Integration of epigenomic and transcriptomic profiling uncovers EZH2 target genes linked to cysteine metabolism in hepatocellular carcinoma
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 24 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)
- Topic
- Hepatocellular carcinomaThis series is part of our curated briefing on it.
- Samples
- 24 samples: 24 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.
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 GSE237952_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 PRJNA997288 and SRA study SRP450785. 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 24 sample titles: 24 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.
- GSM7656797 HepG2_Ctrl_1, ATAC-seq
- GSM7656798 HepG2_Ctrl_2, ATAC-seq
- GSM7656799 HepG2_Taze_1, ATAC-seq
- GSM7656800 HepG2_Taze_2, ATAC-seq
- GSM7656838 HepG2_Ctrl_1, RNA-seq
- GSM7656839 HepG2_Ctrl_2, RNA-seq
- GSM7656840 HepG2_Taze_1, RNA-seq
- GSM7656841 HepG2_Taze_2, RNA-seq
- GSM8287594 HepG2_siNC_1, RNA-seq
- GSM8287595 HepG2_siNC_2, RNA-seq
- GSM8287596 HepG2_siEZH2_1, RNA-seq
- GSM8287597 HepG2_siEZH2_2, RNA-seq
- GSM8287598 HepG2_H3K27me3_Ctrl_1, CUT&Tag
- GSM8287599 HepG2_H3K27me3_Ctrl_2, CUT&Tag
- GSM8287600 HepG2_H3K27me3_Ctrl_3, CUT&Tag
- GSM8287601 HepG2_H3K27me3_Taze_1, CUT&Tag
- GSM8287602 HepG2_H3K27me3_Taze_2, CUT&Tag
- GSM8287603 HepG2_H3K27me3_Taze_3, CUT&Tag
- GSM8287604 HepG2_H3K27me3_siNC_1, CUT&Tag
- GSM8287605 HepG2_H3K27me3_siNC_2, CUT&Tag
- GSM8287606 HepG2_H3K27me3_siNC_3, CUT&Tag
- GSM8287607 HepG2_H3K27me3_siEZH2_1, CUT&Tag
- GSM8287608 HepG2_H3K27me3_siEZH2_2, CUT&Tag
- GSM8287609 HepG2_H3K27me3_siEZH2_3, CUT&Tag
- GSE14520 Gene expression data of human hepatocellular carcinoma (HCC) 488 samples same disease briefing · shares hepatocellular
- GSE10143 Gene Expression in Fixed Tissues and Outcome in Hepatocellular Carcinoma 387 samples same disease briefing · shares hepatocellular
- GSE107170 Molecular Signature of Hepatitis D Virus-Associated Hepatocellular Carcinoma 307 samples same disease briefing · shares hepatocellular
- GSE104580 Using a novel gene signature for predicting the efficacy of the transarterial chemoembolization in patients with hepatocellular carcinoma. 147 samples same disease briefing · shares hepatocellular
- GSE109211 Molecular predictors of prevention of recurrence in hepatocellular carcinoma with sorafenib as adjuvant treatment in the phase 3 STORM trial 140 samples same disease briefing · shares hepatocellular
- GSE10186 Integrative Transcriptome Analysis Reveals Common Molecular Subtypes of Human Hepatocellular Carcinoma 118 samples same disease briefing · shares hepatocellular
- GSE105130 Comprehensive analysis of Transcriptome Profiles in Hepatocellular Carcinoma patients 52 samples same disease briefing · shares hepatocellular
- GSE140228 Landscape and Dynamics of Single Immune Cells in Hepatocellular Carcinoma 41 samples same disease briefing · shares hepatocellular
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.