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COVID-19-RNA-Seq-datasets

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A repository for sharing information on available COVID-19 RNA-Seq datasets

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**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](https://github.com/urmi-21/COVID-19-RNA-Seq-datasets/blob/master/CONTRIBUTING.md)). If you have suggestions, please notify me by opeining a new [issue](https://github.com/urmi-21/COVID-19-RNA-Seq-datasets/issues).

**NOTE 1: If you are facing problems while downloading data with SRA Toolkit, please try using the latest version of [SRA Toolkit](https://github.com/ncbi/sra-tools/wiki/01.-Downloading-SRA-Toolkit)**. If you have aspera you can also use [ena-fast-download](https://github.com/wwood/ena-fast-download) to download fastq files from SRA.

**NOTE 2: Please do NOT directly edit below this line. Please see [contribution guide](https://github.com/urmi-21/COVID-19-RNA-Seq-datasets/blob/master/CONTRIBUTING.md)**

## 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](https://doi.org/10.1016/j.cell.2021.01.053)|scRNA-Seq of various tissue types obtained from COVID-19 patients|[**GSE158055 only processed data**](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE158055)|284|196|single-cell
2|2021-02-01|[SARS-CoV-2 infects and replicates in cells of the human endocrine and exocrine pancreas](https://www.nature.com/articles/s42255-021-00347-1)|RNA-Seq in uninfected, SARS-CoV-2-infected, and remdesivir treated ex vivo cultured human islets|[GSE159717](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE159717) [SRP287872](https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP287872)|6|4|bulk
3|2021-01-12|[Neurological Manifestations of COVID-19 Feature T Cell Exhaustion and Dedifferentiated Monocytes in Cerebrospinal Fluid](https://doi.org/10.1016/j.immuni.2020.12.011)|scRNA-Seq from the (CSF) of Neuro-COVID patients, patients neurological diseases with viral encephalitis|[GSE163005](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE163005) [SRP297575](https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP297575)|31|8|single-cell
4|2020-12-09|[Temporal and spatial heterogeneity of host response to SARS-CoV-2 pulmonary infection](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7725958/)|RNA-Seq analysis on autopsy samples from patients deceased due to SARS-Cov2 infection|[GSE150316](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE150316) [SRP261138](https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP261138)|88|37|bulk
5|2020-11-23|[Whole transcriptome sequencing of peripheral blood mononuclear cells from patients with COVID-19](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA662985)|Longitudinal RNA-seq on PBMC samples of 18 COVID-19 patients|[GSE157859](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE157859) [SRP282150](https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP282150)|85|85|bulk
6|2020-10-29|[SARS-CoV-2 infection of primary human lung epithelium for COVID-19 modeling and drug discovery](https://www.biorxiv.org/content/10.1101/2020.06.29.174623v1)|Bulk RNAseq of SARS-COV2 infected human lung organoid|[GSE160435](https://www.ncbi.nlm.nih.gov//geo/query/acc.cgi?acc=GSE160435) [SRP289766](https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP289766)|10|5|bulk
7|2020-10-28|[Macrophage expression and prognostic significance of the long pentraxin PTX3 in COVID-19](https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP289541)|Total RNA-Seq of Monocytes isolated from peripheral blood samples of 3 healthy 6 COVID-19 patients|[GSE160351](https://www.ncbi.nlm.nih.gov//geo/query/acc.cgi?acc=GSE160351) [SRP289541](https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP289541)|9|3|bulk
8|2020-10-22|[Broad transcriptional dysregulation of brain and choroid plexus cell types with COVID-19](https://www.biorxiv.org/content/10.1101/2020.10.22.349415v1)|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](https://www.ncbi.nlm.nih.gov//geo/query/acc.cgi?acc=GSE159812) [SRP288163](https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP288163)|20|4|single-cell
9|2020-10-20|[Hydroxychloroquine inhibits trained immunity](https://www.medrxiv.org/content/10.1101/2020.06.08.20122143v1)|RNA-seq on monocytes from COVID-19 patients that were treated with HCQ|[GSE159678](https://www.ncbi.nlm.nih.gov//geo/query/acc.cgi?acc=GSE159678) [SRP287810](https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=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](https://www.biorxiv.org/content/10.1101/2020.10.19.343954v1)|Single-cell RNAseq to understand elements of viral tropism and pathogenesis, antiviral immunity, and treatment response to remdesivir.|[GSE157526](https://www.ncbi.nlm.nih.gov//geo/query/acc.cgi?acc=GSE157526) [SRP280154](https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP282132)|5|4|single-cell
11|2020-10-08|[SARS-CoV-2 infected cells present HLA-I peptides from canonical and out-of-frame ORFs](https://www.biorxiv.org/content/10.1101/2020.10.02.324145v2)|RNA-seq human lung A549 kidney HEK293T cells infected with SARS-CoV-2 12h, 18h and 24h post infection|[GSE159191](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE159191) [SRP286660](https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP286660)|16|12|bulk
12|2020-10-07|[Large-scale Multi-omic Analysis of COVID-19 Severity](https://www.cell.com/cell-systems/fulltext/S2405-4712(20)30371-9)|RNA-Seq and high-resolution mass spectrometry on 128 blood samples from COVID-19 positive and negative patients with diverse disease severities.|[GSE157103](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE157103) [SRP279280](https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=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](https://www.sciencedirect.com/science/article/pii/S193459092030463X)|Bulk RNA-seq of choroid plexus organoids performed on mock, SARS-CoV-2 samples.|[GSE157852](https://www.ncbi.nlm.nih.gov//geo/query/acc.cgi?acc=GSE157852) [SRP282132](https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP282132)|9|6|bulk
14|2020-09-04|[Systems biological assessment of immunity to mild versus severe COVID-19 infection in humans](https://science.sciencemag.org/content/369/6508/1210)|RNAseq analysis of PBMCs in a group of 17 COVID-19 subjects and 17 healthy controls.|[GSE152418](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE152418) [SRP267176](https://www.ncbi.nlm.nih.gov/Traces/study/?query_key=3&WebEnv=MCID_5f5d575544419776cb56d6aa&o=acc_s%3Aa)|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](https://www.biorxiv.org/content/10.1101/2020.07.31.230870v1)|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](https://www.biorxiv.org/content/10.1101/2020.07.28.226092v1)|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](https://www.biorxiv.org/content/10.1101/2020.07.23.217703v1)|Single-cell RNA sequencing in peripheral blood samples of 5 healthy donors and 13 COVID-19 patients.|[HRA000150 "**Not public**"](https://bigd.big.ac.cn/gsa-human/browse/HRA000150)|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](https://www.biorxiv.org/content/10.1101/2020.07.20.212837v1)|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](https://www.biorxiv.org/content/10.1101/2020.07.09.194027v1)|single-cell transcriptomes of >80,000 virus-reactive CD8+ T cells from 39 COVID-19 patients and 10 healthy subjects.|[GSE153931](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=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](https://www.biorxiv.org/content/10.1101/2020.07.10.194498v1)|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](https://www.medrxiv.org/content/10.1101/2020.07.07.20148395v2)|Whole blood transcriptomes of 39 COVID-19 patients and 10 control donors.|[**Stalled** EGAS00001004503](https://ega-archive.org/studies/EGAS00001004503)|None|None|bulk
22|2020-06-26|[COVID-19 severity correlates with airway epithelium-immune cell interactions identified by single-cell analysis](https://www.nature.com/articles/s41587-020-0602-4)|Single-cell RNA sequencing on nasopharyngeal and bronchial samples from 19 patients and five controls.|[**Stalled**]() [EGAS00001004481](https://ega-archive.org/studies/EGAS00001004481)|None|None|single-cell
23|2020-06-26|[Neuroinvasive potential of SARS-CoV-2 revealedin a human brain organoid model](https://www.biorxiv.org/content/10.1101/2020.06.25.169946v1)|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](https://ashpublications.org/blood/article/doi/10.1182/blood.2020007214/461106/Platelet-Gene-Expression-and-Function-in-COVID-19)|Platelet gene expression and functional responses in patients infected with SARS-CoV-2.|[SRP262885](https://trace.ncbi.nlm.nih.gov/Traces/study/?acc=SRP262885&o=acc_s%3Aa)|15|10|bulk
25|2020-06-22|[In vivo antiviral host response to SARS-CoV-2 by viral load, sex, and age](https://www.biorxiv.org/content/10.1101/2020.06.22.165225v1)|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](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE152075)|484|430|bulk
26|2020-06-18|[Early temporal dynamics of cellular responses to SARS-CoV-2](https://www.biorxiv.org/content/10.1101/2020.06.18.158154v1)|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](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE151513)|None|None|bulk
27|2020-06-10|[Heightened Innate Immune Responsesin the Respiratory Tract of COVID-19 Patients](https://doi.org/10.1016/j.chom.2020.04.017)|Metatranscriptomic sequencing to profile immune signatures in the bronchoalveolar lavage fluidof eight COVID-19 cases.|[**Data Not public**]() [PRJCA002273](https://bigd.big.ac.cn/gsa-human/browse/HRA000143)|None|None|single-cell
28|2020-06-05|[Suppressive myeloid cells are a hallmark of severe COVID-19](https://www.medrxiv.org/content/10.1101/2020.06.03.20119818v1)|Combined two single-cell RNA-sequencing technologies and single-cell proteomics in whole blood and peripheral blood mononuclear cells (PBMC)|[EGAS00001004450](https://www.ebi.ac.uk/ega/search/site/EGAS00001004450)|100|54|single-cell
29|2020-05-28|[Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19](https://www.sciencedirect.com/science/article/pii/S009286742030489X)|Host response to SARS-CoV-2 and other human respiratory viruses in cell lines, primary cell cultures, ferrets, and COVID-19 patients|[GSE147507](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE147507) [SRP253951](https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP253951)|195|24|bulk
30|2020-05-27|[Single-cell RNA-seq and V(D)J profiling of immune cells in COVID-19 patients](https://www.medrxiv.org/content/10.1101/2020.05.24.20101238v1)|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](https://www.biorxiv.org/content/10.1101/2020.05.25.115600v2)|Human bronchial organoids were infected with SARS-CoV-2 in the presence of absence of camostat.|[GSE150819](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE150819) [SRP262285](https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP262285)|18|6|bulk
32|2020-05-12|[Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19](https://www.nature.com/articles/s41591-020-0901-9)|Characterized bronchoalveolar lavage fluid immune cells from patients with varying severity of COVID-19 and from healthy people.|[GSE145926](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE145926) [SRP250732](https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP250732)|21|18|single-cell
33|2020-05-07|[Single-cell longitudinal analysis of SARS-CoV-2 infection in human bronchial epithelial cells](https://www.biorxiv.org/content/10.1101/2020.05.06.081695v1)|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](https://www.biorxiv.org/content/10.1101/2020.05.06.081695v1)|PBMC from late stage recovery and early stage recovery patients|[CRA002497](https://bigd.big.ac.cn/gsa/browse/detail?pageSize=50&accession=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](https://www.medrxiv.org/content/10.1101/2020.05.02.20084673v1)|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](https://www.medrxiv.org/content/10.1101/2020.04.29.20084327v1)|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](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE148729)|Different human cell lines were infected with SARS-CoV-1 and SARS-CoV-2 and harvested at different time points.|[GSE148729](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE148729) [SRP256479](https://www.ncbi.nlm.nih.gov/sra?term=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](https://www.biorxiv.org/content/10.1101/2020.05.02.073320v1)|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**](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE147975)|None|None|single-cell
39|2020-04-23|[A single-cell atlas of the peripheral immune response to severe COVID-19](https://www.nature.com/articles/s41591-020-0944-y)|Un-cryopreserved peripheral blood mononuclear cells (PBMCs)|[GSE150728](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE150728) [SRP262058](https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP262058)|13|7|single-cell
40|2020-03-31|[Transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in COVID-19 patients](https://www.tandfonline.com/doi/full/10.1080/22221751.2020.1747363)|Transcriptome sequencing of the RNAs isolated from the bronchoalveolar lavage fluid (BALF) and peripheral blood mononuclear cells (PBMC) specimens of COVID-19 patients|[CRA002390](https://bigd.big.ac.cn/gsa/browse/detail?pageSize=50&accession=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](https://www.medrxiv.org/content/10.1101/2020.03.15.20033472v1)|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](https://pages.10xgenomics.com/3p-immunology-coronavirus-additional-publications.html)|10x Genomics publications and preprints that showcase the latest research on COVID-19
2|[BROAD Single Cell Portal](https://singlecell.broadinstitute.org/single_cell/covid19)|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](https://www.immgen.org/Databrowser19/COVID19Databrowser.html)|Visualization tools for SARS-CoV2 expression data.
4|[NCBI SARS-CoV-2 Resources](https://www.ncbi.nlm.nih.gov/sars-cov-2/)|SARS-CoV-2 Sequence, Literature, Clinical Resources

COVID-19-RNA-Seq-datasets

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