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Effect of damaging mutations in LXRalpha on the liver transcriptome

GSE273156 Mus musculus (mouse) RNA-seq (gene expression) 48 samples Submitted 2024/07/31 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 48 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
48 samples: 24 × dn vs 24 × koGroups 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
Damaging mutations in liver X receptor-α are hepatotoxic and implicate cholesterol sensing in liver healthNature metabolism · 2024
Summary (written by the submitters)
Damaging mutations in LXRalpha are associated with hepatotoxicity. We generated mice homozygous for a dominant-negative mutation in LXRalpha (LXRalpha-W441R) and discovered they develop severe liver injury when fed a Western diet, though knockout mice develop little to no liver injury. To examine this in further detail, we performed Bulk RNA-seq of livers from LXRalpha knockout and LXRalpha p.W441R knockin mice after 8 weeks of western diet (TD.88137).
Published in
Damaging mutations in liver X receptor-α are hepatotoxic and implicate cholesterol sensing in liver health
Lockhart SM, Muso M, Zvetkova I et al. · Nature metabolism 2024 · PMID 39322746 · doi:10.1038/s42255-024-01126-4
This dataset
Open GSE273156 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 GSE273156_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 PRJNA1140260 and SRA study SRP522287. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39322746) ↗
Study design
24 × dn vs 24 × ko

Supports a between-group comparison across 48 samples.

How we read this: 2 replicated groups read from 48 sample titles; they account for 48 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

+ 8 more — browse all 48 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.