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Interactions of Polychlorinated Biphenyls and Their Metabolites with the Brain and Liver Transcriptome of Female Mice

GSE252621 Mus musculus (mouse) RNA-seq (gene expression) 62 samples Submitted 2024/11/08 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 62 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
62 samples: 21 × P vs 21 × S vs 20 × LGroups 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
Interactions of Polychlorinated Biphenyls and Their Metabolites with the Brain and Liver Transcriptome of Female MiceACS chemical neuroscience · 2024
Summary (written by the submitters)
In this study, we explore the implications of oral exposure to the MARBLES mixture on the brain in adult female mice through two omics approaches, metabolomics and transcriptomics. The individual PCB congeners (PCB 11, 28, 52, 84, 95, 101, 118, 135, 138, 149, 153, and 180) used to make the MARBLES PCB mix.
Read the full summary ↓
Female C57Bl/6J mice (> 6-week-old) were randomized into exposure groups (N = 4-6) and orally exposed to 0, 0.1, 1, or 6 mg/kg bw/day of the MARBLES mix in organic peanut butter/organic peanut oil for 7 weeks.The striatum and prefrontal cortex were isolated and, together with the liver, prepared for RNA sequencing.
Published in
Interactions of Polychlorinated Biphenyls and Their Metabolites with the Brain and Liver Transcriptome of Female Mice
Bullert AJ, Wang H, Valenzuela AE et al. · ACS chemical neuroscience 2024 · PMID 39392776 · doi:10.1021/acschemneuro.4c00367
This dataset
Open GSE252621 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 GSE252621_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 PRJNA1061527 and SRA study SRP482207. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39392776) ↗
Study design
21 × P vs 21 × S vs 20 × L

Supports a between-group comparison across 62 samples.

How we read this: 3 replicated groups read from 62 sample titles; they account for 62 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

+ 22 more — browse all 62 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.