Persistent pneumococcal colonisation in anti-retroviral-treated HIV infection is associated with nasal inflammation
Single-cell RNA-seq · human · 11 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
- Organism
- Homo sapiens (human)
- Samples
- 11 samples: 11 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.
- Paper
- Persistent pneumococcal colonisation in antiretroviral-treated HIV infection is associated with nasal inflammationNature communications · 2025
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE296893_RAW.tar (it can run to tens of gigabytes).
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.
What the files usually look like: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA1261889 and SRA study SRP584763. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 11 sample titles: 11 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.
- GSM8979537 CFU131 Nasal cells HIV uninfected
- GSM8979538 CUF136 Nasal cells HIV uninfected
- GSM8979539 CUF137 Nasal cells HIV uninfected
- GSM8979540 CFU134 Nasal cells HIV infected, ART less than 3 months
- GSM8979541 CUF13J Nasal cells HIV infected, ART less than 3 months
- GSM8979542 CUF13K Nasal cells HIV infected, ART less than 3 months
- GSM8979543 CFU130 Nasal cells HIV infected, ART greater than 1 year
- GSM8979544 CUF135 Nasal cells HIV infected, ART greater than 1 year
- GSM8979545 CUF13I Nasal cells HIV infected, ART greater than 1 year
- GSM8979546 CUG11X Nasal cells HIV infected, ART greater than 1 year
- GSM8979547 CUH124 Nasal cells HIV infected, ART greater than 1 year
- GSE273967 Loss of CD4 T cell responses to prior vaccines associate with inflammation and altered transcriptional signatures in HIV infection 174 samples shares hiv
- GSE287060 Biomarkers that prospectively predict HIV-1 infection in high risk adults 146 samples shares hiv
- GSE271442 CD16 and CD57 Expressing Gamma Delta T Cells in Acute HIV-1 Infection are Associated with the Development of Neutralization Breadth 82 samples shares hiv
- GSE332837 Single-cell sequencing reveals NK cell dysregulation during chronic HIV infection and identifies transitional NK cell cytotoxicity related to HIV reservoir decay 39 samples shares hiv
- GSE329693 Microbiome-Derived Metabolites Shape CD4⁺ T-Cell Differentiation and Immune Aging in Chronic HIV-1 Infection [RNA-Seq] 36 samples shares hiv
- GSE253769 Autophagy-enhancing ATG16L1 polymorphism improves clinical outcomes and promotes superior T-cell immunity in chronic HIV-1 infection 32 samples shares hiv
- GSE319583 TRIMs in the placental tissue of HIV-1 infection 32 samples shares hiv
- GSE248997 Stem Cell-derived Microglia Exhibit HAND Gene Expression Signature Early Upon Infection with HIV-1 [iPSCMG] 23 samples shares hiv
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.