GEO series

Normal and Oropharyngeal-carcinoma derived monocyte responses to OPC-cell line conditioned media.

GSE281098 Homo sapiens (human) Single-cell RNA-seq 2 samples Submitted 2024/11/25 Platform GPL18573

At a glance

Single-cell RNA-seq · human · 2 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Homo sapiens (human)
Samples: 2 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.
Paper: Oropharyngeal carcinomas induce circulating monocytes to express a TAM-like pro-tumor expression profile that suppresses T-cell proliferationFrontiers in immunology · 2025

Summary (written by the submitters)

Tumor Associated Macrophages (TAMs) represent a critical immunological barrier to effective anti-tumor mechanisms of developing carcinomas of the oropharynx. Tumor infiltrating monocytes become activated and differentiate into TAMs which contribute to the immunological landscape of tumors as either containing or devoid of effector T-cells.

Read the full summary ↓

We first compared transcriptional responses of normal and OPC derived monocytes from single individuals, at the single cell level, after exposure to media conditioned by SCC-25 and SCC-154 OPC cell lines. Since media conditioned by both SCC-154 and SCC-25 contain secreted IL1α, stimulation of these monocytes with recombinant IL1α was included as a control. We showed that to these conditioned media, CXCL1, CXCL5 and CCL2 transcripts reached higher levels in a greater proportion of OPC-patient monocytes compared to control monocytes. These early monocyte responses were validated in a cohort of isolated monocytes exposed to the same media. These findings represent that monocytes may be secreting TME influencing cytokines, prior to their own differentiation, which in turn recruit detrimental cell populations including T-regs, MDSCs and other monocytes.

Published in

Oropharyngeal carcinomas induce circulating monocytes to express a TAM-like pro-tumor expression profile that suppresses T-cell proliferation

Papayannakos CJ, Israr M, DeVoti JA et al. · Frontiers in immunology 2025 · PMID 40176808 · doi:10.3389/fimmu.2025.1539780

This dataset

Open GSE281098 in finder → Find more human RNA-seq datasets →

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 GSE281098_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 PRJNA1182284 and SRA study SRP543271. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40176808) ↗

Samples in this study

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+ 2 more — browse all 2 samples with per-sample file links →

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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.