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Comparative analysis of the cell transcriptome of primary B lymphocytes infected with the Epstein-Barr virus (EBV), its EBNA2 or EBNALP KO derivatives, or activated by CD40L and IL4 at 48 hours post-infection or treatment.

GSE284674 Homo sapiens (human) RNA-seq (gene expression) 25 samples Submitted 2025/07/09 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 25 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
25 samples: 7 conditions, mostly with about 4 replicates eachGroups 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
Alternative splicing in the RBMXL1 5'-UTR induces uORF-mediated translation control in activated B lymphocytesScientific reports · 2025
Summary (written by the submitters)
Epstein-Barr virus (EBV) is a human herpesvirus that has been associated with the development of human cancers across the globe. In laboratory settings, the virus efficiently infects resting human B lymphocytes, inducing their growth transformation and leading to the establishment of lymphoblastoid cell lines (LCLs) within a few weeks.
Read the full summary ↓
This process is accompanied by a global reprogramming of cellular gene transcription. A systematic time-resolved analysis of cellular mRNA splice variant expression during EBV infection of resting B lymphocytes has previously been performed. The results demonstrated that significant alterations in alternative splice variant expression occur as early as day 1 post-infection, indicating that splicing regulation, in addition to transcription, represents an additional mechanism of gene expression regulation at the onset of B cell activation and proliferation. The present study had two principal objectives. The first was to identify which transcriptional and splice events are specific to the EBV infection, in comparison to the activation of primary B lymphocytes by a combination of CD40 ligand (CD40L) and interleukin 4 (IL4). The second was to ascertain which events are dependent on the EBNA2 and EBNALP viral factors. In order to achieve these objectives, a comparative RNA-seq analysis of the transcriptome of the infected cells or those treated with CD40L/IL4, as well as LCLs derived from the wild-type and EBNALP KO EBV-infected cells, was conducted.
Published in
Alternative splicing in the RBMXL1 5'-UTR induces uORF-mediated translation control in activated B lymphocytes
de Breyne S, Polvèche H, Auboeuf D et al. · Scientific reports 2025 · PMID 40595907 · doi:10.1038/s41598-025-03274-3
This dataset
Open GSE284674 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 GSE284674_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 PRJNA1200025 and SRA study SRP552544. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40595907) ↗
Study design
7 conditions, mostly with about 4 replicates each
Bact_CD40L_IL4_48h ×4 Binf_EBV_dEBNA2_48h ×4 Binf_EBV_dEBNALP_48h ×4 Binf_EBV_WT_48h ×4 Bprim ×4 LCLinf_EBV_WT ×3 LCLinf_EBV_dEBNALP ×2

Supports a between-group comparison across 25 samples.

How we read this: 7 replicated groups read from 25 sample titles; they account for 25 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
Datasets on a similar topic

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