GEO series

The Capicua-Ataxin 1L DNA Binding Transcriptional Repressor Complex Serves as a Gatekeepers of Cell Autonomous Antiviral Responses[Mouse RNA-Seq ]

GSE271899 Mus musculus (mouse) RNA-seq (gene expression) 28 samples Submitted 2025/03/24 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 28 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: 28 samples: 14 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)

Early detection of viral infection and rapid activation of host antiviral defenses are critical for limiting viral replication and spread. At a cellular level, this is achieved through host pattern recognition receptors that sense viral nucleic acid as foreign and initiate antiviral defenses through transcriptional upregulation of antiviral cytokines interferons (IFNs) and interferon stimulated genes (ISGs).

Read the full summary ↓

However, aberrant production of IFN in the absence of viral infection leads to auto-inflammation and can be detrimental to the host. Here, we show that the DNA binding transcriptional repressor complex composed of Capicua (CIC) and Ataxin-1 like (ATXN1L) bind to 8-nucleotide motif near IFN and ISG promoters and block aberrant expression under homeostasis. However, during respiratory viral infections, this active repression is relieved by rapid degradation of the CIC-ATXN1L complex via the activation Mitogen‑activated protein kinase (MAPK) pathway, thereby priming the host cells ready to mount robust antiviral responses through canonical interferon regulatory factors (IRF), and signal transducer and activator of transcription (STAT) transcription factors. Importantly, murine Cic-Atxn1L also repress expression from IFN and ISGs promoters, demonstrating the conservation of this regulatory mechanism in murine species. Together, our studies define a new paradigm for regulation of IFN and ISGs through the evolutionarily conserved CIC-ATXN1L DNA binding transcription repressor complex under homeostasis and viral infection conditions.

This dataset

Open GSE271899 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 GSE271899_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 PRJNA1133826 and SRA study SRP518932. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

14 conditions, mostly in duplicate

lungs, CICKO_mock_rep1, ×2 lungs, CICKO_mock_rep2, ×2 lungs, CICKO_PR8_rep1, ×2 lungs, CICKO_PR8_rep2, ×2 lungs, CICKO_PR8_rep3, ×2 lungs, CICKO_PR8_rep4, ×2 lungs, CICKO_PR8_rep5, ×2 lungs, Control_mock_rep1, ×2 +6 more

Supports a between-group comparison across 28 samples.

How we read this: 14 replicated groups read from 28 sample titles; they account for 28 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

GSM8388695 lungs, CICKO_mock_rep1, lane1 lungs, CICKO_mock_rep1,
GSM8388696 lungs, CICKO_mock_rep2, lane1 lungs, CICKO_mock_rep2,
GSM8388697 lungs, CICKO_PR8_rep1, lane1 lungs, CICKO_PR8_rep1,
GSM8388698 lungs, CICKO_PR8_rep2, lane1 lungs, CICKO_PR8_rep2,
GSM8388699 lungs, CICKO_PR8_rep3, lane1 lungs, CICKO_PR8_rep3,
GSM8388700 lungs, CICKO_PR8_rep4, lane1 lungs, CICKO_PR8_rep4,
GSM8388701 lungs, CICKO_PR8_rep5, lane1 lungs, CICKO_PR8_rep5,
GSM8388702 lungs, Control_mock_rep1, lane1 lungs, Control_mock_rep…
GSM8388703 lungs, Control_mock_rep2, lane1 lungs, Control_mock_rep…
GSM8388704 lungs, Control_mock_rep3, lane1 lungs, Control_mock_rep…
GSM8388705 lungs, Control_PR8_rep1, lane1 lungs, Control_PR8_rep1,
GSM8388706 lungs, Control_PR8_rep3, lane1 lungs, Control_PR8_rep3,
GSM8388707 lungs, Control_PR8_rep4, lane1 lungs, Control_PR8_rep4,
GSM8388708 lungs, Control_PR8_rep5, lane1 lungs, Control_PR8_rep5,
GSM8388709 lungs, CICKO_mock_rep1, lane2 lungs, CICKO_mock_rep1,
GSM8388710 lungs, CICKO_mock_rep2, lane2 lungs, CICKO_mock_rep2,
GSM8388711 lungs, CICKO_PR8_rep1, lane2 lungs, CICKO_PR8_rep1,
GSM8388712 lungs, CICKO_PR8_rep2, lane2 lungs, CICKO_PR8_rep2,
GSM8388713 lungs, CICKO_PR8_rep3, lane2 lungs, CICKO_PR8_rep3,
GSM8388714 lungs, CICKO_PR8_rep4, lane2 lungs, CICKO_PR8_rep4,
GSM8388715 lungs, CICKO_PR8_rep5, lane2 lungs, CICKO_PR8_rep5,
GSM8388716 lungs, Control_mock_rep1, lane2 lungs, Control_mock_rep…
GSM8388717 lungs, Control_mock_rep2, lane2 lungs, Control_mock_rep…
GSM8388718 lungs, Control_mock_rep3, lane2 lungs, Control_mock_rep…
GSM8388719 lungs, Control_PR8_rep1, lane2 lungs, Control_PR8_rep1,
GSM8388720 lungs, Control_PR8_rep3, lane2 lungs, Control_PR8_rep3,
GSM8388721 lungs, Control_PR8_rep4, lane2 lungs, Control_PR8_rep4,
GSM8388722 lungs, Control_PR8_rep5, lane2 lungs, Control_PR8_rep5,

Datasets on a similar topic

GSE160057 BAHD1 links H3K27me3 to gene silencing via a conserved BAH reader module and associated corepressor complex in mammalian cells (RNA-Seq) 12 samples shares repressor, complex, rna-seq
GSE290816 Cell autonomous regional differences in oligodendrocyte precursor cell development and response to oncohistone H3.3 K27M [RNA-seq] 142 samples shares autonomous, rna-seq
GSE245648 The Heme-regulated transcriptional repressor, BACH1 safeguards macrophage enhancer selection, activation andtissue adaptation [RNA-seq_BMDM] 24 samples shares repressor, rna-seq
GSE290817 Cell autonomous regional differences in oligodendrocyte precursor cell development and response to oncohistone H3.3 K27M [scRNA-seq] 22 samples shares autonomous, rna-seq
GSE306891 Androgen receptor cell-autonomously regulates luminal cell plasticity and regeneration [scRNA-seq] 22 samples shares autonomous, rna-seq
GSE230264 The transcriptional co-repressor Runx1t1 is essential for N-Myc-driven neuroblastoma tumorigenesis [RNA-Seq 2] 16 samples shares repressor, rna-seq
GSE245649 The Heme-regulated transcriptional repressor, BACH1 safeguards macrophage enhancer selection, activation andtissue adaptation [RNA-seq_muscle] 11 samples shares repressor, rna-seq
GSE306685 Androgen receptor cell-autonomously regulates luminal cell plasticity [RNA-Seq] 9 samples shares autonomous, rna-seq

Search all mouse 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.