GEO series
Single-cell RNA sequencing defines the interplay between tumor cells, virus and microenvironment in nasopharyngeal carcinoma
GSE120926
Homo sapiens (human)
Single-cell RNA-seq
56 samples
Submitted 2024/11/18
Platform GPL11154Platform GPL20795
At a glance
Single-cell RNA-seq · human · 56 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
- 56 samples: 6 conditions, mostly in triplicateGroups 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 transcriptomic analysis defines the interplay between tumor cells, viral infection, and the microenvironment in nasopharyngeal carcinomaCell research · 2020
Summary (written by the submitters)
Purpose: While viruses play critival roles in many human malignancies, the influence of virus infection on the tumor microenviroment(TME) and how this impacts disease progression are poorly characterized. Methods: we applied both Smart-seq2 and 10X Genomics chemistry to ~104000 cells from 19 EBV+ NPC patients and 7 nonmalignant nasopharyngeal biopsies.
Read the full summary ↓
Results: 1. We have defined the complex interplay between tumor cells, virus infection, and the TME at single-cell resolution. 2. An epithelial-immune dual feature of malignant cells was discovered and associated with poor prognosis. 3. Stromal and immune cells in the TME were remodeled by tumor cells and virus infection. 4. EBV gene expression was found to correlate with complement factor expression in malignant cells, which, in turn, mediated T cell modulation and recruitment. 5. We subtyped NPC patients into 5 groups with different prognoses according to their respective TME compositions. Conclusion: Our results provide new insights into the multicellular ecosystem of NPC and offer important clinical implications.
Published in
Jin S, Li R, Chen MY et al.
· Cell research 2020
· PMID 32901110
· doi:10.1038/s41422-020-00402-8
This dataset
Download · which file do I need?
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.
1 · Just have a look
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.
2 · Re-analyse it
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE120926_RAW.tar (it can run to tens of gigabytes).
3 · Start from the raw reads
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 PRJNA495040 and SRA study SRP164416. Searching any of these in the dataset finder brings you back here.
Study design
6 conditions, mostly in triplicate
primary tumor of NPC patient ×18
primar tumor of NPC patient ×16
primary tumor of NPC patient C ×9
nonmalignant narsopharyngeal biopsy of patien… ×7
Single_cell_RNA-seq(Smart-seq2) of Homo sapie… ×3
Single_cell_RNA-seq(Smart-seq2) of Homo sapie… ×3
Supports a between-group comparison across 56 samples.
How we read this: 6 replicated groups read from 56 sample titles; they account for 56 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.
Samples in this study
- GSM3421604 Single_cell_RNA-seq(Smart-seq2) of Homo sapiens: primary tumor of NPC patient 16 Single_cell_RNA-seq(Sma…
- GSM3421605 Single_cell_RNA-seq(Smart-seq2) of Homo sapiens: primary tumor of NPC patient 17 Single_cell_RNA-seq(Sma…
- GSM3421606 Single_cell_RNA-seq(Smart-seq2) of Homo sapiens: primary tumor of NPC patient 36 Single_cell_RNA-seq(Sma…
- GSM3421607 Single_cell_RNA-seq(Smart-seq2) of Homo sapiens: lympho node metastatic tumor of NPC patient 16 Single_cell_RNA-seq(Sma…
- GSM3421608 Single_cell_RNA-seq(Smart-seq2) of Homo sapiens: lympho node metastatic tumor of NPC patient 17 Single_cell_RNA-seq(Sma…
- GSM3421609 Single_cell_RNA-seq(Smart-seq2) of Homo sapiens: lympho node metastatic tumor of NPC patient 36 Single_cell_RNA-seq(Sma…
- GSM3421610 10X_Genomic_RNA-seq of Homo sapiens:primar tumor of NPC patient 33 primar tumor of NPC pat…
- GSM3421611 10X_Genomic_RNA-seq of Homo sapiens:primar tumor of NPC patient 36 primar tumor of NPC pat…
- GSM3421612 10X_Genomic_RNA-seq of Homo sapiens:primar tumor of NPC patient 46 primar tumor of NPC pat…
- GSM3421613 10X_Genomic_RNA-seq of Homo sapiens:primar tumor of NPC patient 47 primar tumor of NPC pat…
- GSM3421614 10X_Genomic_RNA-seq of Homo sapiens:primar tumor of NPC patient 49 primar tumor of NPC pat…
- GSM3421615 Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient 138 primary tumor of NPC pa…
- GSM3421616 Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient 211 primary tumor of NPC pa…
- GSM3421617 Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient 258 primary tumor of NPC pa…
- GSM3421618 Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient 259 primary tumor of NPC pa…
- GSM3421619 Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient 271 primary tumor of NPC pa…
- GSM3421620 Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient 282 primary tumor of NPC pa…
- GSM3421621 Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient 288 primary tumor of NPC pa…
- GSM3421622 Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient 292 primary tumor of NPC pa…
- GSM3421623 Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient 293 primary tumor of NPC pa…
- GSM3421624 Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient 355 primary tumor of NPC pa…
- GSM3421625 Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient 371 primary tumor of NPC pa…
- GSM3421626 Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient 437 primary tumor of NPC pa…
- GSM3421627 Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient 456 primary tumor of NPC pa…
- GSM3421628 Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient 480 primary tumor of NPC pa…
- GSM3421629 Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient 527 primary tumor of NPC pa…
- GSM3421630 Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient 581 primary tumor of NPC pa…
- GSM3421631 Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient 664 primary tumor of NPC pa…
- GSM3421632 Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient 737 primary tumor of NPC pa…
- GSM3423864 Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient C_51 primary tumor of NPC pa…
- GSM3423865 Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient C_52 primary tumor of NPC pa…
- GSM3423866 Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient C_53 primary tumor of NPC pa…
- GSM3423867 Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient C_54 primary tumor of NPC pa…
- GSM3423868 Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient C_57 primary tumor of NPC pa…
- GSM3423869 Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient C_60 primary tumor of NPC pa…
- GSM3423870 Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient C_62 primary tumor of NPC pa…
- GSM3423871 Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient C_64 primary tumor of NPC pa…
- GSM3423872 Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient C_66 primary tumor of NPC pa…
- GSM3687446 10X_Genomic_RNA-seq of Homo sapeins:primar tumor of NPC patient 50 primar tumor of NPC pat…
- GSM3687447 10X_Genomic_RNA-seq of Homo sapeins:primar tumor of NPC patient 51 primar tumor of NPC pat…
+ 16 more — browse all 56 samples with per-sample file links →
More Nasopharyngeal carcinoma datasets
- 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, virus
- 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 microenvironment, nasopharyngeal, single-cell
- GSE179224 A phase 2 Randomized Controlled Trial of Adjuvant Tumor-Infiltrating Lymphocytes for Pretreatment Epstein-Barr Virus DNA-selected High-Risk Nasopharyngeal Carcinoma Patients 4 samples same disease briefing · shares nasopharyngeal, virus
- GSE280127 Nasopharyngeal carcinoma (NPC)-derived exosomes reconstitute tumor microenvironment 2 samples same disease briefing · shares microenvironment, nasopharyngeal
- 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
- GSE231687 Bulk-RNA Sequencing of Nasopharyngeal Carcinoma Cell Lines infected with Epstein-Barr virus (EBV) subjected to air-liquid interface (ALI)-induced reactivation 6 samples same disease briefing · shares nasopharyngeal, virus
- GSE268996 Epstein-Barr virus BOLF1-containing extracellular vesicles promote nasopharyngeal carcinoma metastasis via SPP1+ macrophages 6 samples same disease briefing · shares nasopharyngeal, virus
- GSE295454 Large-scale and high-resolution mass spectrometry-based proteomics profiling defines molecular subtypes of nasopharyngeal carcinoma for therapeutic targeting 6 samples same disease briefing · shares nasopharyngeal, defines
Share this dataset
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.