GEO series

Bulk RNA-seq analysis of Delta-like 4 (Dll4) knockdown in LPS- or TNF-α-stimulated THP-1 cells

GSE327277 Homo sapiens (human) RNA-seq (gene expression) 20 samples Submitted 2026/07/02 Platform GPL21697

At a glance

RNA-seq (gene expression) · human · 20 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: 20 samples: 5 × THP-1 cells, control siRNA, LPS, 24 h, vs 5 × THP-1 cells, Dll4 siRNA, LPS, 24 h, vs 5 × THP-1 cells, control siRNA, TNF-α, 24 h, vs 5 × THP-1 cells, Dll4 siRNA, TNF-α, 24 h,Groups 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: Monocyte Dll4 Contributes to Systemic Inflammation in People Living With HIVCirculation research · 2026

Summary (written by the submitters)

Monocyte-mediated inflammation, rather than T cell activation, is a major cause of chronic inflammation. Here, we investigated the contribution of delta-like 4 (Dll4)-Notch signaling in monocyte-mediated inflammation. To investigate the biological functions and molecular mechanisms of monocyte Dll4, bulk RNA sequencing (RNA-seq) was performed in THP-1 cells transfected with Dll4 siRNA or control siRNA for 24 hours in the presence of LPS or TNF-α stimulation.

Read the full summary ↓

Four experimental groups were analyzed: control siRNA + LPS, Dll4 siRNA + LPS, control siRNA + TNF-α, and Dll4 siRNA + TNF-α. Each group included five biological replicates (n=5 per group). The RNA-seq analysis was designed as a discovery experiment powered to detect moderate-to-large expression differences.

Published in

Monocyte Dll4 Contributes to Systemic Inflammation in People Living With HIV

Wang S, Singh MV, Morrell CN et al. · Circulation research 2026 · PMID 42283084 · doi:10.1161/CIRCRESAHA.125.326836

This dataset

Open GSE327277 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 GSE327277_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 PRJNA1450105 and SRA study SRP689940. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42283084) ↗

Study design

5 × THP-1 cells, control siRNA, LPS, 24 h, vs 5 × THP-1 cells, Dll4 siRNA, LPS, 24 h, vs 5 × THP-1 cells, control siRNA, TNF-α, 24 h, vs 5 × THP-1 cells, Dll4 siRNA, TNF-α, 24 h,

Supports a between-group comparison across 20 samples.

How we read this: 4 replicated groups read from 20 sample titles; they account for 20 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

GSM9652681 THP-1 cells, control siRNA, LPS, 24 h, biological replicate 1 THP-1 cells, control si…
GSM9652682 THP-1 cells, control siRNA, LPS, 24 h, biological replicate 2 THP-1 cells, control si…
GSM9652683 THP-1 cells, control siRNA, LPS, 24 h, biological replicate 3 THP-1 cells, control si…
GSM9652684 THP-1 cells, control siRNA, LPS, 24 h, biological replicate 4 THP-1 cells, control si…
GSM9652685 THP-1 cells, control siRNA, LPS, 24 h, biological replicate 5 THP-1 cells, control si…
GSM9652686 THP-1 cells, Dll4 siRNA, LPS, 24 h, biological replicate 1 THP-1 cells, Dll4 siRNA…
GSM9652687 THP-1 cells, Dll4 siRNA, LPS, 24 h, biological replicate 2 THP-1 cells, Dll4 siRNA…
GSM9652688 THP-1 cells, Dll4 siRNA, LPS, 24 h, biological replicate 3 THP-1 cells, Dll4 siRNA…
GSM9652689 THP-1 cells, Dll4 siRNA, LPS, 24 h, biological replicate 4 THP-1 cells, Dll4 siRNA…
GSM9652690 THP-1 cells, Dll4 siRNA, LPS, 24 h, biological replicate 5 THP-1 cells, Dll4 siRNA…
GSM9652691 THP-1 cells, control siRNA, TNF-α, 24 h, biological replicate 1 THP-1 cells, control si…
GSM9652692 THP-1 cells, control siRNA, TNF-α, 24 h, biological replicate 2 THP-1 cells, control si…
GSM9652693 THP-1 cells, control siRNA, TNF-α, 24 h, biological replicate 3 THP-1 cells, control si…
GSM9652694 THP-1 cells, control siRNA, TNF-α, 24 h, biological replicate 4 THP-1 cells, control si…
GSM9652695 THP-1 cells, control siRNA, TNF-α, 24 h, biological replicate 5 THP-1 cells, control si…
GSM9652696 THP-1 cells, Dll4 siRNA, TNF-α, 24 h, biological replicate 1 THP-1 cells, Dll4 siRNA…
GSM9652697 THP-1 cells, Dll4 siRNA, TNF-α, 24 h, biological replicate 2 THP-1 cells, Dll4 siRNA…
GSM9652698 THP-1 cells, Dll4 siRNA, TNF-α, 24 h, biological replicate 3 THP-1 cells, Dll4 siRNA…
GSM9652699 THP-1 cells, Dll4 siRNA, TNF-α, 24 h, biological replicate 4 THP-1 cells, Dll4 siRNA…
GSM9652700 THP-1 cells, Dll4 siRNA, TNF-α, 24 h, biological replicate 5 THP-1 cells, Dll4 siRNA…

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