GEO series

Single-cell RNA sequencing of metastatic testicular seminoma reveals the cellular and molecular characteristics of metastatic cell lineage

GSE197778 Homo sapiens (human) Single-cell RNA-seq 4 samples Submitted 2022/03/25 Platform GPL20795

At a glance

Single-cell RNA-seq · human · 4 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: Testicular cancerThis series is part of our curated briefing on it.
Samples: 4 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)

Testicular cancer is the most common solid malignancy in young men. Given the many histological classifications of testicular tumours, seminoma is one of the most treatable cancers. The survival rate in early-stage disease was more than 90%. Thus, seminoma at the cellular and molecular levels, especially at the single-cell level, is worth studying.

Read the full summary ↓

We performed a single-cell RNA sequencing (scRNA-seq) study on a patient who was diagnosed with testicular seminoma with lymph node metastasis. This study presented tumour tissue, PBMC, pelvic and renal hilus lymph node in a total of 18,206 high-quality single-cell transcriptome information. The characteristics of metastatic cell lineage were revealed by the comparison between different tumour cell subtypes at the scRNA level. A single-cell map of testicular seminoma with lymph node metastasis was constructed by scRNA-seq. We discovered the gene expression characteristics of the tumour cells in testicular seminoma, especially metastatic tumour cells. KRT8 and KRT18 were commonly expressed in the three tumour cell subtypes. However, TCF7L1, SCG3 and SV2C were the specifically expressed genes of tumour cell subtypes in primary tumour sites. Some molecular markers specifically expressed by the metastatic cell lineage, such as POU5F1, were identified. We revealed the molecular characteristics of testicular seminoma at the single-cell level, especially the metastatic tumour cells. This study could provide new insights into the diagnosis and treatment of testicular seminoma.

This dataset

Open GSE197778 in finder → Find more human RNA-seq datasets → Testicular cancer 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 GSE197778_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 PRJNA812034 and SRA study SRP362212. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 35494058) ↗

Samples in this study

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

+ 4 more — browse all 4 samples with per-sample file links →

More Testicular cancer datasets

GSE228501 Single-cell Multi-omics Analysis of Human Testicular Germ Cell Tumor Reveals its Molecular Features and Microenvironment 4 samples same disease briefing · shares single-cell, testicular
GSE229823 Single-cell Multi-omics Analysis of Human Testicular Germ Cell Tumor Reveals its Molecular Features and Microenvironment II 3 samples same disease briefing · shares single-cell, testicular
GSE8607 Gene expression profiling of testicular seminoma 43 samples same disease briefing · shares testicular, seminoma
GSE278498 Refractory testicular germ cell tumors are highly sensitive to the targeting of polycomb pathway demethylases KDM6A and KDM6B 36 samples same disease briefing · shares testicular
GSE317098 Comparative analysis of the transcriptomic response to cisplatin in drug-sensitive and drug-resistant testicular germ cell tumors. 30 samples same disease briefing · shares testicular
GSE232791 Role of MIR9-2 in testicular germ cell tumours 16 samples same disease briefing · shares testicular
GSE282367 BRD9 inhibition as potential treatment option for testicular germ cell tumors 12 samples same disease briefing · shares testicular
GSE261811 T cells in testicular germ cell tumors: new evidence of fundamental contributions by rare subsets 4 samples same disease briefing · shares testicular

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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.