GEO series
Single-molecule, single-cell profiling of linked chromatin states [Single_cell_CoCUT&Tag]
GSE327821
Homo sapiens
Genome binding/occupancy profiling by high throughput sequencing
200 samples
Submitted 2026/04/30
Platform GPL34295
Summary
Genomic methods for profiling multiple chromatin features face tradeoffs between specificity, sensitivity, and the ability to measure chromatin co-occupancy. As a result, context-dependent interactions between chromatin proteins remain difficult to resolve in rare cell types and primary tissues. Here, we present CoCUT&Tag, which uses synthetic antigen-peptide repeats paired with nanobodies to amplify Tn5 transposase targeting and directly measure co-occupancy of two chromatin features in single cells. We applied CoCUT&Tag to test the model that bivalent chromatin, marked by the coexistence of H3K27me3 and H3K4 methylation, preserves stem-cell multipotency by keeping developmental genes poised for future activation. Instead, we find that during human hematopoiesis, stem cells are defined by a more active chromatin landscape, whereas lineage-restricted populations contain more bivalent genes. Bivalent and unmarked genes are activated with similar timing, but bivalent genes achieve higher expression, are associated with more numerous and stronger enhancers, and are preferentially derepressed following BMI1 loss. Our study shows that bivalent chromatin increases enhancer demand to enable high-amplitude gene activation, demonstrating that CoCUT&Tag can resolve longstanding questions about combinatorial chromatin regulation.
This dataset
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Direct links to NCBI, no account and no request form: the whole study as GSE327821_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 200 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1452847 and SRA study SRP691388. Searching any of these in the dataset finder brings you back here.
Study design
40 conditions, each sampled once — no replicated groups
Read from the first 40 of 200 sample titles: 40 distinct titles with little repetition. Check it against the sample list below before relying on it.
Samples in this study
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- GSM9666540 Single-cell CoCUT&Tag for H3K27me3 (Abcam ab6002) (S1) in peripheral blood mononuclear cells
- GSM9666541 Single-cell CoCUT&Tag for H3K4me3 (Active Motif 39159) (S1) in peripheral blood mononuclear cells
- GSM9666542 Single-cell CoCUT&Tag co-occupancy reads (R1) for H3K4me3 and H3K27me3 (S1) in peripheral blood mononuclear cells
- GSM9666543 Single-cell CoCUT&Tag co-occupancy reads (R2) for H3K4me3 and H3K27me3 (S1) in peripheral blood mononuclear cells
- GSM9666544 Single-cell CoCUT&Tag for H3K27me3 (Abcam ab6002) (S2) in peripheral blood mononuclear cells
- GSM9666545 Single-cell CoCUT&Tag for H3K4me3 (Active Motif 39159) (S2) in peripheral blood mononuclear cells
- GSM9666546 Single-cell CoCUT&Tag co-occupancy reads (R1) for H3K4me3 and H3K27me3 (S2) in peripheral blood mononuclear cells
- GSM9666547 Single-cell CoCUT&Tag co-occupancy reads (R2) for H3K4me3 and H3K27me3 (S2) in peripheral blood mononuclear cells
- GSM9666548 Single-cell CoCUT&Tag for H3K27me3 (Abcam ab6002) (S3) in peripheral blood mononuclear cells
- GSM9666549 Single-cell CoCUT&Tag for H3K4me3 (Active Motif 39159) (S3) in peripheral blood mononuclear cells
- GSM9666550 Single-cell CoCUT&Tag co-occupancy reads (R1) for H3K4me3 and H3K27me3 (S3) in peripheral blood mononuclear cells
- GSM9666551 Single-cell CoCUT&Tag co-occupancy reads (R2) for H3K4me3 and H3K27me3 (S3) in peripheral blood mononuclear cells
- GSM9666552 Single-cell CoCUT&Tag for H3K27me3 (Diagenode C15200181) (S4) in peripheral blood mononuclear cells
- GSM9666553 Single-cell CoCUT&Tag for H3K4me3 (Active Motif 39159) (S4) in peripheral blood mononuclear cells
- GSM9666554 Single-cell CoCUT&Tag co-occupancy reads (R1) for H3K4me3 and H3K27me3 (S4) in peripheral blood mononuclear cells
- GSM9666555 Single-cell CoCUT&Tag co-occupancy reads (R2) for H3K4me3 and H3K27me3 (S4) in peripheral blood mononuclear cells
- GSM9666556 Single-cell CoCUT&Tag for H3K27me3 (Diagenode C15200181) (S5) in peripheral blood mononuclear cells
- GSM9666557 Single-cell CoCUT&Tag for H3K4me3 (Active Motif 39159) (S5) in peripheral blood mononuclear cells
- GSM9666558 Single-cell CoCUT&Tag co-occupancy reads (R1) for H3K4me3 and H3K27me3 (S5) in peripheral blood mononuclear cells
- GSM9666559 Single-cell CoCUT&Tag co-occupancy reads (R2) for H3K4me3 and H3K27me3 (S5) in peripheral blood mononuclear cells
- GSM9666560 Single-cell CoCUT&Tag for H3K27me3 (Diagenode C15200181) (S6) in peripheral blood mononuclear cells
- GSM9666561 Single-cell CoCUT&Tag for H3K4me3 (Active Motif 39159) (S6) in peripheral blood mononuclear cells
- GSM9666562 Single-cell CoCUT&Tag co-occupancy reads (R1) for H3K4me3 and H3K27me3 (S6) in peripheral blood mononuclear cells
- GSM9666563 Single-cell CoCUT&Tag co-occupancy reads (R2) for H3K4me3 and H3K27me3 (S6) in peripheral blood mononuclear cells
- GSM9666564 Single-cell CoCUT&Tag for H3K27me3 (BPS Bioscience 25243) (S7) in peripheral blood mononuclear cells
- GSM9666565 Single-cell CoCUT&Tag for H3K4me3 (Active Motif 39159) (S7) in peripheral blood mononuclear cells
- GSM9666566 Single-cell CoCUT&Tag co-occupancy reads (R1) for H3K4me3 and H3K27me3 (S7) in peripheral blood mononuclear cells
- GSM9666567 Single-cell CoCUT&Tag co-occupancy reads (R2) for H3K4me3 and H3K27me3 (S7) in peripheral blood mononuclear cells
- GSM9666568 Single-cell CoCUT&Tag for H3K27me3 (BPS Bioscience 25243) (S8) in peripheral blood mononuclear cells
- GSM9666569 Single-cell CoCUT&Tag for H3K4me3 (Active Motif 39159) (S8) in peripheral blood mononuclear cells
- GSM9666570 Single-cell CoCUT&Tag co-occupancy reads (R1) for H3K4me3 and H3K27me3 (S8) in peripheral blood mononuclear cells
- GSM9666571 Single-cell CoCUT&Tag co-occupancy reads (R2) for H3K4me3 and H3K27me3 (S8) in peripheral blood mononuclear cells
- GSM9666572 Single-cell CoCUT&Tag for H3K27me3 (BPS Bioscience 25243) (S9) in peripheral blood mononuclear cells
- GSM9666573 Single-cell CoCUT&Tag for H3K4me3 (Active Motif 39159) (S9) in peripheral blood mononuclear cells
- GSM9666574 Single-cell CoCUT&Tag co-occupancy reads (R1) for H3K4me3 and H3K27me3 (S9) in peripheral blood mononuclear cells
- GSM9666575 Single-cell CoCUT&Tag co-occupancy reads (R2) for H3K4me3 and H3K27me3 (S9) in peripheral blood mononuclear cells
- GSM9666576 Single-cell CoCUT&Tag for H3K4me3 (Diagenode C15200152) (S10) in peripheral blood mononuclear cells
- GSM9666577 Single-cell CoCUT&Tag for H3K27me3 (CST 9733) (S10) in peripheral blood mononuclear cells
- GSM9666578 Single-cell CoCUT&Tag co-occupancy reads (R1) for H3K27me3 and H3K4me3 (S10) in peripheral blood mononuclear cells
- GSM9666579 Single-cell CoCUT&Tag co-occupancy reads (R2) for H3K27me3 and H3K4me3 (S10) in peripheral blood mononuclear cells
+ 160 more — browse all 200 samples with per-sample file links →
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