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The impact of Tat expression on the host transcriptome landscape as the cells transit through the successive phases of the latency cycle

GSE309785 Homo sapiens (human) RNA-seq (gene expression) 15 samples Submitted 2025/11/20 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 15 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
15 samples: 5 conditions, mostly in triplicateGroups 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.
Summary (written by the submitters)
We hypothesized that Tat may exert opposing effects on viral gene expression depending on its PTMs. Furthermore, we propose that Tat can actively regulate the expression of host factors responsible for these PTMs, thereby influencing the establishment of latency. To investigate this, we define a latency cycle, capturing the distinct stages of cellular transition through the OFF-ON-OFF phases of viral gene expression.
Read the full summary ↓
Jurkat cells were infected with a dual-reporter viral construct co-expressing a short-lived d2EGFP and a long-lived mScarlet fluorescent protein fused to Tat. The extended half-life of the Tat-mScarlet fusion enabled us to track and stabilize Tat expression even during the LTR-OFF state, providing a means to assess differential host gene expression. In the defined latency cycle, prior to stimulation, infected cells were dual-negative for both reporters (DN: GFP⁻ RFP⁻), indicative of a latent state. Upon activation of the LTR, cells transitioned to a dual-positive phase (DP: GFP⁺ RFP⁺), followed by a single-positive phase (SP: GFP⁻ RFP⁺), and eventually returned to the DN phase. These subsets correspond to distinct stages in the latency cycle: latent, transcriptionally active, early latent, and latent, respectively. We developed a doxycycline-inducible system to selectively activate the viral LTR, without stimulating the host cells. Upon doxycycline treatment, diTat is expressed, providing a controlled, pulse-like activation of the viral LTR and enabling the establishment of a latency cycle. The distinct phases of the latency cycle were sorted, and a transcriptomic analysis was conducted.
This dataset
Open GSE309785 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 GSE309785_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 PRJNA1363170 and SRA study SRP644299. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
5 conditions, mostly in triplicate
Control (Jurkat cells expressing rtTA3) ×3 Control (Jurkat cells expressing Tet-ON-Tat) ×3 Latent phase ×3 Active phase ×3 Early latent phase ×3

Supports a between-group comparison across 15 samples.

How we read this: 5 replicated groups read from 15 sample titles; they account for 15 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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