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Exceptional Uptake, Limited Protein Expression: Liver Macrophages Lost in Translation of Synthetic mRNA

GSE271200 Mus musculus (mouse) RNA-seq (gene expression) 35 samples Submitted 2024/12/26 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 35 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
35 samples: 6 conditions, mostly with about 6 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
Exceptional Uptake, Limited Protein Expression: Liver Macrophages Lost in Translation of Synthetic mRNAAdvanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025
Summary (written by the submitters)
To investigate the translation and function of nucleic acid, we designed and prepared LNPs co-encapsulating GFP mRNA and TLR4 siRNA. These LNPs were administered via tail vein injection and primarily accumulated in the liver. Therefore, in this experiment, we isolated liver cells and used flow cytometry to sort Kupffer cells for gene sequencing, aiming to study the mRNA expression levels in different cell types.
Published in
Exceptional Uptake, Limited Protein Expression: Liver Macrophages Lost in Translation of Synthetic mRNA
Lin C, Kuzmanović A, Wang N et al. · Advanced science (Weinheim, Baden-Wurttemberg, Germany) 2025 · PMID 39792811 · doi:10.1002/advs.202409729
This dataset
Open GSE271200 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 GSE271200_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 PRJNA1130447 and SRA study SRP517372. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39792811) ↗
Study design
6 conditions, mostly with about 6 replicates each
WT ×6 WT2 ×6 GFPactiveTLR4siRNA ×6 WT2HC ×6 GFPactiveTLR4siRNAHC ×6 GFPinactiveTLR4siRNA ×5

Supports a between-group comparison across 35 samples.

How we read this: 6 replicated groups read from 35 sample titles; they account for 35 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
Datasets on a similar topic

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