Late-stage tertiary lymphoid structures in hepatocellular carcinoma treated with neoadjuvant immune checkpoint blockade [scRNA-seq]
Single-cell RNA-seq · human · 17 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
- Organism
- Homo sapiens (human)
- Samples
- 17 samples: 17 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
- Immunotherapy response induces divergent tertiary lymphoid structure morphologies in hepatocellular carcinomaNature immunology · 2024
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 GSE272347_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 PRJNA1136494. 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 17 sample titles: 17 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.
- GSM8398980 All samples, peripheral blood (n=7) and tumor (n=1), aggregated scRNA-seq
- GSM8398981 P02, peripheral blood, scBCR-seq
- GSM8398982 P02, peripheral blood, scTCR-seq
- GSM8398983 P03, peripheral blood, scBCR-seq
- GSM8398984 P03, peripheral blood, scTCR-seq
- GSM8398985 P07, peripheral blood, scBCR-seq
- GSM8398986 P07, peripheral blood, scTCR-seq
- GSM8398987 P08, peripheral blood, scBCR-seq
- GSM8398988 P08, peripheral blood, scTCR-seq
- GSM8398989 P12, peripheral blood, scBCR-seq
- GSM8398990 P12, peripheral blood, scTCR-seq
- GSM8398991 OT1, peripheral blood, scBCR-seq
- GSM8398992 OT1, peripheral blood, scTCR-seq
- GSM8398993 OT6, peripheral blood, scBCR-seq
- GSM8398994 OT6, peripheral blood, scTCR-seq
- GSM8398995 OT6, TIL, scBCR-seq
- GSM8398996 OT6, TIL, scTCR-seq
- GSE272348 Late-stage tertiary lymphoid structures in hepatocellular carcinoma treated with neoadjuvant immune checkpoint blockade 31 samples shares hepatocellular, neoadjuvant, late-stage, structures, checkpoint, tertiary, lymphoid
- GSE272346 Late-stage tertiary lymphoid structures in hepatocellular carcinoma treated with neoadjuvant immune checkpoint blockade [bulk RNA-seq] 14 samples shares hepatocellular, neoadjuvant, late-stage, structures, checkpoint, tertiary, lymphoid
- GSE272409 Molecular and spatial analysis unveils the functional basis of tertiary lymphoid structures in Sjogren’s syndrome[scRNA-seq] 13 samples shares structures, scrna-seq, tertiary, lymphoid
- GSE206245 Single-Cell and Spatial Transcriptome Analyses Reveal Tertiary Lymphoid Structures Linked to Tumour Progression and Immunotherapy Response in Nasopharyngeal Carcinoma 18 samples shares structures, tertiary, lymphoid
- GSE276935 The activity of tertiary lymphoid structures in high grade serous ovarian cancer is governed by site, stroma, and cellular interactions 417 samples shares structures, tertiary, lymphoid
- GSE272410 Molecular and spatial analysis unveils the functional basis of tertiary lymphoid structures in Sjogren’s syndrome[bulk RNA-seq] 73 samples shares structures, tertiary, lymphoid
- GSE271059 Spatial immune profiling defines a subset of human gliomas with functional tertiary lymphoid structures [bulk RNA seq] 64 samples shares structures, tertiary, lymphoid
- GSE280232 Divergent clinical and immunologic outcomes based on STK11 co-mutation status in resectable KRAS-mutant lung cancers following neoadjuvant immune checkpoint blockade 42 samples shares neoadjuvant, checkpoint
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.