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Transcriptome profiling of B-cell lymphoma cells with pharmacological inhibition of KDM5A/B by using the inhibitor JQKD82

GSE310839 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2026/03/10 Platform GPL34284
At a glance

RNA-seq (gene expression) · human · 12 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
12 samples: 3 × BCBL-1 cells, control treatment, repeat vs 3 × BCBL-1 cells, 20µM drug treatment, repeat vs 3 × BJAB cells, control treatment, repeat vs 3 × BJAB cells, 20µM drug treatment, repeatGroups 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
Inhibition of KDM5A/B promotes antitumor innate immune responses in HHV-8/KSHV-positive B-cell lymphomasbioRxiv : the preprint server for biology · 2026
Summary (written by the submitters)
Histone methylation critically controls the progression of human diseases, including infections and cancers. Our study reported that histone lysine demethylases (KDMs) in the KDM5 family KDM5A/B play profound roles in suppressing lytic reactivation of oncogenic human herpesvirus 8 (HHV-8), i.e., Kaposi's sarcoma-associated herpesvirus (KSHV), a human gamma-herpesvirus and an etiological agent of multiple malignancies.
Read the full summary ↓
During KSHV lytic reactivation from latency, host innate immune responses are also activated, which is expected to favor the tumor cell killing by generating the additional oncolytic effects. To further study the systemic effect of KSHV on host immune response under the regulation of KDM5A/B, we performed the transcriptome profiling analysis for both KSHV-infected BCBL-1 vs KSHV-negative BJAB cells with or without JQKD82 treatment by RNA-seq. Our RNA-seq analysis and further experimental validation suggested that the KDM5 inhibitor JQKD82 is capable of inducing antiviral/antitumor innate immune responses in KSHV-negative B-cell lymphomas, but such effects are more striking in KSHV-positive B-cell lymphomas likely due to KSHV lytic reactivation that further triggers the innate immune activation in tumor cells.
Published in
Inhibition of KDM5A/B promotes antitumor innate immune responses in HHV-8/KSHV-positive B-cell lymphomas
Zhou D, Fiches GN, Wu Z et al. · bioRxiv : the preprint server for biology 2026 · PMID 41659624 · doi:10.64898/2026.01.28.702275
This dataset
Open GSE310839 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 GSE310839_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 PRJNA1367136 and SRA study SRP647357. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41659624) ↗
Study design
3 × BCBL-1 cells, control treatment, repeat vs 3 × BCBL-1 cells, 20µM drug treatment, repeat vs 3 × BJAB cells, control treatment, repeat vs 3 × BJAB cells, 20µM drug treatment, repeat

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
Datasets on a similar topic

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