GEO series

Integrated Transcriptomic Profiling of Rectal and Adipose HIV-1 Reservoirs Relative to Matched PBMCs in ART-Treated Individuals

GSE336629 Homo sapiens (human) RNA-seq (gene expression) 14 samples Submitted 2026/06/25 Platform GPL29480

At a glance

RNA-seq (gene expression) · human · 14 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: 14 samples: 14 samples, each with a distinct title — no replicated groupsGroups 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)

HIV-1 persistence in anatomical reservoirs remains a major obstacle to a functional cure under suppressive antiretroviral therapy. This study used bulk RNA-seq to characterize host transcriptomic features across matched peripheral blood mononuclear cells (PBMCs), rectal tissue, and subcutaneous adipose tissue (SAT) from ART-treated people with HIV. Transcriptomic profiling revealed tissue-specific remodeling in rectal and adipose reservoirs relative to matched PBMCs, including extracellular matrix remodeling, immunometabolic alterations, and shared PI3K-Akt-related transcriptional features.

This dataset

Open GSE336629 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 GSE336629_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 PRJNA1482132 and SRA study SRP712673. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

14 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 14 sample titles: 14 distinct titles with little repetition. 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

GSM9838989 PBMC RNA-seq sample 048P from ART-treated PWH donor 048
GSM9838990 Rectal tissue RNA-seq sample 048R from ART-treated PWH donor 048
GSM9838991 PBMC RNA-seq sample 084P from ART-treated PWH donor 084
GSM9838992 Rectal tissue RNA-seq sample 084R from ART-treated PWH donor 084
GSM9838993 PBMC RNA-seq sample 092P from ART-treated PWH donor 092
GSM9838994 Rectal tissue RNA-seq sample 092R from ART-treated PWH donor 092
GSM9838995 PBMC RNA-seq sample 095P from ART-treated PWH donor 095
GSM9838996 Subcutaneous adipose tissue RNA-seq sample 095S from ART-treated PWH donor 095
GSM9838997 PBMC RNA-seq sample 097P from ART-treated PWH donor 097
GSM9838998 Subcutaneous adipose tissue RNA-seq sample 097S from ART-treated PWH donor 097
GSM9838999 PBMC RNA-seq sample 104P from ART-treated PWH donor 104
GSM9839000 Subcutaneous adipose tissue RNA-seq sample 104S from ART-treated PWH donor 104
GSM9839001 PBMC RNA-seq sample 111P from ART-treated PWH donor 111
GSM9839002 Rectal tissue RNA-seq sample 111R from ART-treated PWH donor 111

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Search all human RNA-seq datasets in GEO →

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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.