This is a repository for sharing information on available COVID-19 RNA-Seq datasets. I will update this weekly to add any newly released COVID-19 related 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: Please do NOT directly edit below this line. Please see contribution guide
| S.No. | Date | Title | Description | Download | #Samples | #COVID | Type |
|---|---|---|---|---|---|---|---|
| 1 | 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 |
| 2 | 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 |
| 3 | 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 |
| 4 | 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. | Data is private GSE151513 Data not public |
None | None | bulk |
| 5 | 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 |
| 6 | 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 |
| 7 | 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 |
| 8 | 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 |
| 9 | 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 |
| 10 | 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 |
| 11 | 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 |
| 12 | 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 |
| 13 | 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 |
| 14 | 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 |
| 15 | 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 |
| 16 | 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 |
| 17 | 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 |
| 18 | 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 |
| 19 | 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 |