GEO series

Comparative Immunotoxicity and Transcriptomic Profiling of Seven PFAS in THP-1 Macrophages

GSE313992 Homo sapiens (human) RNA-seq (gene expression) 252 samples Submitted 2026/08/03 Platform GPL34281

At a glance

RNA-seq (gene expression) · human · 252 samples

What it is: RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism: Homo sapiens (human)
Samples: 252 samples: 84 conditions, mostly in triplicateGroups are read from the sample names, not from the paper. Check the list below.
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)

Per- and polyfluoroalkyl substances (PFAS) are a large class of persistent synthetic chemicals widely used across industrial and consumer products. While legacy PFAS, such as perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS), have been extensively studied and linked to immunotoxicity, far less is known about the immune-related hazards of newer-generation alternatives.

Read the full summary ↓

In this study, we systematically evaluated the immunotoxic potential of seven PFAS, including three perfluoroalkyl acids (PFOA, PFOS, PFHpS) and four (poly-)ether PFAS (PFESA BP2, PFESA BP1, DOPFLCA, 8:2 Cl-PFESA) using a THP-1 macrophage model with dose-range exposures for up to 72 hours. Despite an equipotent dosing scheme, the molecular responses to different PFAS congeners were distinct. RNA sequencing revealed that PFOA and PFHpS, but not PFOS, elicited a larger number of differentially expressed genes than ether PFAS. We observed that the absolute PFAS concentration correlated more strongly with the number of DEGs than viability-based potency, suggesting differences in the underlying mechanisms of toxicity. The shared transcriptional signature highlighted PPAR signalling at the core of molecular responses to both legacy and newer-generation alternatives, while an adverse outcome pathway analysis revealed functional differences between the congeners. Together, these findings reveal compound-specific and structure-related differences in immunomodulatory potential among PFAS, with clear distinction by PFAS type. This study provides comprehensive comparative insights to inform hazard evaluation and support the development of safer PFAS alternatives.

This dataset

Open GSE313992 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 GSE313992_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1388171 and SRA study SRP655747. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

84 conditions, mostly in triplicate

pfos_control_24 ×3 pfos_control_48 ×3 pfos_control_72 ×3 pfos_EC10_24 ×3 pfos_EC10_48 ×3 pfos_EC10_72 ×3 pfos_EC20_24 ×3 pfos_EC20_48 ×3 +76 more

Supports a between-group comparison across 252 samples.

How we read this: 84 replicated groups read from 252 sample titles; they account for 252 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

GSM9378915 pfos_control_24_rep1 pfos_control_24
GSM9378916 pfos_control_24_rep2 pfos_control_24
GSM9378917 pfos_control_24_rep3 pfos_control_24
GSM9378918 pfos_control_48_rep1 pfos_control_48
GSM9378919 pfos_control_48_rep2 pfos_control_48
GSM9378920 pfos_control_48_rep3 pfos_control_48
GSM9378921 pfos_control_72_rep1 pfos_control_72
GSM9378922 pfos_control_72_rep2 pfos_control_72
GSM9378923 pfos_control_72_rep3 pfos_control_72
GSM9378924 pfos_EC10_24_rep1 pfos_EC10_24
GSM9378925 pfos_EC10_24_rep2 pfos_EC10_24
GSM9378926 pfos_EC10_24_rep3 pfos_EC10_24
GSM9378927 pfos_EC10_48_rep1 pfos_EC10_48
GSM9378928 pfos_EC10_48_rep2 pfos_EC10_48
GSM9378929 pfos_EC10_48_rep3 pfos_EC10_48
GSM9378930 pfos_EC10_72_rep1 pfos_EC10_72
GSM9378931 pfos_EC10_72_rep2 pfos_EC10_72
GSM9378932 pfos_EC10_72_rep3 pfos_EC10_72
GSM9378933 pfos_EC20_24_rep1 pfos_EC20_24
GSM9378934 pfos_EC20_24_rep2 pfos_EC20_24
GSM9378935 pfos_EC20_24_rep3 pfos_EC20_24
GSM9378936 pfos_EC20_48_rep1 pfos_EC20_48
GSM9378937 pfos_EC20_48_rep2 pfos_EC20_48
GSM9378938 pfos_EC20_48_rep3 pfos_EC20_48
GSM9378939 pfos_EC20_72_rep1 pfos_EC20_72
GSM9378940 pfos_EC20_72_rep2 pfos_EC20_72
GSM9378941 pfos_EC20_72_rep3 pfos_EC20_72
GSM9378942 pfos_EC5_24_rep1 pfos_EC5_24
GSM9378943 pfos_EC5_24_rep2 pfos_EC5_24
GSM9378944 pfos_EC5_24_rep3 pfos_EC5_24
GSM9378945 pfos_EC5_48_rep1 pfos_EC5_48
GSM9378946 pfos_EC5_48_rep2 pfos_EC5_48
GSM9378947 pfos_EC5_48_rep3 pfos_EC5_48
GSM9378948 pfos_EC5_72_rep1 pfos_EC5_72
GSM9378949 pfos_EC5_72_rep2 pfos_EC5_72
GSM9378950 pfos_EC5_72_rep3 pfos_EC5_72
GSM9378951 pfesa_bp2_control_24_rep1 pfesa_bp2_control_24
GSM9378952 pfesa_bp2_control_24_rep2 pfesa_bp2_control_24
GSM9378953 pfesa_bp2_control_24_rep3 pfesa_bp2_control_24
GSM9378954 pfesa_bp2_control_48_rep1 pfesa_bp2_control_48

+ 212 more — browse all 252 samples with per-sample file links →

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