET2KO U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 100ng/ml, IP: H3K4me3
- GSM9278844 WT U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 0.1ng/ml, IP: H3K27ac
- GSM9278845 WT U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 1ng/ml, IP: H3K27ac
- GSM9278846 WT U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 100ng/ml, IP: H3K27ac
- GSM9278847 TET2KO U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 0.1ng/ml, IP: H3K27ac
- GSM9278848 TET2KO U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 1ng/ml, IP: H3K27ac
- GSM9278849 TET2KO U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 100ng/ml, IP: H3K27ac
- GSM9278850 WT U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 0.1ng/ml, IP: Strepavidin
- GSM9278851 WT U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 1ng/ml, IP: Strepavidin
- GSM9278852 WT U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 100ng/ml, IP: Strepavidin
- GSM9278853 TET2KO U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 0.1ng/ml, IP: Strepavidin
- GSM9278854 TET2KO U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 1ng/ml, IP: Strepavidin
- GSM9278855 TET2KO U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 100ng/ml, IP: Strepavidin
- GSM9278856 WT U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 0.1ng/ml, input
- GSM9278857 WT U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 1ng/ml, input
- GSM9278858 WT U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 100ng/ml, input
- GSM9278859 TET2KO U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 0.1ng/ml, input
- GSM9278860 TET2KO U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 1ng/ml, input
- GSM9278861 TET2KO U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 100ng/ml, input
- GSM9278862 Tet2 KO BMDMs treated with galactose, 55mM, 24 hrs; IP: Ogt
- GSM9278863 Tet2 KO BMDMs treated with glucose, 12mM, 24 hrs; IP: GlcNAc
- GSM9278864 Tet2 KO BMDMs treated with glucose, 12mM, 24 hrs; IP: Ogt
- GSM9278865 Tet2 KO BMDMs treated with sucrose, 55mM, 24 hrs; IP: Ogt
- GSM9278866 Tet2 KO BMDMs treated with glucose, 55mM, 24 hrs; IP: GlcNAc
- GSM9278867 Tet2 KO BMDMs treated with glucose, 55mM, 24 hrs; IP: H3K4me1
- GSM9278868 Tet2 KO BMDMs treated with glucose, 55mM, 24 hrs; IP: H3K4me3
- GSM9278869 Tet2 KO BMDMs treated with glucose, 55mM, 24 hrs; IP: H3K27me3
- GSM9278870 Tet2 KO BMDMs treated with glucose, 55mM, 24 hrs; IP: Ogt
- GSM9278871 Tet2 KO BMDMs input
- GSM9278872 WT BMDMs treated with galactose, 55mM, 24 hrs; IP: Ogt
- GSM9278873 WT BMDMs treated with glucose, 12mM, 24 hrs; IP: GlcNAc
- GSM9278874 Wt BMDMs treated with glucose, 12mM, 24 hrs; IP: Ogt
- GSM9278875 WT BMDMs treated with glucose, 55mM, 24 hrs; IP: GlcNAc
- GSM9278876 WT BMDMs treated with glucose, 55mM, 24 hrs; IP: H3K4me1
- GSM9278877 WT BMDMs treated with glucose, 55mM, 24 hrs; IP: H3K4me3
+ 4 more — browse all 44 samples with per-sample file links →
Datasets on a similar topic
- GSE292300 A core transcriptional regulatory circuitry controls super-enhancer-driven activation of LGR5 in colorectal cancer: ChIP-seq 76 samples shares activation, chip-seq, control
- GSE270547 Mutant CEBPA promotes tolerance to inflammatory stress through deficient AP-1 activation [ChIP-seq] 40 samples shares activation, chip-seq
- GSE292302 A core transcriptional regulatory circuitry controls super-enhancer-driven activation of LGR5 in colorectal cancer: RNA-seq 42 samples shares activation, control
- GSE242099 The role of histone lysine demethylases in a genetically defined subset of clonal hematopoiesis 30 samples shares hematopoiesis, clonal
- GSE272816 POISONING OF HEALTHY HEMATOPOIESIS IS AN UNANTICIPATED MECHANISM DRIVING CLONAL DOMINANCE IN VEXAS SYNDROME [scRNA-seq] 14 samples shares hematopoiesis, clonal
- GSE245731 HNF4G and FOXA1 are context-specific drivers of pancreatic cancer progression [ChIP-seq] 172 samples shares chip-seq
- GSE260742 DOT1L provides transcriptional memory through PRC1.1 antagonism [ChIP-Seq] 158 samples shares chip-seq
- GSE240599 An eRNA Transcription Checkpoint For Diverse Signal-dependent Enhancer Activation Programs 130 samples shares activation
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.