GEO series

IBR1: A Novel Endogenous dsRNA Binding to the Helicase Domain of IFIH1 and Its Role in LPS-induced IFIH1 Activation and Macrophage M1 Polarization in ARDS [RNA-seq]

GSE244502 Mus musculus (mouse) RNA-seq (gene expression) 10 samples Submitted 2024/09/05 Platform GPL17021

At a glance

RNA-seq (gene expression) · mouse · 10 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: 10 samples: 8 distinct titles, 2 of them repeatedGroups 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: IBR1, a novel endogenous IFIH1-binding dsRNA, governs IFIH1 activation and M1 macrophage polarisation in ARDSClinical and translational medicine · 2024

Summary (written by the submitters)

Uncontrolled inflammatory responses driven by macrophages and monocytes play a crucial role in perpetuating lung injury and the severity of acute respiratory distress syndrome (ARDS). Previous studies have identified IFIH1 as a key regulator of macrophage M1 polarization in pneumonia-induced ARDS. IFIH1 is a cytosolic receptor responsible for recognizing viral double-stranded RNA (dsRNA) and activating inflammatory and antiviral signaling pathways.

Read the full summary ↓

Interestingly, our observations indicate that IFIH1 can also be activated by lipopolysaccharide (LPS), a component of bacterial cell walls. However, the precise molecular mechanism underlying LPS-induced IFIH1 activation remains unclear. In our preliminary investigations, we have discovered a novel transcript, named IFIH1-binding RNA1 (IBR1), which is upregulated by LPS and gram-negative bacilli in monocytes and macrophages. We have confirmed that IBR1 interacts with the IFIH1 protein, forming a complex. Further experiments have revealed that IBR1, acting as an endogenous dsRNA, binds to the helicase domain of IFIH1 due to its local double-stranded structure. This specific interaction serves as the underlying molecular mechanism responsible for LPS-induced IFIH1 activation and subsequent macrophage M1 polarization in ARDS. Importantly, our observations indicate a significant upregulation of IBR1 expression in ARDS patients with gram-negative bacilli-induced pneumonia. Understanding the molecular mechanisms driving IFIH1 activation and macrophage M1 polarization in ARDS is of great importance for developing new therapeutic strategies to alleviate lung inflammation and improve patient outcomes. Further research is warranted to elucidate the precise roles of IBR1 and its potential as a therapeutic target in the management of ARDS.

Published in

IBR1, a novel endogenous IFIH1-binding dsRNA, governs IFIH1 activation and M1 macrophage polarisation in ARDS

Zhang S, Huang W, Wu X et al. · Clinical and translational medicine 2024 · PMID 39313944 · doi:10.1002/ctm2.70027

This dataset

Open GSE244502 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 GSE244502_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 PRJNA1023280 and SRA study SRP464215. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39313944) ↗

Study design

8 distinct titles, 2 of them repeated

IFIH1-RIP ×2 Input ×2

How we read this: Read from 10 sample titles: 8 distinct titles with little repetition. 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

GSM7818294 mmu-M0A
GSM7818295 mmu-M0B
GSM7818296 mmu-M0C
GSM7818297 mmu-M1A
GSM7818298 mmu-M1B
GSM7818299 mmu-M1C
GSM7818300 IFIH1-RIP
GSM7818301 IFIH1-RIP2
GSM7818302 Input
GSM7818303 Input2

Datasets on a similar topic

GSE247177 IBR1: A Novel Endogenous dsRNA Binding to the Helicase Domain of IFIH1 and Its Role in LPS-induced IFIH1 Activation and Macrophage M1 Polarization in ARDS 20 samples shares ifih1, ibr1, ards, polarization, lps-induced, endogenous, activation, macrophage
GSE245648 The Heme-regulated transcriptional repressor, BACH1 safeguards macrophage enhancer selection, activation andtissue adaptation [RNA-seq_BMDM] 24 samples shares ards, activation, macrophage
GSE245649 The Heme-regulated transcriptional repressor, BACH1 safeguards macrophage enhancer selection, activation andtissue adaptation [RNA-seq_muscle] 11 samples shares ards, activation, macrophage
GSE245647 The Heme-regulated transcriptional repressor, BACH1 safeguards macrophage enhancer selection, activation andtissue adaptation [ChIP-seq] 62 samples shares ards, activation, macrophage
GSE245646 The Heme-regulated transcriptional repressor, BACH1 safeguards macrophage enhancer selection, activation andtissue adaptation [ATAC-seq_muscle] 22 samples shares ards, activation, macrophage
GSE245645 The Heme-regulated transcriptional repressor, BACH1 safeguards macrophage enhancer selection, activation andtissue adaptation [ATAC-seq_BMDM] 12 samples shares ards, activation, macrophage
GSE245650 The Heme-regulated transcriptional repressor, BACH1 safeguards macrophage enhancer selection, activation andtissue adaptation [Capture Hi-C] 6 samples shares ards, activation, macrophage
GSE202753 DsbA-L deficiency attenuates LPS-induced acute kidney injury via NF-κB/AP-1 regulation of macrophage polarization 13 samples shares polarization, lps-induced, macrophage

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