GEO series

Effect of the rhesus theta defensin-1 (RTD-1) on gene expression in human monocytic THP-1 cells. [I]

GSE278567 Homo sapiens (human) RNA-seq (gene expression) 24 samples Submitted 2025/12/09 Platform GPL20301

At a glance

RNA-seq (gene expression) · human · 24 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: 24 samples: 8 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: The macrocyclic peptide rhesus theta defensin 1 activates interferon and antiviral pathways in human monocytesJournal of leukocyte biology · 2025

Summary (written by the submitters)

Theta defensins are unique since they are the only cyclic peptides in the animal kingdom. The theta defensin, Rhesus theta defensin (RTD)-1, first isolated from rhesus macaque neutrophils as a broad-spectrum antimicrobial peptide was subsequently found to regulate gene expression and immune signaling pathways in cell culture and animal models of immune mediated diseases.

Read the full summary ↓

To gain insights into RTD-1 regulation, we performed RNA sequencing (RNA-seq) to determine the effect of RTD-1 on global gene expression in THP-1 monocytes. Differential gene expression analysis revealed RTD-1 mediated stimulation of interferon and antiviral gene expression pathways potentially priming cells for resistance to viral infections.

Published in

The macrocyclic peptide rhesus theta defensin 1 activates interferon and antiviral pathways in human monocytes

Tongaonkar P, Trinh KK, Henley JE et al. · Journal of leukocyte biology 2025 · PMID 41139211 · doi:10.1093/jleuko/qiaf150

This dataset

Open GSE278567 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 GSE278567_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 PRJNA1167792 and SRA study SRP536110. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41139211) ↗

Study design

8 conditions, mostly in triplicate

THP-1, 20h, vehicle exp ×3 THP-1, 20h, 1 µg/ml RTD-1 exp ×3 THP-1, 20h, 3 µg/ml RTD-1 exp ×3 THP-1, 20h, 10 µg/ml RTD-1 exp ×3 THP-1, 20h, LPS exp ×3 THP-1, 20h, 1 µg/ml RTD-1 LPS exp ×3 THP-1, 20h, 3 µg/ml RTD-1 LPS exp ×3 THP-1, 20h, 10 µg/ml RTD-1 LPS exp ×3

Supports a between-group comparison across 24 samples.

How we read this: 8 replicated groups read from 24 sample titles; they account for 24 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

GSM8549051 THP-1, 20h, vehicle exp1 THP-1, 20h, vehicle exp
GSM8549052 THP-1, 20h, vehicle exp2 THP-1, 20h, vehicle exp
GSM8549053 THP-1, 20h, vehicle exp3 THP-1, 20h, vehicle exp
GSM8549054 THP-1, 20h, 1 µg/ml RTD-1 exp1 THP-1, 20h, 1 µg/ml RTD…
GSM8549055 THP-1, 20h, 1 µg/ml RTD-1 exp2 THP-1, 20h, 1 µg/ml RTD…
GSM8549056 THP-1, 20h, 1 µg/ml RTD-1 exp3 THP-1, 20h, 1 µg/ml RTD…
GSM8549057 THP-1, 20h, 3 µg/ml RTD-1 exp1 THP-1, 20h, 3 µg/ml RTD…
GSM8549058 THP-1, 20h, 3 µg/ml RTD-1 exp2 THP-1, 20h, 3 µg/ml RTD…
GSM8549059 THP-1, 20h, 3 µg/ml RTD-1 exp3 THP-1, 20h, 3 µg/ml RTD…
GSM8549060 THP-1, 20h, 10 µg/ml RTD-1 exp1 THP-1, 20h, 10 µg/ml RT…
GSM8549061 THP-1, 20h, 10 µg/ml RTD-1 exp2 THP-1, 20h, 10 µg/ml RT…
GSM8549062 THP-1, 20h, 10 µg/ml RTD-1 exp3 THP-1, 20h, 10 µg/ml RT…
GSM8549063 THP-1, 20h, LPS exp1 THP-1, 20h, LPS exp
GSM8549064 THP-1, 20h, LPS exp2 THP-1, 20h, LPS exp
GSM8549065 THP-1, 20h, LPS exp3 THP-1, 20h, LPS exp
GSM8549066 THP-1, 20h, 1 µg/ml RTD-1 LPS exp1 THP-1, 20h, 1 µg/ml RTD…
GSM8549067 THP-1, 20h, 1 µg/ml RTD-1 LPS exp2 THP-1, 20h, 1 µg/ml RTD…
GSM8549068 THP-1, 20h, 1 µg/ml RTD-1 LPS exp3 THP-1, 20h, 1 µg/ml RTD…
GSM8549069 THP-1, 20h, 3 µg/ml RTD-1 LPS exp1 THP-1, 20h, 3 µg/ml RTD…
GSM8549070 THP-1, 20h, 3 µg/ml RTD-1 LPS exp2 THP-1, 20h, 3 µg/ml RTD…
GSM8549071 THP-1, 20h, 3 µg/ml RTD-1 LPS exp3 THP-1, 20h, 3 µg/ml RTD…
GSM8549072 THP-1, 20h, 10 µg/ml RTD-1 LPS exp1 THP-1, 20h, 10 µg/ml RT…
GSM8549073 THP-1, 20h, 10 µg/ml RTD-1 LPS exp2 THP-1, 20h, 10 µg/ml RT…
GSM8549074 THP-1, 20h, 10 µg/ml RTD-1 LPS exp3 THP-1, 20h, 10 µg/ml RT…

Datasets on a similar topic

GSE278568 Effect of the rhesus theta defensin-1 (RTD-1) on gene expression in human monocytes. [II] 6 samples shares defensin-1, rtd-1, rhesus, theta
GSE261112 Characterization of human monocytic cell line THP-1 associated with human 3D skin models under UVA exposure 12 samples shares thp-1, monocytic
GSE240644 The role of human endogenous retrovirus (HERV)-K env in THP-1 monocytic cell differentiation 6 samples shares thp-1, monocytic
GSE289760 Epitranscriptomic profiling of m6A RNA modifications in THP-1 monocytic cell line. 2 samples shares thp-1, monocytic
GSE281531 Effect of depletion of MALAT1 on gene expression during LPS stimulation on THP-1 derived differentiated macrophages 24 samples shares thp-1
GSE269185 Effect of decitabine on gene expression in THP-1 or decitabine-resistant THP-1 leukemia cells 8 samples shares thp-1
GSE318527 Effect of CST3 knockout on gene expression in THP-1-derived macrophages 6 samples shares thp-1
GSE270338 Effect of FL-Fc-DM1 drug on gene expression of THP-1 cells pretreated with cytarabine. 4 samples shares thp-1

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