GEO series

HIV-1 m6A methylome investigation by m6A-SAC-seq [CD4+ T cells]

GSE280563 Homo sapiens (human) DNA methylation 12 samples Submitted 2025/05/01 Platform GPL34281

At a glance

DNA methylation · human · 12 samples

What it is: DNA methylationChemical marks on DNA that help switch genes on or off.
Organism: Homo sapiens (human)
Samples: 12 samples: 3 × Primary-activated-CD4-Mock-m6A-SAC-seq-input-rp vs 3 × Primary-activated-CD4-HIV-m6A-SAC-seq-input-rp vs 3 × Primary-activated-CD4-Mock-m6A-SAC-seq-label-rp vs 3 × Primary-activated-CD4-HIV-m6A-SAC-seq-label-rpGroups 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: Single-base m(6)A epitranscriptomics reveals novel HIV-1 host interaction targets in primary CD4(+) T cellsJournal of virology · 2025

Summary (written by the submitters)

N6-methyladenosine (m6A) is the most prevalent cellular mRNA modification and plays an important role in RNA stability, localization, and gene expression. There are several papers reported that HIV-1 infection upregulates cellular RNA m6A in CD4+ T cells, and this upregulation occurs without changes to the expression levels of the cellular enzymes which add or remove m6A.

Read the full summary ↓

However, the mechanism of HIV-1 inducing cellular mRNA m6A upregulation is unknown. Here we show that HIV-1 infection upregulates m6A of cellular mRNA and promotes METTL3/METTL14 interaction. We found that HIV-1 infection resulted in increased cellular mRNA m6A level in activated primary CD4+ T cells detected by m6A dot blot and m6A ELISA. We found that HIV-1 infection of CD4+ T cells promotes METTL3/METTL14 interaction compared to mock control using co-immunoprecipitation (co-IP). Our ongoing studies will determine the transcriptomic, epitranscriptomic, and proteomic profiles of CD4+ T cells infected with HIV-1 for 4 days. These studies will facilitate the elucidation of the mechanisms by which HIV-1 infection leads to increased levels of cellular m6A and methyltransferase writers comlex.

Published in

Single-base m(6)A epitranscriptomics reveals novel HIV-1 host interaction targets in primary CD4(+) T cells

Huang S, Zhao Y, Phillips S et al. · Journal of virology 2025 · PMID 41085277 · doi:10.1128/jvi.01536-25

This dataset

Open GSE280563 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 GSE280563_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: Look for beta-value tables or raw IDAT files among the supplementary files.

Also filed as BioProject PRJNA1179418 and SRA study SRP541802. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41085277) ↗

Study design

3 × Primary-activated-CD4-Mock-m6A-SAC-seq-input-rp vs 3 × Primary-activated-CD4-HIV-m6A-SAC-seq-input-rp vs 3 × Primary-activated-CD4-Mock-m6A-SAC-seq-label-rp vs 3 × Primary-activated-CD4-HIV-m6A-SAC-seq-label-rp

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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

GSM8600778 Primary-activated-CD4-Mock-m6A-SAC-seq-input-rp1 Primary-activated-CD4-M…
GSM8600779 Primary-activated-CD4-Mock-m6A-SAC-seq-input-rp2 Primary-activated-CD4-M…
GSM8600780 Primary-activated-CD4-Mock-m6A-SAC-seq-input-rp3 Primary-activated-CD4-M…
GSM8600781 Primary-activated-CD4-HIV-m6A-SAC-seq-input-rp1 Primary-activated-CD4-H…
GSM8600782 Primary-activated-CD4-HIV-m6A-SAC-seq-input-rp2 Primary-activated-CD4-H…
GSM8600783 Primary-activated-CD4-HIV-m6A-SAC-seq-input-rp3 Primary-activated-CD4-H…
GSM8600784 Primary-activated-CD4-Mock-m6A-SAC-seq-label-rp1 Primary-activated-CD4-M…
GSM8600785 Primary-activated-CD4-Mock-m6A-SAC-seq-label-rp2 Primary-activated-CD4-M…
GSM8600786 Primary-activated-CD4-Mock-m6A-SAC-seq-label-rp3 Primary-activated-CD4-M…
GSM8600787 Primary-activated-CD4-HIV-m6A-SAC-seq-label-rp1 Primary-activated-CD4-H…
GSM8600788 Primary-activated-CD4-HIV-m6A-SAC-seq-label-rp2 Primary-activated-CD4-H…
GSM8600789 Primary-activated-CD4-HIV-m6A-SAC-seq-label-rp3 Primary-activated-CD4-H…

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.