Single cell RNA seq of Healthy, covid-19 infected, recovered and long recovered individuals.
Single-cell RNA-seq · human · 57 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
- 57 samples: 57 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
- Intracellular microbial shifts during COVID-19 infection and longitudinal recovery revealed by single-cell RNA sequencingiScience · 2026
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 GSE303208_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 PRJNA1293800 and SRA study SRP602226. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 24 samples read as cases, 9 as controls.
How we read this: Read from 57 sample titles: 57 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.
- GSM9120529 Single cell RNA Seq of Infected Individual b01st01 Sample
- GSM9120530 Single cell RNA Seq of Infected Individual b01st02 Sample
- GSM9120531 Single cell RNA Seq of Infected Individual b01st03 Sample
- GSM9120532 Single cell RNA Seq of Infected Individual b02st04 Sample
- GSM9120533 Single cell RNA Seq of Infected Individual b02st05 Sample
- GSM9120534 Single cell RNA Seq of Infected Individual b02st06 Sample
- GSM9120535 Single cell RNA Seq of Infected Individual b02st07 Sample
- GSM9120536 Single cell RNA Seq of Infected Individual b03st08 Sample
- GSM9120537 Single cell RNA Seq of Infected Individual b03st09 Sample
- GSM9120538 Single cell RNA Seq of Infected Individual b03st10 Sample
- GSM9120539 Single cell RNA Seq of Infected Individual b03st11 Sample
- GSM9120540 Single cell RNA Seq of Infected Individual b04st12 Sample
- GSM9120541 Single cell RNA Seq of Infected Individual b04st01 Sample
- GSM9120542 Single cell RNA Seq of Infected Individual b04st02 Sample
- GSM9120543 Single cell RNA Seq of Infected Individual b04st03 Sample
- GSM9120544 Single cell RNA Seq of Infected Individual b05st04 Sample
- GSM9120545 Single cell RNA Seq of Recovered Individual b05st05 Sample
- GSM9120546 Single cell RNA Seq of Infected Individual b05st06 Sample
- GSM9120547 Single cell RNA Seq of Recovered Individual b05st07 Sample
- GSM9120548 Single cell RNA Seq of Infected Individual b06st08 Sample
- GSM9120549 Single cell RNA Seq of Recovered Individual b06st09 Sample
- GSM9120550 Single cell RNA Seq of Infected Individual b06st10 Sample
- GSM9120551 Single cell RNA Seq of Recovered Individual b06st11 Sample
- GSM9120552 Single cell RNA Seq of Infected Individual b07st12 Sample
- GSM9120553 Single cell RNA Seq of Infected Individual b07st01 Sample
- GSM9120554 Single cell RNA Seq of Recovered Individual b07st03 Sample
- GSM9120555 Single cell RNA Seq of Longitudinal Recovered Individual b08st04 Sample
- GSM9120556 Single cell RNA Seq of Infected Individual b08st05 Sample
- GSM9120557 Single cell RNA Seq of Infected Individual b08st06 Sample
- GSM9120558 Single cell RNA Seq of Healthy Individual b08st07 Sample
- GSM9120559 Single cell RNA Seq of Recovered Individual b09st08 Sample
- GSM9120560 Single cell RNA Seq of Recovered Individual b09st09 Sample
- GSM9120561 Single cell RNA Seq of Recovered Individual b09st10 Sample
- GSM9120562 Single cell RNA Seq of Recovered Individual b09st11 Sample
- GSM9120563 Single cell RNA Seq of Recovered Individual b10st12 Sample
- GSM9120564 Single cell RNA Seq of Infected Individual b10st01 Sample
- GSM9120565 Single cell RNA Seq of Recovered Individual b10st02 Sample
- GSM9120566 Single cell RNA Seq of Recovered Individual b10st03 Sample
- GSM9120567 Single cell RNA Seq of Longitudinal Recovered Individual b11st04 Sample
- GSM9120568 Single cell RNA Seq of Longitudinal Recovered Individual b11st05 Sample
+ 17 more — browse all 57 samples with per-sample file links →
- GSE167410 Histone H4 is increased in SARS-CoV-2-infected lung epithelial cells and linked to COVID-19 severity 16 samples shares covid-19, infected
- GSE273149 Longitudinal transcriptomic analysis reveals persistent enrichment of iron homeostasis and erythrocyte function pathways in severe COVID-19 ARDS 49 samples shares covid-19, long
- GSE196198 Longitudinal single-cell multiomics data for different severity of COVID-19 100 samples shares covid-19, long
- GSE274680 Inflammation and lymphocyte activation during longitudinal progression to rheumatoid arthritis in at-risk individuals 243 samples shares individuals, long
- GSE274788 X-ray-induced more serious damage to CD8+ T cells in patients with hypopharyngeal squamous cell carcinoma (HPSCC) than those in healthy individuals 12 samples shares individuals, healthy
- GSE158592 RNAseq analysis of blood from influenza infected patients and healthy controls SIG-2018 74 samples shares infected, healthy
- GSE196350 RNAseq analysis of blood from influenza infected patients and healthy controls 69 samples shares infected, healthy
- GSE226039 scRNAseq from pbmc, ileum, and rectal tissue of healthy and crohns disease individuals 46 samples shares individuals, healthy
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.