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Insights into Brominated Flame Retardant Neurotoxicity: Mechanisms of Hippocampal Neural Cell Death and Brain Region-Specific Transcriptomic Shifts in Mice

GSE242684 Mus musculus (mouse) RNA-seq (gene expression) 76 samples Submitted 2024/07/28 Platform GPL30172
At a glance

RNA-seq (gene expression) · mouse · 76 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
76 samples: 19 conditions, mostly with about 4 replicates eachGroups 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
Insights into brominated flame retardant neurotoxicity: mechanisms of hippocampal neural cell death and brain region-specific transcriptomic shifts in miceToxicological sciences : an official journal of the Society of Toxicology · 2024
Summary (written by the submitters)
Brominated Flame Retardants (BFRs) reduce flammability in a wide range of products including electronics, carpets, and paint, but leach into the environment to result in continuous, population-level exposure. Epidemiology studies have correlated BFR exposure with neurological problems, including alterations in learning and memory. This study investigated the molecular mechanisms mediating BFR-induced cell death in hippocampal cells and clarified the impact of HBCD exposure on gene transcription in the hippocampus, dorsal striatum, and frontal cortex of male mice.
Read the full summary ↓
Hippocampal derived HT-22 cell exposure to tetrabromobisphenol-A (TBBPA), hexabromocyclododecane (HBCD), or 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) (current, phasing out, and phased out BFRs, respectively) induced time, concentration, and chemical-dependent cellular and nuclear morphological alterations indicative of apoptosis, which aligned with alterations in cell cycle and increases in annexin V staining. All three BFRs increased p53 and p21 expression; however, inhibition of p53 nuclear translocation using pifthrin-a did not decrease cell death. Transcriptomic analysis upon low (10 nM) and cytotoxic (10 μM) BFR exposure indicated that HBCD and BDE-47 altered genes mediating autophagy-related pathways. Further evaluation showed BFR exposure increased LC3-II conversion and autophagosome formation, and co-exposure with the autophagy inhibitor 3-methyladenine (3-MA) attenuated cytotoxicity. Transcriptomic assessment of select brain regions from subchronically HBCD-exposed male mice demonstrated alteration of genes mediating vesicular transport, with greater impact on the frontal cortex and dorsal striatum compared to the dorsal and ventral hippocampus. These data demonstrate that BFRs can induce chemical-dependent autophagy in neural cells in vitro and provide evidence that BFRs induce region-specific transcriptomic effects in the brain.
Published in
Insights into brominated flame retardant neurotoxicity: mechanisms of hippocampal neural cell death and brain region-specific transcriptomic shifts in mice
Kramer NE, Fillmore CE, Slane EG et al. · Toxicological sciences : an official journal of the Society of Toxicology 2024 · PMID 38995820 · doi:10.1093/toxsci/kfae090
This dataset
Open GSE242684 in finder → Find more mouse 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 GSE242684_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 PRJNA1014109 and SRA study SRP459170. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38995820) ↗
Study design
19 conditions, mostly with about 4 replicates each
Frontal_cortex_Vehicle ×4 Frontal_cortex_HBCD ×4 Dorsal_Striatum_Vehicle ×4 Dorsal_Striatum_HBCD ×4 Dorsal_Hippocampus_Vehicle ×4 Dorsal_Hippocampus_HBCD ×4 Ventral_Hippocampus_Vehicle ×4 Ventral_Hippocampus_HBCD ×4 +11 more

Supports a between-group comparison across 76 samples.

How we read this: 19 replicated groups read from 76 sample titles; they account for 76 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

+ 36 more — browse all 76 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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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.