Genome-wide studies identify genes directly regulated by PML_RARα fusion protein and co-activator BRD4 [ChIP-Seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 17 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
- 17 samples: 17 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.
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 GSE232371_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 PRJNA971877 and SRA study SRP437356. 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 17 sample titles: 17 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.
- GSM7329540 NB4_BRD4_BETHYL
- GSM7329541 K562_vector_FLAG_SIGMA
- GSM7329542 K562_flag-PML_RARα_FLAG_SIGMA
- GSM7329543 K562_flag-PML_RARα-ΔIDR_FLAG_SIGMA
- GSM7329544 NB4_PBS_PML_RARα_customized
- GSM7329545 NB4_1,6-Hex_PML_RARα_customized
- GSM7329546 NB4_PBS_BRD4_BETHYL
- GSM7329547 NB4_1,6-Hex_BRD4_BETHYL
- GSM7329548 NB4_PBS_RNA pol II_BETHYL
- GSM7329549 NB4_1,6-Hex_RNA pol II_BETHYL
- GSM7329550 NB4_DMSO_PML_RARα_customized
- GSM7329551 NB4_ATO_PML_RARα_customized
- GSM7329552 NB4_JQ1_PML_RARα_customized
- GSM7329553 NB4_DMSO_BRD4_BETHYL
- GSM7329554 NB4_ATO_BRD4_BETHYL
- GSM7329555 NB4_JQ1_BRD4_BETHYL
- GSM7329556 NB4_Input
- GSE275303 Identifying RARG fusions or PML-RARA binding genes or analysis the epigenetic changes (H3K27ac, H3K4me1, and H3K4me3) in hCD34+ cells overexpressing CPSF6::RARG and NUP98::RARG. 34 samples shares pml, rar
- GSE299161 MALNC: A new mutant NPM1/IDH2R140 and PML-RARA-associated lncRNA with impact on AML cell proliferation, maturation and drug response 15 samples shares pml, rar
- GSE243437 The effect RARG fusion genes or PML-RARA overexpression in human CD34+ cells on the gene expression. 14 samples shares pml, rar
- GSE314776 Decoding 3D chromatin architecture reveals distinct enhancer classes underlying hierarchical gene regulation in prostate cancer [ChIP-Seq] 24 samples shares rar, chip-seq
- GSE252981 Toggling of BRD4 functions is triggered through its phosphorylation by JNK [ChIP-seq] 22 samples shares brd4, chip-seq
- GSE265759 Individual ChIP-seq for BRD4 and H3K27ac 16 samples shares brd4, chip-seq
- GSE267369 Elevating PLK1 Overcomes BETi-Resistance in Prostate Cancer via Triggering BRD4 Phosphorylation-dependent Degradation in Mitosis [ChIP-seq] 14 samples shares brd4, chip-seq
- GSE233712 Aberrant induction of the rare RNA binding protein PABPC4 in MYC-driven hepatocellular carcinoma 14 samples shares rar, protein
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.