NOTE: I am no longer actively adding new studies but new contributions are still welcome.

Introduction

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

COVID-19-RNA-Seq-datasets

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

COVID-19-RNA-Seq Resources

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