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Identification of phthalate mixture exposure targets in the human and mouse ovary in vitro 

GSE223645 Mus musculus (mouse) RNA-seq (gene expression) 144 samples Submitted 2025/01/27 Platform GPL18573Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 144 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
Mus musculus (mouse)
Samples
144 samples: 45 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
Identification of phthalate mixture exposure targets in the human and mouse ovary in vitroReproductive toxicology (Elmsford, N.Y.) · 2023
Summary (written by the submitters)
Chemical health risk assessment is based on single chemicals, but humans and wildlife are exposed to extensive mixtures of industrial substances and pharmaceuticals. Such exposures are life-long and correlate with multiple morbidities, including infertility. How combinatorial effects of chemicals should be handled in hazard characterization and risk assessment are open questions.
Read the full summary ↓
Further, test systems are missing for several relevant health outcomes including reproductive health and fertility in women. Here, our aim was to screen multiple ovarian cell models for phthalate induced effects to identify biomarkers of exposure. We used an epidemiological cohort study to define different phthalate mixtures for in vitro testing. The mixtures were then tested in five cell models representing ovarian granulosa or stromal cells, namely COV434, KGN, primary human granulosa cells, primary mouse granulosa cells, and primary human ovarian stromal cells. Exposures at epidemiologically relevant exposure level did not markedly elicit cytotoxicity or affect steroidogenesis in short 24-hour exposure. However, significant effects on gene expression were discovered by RNA-sequencing. Altogether, the exposures changed the average expression of 124 genes (9-479 genes per exposure) in human cell models, without obvious concentration or mixture-dependent effects on gene numbers. The mixtures stimulated distinct changes in different cell models. Despite differences, our analyses suggest commonalities in responses towards phthalates, which forms a starting point for follow-up studies on identification and validation of candidate biomarkers that could be developed to novel assays for regulatory testing or even into clinical tests.
Published in
Identification of phthalate mixture exposure targets in the human and mouse ovary in vitro
Tarvainen I, Soto DA, Laws MJ et al. · Reproductive toxicology (Elmsford, N.Y.) 2023 · PMID 37160244 · doi:10.1016/j.reprotox.2023.108393
This dataset
Open GSE223645 in finder → Find more 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 GSE223645_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 PRJNA927020 and SRA study SRP418925. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 37160244) ↗
Study design
45 conditions, mostly in triplicate
MmGC_DMSO ×4 MmGC_WQS ×4 MmGC_WQS100 ×4 MmGC_EPIDEM ×4 MmGC_EPIDEM100 ×4 MmGC_EQUI ×4 MmGC_EQUI100 ×4 MmGC_MHHP ×4 +37 more

Supports a between-group comparison across 144 samples.

How we read this: 45 replicated groups read from 144 sample titles; they account for 144 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

+ 104 more — browse all 144 samples with per-sample file links →

Datasets on a similar topic

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