Open chromatin, HIF binding and mRNA expression analysis in primary tubule and ccRCC cells [ChIP-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 15 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
- 15 samples: 15 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
- HIF sustain a transcriptional regulatory circuit of EPAS1 expression in renal clear cell carcinomaNature communications · 2026
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 GSE255997_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 PRJNA1077366 and SRA study SRP490100. 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 15 sample titles: 15 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.
- GSM8083960 ChIP_PTC_1_ctrl_Input
- GSM8083961 ChIP_PTC_1_ctrl_H3K27ac
- GSM8083962 ChIP_PTC_2_ctrl_Input
- GSM8083963 ChIP_PTC_2_ctrl_H3K27ac
- GSM8083964 ChIP_PTC_3_ctrl_Input
- GSM8083965 ChIP_PTC_3_ctrl_H3K27ac
- GSM8083966 ChIP_ccRCC_1_ctrl_Input
- GSM8083967 ChIP_ccRCC_1_ctrl_H3K27ac
- GSM8083968 ChIP_ccRCC_2_ctrl_Input
- GSM8083969 ChIP_ccRCC_2_ctrl_H3K27ac
- GSM8083970 ChIP_ccRCC_3_ctrl_Input
- GSM8083971 ChIP_ccRCC_3_ctrl_H3K27ac
- GSM8083972 ChIP_U87_DMOG_Input
- GSM8083973 ChIP_U87_DMOG_H3K27ac
- GSM8083974 ChIP_U87_DMOG_HIF1_beta
- GSE301512 Chromatin topology dynamics of dexamethasone-treated trabecular meshwork identifies 78 causal genes for intraocular pressure and primary open angle glaucoma [CUT&Run] 30 samples shares chromatin, primary, open
- GSE296190 Hypoxic regulation of chromatin and gene transcription [ChIP-seq] 84 samples shares chromatin, chip-seq
- GSE316389 Chromatin accessibility and gene expression profiling of primary and metastatic ER+ breast cancer [ATAC-seq] 36 samples shares chromatin, primary
- GSE282760 Epigenomic manipulation reveals the relationship between locus specific chromatin dynamics and gene expression [ChIP-seq] 36 samples shares chromatin, chip-seq
- GSE337829 Integrated single-cell profiling of RNA and DNA interactomes reveals targetable chromatin architectures in cancer [ChIP-Seq] 32 samples shares chromatin, chip-seq
- GSE314776 Decoding 3D chromatin architecture reveals distinct enhancer classes underlying hierarchical gene regulation in prostate cancer [ChIP-Seq] 24 samples shares chromatin, chip-seq
- GSE316391 Chromatin accessibility and gene expression profiling of primary and metastatic ER+ breast cancer [RNA-seq] 32 samples shares chromatin, primary
- GSE171817 SUMOylation Regulates Super-Enhancers Through Transcription Factor TFAP2C Binding on Chromatin 30 samples shares chromatin, binding
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.