GEO series
Essential function of the integrator complex in Kaposi's sarcoma-associated herpesvirus lytic replication
GSE300543
Homo sapiens (human)
RNA-seq (gene expression)
16 samples
Submitted 2025/06/25
Platform GPL34281
At a glance
RNA-seq (gene expression) · human · 16 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
- 16 samples: 8 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
- Essential function of the integrator complex in Kaposi's sarcoma-associated herpesvirus lytic replicationJournal of virology · 2025
Summary (written by the submitters)
The integrator complex (INT) is an essential regulator of RNA biogenesis across evolution. Most current findings describe INT's function in states of equilibrium, presenting a research gap in INT's role in dynamic states, such as in infections and cancers. Viruses hijack cellular RNA machinery to transcribe their genes and produce viral progeny, presenting a unique condition to investigate INT-dependent RNA regulation under perturbation.
Read the full summary ↓
Kaposi's sarcoma-associated herpesvirus (KSHV) is an oncogenic DNA virus that causes two deadly cancers, Kaposi's sarcoma and primary effusion lymphoma. KSHV undergoes a highly regulated and robust transcription of viral genes upon lytic reactivation, providing a complex and dynamic system to investigate integrator-mediated viral/host RNA regulation. We find that integrator subunit 11 (INTS11), the enzymatic core of INT, is essential for KSHV lytic replication triggered by reactivation or primary infection. Further RNA-seq analyses revealed a dynamic and unique signature of human transcriptomes during each lytic stage, respectively. Although the knockdown of INTS11 resulted in selective upregulation and downregulation of certain human gene transcription, INTS11's loss globally repressed the KSHV transcriptome throughout KSHV lytic replication. This inhibited viral lytic gene expression, viral genome replication, and virion production. Integrator subunits 9 and 6 are also important for KSHV lytic replication. Mechanistically, ChIP-seq analysis showed that INTS11 is increasingly recruited to the KSHV genome with some unique binding patterns as the lytic cycle progresses, suggesting that KSHV hijacks INTS11 during lytic gene transcriptions. In all, our findings reveal the essential roles of the Integrator complex in KSHV lytic replication.IMPORTANCEThe integrator complex (INT) is essential for RNA metabolism and is fundamental to all organisms, but its function and regulation during viral infection are not well described. Kaposi's sarcoma-associated herpesvirus (KSHV) infection establishes lifelong infection and causes two deadly cancers; however, no vaccine is available. Using KSHV as a model, we found that integrator subunit 11 (INTS11), the enzymatic core of INT, is recruited to the KSHV genome under lytic phases and plays an essential role in facilitating global KSHV lytic mRNA transcription and viral production. This reveals the critical role of INT in viral infection, a common and inevitable event in human life.
Published in
Nguyen A, Li T, Traugot C et al.
· Journal of virology 2025
· PMID 40801543
· doi:10.1128/jvi.00266-25
This dataset
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.
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 GSE300543_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1281142 and SRA study SRP594108. Searching any of these in the dataset finder brings you back here.
Study design
8 conditions, mostly in duplicate
INTS11 knockdown RNA-seq, scramble, 0h, ×2
INTS11 knockdown RNA-seq, KD, 0h, ×2
INTS11 knockdown RNA-seq, scramble, 24h, ×2
INTS11 knockdown RNA-seq, KD, 24h, ×2
INTS11 knockdown RNA-seq, scramble, 48h, ×2
INTS11 knockdown RNA-seq, KD, 48h, ×2
INTS11 knockdown RNA-seq, scramble, 72h, ×2
INTS11 knockdown RNA-seq, KD, 72h, ×2
Supports a between-group comparison across 16 samples.
How we read this: 8 replicated groups read from 16 sample titles; they account for 16 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
- GSM9064269 INTS11 knockdown RNA-seq, scramble, 0h, rep1 INTS11 knockdown RNA-se…
- GSM9064270 INTS11 knockdown RNA-seq, scramble, 0h, rep2 INTS11 knockdown RNA-se…
- GSM9064271 INTS11 knockdown RNA-seq, KD, 0h, rep1 INTS11 knockdown RNA-se…
- GSM9064272 INTS11 knockdown RNA-seq, KD, 0h, rep2 INTS11 knockdown RNA-se…
- GSM9064273 INTS11 knockdown RNA-seq, scramble, 24h, rep1 INTS11 knockdown RNA-se…
- GSM9064274 INTS11 knockdown RNA-seq, scramble, 24h, rep2 INTS11 knockdown RNA-se…
- GSM9064275 INTS11 knockdown RNA-seq, KD, 24h, rep1 INTS11 knockdown RNA-se…
- GSM9064276 INTS11 knockdown RNA-seq, KD, 24h, rep2 INTS11 knockdown RNA-se…
- GSM9064277 INTS11 knockdown RNA-seq, scramble, 48h, rep1 INTS11 knockdown RNA-se…
- GSM9064278 INTS11 knockdown RNA-seq, scramble, 48h, rep2 INTS11 knockdown RNA-se…
- GSM9064279 INTS11 knockdown RNA-seq, KD, 48h, rep1 INTS11 knockdown RNA-se…
- GSM9064280 INTS11 knockdown RNA-seq, KD, 48h, rep2 INTS11 knockdown RNA-se…
- GSM9064281 INTS11 knockdown RNA-seq, scramble, 72h, rep1 INTS11 knockdown RNA-se…
- GSM9064282 INTS11 knockdown RNA-seq, scramble, 72h, rep2 INTS11 knockdown RNA-se…
- GSM9064283 INTS11 knockdown RNA-seq, KD, 72h, rep1 INTS11 knockdown RNA-se…
- GSM9064284 INTS11 knockdown RNA-seq, KD, 72h, rep2 INTS11 knockdown RNA-se…
Datasets on a similar topic
- GSE300544 The Integrator complex is required for optimal lytic lifecycle of Kaposi’s Sarcoma-Associated Herpesvirus [ChIP-seq] 16 samples shares sarcoma-associated, herpesvirus, integrator, complex, kaposi, lytic
- GSE293213 A viral circular RNA in Kaposi’s sarcoma-associated herpesvirus contributes to viral and host gene expression during latent and lytic replication 10 samples shares sarcoma-associated, herpesvirus, replication, kaposi, lytic
- GSE276747 Integrator complex subunit 12 knockout overcomes a transcriptional block to HIV latency reversal [RNA-seq] 18 samples shares integrator, complex
- GSE267104 Disruption of the Integrator complex triggers the Integrated Stress Response through formation of double-stranded RNA [RNAseq] 17 samples shares integrator, complex
- GSE291919 ORCA-mediated Polycomb Repressive Complex stabilization maintains 3D-genome architecture and controls replication timing 12 samples shares replication, complex
- GSE342072 Cytoplasmic ATM restricts oncolytic VSVΔ51 replication by sustaining TBK1-IRF3 signaling in glioblastoma cells 12 samples shares replication, lytic
- GSE250431 High-density resolution of the Kaposi’s Sarcoma associated Herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicing [KSHV_TRIMD_Ritu_Illumina] 4 samples shares herpesvirus, kaposi
- GSE276856 Selective interactions at pre-replication complexes categorize baseline and dormant origins 211 samples shares replication, complex
Share this dataset
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.