GEO series

Single-cell transcriptomic landscape reveals the differences in cell differentiation and immune microenvironment of papillary thyroid carcinoma between male and female patients

GSE158291 Homo sapiens (human) Single-cell RNA-seq 3 samples Submitted 2020/12/31 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 3 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: Thyroid cancerThis series is part of our curated briefing on it.
Samples: 3 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)

Objective: Papillary thyroid carcinoma (PTC) is the main pathological type of thyroid carcinoma (TC), whose incidence and prognosis are related to the gender of patients. We focused on the differences of cell clusters and immune microenvironment induced by gender in PTC. Methods: We collected tissues from nodular goiter, male PTC patients and female PTC patients respectively, performed single-cell RNA sequencing (scRNA-seq) based on BD Rhapsody and characterized the first single-cell transcriptomic landscape of PTC involving gender.

Read the full summary ↓

The differential cell clusters and their genes profile were identified in male- and female- PTC, analyzed by multi-resolution network. Finally, we analyzed the interaction of fibroblasts, endothelial cells with malignant epithelial cells, and the difference of immune infiltration of B lymphocytes and T lymphocytes driven by gender. Results: Malignant epithelial cells were divided into two distinct subsets in male PTC patients and female PTC patients, with significant difference involving gene mutation, gene profile and cell differentiation. In the interaction between fibroblasts, endothelial cells and malignant epithelial cells, members of human leukocyte antigen and their receptors were considered as typical in female PTC patients, while TGFB1 and its receptors in male PTC patients. Both B cells and T cells were significantly different between male- and female PTC patients, involving cell clusters, cell differentiation and dominant genes set. Conclusions: Our research indicated the detailed differences of cell clusters and immune microenvironment in PTC driven by gender, and provided an insight to further understand the impact of gender on PTC at single-cell level.

This dataset

Open GSE158291 in finder → Find more human RNA-seq datasets → Thyroid 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 GSE158291_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 PRJNA664760 and SRA study SRP284258. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 33588924) ↗

Samples in this study

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

+ 3 more — browse all 3 samples with per-sample file links →

More Thyroid cancer datasets

GSE281736 Single-cell RNA Sequencing Reveals the Heterogeneity in Differentiation Trajectory and Tumor Microenvironment Leading to More Aggressive Phenotypes of Papillary Thyroid Cancer in Children and Young Adult Patients 12 samples same disease briefing · shares microenvironment, single-cell, papillary, thyroid
GSE275666 Genomic Characterization of Papillary Thyroid Carcinoma: Age Differences in Tumor Aggressiveness and Immune Infiltration 22 samples same disease briefing · shares differences, papillary, thyroid
GSE274674 Single-cell RNA sequencing reveals a novel CD4+T cell subset in papillary thyroid cancer 4 samples same disease briefing · shares single-cell, papillary, thyroid
GSE310793 PRECISE: A prognostic thyroid follicular-cell derived gene signature for papillary thyroid carcinoma 109 samples same disease briefing · shares papillary, thyroid
GSE165724 Transcriptome analysis discloses dysregulated genes in normal appearing tumor-adjacent thyroid tissues from patients with papillary thyroid carcinoma 74 samples same disease briefing · shares papillary, thyroid
GSE288945 Transcriptome Analysis Reveals Sex Disparities in Recurremt and Non-Recurrent Papillary Thyroid Cancer (PTC) 16 samples same disease briefing · shares papillary, thyroid
GSE308716 Knockdown of TRIM35 supresses cell proliferation, metastasis, and glycolysis in papillary thyroid cancer cells 12 samples same disease briefing · shares papillary, thyroid
GSE285016 FN1 Shapes the Behavior of Papillary Thyroid Carcinoma through Alternative Splicing of EDB Region 10 samples same disease briefing · shares papillary, thyroid

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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.