Late-stage tertiary lymphoid structures in hepatocellular carcinoma treated with neoadjuvant immune checkpoint blockade
RNA-seq (gene expression) · human · 31 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
- 31 samples: 31 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
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 GSE272348_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 PRJNA1136490. 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 31 sample titles: 31 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.
- GSM8398966 P01, tumor, bulkRNAseq and reconstructed TCR/BCR repertoires
- GSM8398967 P02, tumor, bulkRNAseq and reconstructed TCR/BCR repertoires
- GSM8398968 P03, tumor, bulkRNAseq and reconstructed TCR/BCR repertoires
- GSM8398969 P07, tumor, bulkRNAseq and reconstructed TCR/BCR repertoires
- GSM8398970 P08, tumor, bulkRNAseq and reconstructed TCR/BCR repertoires
- GSM8398971 P11, tumor, bulkRNAseq and reconstructed TCR/BCR repertoires
- GSM8398972 P12, tumor, bulkRNAseq and reconstructed TCR/BCR repertoires
- GSM8398973 P13, tumor, bulkRNAseq and reconstructed TCR/BCR repertoires
- GSM8398974 P14, tumor, bulkRNAseq and reconstructed TCR/BCR repertoires
- GSM8398975 OT1, tumor, bulkRNAseq and reconstructed TCR/BCR repertoires
- GSM8398976 OT2, tumor, bulkRNAseq and reconstructed TCR/BCR repertoires
- GSM8398977 OT4, tumor, bulkRNAseq and reconstructed TCR/BCR repertoires
- GSM8398978 OT5, tumor, bulkRNAseq and reconstructed TCR/BCR repertoires
- GSM8398979 OT6, tumor, bulkRNAseq and reconstructed TCR/BCR repertoires
- 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
- 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
- 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
- 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.