GEO series

Single-cell transcriptomics reveals regulators underlying immune cell diversity and immune subtypes associated with prognosis in nasopharyngeal carcinoma

GSE150430 Homo sapiens (human) Single-cell RNA-seq 16 samples Submitted 2020/07/20 Platform GPL20795

At a glance

Single-cell RNA-seq · human · 16 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: 16 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)

Nasopharyngeal carcinoma (NPC) is an aggressive malignancy with extremely skewed ethnic and geographic distributions. Increasing evidence indicates that targeting the tumour microenvironment (TME) represents a promising therapeutic approach in NPC, highlighting an urgent need to deepen the understanding of the complex NPC TME. Here, we generated single-cell transcriptome profiles for 7,581 malignant cells and 40,285 immune cells from 15 primary NPC tumours and one normal sample.

Read the full summary ↓

We revealed malignant signatures capturing intratumoural transcriptional heterogeneity and predicting aggressiveness of malignant cells. Diverse immune cell subtypes were identified, including novel subtypes such as CLEC9A+ dendritic cells (DCs). We further revealed transcriptional regulators underlying immune cell diversity, and cell-cell interaction analyses highlighted promising immunotherapeutic targets in NPC. Moreover, we established the immune subtype-specific signatures, and demonstrated that the signatures of macrophages, plasmacytoid dendritic cells (pDCs), CLEC9A+ DCs, natural killer (NK) cells, and plasma cells were significantly associated with improved survival outcomes in NPC. Taken together, our findings represent a unique resource providing in-depth insights into the cellular heterogeneity of NPC TME and highlight potential biomarkers for anticancer treatment and risk stratification, laying a new foundation for the precision therapies in NPC.

This dataset

Open GSE150430 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 GSE150430_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 PRJNA632027. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 32686767) ↗

Samples in this study

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

+ 16 more — browse all 16 samples with per-sample file links →

More Nasopharyngeal carcinoma datasets

GSE102349 Genomic Analysis of Nasopharyngeal Carcinoma Reveals TME-based Subtypes 113 samples same disease briefing · shares nasopharyngeal, subtypes
GSE231572 Development and validation of a microbiota signature to predict prognosis in nasopharyngeal carcinoma 64 samples same disease briefing · shares nasopharyngeal, prognosis
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
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
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, subtypes
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
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
GSE305669 Reduced expression of UPF1 promotes tumor progression through stabilizing COX-2 mRNA in nasopharyngeal carcinoma 12 samples same disease briefing · shares nasopharyngeal

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