GEO series
Single-molecule, single-cell profiling of linked chromatin states [Bulk_CoCUT&Tag]
GSE327819
Homo sapiens
Genome binding/occupancy profiling by high throughput sequencing
35 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 GSE327819_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 35 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1452843 and SRA study SRP691375. Searching any of these in the dataset finder brings you back here.
Study design
35 conditions, each sampled once — no replicated groups
Read from 35 sample titles: 35 distinct titles with little repetition. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM9666496 CoCUT&Tag for H3K27me3 (Abcam ab6002) alone in RS411 cells
- GSM9666497 CoCUT&Tag with no Block for H3K27me3 (Abcam ab6002) alone in RS411 cells
- GSM9666498 CoCUT&Tag for H3K27me3 (CST 9733S) alone in RS411 cells
- GSM9666499 CoCUT&Tag with no Block for H3K27me3 (CST 9733S) alone in RS411 cells
- GSM9666500 CoCUT&Tag for H3K4me2 (Active Motif 39679) alone in RS411 cells
- GSM9666501 CoCUT&Tag with no Block for H3K4me2 (Active Motif 39679) alone in RS411 cells
- GSM9666502 CoCUT&Tag for H3K4me2 (Sigma Aldrich 07-030) alone in RS411 cells
- GSM9666503 CoCUT&Tag with no Block for H3K4me2 (Sigma Aldrich 07-030) alone in RS411 cells
- GSM9666504 CoCUT&Tag for H3K4me3 (Diagenode C15200152) alone in K562 cells
- GSM9666505 CoCUT&Tag for H3K27ac (Diagenode C15200184) alone in K562 cells
- GSM9666506 CoCUT&Tag for H3K27me3 (CST 9733) alone in K562 cells
- GSM9666507 Bulk CoCUT&Tag for H3K27me3 (BPS Bioscience 25243) in K562 cells (B5)
- GSM9666508 Bulk CoCUT&Tag for H3K4me3 (CST 9751) in K562 cells (B5)
- GSM9666509 Bulk CoCUT&Tag co-occupancy reads (R1) for H3K4me3 and H3K27me3 in K562 cells (B5)
- GSM9666510 Bulk CoCUT&Tag co-occupancy reads (R2) for H3K4me3 and H3K27me3 in K562 cells (B5)
- GSM9666511 Bulk CoCUT&Tag for H3K27me3 (BPS Bioscience 25243) in K562 cells (A5)
- GSM9666512 Bulk CoCUT&Tag for H3K4me3 (CST 9751) in K562 cells (A5)
- GSM9666513 Bulk CoCUT&Tag co-occupancy reads (R1) for H3K4me3 and H3K27me3 in K562 cells (A5)
- GSM9666514 Bulk CoCUT&Tag co-occupancy reads (R2) for H3K4me3 and H3K27me3 in K562 cells (A5).
- GSM9666515 Bulk CoCUT&Tag for H3K27ac (Diagenode C15200184) in K562 cells (A8)
- GSM9666516 Bulk CoCUT&Tag for H3K27me3 (CST 9733) in K562 cells (A8)
- GSM9666517 Bulk CoCUT&Tag co-occupancy reads (R1) for H3K27me3 and H3K27ac in K562 cells (A8)
- GSM9666518 Bulk CoCUT&Tag co-occupancy reads (R2) for H3K27me3 and H3K27ac in K562 cells (A8)
- GSM9666519 Bulk CoCUT&Tag for H3K27ac (Diagenode C15200184) in K562 cells (B8)
- GSM9666520 Bulk CoCUT&Tag for H3K27me3 (CST 9733) in K562 cells (B8)
- GSM9666521 Bulk CoCUT&Tag co-occupancy reads (R1) for H3K27me3 and H3K27ac in K562 cells (B8)
- GSM9666522 Bulk CoCUT&Tag co-occupancy reads (R2) for H3K27me3 and H3K27ac in K562 cells (B8)
- GSM9666523 Bulk CoCUT&Tag for H3K27ac (Diagenode C15200184) in K562 cells (A6)
- GSM9666524 Bulk CoCUT&Tag for H3K4me3 (CST 9751) in K562 cells (A6)
- GSM9666525 Bulk CoCUT&Tag co-occupancy reads (R1) for H3K4me3 and H3K27ac in K562 cells (A6)
- GSM9666526 Bulk CoCUT&Tag co-occupancy reads (R2) for H3K4me3 and H3K27ac in K562 cells (A6)
- GSM9666527 Bulk CoCUT&Tag for H3K27ac (Diagenode C15200184) in K562 cells (B6)
- GSM9666528 Bulk CoCUT&Tag for H3K4me3 (CST 9751) in K562 cells (B6)
- GSM9666529 Bulk CoCUT&Tag co-occupancy reads (R1) for H3K4me3 and H3K27ac in K562 cells (B6)
- GSM9666530 Bulk CoCUT&Tag co-occupancy reads (R2) for H3K4me3 and H3K27ac in K562 cells (B6)
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