Improved spike-in normalization clarifies the relationship between active histone modifications and transcription
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 244 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
- 244 samples: 214 distinct titles, 30 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.
Read the full summary ↓
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE286875_RAW.tar (it can run to tens of gigabytes).
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 PRJNA1217867 and SRA study SRP560966. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 30 samples read as cases, 58 as controls.
How we read this: Read from 244 sample titles: 214 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.
- 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 →
- GSE124718 Resetting histone modifications during human parental-to-zygotic transition 42 samples shares modifications, histone
- GSE240506 Histone lysine demethylase 4 family proteins maintain the transcriptional program and adrenergic cellular state of MYCN-amplified neuroblastoma 26 samples shares transcription, histone
- GSE261351 Direct measurement of RNA Polymerase II hypertranscription in cancer FFPE samples 278 samples shares transcription
- GSE260742 DOT1L provides transcriptional memory through PRC1.1 antagonism [ChIP-Seq] 158 samples shares transcription
- GSE240599 An eRNA Transcription Checkpoint For Diverse Signal-dependent Enhancer Activation Programs 130 samples shares transcription
- GSE292300 A core transcriptional regulatory circuitry controls super-enhancer-driven activation of LGR5 in colorectal cancer: ChIP-seq 76 samples shares transcription
- GSE188412 The PAF1 Complex Regulates Transcriptional Termination and Reinitiation [CUT&Tag] 71 samples shares transcription
- GSE256232 Quantitative analysis of cis-regulatory elements in transcription with KAS-ATAC-seq 67 samples shares transcription
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.