Changes in H3K27 acetylation in THP1 human AML cell line on PHF6 knockout, PHF6R274Q mutation, PHIP knockout, and double knockout of PHF6 and PHIP compared to wildtype clones
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 18 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
- 18 samples: 5 conditions, mostly in triplicateGroups 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
- Leukemia mutated proteins PHF6 and PHIP form a chromatin complex that represses acute myeloid leukemia stemnessGenes & development · 2025
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 GSE281627_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 PRJNA1184838 and SRA study SRP544554. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 16 samples.
How we read this: 5 replicated groups read from 18 sample titles; they account for 16 of them. 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.
- GSM8625075 WT_THP1_ChIP-Input
- GSM8625076 WT_THP1_IgG-ChIP
- GSM8625077 WT_THP1_H3K27ac-ChIP_Rep1 WT_THP1_H3K27ac-ChIP
- GSM8625078 WT_THP1_H3K27ac-ChIP_Rep2 WT_THP1_H3K27ac-ChIP
- GSM8625079 WT_THP1_H3K27ac-ChIP_Rep3 WT_THP1_H3K27ac-ChIP
- GSM8625080 PHF6KO_THP1_H3K27ac-ChIP_Rep1 PHF6KO_THP1_H3K27ac-ChIP
- GSM8625081 PHF6KO_THP1_H3K27ac-ChIP_Rep2 PHF6KO_THP1_H3K27ac-ChIP
- GSM8625082 PHF6KO_THP1_H3K27ac-ChIP_Rep3 PHF6KO_THP1_H3K27ac-ChIP
- GSM8625083 PHF6KO_THP1_H3K27ac-ChIP_Rep4 PHF6KO_THP1_H3K27ac-ChIP
- GSM8625084 R274Q_THP1_H3K27ac-ChIP_Rep1 R274Q_THP1_H3K27ac-ChIP
- GSM8625085 R274Q_THP1_H3K27ac-ChIP_Rep2 R274Q_THP1_H3K27ac-ChIP
- GSM8625086 R274Q_THP1_H3K27ac-ChIP_Rep3 R274Q_THP1_H3K27ac-ChIP
- GSM8625087 PHIPKO_THP1_H3K27ac-ChIP_Rep1 PHIPKO_THP1_H3K27ac-ChIP
- GSM8625088 PHIPKO_THP1_H3K27ac-ChIP_Rep2 PHIPKO_THP1_H3K27ac-ChIP
- GSM8625089 PHIPKO_THP1_H3K27ac-ChIP_Rep3 PHIPKO_THP1_H3K27ac-ChIP
- GSM8625090 DKO_THP1_H3K27ac-ChIP_Rep1 DKO_THP1_H3K27ac-ChIP
- GSM8625091 DKO_THP1_H3K27ac-ChIP_Rep2 DKO_THP1_H3K27ac-ChIP
- GSM8625092 DKO_THP1_H3K27ac-ChIP_Rep3 DKO_THP1_H3K27ac-ChIP
- GSE281628 PHF6 occupancy in THP1 human AML cell line in wildtype, PHF6R274Q mutant, and PHIP knockout cells 12 samples shares phf6r274q, thp1, phf6, phip, aml, knockout
- GSE281475 Transcriptomic changes in THP1 human AML cell line on PHF6 knockout, PHF6R274Q mutation, PHIP knockout, and double knockout of PHF6 and PHIP compared to wildtype cells 21 samples shares phf6r274q, thp1, phf6, phip, aml, knockout
- GSE281624 Transcriptomic changes in PHF6 knockout THP1 human AML cell line on rescue with PHF6 wildtype (with and without PHIP) or rescue with PHF6R274Q mutant 19 samples shares phf6r274q, thp1, phf6, phip, aml, knockout
- GSE288498 The Retinal Determination Gene Network can confer chemoresistant properties to AML [THP1_chip_rna] 23 samples shares thp1, aml
- GSE295226 CUT&RUN in SCC-25 Parental and RARG knockout cells maps RARγ binding sites and genome wide changes in H3K4 & H3K27 trimethylation 23 samples shares h3k27, knockout
- GSE289004 Mitochondrial calcium uniporter links acetyl-CoA metabolism and H3K27 acetylation to maintain glioblastoma stem cells [ChIP-Seq] 12 samples shares h3k27, acetylation
- GSE272469 Spatial control of m6A deposition on enhancer and promoter RNAs through co-acetylation of METTL3 and H3K27 on chromatin 26 samples shares h3k27, acetylation
- GSE289005 Mitochondrial calcium uniporter links acetyl-CoA metabolism and H3K27 acetylation to maintain glioblastoma stem cells 18 samples shares h3k27, acetylation
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.