ChIP-seq of RNA polymerase II and HNF4alpha in mouse liver after cytokine stimulation (WT vs TG)
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 9 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
- Mus musculus (mouse)
- Samples
- 9 samples: 9 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
- Inflammation-Driven Downregulation of CYP2E1 Is Associated with Attenuated Diethylnitrosamine (DEN)-Induced HepatocarcinogenesisCells · 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 GSE322777_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 PRJNA1431464 and SRA study SRP680698. 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 9 sample titles: 9 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.
- GSM9558274 A_WT_vehicle_Input_4h
- GSM9558275 B_WT_TNF_Input_4h
- GSM9558276 C_TG_vehicle_Input_4h
- GSM9558277 D_WT_vehicle_Pol2_4h
- GSM9558278 E_WT_TNF_Pol2_4h
- GSM9558279 F_TG_vehicle_Pol2_4h
- GSM9558280 G_WT_vehicle_HNF4_4h
- GSM9558281 H_WT_TNF_HNF4_4h
- GSM9558282 I_TG_vehicle_HNF4_4h
- GSE242901 An Intrinsically Disordered Region Controlling Condensation of a Circadian Clock Component and Rhythmic Transcription in the Liver [ChIP-seq] 45 samples shares chip-seq, liver
- GSE268146 Integrator complex bridges TFIID and RNA polymerase II to maintain pluripotency during development (ChIP-Seq) 38 samples shares polymerase, chip-seq
- GSE304113 Establishment of sex-specific liver transcriptomes and H3K9me3 profiles during sexual maturity: the impact of maternal obesity [ChIP-seq] 36 samples shares chip-seq, liver
- GSE324933 DGCR8 promotes RNA polymerase II pause release independently of DROSHA [ChIP-seq] 32 samples shares polymerase, chip-seq
- GSE297574 H3K9 di-methylation dynamics underlies mouse minor zygotic genome activation [spike-in ChIP-seq of mESC] 64 samples shares chip-seq
- GSE278338 ChIP-seq to measure binding of NIPBL/MAU2, RAD21, and CTCF in mouse embryonic stem cells and neural progenitor cells 50 samples shares chip-seq
- GSE261221 Scaffolding element rewires genome architecture during differentiation at the Zfp608 locus (ChIP-Seq) 189 samples shares chip-seq
- GSE261412 Acute hormonal signaling-induced 3D chromatin loop reorganization controls adipocyte thermogenesis [ChIP-Seq mouse, H3K27ac, H3K4me3, H2AZ] 24 samples shares chip-seq
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.