Transcription of HIV-1 at sites of intact latent provirus integration [scRNA-seq]
Single-cell RNA-seq · human · 10 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
- Organism
- Homo sapiens (human)
- Samples
- 10 samples: 10 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
- Transcription of HIV-1 at sites of intact latent provirus integrationThe Journal of experimental medicine · 2024
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 GSE267988_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 PRJNA1114000 and SRA study SRP508970. 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 10 sample titles: 10 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.
- GSM8283384 Participant 5104 10x RNA Replicate1 - Activated
- GSM8283385 Participant 5104 10x VDJ Replicate1 - Activated
- GSM8283386 Participant 5104 10x RNA Replicate1 - Resting
- GSM8283387 Participant 5104 10x VDJ Replicate1 - Resting
- GSM8283388 Participant 603 10x RNA Replicate1 - Activated
- GSM8283389 Participant 603 10x VDJ Replicate1 - Activated
- GSM8283390 Participant 603 10x RNA Replicate1 - Resting
- GSM8283391 Participant 603 10x VDJ Replicate1 - Resting
- GSM8283392 Participant 603 10x RNA Replicate2 - Resting
- GSM8283393 Participant 603 10x VDJ Replicate2 - Resting
- GSE279688 The role of LEDGF in transcription is exploited by HIV-1 to position integration 56 samples shares hiv-1, transcription, integration
- GSE299348 Single-cell epigenetic, transcriptional, protein, and TCR states of HIV-1-infected cells in gut 117 samples shares hiv-1, transcription
- GSE189357 Spatiotemporal transcriptional atlas of lung adenocarcinoma from adenocarcinoma in situ to invasive carcinoma [scRNA-seq] 9 samples shares transcription, scrna-seq
- GSE239858 BRCA2 suppresses “head-on” transcription-replication conflicts incurred by dormant origin firing at transcription termination sites 14 samples shares transcription, sites
- GSE314310 Cardiopedia-Ligand: a Ligand Stimulation Atlas for Cardiac Function and Transcriptional Response 468 samples shares transcription
- GSE309595 Longitudinal Analysis of Multiple Myeloma: Therapeutic Response and Immune Microenvironment Dynamics in the Context of Tumor Heterogeneity [scRNA-seq] 270 samples shares scrna-seq
- GSE271676 Spatial Transcriptional Landscape of Human Heart Failure 178 samples shares transcription
- GSE251778 Sex-specific and multiomic integration enhance accuracy of peripheral blood biomarkers of major depressive disorder [RNA-Seq] 169 samples shares integration
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.