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The long noncoding RNA Malat1 contains an internal ribosome entry site mediating micropeptide translation

GSE310313 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2026/03/05 Platform GPL30172
At a glance

RNA-seq (gene expression) · mouse · 12 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
12 samples: 6 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)
To determine the structure of the Malat1 IRES, fbDMS-MaP structure probing experiments were performed in BV2 cells for endogenous mouse Malat1 probing, and N2a cells for probing of reporter constructs pDual-GFP-(1-739) IRES-RFP and pDual-GFP-(558-695) IRES-RFP. Two biological replicates were collected for each probing target. For each replicate, fbDMS-MaP includes a sample treated with dimethyl sulfate (modified), and one sample treated with ethanol (unmodified).
Read the full summary ↓
DMS reacts with the Watson-Crick face of unpaired bases in RNA, covalently modifying them with a methyl adduct. These modifications are encoded as mutations during reverse transcription with MarathonRT. Amplicons are then PCR amplified, next-generation sequencing libraries are prepared, and sequenced using an Illumina NextSeq 2000 platform. The sequencing data are aligned to the reference sequence, and a reactivity profile of 'modified' and 'unmodified' samples is used to calculate the DMS reactivity values of each base. These data can subsequently be used for RNA secondary structure modelling.
This dataset
Open GSE310313 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 GSE310313_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 PRJNA1365748 and SRA study SRP646294. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
6 conditions, mostly in duplicate
Endogenous mMALAT1, Modified, ×2 Endogenous mMALAT1, Unmodified, ×2 MALAT1 reporter pDual-GFP-(1-739) IRES-RFP, M… ×2 MALAT1 reporter pDual-GFP-(1-739) IRES-RFP, U… ×2 MALAT1 reporter pDual-GFP-(558-695) IRES-RFP,… ×2 MALAT1 reporter pDual-GFP-(558-695) IRES-RFP,… ×2

Supports a between-group comparison across 12 samples.

How we read this: 6 replicated groups read from 12 sample titles; they account for 12 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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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.