GEO series

High-Throughput Transcriptomic Profiling for Bioactivity Screening: Mapping Molecular Targets and Potencies for PFAS chemicals in HepaRG Cells

GSE296248 Homo sapiens (human) RNA-seq (gene expression) Submitted 2025/11/21

At a glance

RNA-seq (gene expression) · human

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)
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)

This study used high-throughput transcriptomics (HTTr) to evaluate the gene expression effects of 133 per- and polyfluoroalkyl substances (PFAS) in HepaRG cells. The PFAS chemicals were selected using a category-based prioritization approach developed by the U.S. Environmental Protection Agency (EPA) to ensure representation of structurally diverse compounds with relevance to human exposure and regulatory interest (Patlewicz et al., 2019; https://doi.org/10.1289/EHP4555).

Read the full summary ↓

Differentiated HepaRG cells were exposed to each PFAS in concentration-response format (0.1 to 100 µM) for 24 hours. Transcriptomic changes were measured using the TempO-Seq platform (BioSpyder Technologies), enabling expression profiling of approximately 20,000 human genes. The resulting gene expression data were used to characterize the concentration-dependent molecular responses to PFAS exposure using connectivity mapping and to derive transcriptomic points of departure (tPODs). This dataset contributes to a broader effort to screen the bioactivity of environmental chemicals using HTTr in human liver-derived cells. It supports the use of transcriptomic profiling to identify bioactive PFAS, elucidate affected molecular pathways, and inform chemical hazard assessment.

This dataset

Open GSE296248 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 GSE296248_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 PRJNA1254200 and SRA study SRP580583. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Samples in this study

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

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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.