GEO series

HCMV Immediate Early Proteins Promote Lytic Infection and Reactivation in Monocytes

GSE307171 Homo sapiens (human) RNA-seq (gene expression) 34 samples Submitted 2026/05/12 Platform GPL34281

At a glance

RNA-seq (gene expression) · human · 34 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: 34 samples: 15 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: Parsing the functions of immediate-early proteins in the lytic-latent balance of HCMV infectionProceedings of the National Academy of Sciences of the United States of America · 2026

Summary (written by the submitters)

Human cytomegalovirus (HCMV) is a prevalent pathogen of the herpesvirus family, infecting most of the human population worldwide. Like all herpesviruses, HCMV can establish a latent infection that persists throughout the lifetime of the host. The HCMV immediate early (IE) proteins, IE1 and IE2, are viewed as master regulators of HCMV infection and are commonly assumed to play pivotal roles in regulating the balance between latent and lytic infection, as their repression is a hallmark of latency.

Read the full summary ↓

However, it is still unclear whether their expression can indeed determine the establishment of productive infection and what are the functions, either related to viral gene expression or to cellular pathways, involved in this activity. Using THP1 monocytes, ectopically expressing the HCMV receptor, PDGFRα to boost viral entry, we show that overexpression of either IE1 or IE2 significantly enhances productive infection, illustrating their critical role in determining infection outcome. Mechanistically, IE2 drives expression of the viral early genes at early stages of infection, whereas IE1 acts more broadly to enhance global viral gene expression. We further show that from the many functions of IE1, its ability to promote lytic infection is mainly linked to disruption of PML nuclear bodies. Importantly, induction of either IE1 or IE2 expression in latently infected cells enhances viral reactivation, with IE1-mediated PML representing a central mechanism. Taken together, our findings elucidate the distinct and complementary roles of IE1 and IE2 in overcoming barriers to productive infection and reactivation.

Published in

Parsing the functions of immediate-early proteins in the lytic-latent balance of HCMV infection

Kitsberg Y, Nachshon A, Brandis A et al. · Proceedings of the National Academy of Sciences of the United States of America 2026 · PMID 42213753 · doi:10.1073/pnas.2536082123

This dataset

Open GSE307171 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 GSE307171_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 PRJNA1314688 and SRA study SRP616888. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42213753) ↗

Study design

15 conditions, mostly in duplicate

I8_KO_mCherry ×3 I8_KO_IE1 ×3 PML_KO_mCherry ×3 PML_KO_IE1 ×3 IE1_0hpi ×2 IE2_0hpi ×2 mCherry_0hpi ×2 IE1_0hpi_noDox ×2 +7 more

Supports a between-group comparison across 34 samples.

How we read this: 15 replicated groups read from 34 sample titles; they account for 34 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

GSM9217644 IE1_0hpi_1 IE1_0hpi
GSM9217645 IE1_0hpi_2 IE1_0hpi
GSM9217646 IE2_0hpi_1 IE2_0hpi
GSM9217647 IE2_0hpi_2 IE2_0hpi
GSM9217648 mCherry_0hpi_1 mCherry_0hpi
GSM9217649 mCherry_0hpi_2 mCherry_0hpi
GSM9217650 IE1_0hpi_noDox_1 IE1_0hpi_noDox
GSM9217651 IE1_0hpi_noDox_2 IE1_0hpi_noDox
GSM9217652 IE2_0hpi_noDox_1 IE2_0hpi_noDox
GSM9217653 IE2_0hpi_noDox_2 IE2_0hpi_noDox
GSM9217654 mCherry_0hpi_noDox_1 mCherry_0hpi_noDox
GSM9217655 mCherry_0hpi_noDox_2 mCherry_0hpi_noDox
GSM9217656 IE1_12hpi_1 IE1_12hpi
GSM9217657 IE1_12hpi_2 IE1_12hpi
GSM9217658 IE2_12hpi_1 IE2_12hpi
GSM9217659 IE2_12hpi_2 IE2_12hpi
GSM9217660 mCherry_12hpi_1 mCherry_12hpi
GSM9217661 mCherry_12hpi_2 mCherry_12hpi
GSM9217662 IE1_1 IE1
GSM9217663 IE1_2 IE1
GSM9217664 IE1_STAT_1 IE1_STAT
GSM9217665 IE1_STAT_2 IE1_STAT
GSM9597437 I8_KO_mCherry_1 I8_KO_mCherry
GSM9597438 I8_KO_mCherry_2 I8_KO_mCherry
GSM9597439 I8_KO_mCherry_3 I8_KO_mCherry
GSM9597440 I8_KO_IE1_1 I8_KO_IE1
GSM9597441 I8_KO_IE1_2 I8_KO_IE1
GSM9597442 I8_KO_IE1_3 I8_KO_IE1
GSM9597443 PML_KO_mCherry_1 PML_KO_mCherry
GSM9597444 PML_KO_mCherry_2 PML_KO_mCherry
GSM9597445 PML_KO_mCherry_3 PML_KO_mCherry
GSM9597446 PML_KO_IE1_1 PML_KO_IE1
GSM9597447 PML_KO_IE1_2 PML_KO_IE1
GSM9597448 PML_KO_IE1_3 PML_KO_IE1

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