GEO series
Improved spike-in normalization clarifies the relationship between active histone modifications and transcription
GSE286875
Homo sapiens; Mus musculus
Genome binding/occupancy profiling by high throughput sequencing
244 samples
Submitted 2025/10/29
Platform GPL30173Platform GPL21697Platform GPL30172
Summary
Spike-in normalization enables quantitative analysis of ChIP-sequencing (ChIP-seq) signal. Here we introduce a novel robust dual-spike-in normalization approach for ChIP-seq (ChIP-wrangler) and revisit recent claims that active histone marks are dependent on transcription. Concerned that previous studies improperly used spike-in normalization to arrive at their conclusions, we used ChIP-wrangler to show that acute depletion of RNA polymerase II has only a modest impact on the levels of H3K4me3 and H3K27ac. In line with other studies, our results provide proof that the maintenance of histone acetylation is not merely a consequence of ongoing transcription. Our innovative ChIP-seq normalization approach provides increased rigor and “guardrails” for successful spike-in normalization, and as applied here refines the understanding of the intricate crosstalk between RNA polymerase II activity and histone marks associated with transcription
This dataset
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Direct links to NCBI, no account and no request form: the whole study as GSE286875_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 244 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1217867 and SRA study SRP560966. Searching any of these in the dataset finder brings you back here.
Study design
34 conditions, each sampled once — no replicated groups
HeLa-S3, Triptolide treated, 0hr, biological … ×2
HeLa-S3, Triptolide treated, 0hr, biological … ×2
HeLa-S3, Triptolide treated, 1hr, biological … ×2
HeLa-S3, Triptolide treated, 1hr, biological … ×2
HeLa-S3, Triptolide treated, 4hr, biological … ×2
HeLa-S3, Triptolide treated, 4hr, biological … ×2
Read from the first 40 of 244 sample titles: 34 distinct titles with little repetition. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM8732798 HeLa-S3, Triptolide treated, 0hr, biological replicate 1, H3K27ac
- GSM8732800 HeLa-S3, Triptolide treated, 0hr, biological replicate 2, H3K27ac
- GSM8732801 HeLa-S3, Triptolide treated, 1hr, biological replicate 1, H3K27ac
- GSM8732802 HeLa-S3, Triptolide treated, 1hr, biological replicate 2, H3K27ac
- GSM8732803 HeLa-S3, Triptolide treated, 4hr, biological replicate 1, H3K27ac
- GSM8732805 HeLa-S3, Triptolide treated, 4hr, biological replicate 2, H3K27ac
- GSM8732806 HeLa-S3, Triptolide treated, 0hr, biological replicate 1, H3K4me3
- GSM8732807 HeLa-S3, Triptolide treated, 0hr, biological replicate 2, H3K4me3
- GSM8732809 HeLa-S3, Triptolide treated, 1hr, biological replicate 1, H3K4me3
- GSM8732810 HeLa-S3, Triptolide treated, 1hr, biological replicate 2, H3K4me3
- GSM8732811 HeLa-S3, Triptolide treated, 4hr, biological replicate 1, H3K4me3
- GSM8732813 HeLa-S3, Triptolide treated, 4hr, biological replicate 2, H3K4me3
- GSM8732814 HeLa-S3, Triptolide treated, 0hr, biological replicate 1, H3K4me1
- GSM8732815 HeLa-S3, Triptolide treated, 0hr, biological replicate 2, H3K4me1
- GSM8732817 HeLa-S3, Triptolide treated, 1hr, biological replicate 1, H3K4me1
- GSM8732818 HeLa-S3, Triptolide treated, 1hr, biological replicate 2, H3K4me1
- GSM8732819 HeLa-S3, Triptolide treated, 4hr, biological replicate 1, H3K4me1
- GSM8732821 HeLa-S3, Triptolide treated, 4hr, biological replicate 2, H3K4me1
- GSM8732822 HeLa-S3, Triptolide treated, 0hr, biological replicate 1, Rpb1
- GSM8732823 HeLa-S3, Triptolide treated, 0hr, biological replicate 2, Rpb1
- GSM8732825 HeLa-S3, Triptolide treated, 1hr, biological replicate 1, Rpb1
- GSM8732826 HeLa-S3, Triptolide treated, 1hr, biological replicate 2, Rpb1
- GSM8732827 HeLa-S3, Triptolide treated, 4hr, biological replicate 1, Rpb1
- GSM8732829 HeLa-S3, Triptolide treated, 4hr, biological replicate 2, Rpb1
- GSM8732830 HeLa-S3, Triptolide treated, 0hr, biological replicate 1, input
- GSM8732831 HeLa-S3, Triptolide treated, 0hr, biological replicate 2, input
- GSM8732833 HeLa-S3, Triptolide treated, 1hr, biological replicate 1, input
- GSM8732834 HeLa-S3, Triptolide treated, 1hr, biological replicate 2, input
- GSM8732835 HeLa-S3, Triptolide treated, 4hr, biological replicate 1, input
- GSM8732837 HeLa-S3, Triptolide treated, 4hr, biological replicate 2, input
- GSM8732838 HCT116, DMSO treated, 0hr, biological replicate 1, H3K27ac
- GSM8732839 HCT116, auxin 1hr, biological replicate 1, H3K27ac
- GSM8732841 HCT116, auxin 4hr, biological replicate 1, H3K27ac
- GSM8732842 HCT116, triptolide 1hr, biological replicate 1, H3K27ac
- GSM8732843 HCT116, triptolide 4hr, biological replicate 1, H3K27ac
- GSM8732845 HCT116, DMSO treated, 0hr, biological replicate 1, H3K4me3
- GSM8732846 HCT116, auxin 1hr, biological replicate 1, H3K4me3
- GSM8732847 HCT116, auxin 4hr, biological replicate 1, H3K4me3
- GSM8732849 HCT116, triptolide 1hr, biological replicate 1, H3K4me3
- GSM8732850 HCT116, triptolide 4hr, biological replicate 1, H3K4me3
+ 204 more — browse all 244 samples with per-sample file links →
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