Late-stage tertiary lymphoid structures in hepatocellular carcinoma treated with neoadjuvant immune checkpoint blockade [bulk RNA-seq]
RNA-seq (gene expression) · human · 14 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)
- Samples
- 14 samples: 14 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 GSE272346_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 PRJNA1136492. 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 14 sample titles: 14 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
- 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, blockade
- GSE272347 Late-stage tertiary lymphoid structures in hepatocellular carcinoma treated with neoadjuvant immune checkpoint blockade [scRNA-seq] 17 samples shares hepatocellular, neoadjuvant, late-stage, structures, checkpoint, tertiary, lymphoid, blockade
- 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
- GSE272409 Molecular and spatial analysis unveils the functional basis of tertiary lymphoid structures in Sjogren’s syndrome[scRNA-seq] 13 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, blockade
- 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
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.