GEO series

Comprehensive single-cell sequencing reveals the stromal dynamics and tumor-specific characteristics in the microenvironment of nasopharyngeal carcinoma

GSE150825 Homo sapiens (human) Single-cell RNA-seq 35 samples Submitted 2021/01/11 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 35 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: 35 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 tumor microenvironment (TME) of nasopharyngeal carcinoma (NPC) harbors a heterogeneous and dynamic stromal population. A comprehensive understanding of this tumor-specific ecosystem is necessary to enhance cancer diagnosis, therapeutics, and prognosis. However, recent advances based on bulk RNA sequencing remain insufficient to construct an in-depth landscape of infiltrating stromal cells in NPC.

Read the full summary ↓

Here we apply single-cell RNA sequencing to 66,627 cells from 14 patients, integrated with clonotype identification on T and B cells. We identify and characterize five major stromal clusters and 36 distinct subpopulations based on genetic profiling. By comparing with the infiltrating cells in the non-malignant microenvironment, we report highly representative features in the TME, including phenotypic abundance, genetic alternations, immune dynamics, clonal expansion, developmental trajectory, and molecular interactions that profoundly influence patient prognosis and therapeutic outcome. The key findings are further independently validated in two single-cell RNA sequencing cohorts and two bulk RNA-sequencing cohorts. In the present study, we reveal the correlation between NPC-specific characteristics and progression-free survival. Together, these data facilitate the understanding of the stromal landscape and immune dynamics in NPC patients and provides deeper insights into the development of prognostic biomarkers and therapeutic targets in the TME.

This dataset

Open GSE150825 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 GSE150825_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 PRJNA633797 and SRA study SRP262300. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 33750785) ↗

Samples in this study

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

+ 35 more — browse all 35 samples with per-sample file links →

More Nasopharyngeal carcinoma datasets

GSE120926 Single-cell RNA sequencing defines the interplay between tumor cells, virus and microenvironment in nasopharyngeal carcinoma 56 samples same disease briefing · shares microenvironment, nasopharyngeal, single-cell
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, 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
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
GSE280127 Nasopharyngeal carcinoma (NPC)-derived exosomes reconstitute tumor microenvironment 2 samples same disease briefing · shares microenvironment, nasopharyngeal
GSE162025 Tumour Heterogeneity and Intercellular Networks of Nasopharyngeal Carcinoma at Single Cell Resolution 40 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

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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.