GEO series

Quantitative analysis of Tat-dependent and host-driven HIV transcription by ChIP-seq and RNA-seq

GSE318861 Homo sapiens Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing 52 samples Submitted 2026/07/01 Platform GPL30173

Summary

HIV transcription is initiated by host transcriptional machinery prior to the production of the viral transactivator Tat, yet the magnitude and regulatory features of this Tat-independent transcriptional state remain poorly defined. In this study, we performed integrated chromatin and transcriptional profiling to quantitatively compare Tat-dependent and host-driven regulation of HIV and cellular gene expression. Jurkat T cells were infected with isogenic HIV constructs expressing functional Tat (TatWT) or lacking Tat expression (TatNull) and analyzed under non-stimulated and stimulated conditions. Genome-wide chromatin occupancy of Tat and transcriptional machinery was measured by ChIP-seq, and corresponding transcriptional output from both the HIV provirus and host genome was quantified by RNA sequencing. These datasets define the baseline host-driven transcriptional state of HIV in the absence of Tat and enable direct comparison with Tat-amplified transcriptional responses. Together, this integrated ChIP-seq and RNA-seq resource provides a quantitative framework for dissecting Tat-dependent and Tat-independent mechanisms of HIV transcriptional regulation in chromatin.

Published in

Quantitative limits of host-driven HIV transcription and host gene control by the viral transactivator Tat

Li C, Ma Y, Wang Y et al. · Nucleic acids research 2026 · PMID 42328785 · doi:10.1093/nar/gkag631

This dataset

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Download

Direct links to NCBI, no account and no request form: the whole study as GSE318861_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 52 samples. Raw sequencing reads are also available from ENA.

Whole study · RAW.tar ↓ Series matrix ↓ All supplementary files ↗ Raw reads on ENA ↗

Also filed as BioProject PRJNA1420730 and SRA study SRP675717. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42328785) ↗

Study design

18 conditions, mostly in duplicate

TatWT_Tat-ChIP ×2 TatWT+Stim_Tat-ChIP ×2 TatNull_Tat-ChIP ×2 TatNull+Stim_TatChIP ×2 TatWT_RNAPII-Ser2p-ChIP ×2 TatWT+Stim_RNAPII-Ser2p-ChIP ×2 TatNull_RNAPII-Ser2p-ChIP ×2 TatNull+Stim_RNAPII-Ser2p-ChIP ×2 +14 more

Supports a between-group comparison across 36 samples.

18 replicated groups read from the first 40 of 52 sample titles; they account for 36 of them. Check it against the sample list below before relying on it.

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