Single-Cell and Spatial Transcriptome Analyses Reveal Tertiary Lymphoid Structures Linked to Tumour Progression and Immunotherapy Response in Nasopharyngeal Carcinoma
Single-cell RNA-seq · human · 18 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)
- Topic
- Nasopharyngeal carcinomaThis series is part of our curated briefing on it.
- Samples
- 18 samples: 15 × NPC_ST vs 2 × GaC_MGroups 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
- Single-cell and spatial transcriptome analyses reveal tertiary lymphoid structures linked to tumour progression and immunotherapy response in nasopharyngeal carcinomaNature communications · 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 GSE206245_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 PRJNA849801. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 17 samples.
How we read this: 2 replicated groups read from 18 sample titles; they account for 17 of them. 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.
- GSM6248645 BCR of 20 NPC samples
- GSM6248646 NPC_ST5 NPC_ST
- GSM6248647 NPC_ST6 NPC_ST
- GSM6248648 NPC_ST7 NPC_ST
- GSM6248649 NPC_ST8 NPC_ST
- GSM6248650 NPC_ST9 NPC_ST
- GSM6248651 NPC_ST10 NPC_ST
- GSM6248652 NPC_ST11 NPC_ST
- GSM6248653 NPC_ST12 NPC_ST
- GSM6248654 NPC_ST16 NPC_ST
- GSM6248655 NPC_ST17 NPC_ST
- GSM6248656 NPC_ST18 NPC_ST
- GSM6248657 NPC_ST19 NPC_ST
- GSM8361988 NPC_ST1 NPC_ST
- GSM8361990 NPC_ST2 NPC_ST
- GSM8361991 NPC_ST3 NPC_ST
- GSM8361993 GaC_M39 GaC_M
- GSM8361995 GaC_M55 GaC_M
- GSE289272 Interferon responsive high endothelial venules drive tumor tertiary lymphoid structure formation and predict response to anti-PD-1 immunotherapy in nasopharyngeal carcinoma 55 samples same disease briefing · shares nasopharyngeal, immunotherapy, tertiary, lymphoid
- GSE150825 Comprehensive single-cell sequencing reveals the stromal dynamics and tumor-specific characteristics in the microenvironment of nasopharyngeal carcinoma 35 samples same disease briefing · shares nasopharyngeal, single-cell
- GSE120926 Single-cell RNA sequencing defines the interplay between tumor cells, virus and microenvironment in nasopharyngeal carcinoma 56 samples same disease briefing · shares nasopharyngeal, single-cell
- GSE150430 Single-cell transcriptomics reveals regulators underlying immune cell diversity and immune subtypes associated with prognosis in nasopharyngeal carcinoma 16 samples same disease briefing · shares nasopharyngeal, single-cell
- GSE305669 Reduced expression of UPF1 promotes tumor progression through stabilizing COX-2 mRNA in nasopharyngeal carcinoma 12 samples same disease briefing · shares nasopharyngeal, progression
- GSE231689 Bulk-RNA and single-cell RNA sequencing of Nasopharyngeal Carcinoma Cell lines infected with Epstein-Barr virus (EBV) subjected to air-liquid interface (ALI)-induced reactivation 10 samples same disease briefing · shares nasopharyngeal, single-cell
- GSE200310 Spatial transcriptome sequencing of primary nasopharyngeal carcinoma tissues 2 samples same disease briefing · shares nasopharyngeal, spatial
- GSE162025 Tumour Heterogeneity and Intercellular Networks of Nasopharyngeal Carcinoma at Single Cell Resolution 40 samples same disease briefing · shares nasopharyngeal
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.