Upper airway gene expression differentiates COVID-19 from other acute respiratory illnesses and reveals suppression of innate immune responses by SARS-CoV-2
RNA-seq (gene expression) · human · 234 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
- 234 samples
- 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.
Read the full summary ↓
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 GSE156063_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: 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 PRJNA656568. Searching any of these in the dataset finder brings you back here.
The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.
+ 234 more — browse all 234 samples with per-sample file links →
- GSE297329 Evolution of SARS-CoV-2 T cell responses as a function of multiple COVID-19 boosters 98 samples shares sars-cov-2, covid-19
- GSE281237 Widespread gene-environment interactions shape the immune response to SARS-CoV-2 infection in hospitalized COVID-19 patients 29 samples shares sars-cov-2, covid-19
- GSE167410 Histone H4 is increased in SARS-CoV-2-infected lung epithelial cells and linked to COVID-19 severity 16 samples shares sars-cov-2, covid-19
- GSE250023 Impaired innate and adaptive immune responses to BNT162b2 SARS-CoV-2 vaccination in systemic lupus erythematosus 75 samples shares sars-cov-2, innate
- GSE271148 Human airway submucosal gland organoids to study respiratory inflammation and infection [bulk RNA-seq] 16 samples shares respiratory, airway
- GSE271264 Human airway submucosal gland organoids to study respiratory inflammation and infection [bulk RNA-seq] 15 samples shares respiratory, airway
- GSE300696 Identification of reactive CpGs and RNA expression in early COVID-19 through cis-eQTM analysis reflecting disease severity and recovery [RNA-seq] 346 samples shares covid-19
- GSE276544 MVA-based SARS-CoV-2 vaccine candidates encoding different spike protein conformations induce distinct early transcriptional responses which may impact subsequent adaptive immunity 305 samples shares sars-cov-2
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.