GEO series
Transcriptomic and H3K27ac chromatin responses of human microglia to acute PFOS exposure and recovery
GSE342612
Homo sapiens (human)
ChIP-seq / ATAC-seq (genome binding and open chromatin)
36 samples
Submitted 2026/08/06
Platform GPL21697
At a glance
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 36 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Homo sapiens (human)
- Samples
- 36 samples: 6 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.
- Paper
- Perfluoroalkyl substance pollutants disrupt microglia function and trigger transcriptional and epigenomic changesToxicology · 2025
Summary (written by the submitters)
Per- and polyfluoroalkyl substances (PFAS) are persistent environmental contaminants associated with adverse neurological effects, but their impact on microglial gene regulation remains unclear. In this study, human HMC3 microglial cells were exposed to vehicle control or perfluorooctane sulfonate (PFOS) at 25 or 50 µM for 24 hours. RNA sequencing was used to characterize transcriptomic changes, and H3K27ac CUT&Tag was used to profile active chromatin.
Read the full summary ↓
Additional samples were collected after PFOS withdrawal and a 24-hour recovery period to assess persistent molecular alterations. These datasets support integrated analysis of acute and persistent PFOS-induced transcriptomic and epigenetic changes in human microglia.
Published in
Cheng Y, Li JR, Yu H et al.
· Toxicology 2025
· PMID 40419075
· doi:10.1016/j.tox.2025.154198
This dataset
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.
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 GSE342612_RAW.tar (it can run to tens of gigabytes).
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.
What the files usually look like: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA1508658 and SRA study SRP724678. Searching any of these in the dataset finder brings you back here.
Study design
6 conditions, mostly in triplicate
vehicle control, 24 h treatment, ×3
25 µM PFOS, 24 h treatment, ×3
50 µM PFOS, 24 h treatment, ×3
vehicle control, 24 h treatment followed by 2… ×3
25 µM PFOS, 24 h treatment followed by 24 h r… ×3
50 µM PFOS, 24 h treatment followed by 24 h r… ×3
vehicle control, 24 h treatment, biological r… ×1
vehicle control, 24 h treatment, biological r… ×1
+16 more
Supports a between-group comparison across 18 samples.
How we read this: 6 replicated groups read from 36 sample titles; they account for 18 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
- GSM9934646 vehicle control, 24 h treatment, biological replicate 1 vehicle control, 24 h t…
- GSM9934647 vehicle control, 24 h treatment, biological replicate 2 vehicle control, 24 h t…
- GSM9934648 vehicle control, 24 h treatment, biological replicate 3 vehicle control, 24 h t…
- GSM9934649 25 µM PFOS, 24 h treatment, biological replicate 1 25 µM PFOS, 24 h treatm…
- GSM9934650 25 µM PFOS, 24 h treatment, biological replicate 2 25 µM PFOS, 24 h treatm…
- GSM9934651 25 µM PFOS, 24 h treatment, biological replicate 3 25 µM PFOS, 24 h treatm…
- GSM9934652 50 µM PFOS, 24 h treatment, biological replicate 1 50 µM PFOS, 24 h treatm…
- GSM9934653 50 µM PFOS, 24 h treatment, biological replicate 2 50 µM PFOS, 24 h treatm…
- GSM9934654 50 µM PFOS, 24 h treatment, biological replicate 3 50 µM PFOS, 24 h treatm…
- GSM9934655 vehicle control, 24 h treatment followed by 24 h recovery, biological replicate 1 vehicle control, 24 h t…
- GSM9934656 vehicle control, 24 h treatment followed by 24 h recovery, biological replicate 2 vehicle control, 24 h t…
- GSM9934657 vehicle control, 24 h treatment followed by 24 h recovery, biological replicate 3 vehicle control, 24 h t…
- GSM9934658 25 µM PFOS, 24 h treatment followed by 24 h recovery, biological replicate 1 25 µM PFOS, 24 h treatm…
- GSM9934659 25 µM PFOS, 24 h treatment followed by 24 h recovery, biological replicate 2 25 µM PFOS, 24 h treatm…
- GSM9934660 25 µM PFOS, 24 h treatment followed by 24 h recovery, biological replicate 3 25 µM PFOS, 24 h treatm…
- GSM9934661 50 µM PFOS, 24 h treatment followed by 24 h recovery, biological replicate 1 50 µM PFOS, 24 h treatm…
- GSM9934662 50 µM PFOS, 24 h treatment followed by 24 h recovery, biological replicate 2 50 µM PFOS, 24 h treatm…
- GSM9934663 50 µM PFOS, 24 h treatment followed by 24 h recovery, biological replicate 3 50 µM PFOS, 24 h treatm…
- GSM9934664 vehicle control, 24 h treatment, biological replicate 1, H3K27ac CUT&Tag
- GSM9934665 vehicle control, 24 h treatment, biological replicate 2, H3K27ac CUT&Tag
- GSM9934666 vehicle control, 24 h treatment, biological replicate 3, H3K27ac CUT&Tag
- GSM9934667 25 µM PFOS, 24 h treatment, biological replicate 1, H3K27ac CUT&Tag
- GSM9934668 25 µM PFOS, 24 h treatment, biological replicate 2, H3K27ac CUT&Tag
- GSM9934669 25 µM PFOS, 24 h treatment, biological replicate 3, H3K27ac CUT&Tag
- GSM9934670 50 µM PFOS, 24 h treatment, biological replicate 1, H3K27ac CUT&Tag
- GSM9934671 50 µM PFOS, 24 h treatment, biological replicate 2, H3K27ac CUT&Tag
- GSM9934672 50 µM PFOS, 24 h treatment, biological replicate 3, H3K27ac CUT&Tag
- GSM9934673 vehicle control, 24 h treatment followed by 24 h recovery, biological replicate 1, H3K27ac CUT&Tag
- GSM9934674 vehicle control, 24 h treatment followed by 24 h recovery, biological replicate 2, H3K27ac CUT&Tag
- GSM9934675 vehicle control, 24 h treatment followed by 24 h recovery, biological replicate 3, H3K27ac CUT&Tag
- GSM9934676 25 µM PFOS, 24 h treatment followed by 24 h recovery, biological replicate 1, H3K27ac CUT&Tag
- GSM9934677 25 µM PFOS, 24 h treatment followed by 24 h recovery, biological replicate 2, H3K27ac CUT&Tag
- GSM9934678 25 µM PFOS, 24 h treatment followed by 24 h recovery, biological replicate 3, H3K27ac CUT&Tag
- GSM9934679 50 µM PFOS, 24 h treatment followed by 24 h recovery, biological replicate 1, H3K27ac CUT&Tag
- GSM9934680 50 µM PFOS, 24 h treatment followed by 24 h recovery, biological replicate 2, H3K27ac CUT&Tag
- GSM9934681 50 µM PFOS, 24 h treatment followed by 24 h recovery, biological replicate 3, H3K27ac CUT&Tag
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