GEO series

RPL41 stabilizes ribosome dynamics and supports long-protein homeostasis in mammals

GSE308359 Mus musculus (mouse) RNA-seq (gene expression) 74 samples Submitted 2026/07/27 Platform GPL24676Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 74 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: 74 samples: 32 conditions, mostly in duplicateGroups 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.

Summary (written by the submitters)

Ribosomal protein L41 (RPL41 or eL41) is the smallest ribosomal protein and forms the eukaryote-specific bridge, eB14, near the decoding center; however, its role in mammalian translation remains unclear. In this study, we established RPL41-deficient models of human HEK293T cells and mice to define its function. Cryo-electron microscopy revealed that RPL41 constrains intersubunit conformational dynamics without inducing major local static rearrangements.

Read the full summary ↓

Loss of RPL41 altered A-site dynamics, slowed elongation, modestly increased amino acid misincorporation, and modestly enhanced readthrough of collision-inducing reporter sequences. Quantitative proteomic analysis suggested that these translational defects compromise long-protein homeostasis, as evidenced by increased insolubility and reduced abundance of long proteins. In vivo, Rpl41−/− mice were viable but exhibited growth retardation and decreased abundance of long proteins in tissues. Our findings reveal a conserved role for RPL41 in maintaining ribosome dynamics and translational fidelity, indicating that RPL41 supports ribosome function and long-protein homeostasis in mammals.

This dataset

Open GSE308359 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 GSE308359_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 PRJNA1330269 and SRA study SRP621282. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

32 conditions, mostly in duplicate

WT mouse brain Ribo-seq ×3 Rpl41 KO mouse brain Ribo-seq ×3 WT mouse brain RNA-seq ×3 Rpl41 KO mouse brain RNA-seq ×3 WT mouse kidney Ribo-seq ×3 Rpl41 KO mouse kidney Ribo-seq ×3 WT mouse kidney RNA-seq ×3 Rpl41 KO mouse kidney RNA-seq ×3 +24 more

Supports a between-group comparison across 74 samples.

How we read this: 32 replicated groups read from 74 sample titles; they account for 74 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

GSM9243968 WT HEK293T Ribo-seq replicate 1 WT HEK293T Ribo-seq
GSM9243969 WT HEK293T Ribo-seq replicate 2 WT HEK293T Ribo-seq
GSM9243970 RPL41 KO HEK293T Ribo-seq replicate 1 RPL41 KO HEK293T Ribo-s…
GSM9243971 RPL41 KO HEK293T Ribo-seq replicate 2 RPL41 KO HEK293T Ribo-s…
GSM9243972 WT HEK293T RNA-seq replicate 1 WT HEK293T RNA-seq
GSM9243973 WT HEK293T RNA-seq replicate 2 WT HEK293T RNA-seq
GSM9243974 RPL41 KO HEK293T RNA-seq replicate 1 RPL41 KO HEK293T RNA-seq
GSM9243975 RPL41 KO HEK293T RNA-seq replicate 2 RPL41 KO HEK293T RNA-seq
GSM9243976 WT HEK293T harringtonine 0 min Ribo-seq replicate 1 WT HEK293T harringtonin…
GSM9243977 WT HEK293T harringtonine 0 min Ribo-seq replicate 2 WT HEK293T harringtonin…
GSM9243978 RPL41 KO HEK293T harringtonine 0 min Ribo-seq replicate 1 RPL41 KO HEK293T harrin…
GSM9243979 RPL41 KO HEK293T harringtonine 0 min Ribo-seq replicate 2 RPL41 KO HEK293T harrin…
GSM9243980 WT HEK293T harringtonine 1 min Ribo-seq replicate 1 WT HEK293T harringtonin…
GSM9243981 WT HEK293T harringtonine 1 min Ribo-seq replicate 2 WT HEK293T harringtonin…
GSM9243982 RPL41 KO HEK293T harringtonine 1 min Ribo-seq replicate 1 RPL41 KO HEK293T harrin…
GSM9243983 RPL41 KO HEK293T harringtonine 1 min Ribo-seq replicate 2 RPL41 KO HEK293T harrin…
GSM9243984 WT HEK293T harringtonine 2 min Ribo-seq replicate 1 WT HEK293T harringtonin…
GSM9243985 WT HEK293T harringtonine 2 min Ribo-seq replicate 2 WT HEK293T harringtonin…
GSM9243986 RPL41 KO HEK293T harringtonine 2 min Ribo-seq replicate 1 RPL41 KO HEK293T harrin…
GSM9243987 RPL41 KO HEK293T harringtonine 2 min Ribo-seq replicate 2 RPL41 KO HEK293T harrin…
GSM9243988 WT HEK293T harringtonine 3 min Ribo-seq replicate 1 WT HEK293T harringtonin…
GSM9243989 WT HEK293T harringtonine 3 min Ribo-seq replicate 2 WT HEK293T harringtonin…
GSM9243990 RPL41 KO HEK293T harringtonine 3 min Ribo-seq replicate 1 RPL41 KO HEK293T harrin…
GSM9243991 RPL41 KO HEK293T harringtonine 3 min Ribo-seq replicate 2 RPL41 KO HEK293T harrin…
GSM9243992 WT HEK293T disome-seq replicate 1 WT HEK293T disome-seq
GSM9243993 WT HEK293T disome-seq replicate 2 WT HEK293T disome-seq
GSM9243994 RPL41 KO HEK293T disome-seq replicate 1 RPL41 KO HEK293T disome…
GSM9243995 RPL41 KO HEK293T disome-seq replicate 2 RPL41 KO HEK293T disome…
GSM9243996 WT HEK293T SLAM-seq 0 h replicate 1 WT HEK293T SLAM-seq 0 h
GSM9243997 WT HEK293T SLAM-seq 3 h replicate 1 WT HEK293T SLAM-seq 3 h
GSM9243998 WT HEK293T SLAM-seq 6 h replicate 1 WT HEK293T SLAM-seq 6 h
GSM9243999 WT HEK293T SLAM-seq 12 h replicate 1 WT HEK293T SLAM-seq 12 h
GSM9244000 WT HEK293T SLAM-seq 0 h replicate 2 WT HEK293T SLAM-seq 0 h
GSM9244001 WT HEK293T SLAM-seq 3 h replicate 2 WT HEK293T SLAM-seq 3 h
GSM9244002 WT HEK293T SLAM-seq 6 h replicate 2 WT HEK293T SLAM-seq 6 h
GSM9244003 WT HEK293T SLAM-seq 12 h replicate 2 WT HEK293T SLAM-seq 12 h
GSM9244004 RPL41 KO HEK293T SLAM-seq 0 h replicate 1 RPL41 KO HEK293T SLAM-s…
GSM9244005 RPL41 KO HEK293T SLAM-seq 3 h replicate 1 RPL41 KO HEK293T SLAM-s…
GSM9244006 RPL41 KO HEK293T SLAM-seq 6 h replicate 1 RPL41 KO HEK293T SLAM-s…
GSM9244007 RPL41 KO HEK293T SLAM-seq 12 h replicate 1 RPL41 KO HEK293T SLAM-s…

+ 34 more — browse all 74 samples with per-sample file links →

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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.