NOTE: I am no longer actively adding new studies but new contributions are still welcome.
This is a repository for sharing information on available COVID-19 RNA-Seq datasets. Please feel free to contribute to this repository (see contribution guide). If you have suggestions, please notify me by opeining a new issue.
NOTE 1: If you are facing problems while downloading data with SRA Toolkit, please try using the latest version of SRA Toolkit. If you have aspera you can also use ena-fast-download to download fastq files from SRA.
NOTE 2: Please do NOT directly edit below this line. Please see contribution guide
| S.No. | Date | Title | Description | Download | #Samples | #COVID | Type |
|---|---|---|---|---|---|---|---|
| 1 | 2021-02-15 | COVID-19 immune features revealed by a large-scale single cell transcriptome atlas | scRNA-Seq of various tissue types obtained from COVID-19 patients | GSE158055 only processed data | 284 | 196 | single-cell |
| 2 | 2021-02-01 | SARS-CoV-2 infects and replicates in cells of the human endocrine and exocrine pancreas | RNA-Seq in uninfected, SARS-CoV-2-infected, and remdesivir treated ex vivo cultured human islets | GSE159717 SRP287872 |
6 | 4 | bulk |
| 3 | 2021-01-12 | Neurological Manifestations of COVID-19 Feature T Cell Exhaustion and Dedifferentiated Monocytes in Cerebrospinal Fluid | scRNA-Seq from the (CSF) of Neuro-COVID patients, patients neurological diseases with viral encephalitis | GSE163005 SRP297575 |
31 | 8 | single-cell |
| 4 | 2020-12-09 | Temporal and spatial heterogeneity of host response to SARS-CoV-2 pulmonary infection | RNA-Seq analysis on autopsy samples from patients deceased due to SARS-Cov2 infection | GSE150316 SRP261138 |
88 | 37 | bulk |
| 5 | 2020-11-23 | Whole transcriptome sequencing of peripheral blood mononuclear cells from patients with COVID-19 | Longitudinal RNA-seq on PBMC samples of 18 COVID-19 patients | GSE157859 SRP282150 |
85 | 85 | bulk |
| 6 | 2020-10-29 | SARS-CoV-2 infection of primary human lung epithelium for COVID-19 modeling and drug discovery | Bulk RNAseq of SARS-COV2 infected human lung organoid | GSE160435 SRP289766 |
10 | 5 | bulk |
| 7 | 2020-10-28 | Macrophage expression and prognostic significance of the long pentraxin PTX3 in COVID-19 | Total RNA-Seq of Monocytes isolated from peripheral blood samples of 3 healthy 6 COVID-19 patients | GSE160351 SRP289541 |
9 | 3 | bulk |
| 8 | 2020-10-22 | Broad transcriptional dysregulation of brain and choroid plexus cell types with COVID-19 | 47,678 droplet-based single-nucleus transcriptomes from the frontal cortex and choroid plexus across 10 non-viral, 4 COVID-19, and an influenza patient. | GSE159812 SRP288163 |
20 | 4 | single-cell |
| 9 | 2020-10-20 | Hydroxychloroquine inhibits trained immunity | RNA-seq on monocytes from COVID-19 patients that were treated with HCQ | GSE159678 SRP287810 |
29 | 20 | bulk |
| 10 | 2020-10-19 | Single cell resolution of SARS-CoV-2 tropism, antiviral responses, and susceptibility to therapies in primary human airway epithelium | Single-cell RNAseq to understand elements of viral tropism and pathogenesis, antiviral immunity, and treatment response to remdesivir. | GSE157526 SRP280154 |
5 | 4 | single-cell |
| 11 | 2020-10-08 | SARS-CoV-2 infected cells present HLA-I peptides from canonical and out-of-frame ORFs | RNA-seq human lung A549 kidney HEK293T cells infected with SARS-CoV-2 12h, 18h and 24h post infection | GSE159191 SRP286660 |
16 | 12 | bulk |
| 12 | 2020-10-07 | Large-scale Multi-omic Analysis of COVID-19 Severity | RNA-Seq and high-resolution mass spectrometry on 128 blood samples from COVID-19 positive and negative patients with diverse disease severities. | GSE157103 SRP279280 |
252 | 200 | bulk |
| 13 | 2020-09-21 | Human Pluripotent Stem Cell-Derived Neural Cells and Brain Organoids Reveal SARS-CoV-2 Neurotropism Predominates in Choroid Plexus Epithelium | Bulk RNA-seq of choroid plexus organoids performed on mock, SARS-CoV-2 samples. | GSE157852 SRP282132 |
9 | 6 | bulk |
| 14 | 2020-09-04 | Systems biological assessment of immunity to mild versus severe COVID-19 infection in humans | RNAseq analysis of PBMCs in a group of 17 COVID-19 subjects and 17 healthy controls. | GSE152418 SRP267176 |
68 | 34 | bulk |
| 15 | 2020-07-31 | A novel isoform of ACE2 is expressed in human nasal and bronchial respiratory epithelia and is upregulated in response to RNA respiratory virus infection | RNA-Seq from human airway cells. | Data not public | None | None | bulk |
| 16 | 2020-07-29 | Direct exposure to SARS-CoV-2 and cigarette smoke increases infection severity and alters the stem cell-derived airway repair response | Mucociliary air-liquid interface cultures derived from primary human nonsmoker airway basal stem cells exposed to short term cigarette smoke and infected them with live SARS-CoV-2. | Data not public | None | None | single-cell |
| 17 | 2020-07-24 | Single-cell landscape of immunological responses in COVID-19 patients | Single-cell RNA sequencing in peripheral blood samples of 5 healthy donors and 13 COVID-19 patients. | HRA000150 "Not public" | 64 | 51 | single-cell |
| 18 | 2020-07-21 | Single cell RNA sequencing of blood antigen-presenting cells in severe Covid-19 reveals multi-process defects in antiviral immunity | Blood antigen-presenting cells (APC) in 7 COVID-19 patients with moderate or severe pneumonia. | Data not public | None | None | single-cell |
| 19 | 2020-07-10 | Severely ill COVID-19 patients display augmented functional properties in SARS-CoV-2-reactive CD8+ T cells | single-cell transcriptomes of >80,000 virus-reactive CD8+ T cells from 39 COVID-19 patients and 10 healthy subjects. | GSE153931 SRP270654 |
None | None | single cell |
| 20 | 2020-07-10 | Robust three-dimensional expansion of human adult alveolar stem cells and SARS-CoV-2 infection | investigate infection response to SARS-CoV-2 in human alveolar type 2 (hAT2) cells | Data not public | None | None | bulk |
| 21 | 2020-07-08 | Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients | Whole blood transcriptomes of 39 COVID-19 patients and 10 control donors. | Stalled EGAS00001004503 | None | None | bulk |
| 22 | 2020-06-26 | COVID-19 severity correlates with airway epithelium-immune cell interactions identified by single-cell analysis | Single-cell RNA sequencing on nasopharyngeal and bronchial samples from 19 patients and five controls. | Stalled EGAS00001004481 |
None | None | single-cell |
| 23 | 2020-06-26 | Neuroinvasive potential of SARS-CoV-2 revealedin a human brain organoid model | Brain organoids were infected with SARS-CoV-2 and sequenced with 10x single cell sequencing strategies. | Data not public | None | None | single-cell |
| 24 | 2020-06-23 | Platelet Gene Expression and Function in COVID-19 Patients | Platelet gene expression and functional responses in patients infected with SARS-CoV-2. | SRP262885 | 15 | 10 | bulk |
| 25 | 2020-06-22 | In vivo antiviral host response to SARS-CoV-2 by viral load, sex, and age | Examined host gene expression across infection status, viral load, age, and sex among RNA-sequencing profiles of nasopharyngeal swabs from 430 individuals with SARS-CoV-2 and 54 negative controls. | GSE152075 | 484 | 430 | bulk |
| 26 | 2020-06-18 | Early temporal dynamics of cellular responses to SARS-CoV-2 | Performed a time series RNA-seq and selective immunoblot analysis of SARS-CoV-2 infected lung (Calu-3) cells to characterize early virus-host processes. | GSE151513 | None | None | bulk |
| 27 | 2020-06-10 | Heightened Innate Immune Responsesin the Respiratory Tract of COVID-19 Patients | Metatranscriptomic sequencing to profile immune signatures in the bronchoalveolar lavage fluidof eight COVID-19 cases. | Data Not public PRJCA002273 |
None | None | single-cell |
| 28 | 2020-06-05 | Suppressive myeloid cells are a hallmark of severe COVID-19 | Combined two single-cell RNA-sequencing technologies and single-cell proteomics in whole blood and peripheral blood mononuclear cells (PBMC) | EGAS00001004450 | 100 | 54 | single-cell |
| 29 | 2020-05-28 | Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19 | Host response to SARS-CoV-2 and other human respiratory viruses in cell lines, primary cell cultures, ferrets, and COVID-19 patients | GSE147507 SRP253951 |
195 | 24 | bulk |
| 30 | 2020-05-27 | Single-cell RNA-seq and V(D)J profiling of immune cells in COVID-19 patients | transcriptional profiles and changes in CD3+ and CD19+ lymphocytes by comprehensive single-cell transcriptome and V(D)J recombination analyses | Data not public | NA | NA | single-cell |
| 31 | 2020-05-26 | Generation of human bronchial organoids for SARS-CoV-2 research | Human bronchial organoids were infected with SARS-CoV-2 in the presence of absence of camostat. | GSE150819 SRP262285 |
18 | 6 | bulk |
| 32 | 2020-05-12 | Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19 | Characterized bronchoalveolar lavage fluid immune cells from patients with varying severity of COVID-19 and from healthy people. | GSE145926 SRP250732 |
21 | 18 | single-cell |
| 33 | 2020-05-07 | Single-cell longitudinal analysis of SARS-CoV-2 infection in human bronchial epithelial cells | Experimentally infected human bronchial epithelial cells (HBECs) in air-liquid interface cultures over a time-course. | Data not public | NA | NA | single-cell |
| 34 | 2020-05-07 | Immune cell profiling of COVID-19 patients in the recovery stage by single-cell sequencing | PBMC from late stage recovery and early stage recovery patients | CRA002497 | 180 | 120 | single-cell |
| 35 | 2020-05-05 | Disruption of the CCL5/RANTES-CCR5 Pathway Restores Immune Homeostasis and Reduces Plasma Viral Load in Critical COVID-19 | Single-cell RNA-sequencing revealed declines in transcriptomic myeloid cell clusters expressing IL-6 and interferon-related genes. | Data Not public | None | None | single-cell |
| 36 | 2020-05-05 | Cross-talk between the airway epithelium and activated immune cells defines severity in COVID-19 | single-cell transcriptomes of nasopharyngeal and bronchial samples from clinically well-characterized patients presenting with moderate and critical severities | Data not public | NA | NA | single-cell |
| 37 | 2020-05-04 | Gene expression profiling of SARS-CoV-1/2 infected human cell lines at bulk and single-cell level | Different human cell lines were infected with SARS-CoV-1 and SARS-CoV-2 and harvested at different time points. | GSE148729 SRP256479 |
154 | 56 | bulk and single-cell level |
| 38 | 2020-05-02 | Identification of Drugs Blocking SARS-CoV-2 Infection using Human Pluripotent Stem Cell-derived Colonic Organoids | Single cell RNA-seq and immunostaining showed that the putative viral entry receptor ACE2 is expressed in multiple hESC-derived colonic cell types, but highly enriched in enterocytes. | Data Not public GSE147975 | None | None | single-cell |
| 39 | 2020-04-23 | A single-cell atlas of the peripheral immune response to severe COVID-19 | Un-cryopreserved peripheral blood mononuclear cells (PBMCs) | GSE150728 SRP262058 |
13 | 7 | single-cell |
| 40 | 2020-03-31 | Transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in COVID-19 patients | Transcriptome sequencing of the RNAs isolated from the bronchoalveolar lavage fluid (BALF) and peripheral blood mononuclear cells (PBMC) specimens of COVID-19 patients | CRA002390 | 10 | 7 | single-cell |
| 41 | 2020-03-17 | Blood single cell immune profiling reveals the interferon-MAPK pathway mediated adaptive immune response for COVID-19 | Blood cell immune response profiles using 5' mRNA, TCR and BCR V(D)J transcriptome analysis with single-cell resolution | Data not public | NA | NA | single-cell |
| S.No. | Resource | Description |
|---|---|---|
| 1 | 10x Genomics publications and preprints that showcase the latest research on COVID-19 | 10x Genomics publications and preprints that showcase the latest research on COVID-19 |
| 2 | BROAD Single Cell Portal | BROAD Single Cell Portal contains studies which have been identified by the study owners as relevant to COVID-19 |
| 3 | ImmGen COVID-19 expression data browser | Visualization tools for SARS-CoV2 expression data. |
| 4 | NCBI SARS-CoV-2 Resources | SARS-CoV-2 Sequence, Literature, Clinical Resources |
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