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Cellular Defense Mechanisms Show Stronger Response to Linear DNA Compared to Circular Plasmid [RNA-seq]

GSE275387 Homo sapiens (human) RNA-seq (gene expression) 99 samples Submitted 2025/05/21 Platform GPL30209
At a glance

RNA-seq (gene expression) · human · 99 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
Homo sapiens (human)
Samples
99 samples: 33 conditions, mostly in triplicateGroups 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
Unlocking the Puzzle of Mammalian Transfection: The Role of the RNA-sensing-Mediated Interferon Response in the Cellular Defense Against Foreign DNA IntrusionInternational journal of biological sciences · 2025
Summary (written by the submitters)
Low transfection efficiency poses a significant challenge to experimental success, making the improvement of gene-carrying plasmid delivery and expression essential across various research fields. The stability of transfected vector DNA or mRNA significantly impacts transgene expression, as the innate immune system may recognize plasmid DNA as foreign and initiate a degradation response.
Read the full summary ↓
Currently, it is unclear whether RNA transcribed from plasmids can activate RNA sensors, affecting transfection efficiency. This study employed RNA sequencing to analyze cellular responses to various circular and linear DNAs across five cell lines—HEK293T, HCT116, HeLa, L02, and NCM460—revealing that the innate immune response is a primary contributor to low transfection efficiency. Additionally, we used ChIP-seq to detect H3K27ac histone marks to explore whether the immune response triggered by plasmid transfection is regulated by epigenetic mechanisms. Finally, we performed ChIP assays for IRF7 and p-IRF3 in HeLa cells transfected with the linear pcDNA3.1-neo plasmid to demonstrate that these two transcription factors can indeed bind to the RTV genes.
Published in
Unlocking the Puzzle of Mammalian Transfection: The Role of the RNA-sensing-Mediated Interferon Response in the Cellular Defense Against Foreign DNA Intrusion
Li X, Zhou Y, Wei J et al. · International journal of biological sciences 2025 · PMID 40607250 · doi:10.7150/ijbs.107510
This dataset
Open GSE275387 in finder → Find more human 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 GSE275387_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 PRJNA1150588 and SRA study SRP527857. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40607250) ↗
Study design
33 conditions, mostly in triplicate
HeLa cells,control, ×3 HeLa cells,pcDNA3.1-neo, ×3 HeLa cells,linear pcDNA3.1-neo, ×3 HeLa cells,pre-gRNA, ×3 HeLa cells,linear pre-gRNA, ×3 NCM460 cells,control, ×3 NCM460 cells,pcDNA3.1-neo, ×3 NCM460 cells,linear pcDNA3.1-neo, ×3 +25 more

Supports a case/control comparison: 24 samples read as cases, 15 as controls.

How we read this: 33 replicated groups read from 99 sample titles; they account for 99 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

+ 59 more — browse all 99 samples with per-sample file links →

Datasets on a similar topic

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