Histone H3K4ac, as a marker of active transcription start sites and enhancers, plays roles in histone eviction and RNA transcription
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 30 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
- 30 samples: 30 samples, each with a distinct title — no replicated groupsGroups 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.
- Paper
- Histone H3K4ac, as a marker of active transcription start sites and enhancers, plays roles in histone eviction and RNA transcriptionBiochimica et biophysica acta. Gene regulatory mechanisms · 2024
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 GSE248434_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 PRJNA1043745 and SRA study SRP473418. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 30 sample titles: 30 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.
- GSM7913984 K562, Con, H3K4ac_Sp, ChIP, rep1
- GSM7913985 K562, Con, H3K4me1_Sp,ChIP, rep1
- GSM7913986 K562, Con, H3K4me2_Sp,ChIP, rep1
- GSM7913987 K562, Con, H3K4me3_Sp,ChIP, rep1
- GSM7913988 K562, Con, H3_Sp, ChIP, rep1
- GSM7913989 K562, dp300, H3K4ac_Sp, ChIP, rep1
- GSM7913990 K562, dp300, H3K4me1_Sp,ChIP, rep1
- GSM7913991 K562, dp300, H3K4me2_Sp,ChIP, rep1
- GSM7913992 K562, dp300, H3K4me3_Sp,ChIP, rep1
- GSM7913993 K562, dp300, H3_Sp, ChIP, rep1
- GSM7913994 K562, dMLL3/4, H3K4ac_Sp, ChIP, rep1
- GSM7913995 K562, dMLL3/4, H3K4me1_Sp,ChIP, rep1
- GSM7913996 K562, dMLL3/4, H3K4me2_Sp,ChIP, rep1
- GSM7913997 K562, dMLL3/4, H3K4me3_Sp,ChIP, rep1
- GSM7913998 K562, dMLL3/4, H3_Sp, ChIP, rep1
- GSM7913999 K562, Con, H3K4ac, ChIP, rep2
- GSM7914000 K562, Con, H3K4me1, ChIP, rep2
- GSM7914001 K562, Con, H3K4me2,ChIP, rep2
- GSM7914002 K562, Con, H3K4me3,ChIP, rep2
- GSM7914003 K562, Con, H3, ChIP, rep2
- GSM7914004 K562, dp300, H3K4ac, ChIP, rep2
- GSM7914005 K562, dp300, H3K4me1, ChIP, rep2
- GSM7914006 K562, dp300, H3K4me2,ChIP, rep2
- GSM7914007 K562, dp300, H3K4me3,ChIP, rep2
- GSM7914008 K562, dp300, H3, ChIP, rep2
- GSM7914009 K562, dMLL3/4, H3K4ac, ChIP, rep2
- GSM7914010 K562, dMLL3/4, H3K4me1, ChIP, rep2
- GSM7914011 K562, dMLL3/4, H3K4me2,ChIP, rep2
- GSM7914012 K562, dMLL3/4, H3K4me3,ChIP, rep2
- GSM7914013 K562, dMLL3/4, H3, ChIP, rep2
- GSE263584 Glycolysis involved in transcription dysregulation through histone lactylation in T-lineage acute lymphoblastic leukemia 12 samples shares transcription, histone
- GSE22098 Whole blood transcriptional profiles of patients with active tuberculosis (TB) and other inflammatory and infectious diseases 274 samples shares transcription, active
- GSE171817 SUMOylation Regulates Super-Enhancers Through Transcription Factor TFAP2C Binding on Chromatin 30 samples shares transcription, enhancers
- GSE309861 KLF5 controls subtype-independent highly interactive enhancers in pancreatic cancer to regulate cell survival [HiChIPseq] 10 samples shares enhancers, active
- GSE286581 Ablation of Linker Histone H1.4 Reveals Focal Regulation of AP-1 Directed Enhancers and Chromatin Accessibility [4sU] 6 samples shares enhancers, histone
- GSE284519 TRIM33 loss reduces Androgen Receptor transcriptional output and H2BK120 ubiquitination [ChIP-seq] 93 samples shares transcription
- GSE302930 Epigenetic Atlas of Bladder Cancer Reveals Master Transcription Factors and Risk-Associated Regulatory Elements in Luminal and Basal-Squamous Molecular Subtypes 92 samples shares transcription
- GSE296190 Hypoxic regulation of chromatin and gene transcription [ChIP-seq] 84 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.