GEO series

Analysis of transcription in peripheral blood mononuclear cells from HIV-infected patients receiving antiretroviral therapy

GSE297198 Homo sapiens (human) RNA-seq (gene expression) 20 samples Submitted 2025/05/21 Platform GPL18460

At a glance

RNA-seq (gene expression) · human · 20 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: 20 samples: 11 × PBMC, before therapy, week 0, sampleGroups 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)

Human immunodeficiency virus is a cause of progressive infection leading to immune dysfunction. Although antiretroviral treatment can normalize the functional state of immune cells by reducing viral load, for some people the immune efficacy of antiretroviral therapy (ART) is insufficient. The aim of this study was to investigate the transcriptomic changes in peripheral blood mononuclear cells (PBMC) of patients receiving ART.

Read the full summary ↓

To evaluate the changes in PBMC, we conducted a clinical trial involving HIV-positive patients on ART. PBMC were collected before starting ART and after 24 weeks of treatment with ART along with estimation of viral load and CD4+ and CD8+ T-lymphocytes count. To evaluate the transcriptional profiles, we used RNA sequencing of isolated PBMC. The results showed two-fold differential expression of 70 genes in PBMC induced by ART and 56 genes prediction an increase in CD4+ lymphocytes after therapy. This information can be helpful for understanding molecular mechanisms of host response to ART.

This dataset

Open GSE297198 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 GSE297198_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 PRJNA1262980 and SRA study SRP585258. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

11 × PBMC, before therapy, week 0, sample

Supports a between-group comparison across 11 samples.

How we read this: 1 replicated groups read from 20 sample titles; they account for 11 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

GSM8985481 PBMC, before therapy, week 0, sample 1 PBMC, before therapy, w…
GSM8985482 PBMC, before therapy, week 0, sample 2 PBMC, before therapy, w…
GSM8985483 PBMC, before therapy, week 0, sample 3 PBMC, before therapy, w…
GSM8985484 PBMC, before therapy, week 0, sample 4 PBMC, before therapy, w…
GSM8985485 PBMC, before therapy, week 0, sample 5 PBMC, before therapy, w…
GSM8985486 PBMC, before therapy, week 0, sample 6 PBMC, before therapy, w…
GSM8985487 PBMC, before therapy, week 0, sample 7 PBMC, before therapy, w…
GSM8985488 PBMC, before therapy, week 0, sample 8 PBMC, before therapy, w…
GSM8985489 PBMC, before therapy, week 0, sample 9 PBMC, before therapy, w…
GSM8985490 PBMC, before therapy, week 0, sample 10 PBMC, before therapy, w…
GSM8985491 PBMC, before therapy, week 0, sample 11 PBMC, before therapy, w…
GSM8985492 PBMC, after therapy, week 24, sample 1_2
GSM8985493 PBMC, after therapy, week 24, sample 2_2
GSM8985494 PBMC, after therapy, week 24, sample 3_2
GSM8985495 PBMC, after therapy, week 24, sample 4_2
GSM8985496 PBMC, after therapy, week 24, sample 5_2
GSM8985497 PBMC, after therapy, week 24, sample 6_2
GSM8985498 PBMC, after therapy, week 24, sample 7_2
GSM8985499 PBMC, after therapy, week 24, sample 8_2
GSM8985500 PBMC, after therapy, week 24, sample 9_2

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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.