Hight througput RNA sequencing in a cohort of HBV related HCC and healty liver samples
RNA-seq (gene expression) · human · 25 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Homo sapiens (human)
- Topic
- Hepatocellular carcinomaThis series is part of our curated briefing on it.
- Samples
- 25 samples: 25 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
- HBV-driven host chromatin accessibility changes affect liver metabolic pathways, iron homeostasis and promote a preneoplastic phenotypeJournal of experimental & clinical cancer research : CR · 2025
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 GSE251942_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1055956 and SRA study SRP479712. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 20 samples read as cases, 5 as controls.
How we read this: Read from 25 sample titles: 25 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.
- GSM7990394 Sample 113NT Non tumor tissue
- GSM7990395 Sample 113T Tumor tissue
- GSM7990396 Sample 43NT Non tumor tissue
- GSM7990397 Sample 43T Tumor tissue
- GSM7990398 Sample FS1_NT Normal liver tissue
- GSM7990399 Sample FS2_NT Normal liver tissue
- GSM7990400 Sample FS6_NT Normal liver tissue
- GSM7990401 Sample FS12_NT Normal liver tissue
- GSM7990402 Sample FS43_NT Normal liver tissue
- GSM7990403 Sample 105NT Non tumor tissue
- GSM7990404 Sample 34T Tumor tissue
- GSM7990405 Sample 51NT Non tumor tissue
- GSM7990406 Sample 51T Tumor tissue
- GSM7990407 Sample 150NT Non tumor tissue
- GSM7990408 Sample 150T Tumor tissue
- GSM7990409 Sample 141NT Non tumor tissue
- GSM7990410 Sample 141T Tumor tissue
- GSM7990411 Sample 105T Tumor tissue
- GSM7990412 Sample 144NT Non tumor tissue
- GSM7990413 Sample 144T Tumor tissue
- GSM7990414 Sample 13NT Non tumor tissue
- GSM7990415 Sample 13T Tumor tissue
- GSM7990416 Sample 28NT Non tumor tissue
- GSM7990417 Sample 28T Tumor tissue
- GSM7990418 Sample 34NT Non tumor tissue
- GSE114564 Identification of novel serum biomarkers in early-stage HCC patients. 118 samples same disease briefing · shares hcc
- GSE14520 Gene expression data of human hepatocellular carcinoma (HCC) 488 samples same disease briefing · shares hcc
- GSE105130 Comprehensive analysis of Transcriptome Profiles in Hepatocellular Carcinoma patients 52 samples same disease briefing
- GSE140228 Landscape and Dynamics of Single Immune Cells in Hepatocellular Carcinoma 41 samples same disease briefing
- GSE10143 Gene Expression in Fixed Tissues and Outcome in Hepatocellular Carcinoma 387 samples same disease briefing
- GSE107170 Molecular Signature of Hepatitis D Virus-Associated Hepatocellular Carcinoma 307 samples same disease briefing
- 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
- GSE10186 Integrative Transcriptome Analysis Reveals Common Molecular Subtypes of Human Hepatocellular Carcinoma 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.