Spatial and single-nucleus transcriptomic profiling of CHB liver biopsies
Single-nucleus RNA-seq · human · 13 samples
- What it is
- Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue).
- Organism
- Homo sapiens (human)
- Samples
- 13 samples: 13 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
- Spatial transcriptional profiling of CHB liver biopsies reveals an undetected population of zonally biased HBV-integrated cellsJHEP reports : innovation in hepatology · 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 GSE306575_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA1311140 and SRA study SRP612858. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 1 samples read as cases, 3 as controls.
How we read this: Read from 13 sample titles: 13 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.
- GSM9204000 uPA-SCID mouse, vehicle treated
- GSM9204001 uPA-SCID mouse, TAF treated
- GSM9204002 cell pellet array
- GSM9204003 healthy donor Hu-P-003749 spatial transcriptomics
- GSM9204004 healthy donor Hu-P-003752 spatial transcriptomics
- GSM9204005 CHB donor Hu-P-005521 spatial transcriptomics
- GSM9204006 CHB donor Hu-P-005522 spatial transcriptomics
- GSM9204007 CHB donor Hu-P-005524 spatial transcriptomics
- GSM9204008 CHB donor Hu-P-003720 spatial transcriptomics
- GSM9797178 healthy donor Hu-P-003749 single nucleus transcriptomics
- GSM9797179 CHB donor Hu-P-005521 single nucleus transcriptomics
- GSM9797180 CHB donor Hu-P-005522 single nucleus transcriptomics
- GSM9797181 CHB donor Hu-P-005524 single nucleus transcriptomics
- GSE233208 Single-nucleus RNA-Seq and spatial transcriptomics characterization of Alzheimer’s Disease and Down Syndrome 185 samples shares single-nucleus, spatial
- GSE246613 Single-cell and spatial profiling identify three response trajectories to pembrolizumab and radiation therapy in triple negative breast cancer 266 samples shares spatial
- GSE292893 A cost-effective and flexible workflow for high-resolution spatial transcriptomics in fixed tissue 52 samples shares spatial
- GSE285303 Spatially resolved m6A profiling using m6A-ARTR-DBiT 40 samples shares spatial
- GSE325427 Integrative single-nucleus multiomic, CUT&Tag, and bulk RNA-seq profiling of human and mouse prefrontal cortex reveals gene regulatory mechanisms of cortical development and Meis2 function 34 samples shares single-nucleus
- GSE268148 Large field of view and spatial region of interest transcriptomics in frozen and FFPE tissue 26 samples shares spatial
- GSE336954 Central amygdala single-nucleus atlas reveals chromatin and gene transcription dynamics in human alcohol use disorder 126 samples shares single-nucleus
- GSE269875 Spatial transcriptomics unveils novel potential disease mechanisms associated with the microenvironment in Multiple Myeloma 15 samples shares spatial
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.