← BioTransfer GEO Dataset Finder
GEO series

TLDR (True Length of Diverse capped RNAs)-seq: a method for 5’-to-3’ end sequencing of capped full-length RNAs with or without 3’ polyadenylation

GSE279131 Mus musculus (mouse) RNA-seq (gene expression) 18 samples Submitted 2025/04/09 Platform GPL24106Platform GPL24973
At a glance

RNA-seq (gene expression) · mouse · 18 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
18 samples: 12 × TLDR-Seq_HeLa_libNoamp_bc vs 3 × TLDR-Seq_HeLa_libamp_bcGroups 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
True length of diverse capped RNA sequencing (TLDR-seq): 5'-3'-end sequencing of capped RNAs regardless of 3'-end statusNucleic acids research · 2025
Summary (written by the submitters)
Analysis and understanding of transcript functions is greatly helped by knowing the full-length sequence of individual RNAs. New long-read sequencing devices such as Oxford Nanopore and Pacbio have the potential to sequence full-length transcripts, but standard methods lack the ability to capture true RNA 5’ ends and selects for poly-adenylated (pA+) transcripts.
Read the full summary ↓
We present a method that, by utilizing cap-trapping and 3’ end adapter ligation, can sequence transcripts from the exact 5’ end to 3’ end regardless of whether they are poly-adenylated, with no need for ribosomal RNA depletion. We show that the method can faithfully detect 5’ ends, splice junctions and 3’ ends, has high reproducibility between runs and gene expression estimates from the method correlate well with short-read sequencing methods. We also demonstrate that the method can detect and sequence full-length pA- RNAs, including lncRNAs, promoter upstream transcripts (PROMPTs) and enhancer RNAs. TLDR-seq is therefore useful for the characterization of diverse capped RNA species.
Published in
True length of diverse capped RNA sequencing (TLDR-seq): 5'-3'-end sequencing of capped RNAs regardless of 3'-end status
Auxillos J, Stigliani A, Vaagensø CS et al. · Nucleic acids research 2025 · PMID 40183637 · doi:10.1093/nar/gkaf240
This dataset
Open GSE279131 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 GSE279131_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 PRJNA1170942 and SRA study SRP537436. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40183637) ↗
Study design
12 × TLDR-Seq_HeLa_libNoamp_bc vs 3 × TLDR-Seq_HeLa_libamp_bc

Supports a between-group comparison across 15 samples.

How we read this: 2 replicated groups read from 18 sample titles; they account for 15 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

Search all 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.