Landscape of super-enhancer-associated lncRNAs in hepatocellular carcinoma
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 10 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
- 10 samples: 2 × HepG2_Vehicle vs 2 × HepG2_JQ1 vs 2 × LM3_Vehicle vs 2 × LM3_JQ1Groups 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
- Anchoring super-enhancer-driven oncogenic lncRNAs for anti-tumor therapy in hepatocellular carcinomaMolecular therapy : the journal of the American Society of Gene Therapy · 2023
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 GSE181755_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 PRJNA753288 and SRA study SRP331834. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 8 samples.
How we read this: 4 replicated groups read from 10 sample titles; they account for 8 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.
- GSM5510395 LM3 cells - H3K27ac
- GSM5510396 LM3 cells - input DNA
- GSM5510397 HepG2_Vehicle_rep1 HepG2_Vehicle
- GSM5510398 HepG2_Vehicle_rep2 HepG2_Vehicle
- GSM5510399 HepG2_JQ1_rep1 HepG2_JQ1
- GSM5510400 HepG2_JQ1_rep2 HepG2_JQ1
- GSM5510401 LM3_Vehicle_rep1 LM3_Vehicle
- GSM5510402 LM3_Vehicle_rep2 LM3_Vehicle
- GSM5510403 LM3_JQ1_rep1 LM3_JQ1
- GSM5510404 LM3_JQ1_rep2 LM3_JQ1
- 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
- GSE140228 Landscape and Dynamics of Single Immune Cells in Hepatocellular Carcinoma 41 samples same disease briefing · shares hepatocellular
- GSE107170 Molecular Signature of Hepatitis D Virus-Associated Hepatocellular Carcinoma 307 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
- GSE114564 Identification of novel serum biomarkers in early-stage HCC patients. 118 samples same disease briefing
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.