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The lncRNA Firre functions as a rapid regulator of transcription [RNA-seq]

GSE202405 Mus musculus (mouse) RNA-seq (gene expression) 156 samples Submitted 2024/03/01 Platform GPL21103
At a glance

RNA-seq (gene expression) · mouse · 156 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
156 samples: 68 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.
Paper
The temporal dynamics of lncRNA Firre-mediated epigenetic and transcriptional regulationNature communications · 2024
Summary (written by the submitters)
There are currently over 16,000 long-noncoding RNAs (lncRNAs) annotated in mammalian genomes, a number on par with protein-coding genes. Numerous studies have demonstrated that lncRNAs can influence gene expression programs but lack the temporal resolution to identify the immediate regulatory events. Thus, even for the most well studied the early and primary targets of lncRNAs remains elusive.
Read the full summary ↓
Here we describe a multifaceted effort to determine the primary targets of a lncRNA and the underlying temporal dynamics. Our approach combines several genetically defined loss-of and gain-of-function, rescue, and inducible lncRNA models. We further resolved gene regulatory events temporally (30 min to four days). Applying this approach, we find that the lncRNA Firre is an RNA-based transcriptional activator. These transcriptional activation events are not mediated by the epigenetic regulators PRC2, WDR5, or G9A, nor are they due to the proximal binding of the Firre lncRNA. Instead, Firre activates transcription by increasing chromatin accessibility (approximately 30 min after induction) and activating primary target genes (about an hour later). Overall, this study suggests Firre functions as an RNA-based transcriptional activator.
Published in
The temporal dynamics of lncRNA Firre-mediated epigenetic and transcriptional regulation
Much C, Lasda EL, Pereira IT et al. · Nature communications 2024 · PMID 39122712 · doi:10.1038/s41467-024-50402-0
This dataset
Open GSE202405 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 GSE202405_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 PRJNA835859 and SRA study SRP374025. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39122712) ↗
Study design
68 conditions, mostly in duplicate
mESC_Firre_OE_control_0min_dox_long ×3 mESC_Firre_OE_control_720min_dox_long ×3 mESC_Firre_OE_control_1440min_dox_long ×3 mESC_Firre_OE_control_2880min_dox_long ×3 mESC_Firre_OE_control_5760min_dox_long ×3 mESC_Firre_OE_firre_induced_0min_dox_long ×3 mESC_Firre_OE_firre_induced_720min_dox_long ×3 mESC_Firre_OE_firre_induced_1440min_dox_long ×3 +60 more

Supports a case/control comparison: 78 samples read as cases, 78 as controls.

How we read this: 68 replicated groups read from 156 sample titles; they account for 156 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

+ 116 more — browse all 156 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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