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Pathways for macrophage uptake of cell-free circular RNAs

GSE264160 Mus musculus (mouse) RNA-seq (gene expression) 28 samples Submitted 2024/08/01 Platform GPL21626
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: 8 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
Pathways for macrophage uptake of cell-free circular RNAsMolecular cell · 2024
Summary (written by the submitters)
Circular RNAs (CircRNAs) are stable RNAs present in cell-free RNA, comprising cellular debris and pathogen genomes. As a prerequisite for the development of efficient circRNA-based therapies, we investigated the phenomenon and mechanism of cellular uptake and intracellular fate of circRNAs. Human myeloid cells and B cells selectively internalize extracellular circRNAs.
Read the full summary ↓
Macrophage uptake of circRNA is rapid, energy-dependent, and saturable. CircRNA uptake can lead to translation of encoded sequences and antigen presentation. The route of internalization influences immune activation after circRNA uptake, with distinct gene expression programs depending on the mechanism involved. Genome-scale CRISPR screens and chemical inhibitor studies nominate macrophage scavenger receptor MSR1, toll-like receptors, and mTOR signaling as key regulators of receptor-mediated phagocytosis of circRNAs, a dominant pathway to internalize circRNAs in parallel to macropinocytosis. These results suggest that cell-free circRNA serves as an "eat me" signal and a danger-associated molecular pattern, indicating orderly pathways of recognition and disposal.
Published in
Pathways for macrophage uptake of cell-free circular RNAs
Amaya L, Abe B, Liu J et al. · Molecular cell 2024 · PMID 38761795 · doi:10.1016/j.molcel.2024.04.022
This dataset
Open GSE264160 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 GSE264160_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 PRJNA1101075 and SRA study SRP502116. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38761795) ↗
Study design
8 conditions, mostly in duplicate
RAW264_untreated ×2 RAW264_circRNA_uptake ×2 RAW264_circRNA_transfection ×2 MutuDC_untreated ×2 MutuDC_circRNA_uptake ×2 MutuDC_circRNA_transfection ×2 J774_circRNA_uptake ×2 J774_circSTOP_uptake ×2 +12 more

Supports a between-group comparison across 16 samples.

How we read this: 8 replicated groups read from 28 sample titles; they account for 16 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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