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

GSE318861 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 52 samples Submitted 2026/07/01 Platform GPL30173
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 52 samples

What it is
ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism
Homo sapiens (human)
Samples
52 samples: 24 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
Quantitative limits of host-driven HIV transcription and host gene control by the viral transactivator TatNucleic acids research · 2026
Summary (written by the submitters)
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.
Read the full summary ↓
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
Open GSE318861 in finder → Find more human ChIP / ATAC / CUT&Tag 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 GSE318861_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 peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are 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
24 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 +20 more

Supports a between-group comparison across 48 samples.

How we read this: 24 replicated groups read from 52 sample titles; they account for 48 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

+ 12 more — browse all 52 samples with per-sample file links →

Datasets on a similar topic

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