GEO series

Tumour Heterogeneity and Intercellular Networks of Nasopharyngeal Carcinoma at Single Cell Resolution

GSE162025 Homo sapiens (human) Single-cell RNA-seq 40 samples Submitted 2020/11/24 Platform GPL20795

At a glance

Single-cell RNA-seq · human · 40 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: 40 samples
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.

Summary (written by the submitters)

The heterogeneous nature of tumour microenvironment (TME) underlying diverse treatment responses remains unclear in nasopharyngeal carcinoma (NPC). Here, we profile 176,447 cells from 10 NPC tumour-blood pairs, using single-cell transcriptome coupled with T cell receptor sequencing. Our analyses reveal 53 cell subtypes, including tumour-infiltrating CD8+ T, regulatory T (Treg), and dendritic cells (DCs), as well as malignant cells with different Epstein-Barr virus infection status.

Read the full summary ↓

Trajectory analyses reveal exhausted CD8+ T and immune-suppressive TNFRSF4+ Treg cells in tumours might derive from peripheral CX3CR1+CD8+ T and naïve Treg cells, respectively. Moreover, we identify immune-regulatory and tolerogenic LAMP3+ DCs. Noteworthily, intensive inter-cell interactions are observed among LAMP3+ DCs, Treg, exhausted CD8+ T, and malignant cells, suggesting potential cross-talks to foster an immune-suppressive niche for the TME. Collectively, our study uncovers the heterogeneity and interacting molecules of the TME in NPC at single-cell resolution, which provide insights into the mechanisms underlying NPC progression and the development of precise therapies for NPC.

This dataset

Open GSE162025 in finder → Find more human RNA-seq datasets → Nasopharyngeal carcinoma landscape →

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.

Series matrix ↓

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 GSE162025_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

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.

Raw reads on ENA ↗

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 PRJNA680328 and SRA study SRP293799. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 33531485) ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 40 more — browse all 40 samples with per-sample file links →

More Nasopharyngeal carcinoma datasets

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, resolution
GSE206245 Single-Cell and Spatial Transcriptome Analyses Reveal Tertiary Lymphoid Structures Linked to Tumour Progression and Immunotherapy Response in Nasopharyngeal Carcinoma 18 samples same disease briefing · shares nasopharyngeal
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
GSE169589 N7-methylguanosine tRNA modification promotes tumorigenesis and chemoresistance through WNT/β-Catenin pathway in nasopharyngeal carcinoma 20 samples same disease briefing · shares nasopharyngeal
GSE186485 18S rRNA N6-methyladenosine (m6A) modification promotes tumorigenesis and chemoresistance via gain-of-function mutant p53 in nasopharyngeal carcinoma 16 samples same disease briefing · shares nasopharyngeal
GSE262035 RAN directly binds and stabilizes G3BP1 mRNA in the nucleus to facilitate proliferation and metastasis of nasopharyngeal carcinoma 14 samples same disease briefing · shares nasopharyngeal
GSE120926 Single-cell RNA sequencing defines the interplay between tumor cells, virus and microenvironment in nasopharyngeal carcinoma 56 samples same disease briefing · shares 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

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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.