GEO series
mChIP-seq for high-throughput epigenomic profiling reveals a decoupling of H2A.Z and H3K4me3 in cancer
GSE280574
Homo sapiens
Genome binding/occupancy profiling by high throughput sequencing
576 samples
Submitted 2026/08/05
Platform GPL29480Platform GPL24676
Summary
Histone variant H2A.Z has multiple roles in regulating gene transcription and its overexpression has been observed in various cancer types. However, the epigenomic characterization of H2A.Z in cancer is unclear. Combining the pool-and-split strategy with sequencing, we developed mChIP-seq, a multiplexed chromatin immunoprecipitation followed by sequencing method to efficiently profile multifactorial epigenetic landscapes of histone marks for multiple samples in parallel. mChIP-seq generates high-quality profiles comparable to standard ChIP-seq but with merits of high efficiency, low cost, and low-input requirement. Using mChIP-seq to profile H2A.Z and 10 H3 histone modifications for 24 cancer cell lines spanning 9 cancer types, we generated 528 epigenomic profiles from two workflows, comprehensively characterized genomic distribution of H2A.Z, and revealed its associations with main histone modifications and gene expression. Moreover, compared with normal cells by integration analysis of public data, we found a decoupling of H2A.Z and H3K4me3 at promoter sites in cancer cells, where the signal intensity of H2A.Z is not in line with the signal intensity of H3K4me3, which further dysregulates gene expression. Altogether, our results demonstrate that mChIP-seq is a powerful technology for epigenomic profiling and reveal abnormal regulatory features of H2A.Z in cancer.
Published in
Sun C, Zhang Q, Yan J et al.
· bioRxiv : the preprint server for biology 2026
· PMID 42094403
· doi:10.64898/2026.04.27.721226
This dataset
Download
Direct links to NCBI, no account and no request form: the whole study as GSE280574_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 576 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1179441 and SRA study SRP541848. 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 576 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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- GSM8600964 SNB19, H2AZ, rep1
- GSM8600965 NCI-H460, H2AZ, rep1
- GSM8600966 786-O, H2AZ, rep1
- GSM8600967 A549, H2AZ, rep1
- GSM8600968 U251, H2AZ, rep1
- GSM8600969 DU145, H2AZ, rep1
- GSM8600970 A498, H2AZ, rep1
- GSM8600971 NCI-H23, H2AZ, rep1
- GSM8600972 OVCAR-8, H2AZ, rep1
- GSM8600973 NCI-H522, H2AZ, rep1
- GSM8600974 NCI-H226, H2AZ, rep1
- GSM8600975 MOLT-4, H2AZ, rep1
- GSM8600976 HL-60, H2AZ, rep1
- GSM8600977 HCT116, H2AZ, rep1
- GSM8600978 SW620, H2AZ, rep1
- GSM8600979 SK-OV-3, H2AZ, rep1
- GSM8600980 K562, H2AZ, rep1
- GSM8600981 PC-3, H2AZ, rep1
- GSM8600982 T47D, H2AZ, rep1
- GSM8600983 CCRF-CEM, H2AZ, rep1
- GSM8600984 SK-MEL-2, H2AZ, rep1
- GSM8600985 RPMI-8226, H2AZ, rep1
- GSM8600986 MDA-MB-468, H2AZ, rep1
- GSM8600987 SK-MEL-28, H2AZ, rep1
- GSM8600988 SNB19, H3K18ac, rep1
- GSM8600989 NCI-H460, H3K18ac, rep1
- GSM8600990 786-O, H3K18ac, rep1
- GSM8600991 A549, H3K18ac, rep1
- GSM8600992 U251, H3K18ac, rep1
- GSM8600993 DU145, H3K18ac, rep1
- GSM8600994 A498, H3K18ac, rep1
- GSM8600995 NCI-H23, H3K18ac, rep1
- GSM8600996 OVCAR-8, H3K18ac, rep1
- GSM8600997 NCI-H522, H3K18ac, rep1
- GSM8600998 NCI-H226, H3K18ac, rep1
- GSM8600999 MOLT-4, H3K18ac, rep1
- GSM8601000 HL-60, H3K18ac, rep1
- GSM8601001 HCT116, H3K18ac, rep1
- GSM8601002 SW620, H3K18ac, rep1
- GSM8601003 SK-OV-3, H3K18ac, rep1
+ 536 more — browse all 576 samples with per-sample file links →
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