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readme.Rmd
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readme.Rmd
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---
title: "README"
date: "`r Sys.Date()`"
author:
- name: Arun Seetharam
- name: Jeffrey Haltom
affiliation: Wurtele Lab
affiliation_url:
output:
rmdformats::html_clean:
self_contained: true
thumbnails: false
lightbox: true
gallery: true
highlight: tango
---
```{r setup, include=FALSE}
options(max.print = "75")
knitr::opts_chunk$set(
echo = TRUE,
collapse = TRUE,
comment = "#>",
fig.path = "assets/",
fig.width = 8,
prompt = FALSE,
tidy = FALSE,
message = FALSE,
warning = TRUE
)
knitr::opts_knit$set(width = 75)
```
## Header
## Publication
_coming soon_
## Contacts
## Documentation
## Data availability
The data used in this study are publicly available:
| study_accession | Title | Runs | Study Type | Type |
|--------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------|--------------|-----------|
| [ERP122190](ERP122190_multiqc_report.html) | Multi-level proteomics reveals host-perturbation strategies of SARS-CoV-2 and SARS-CoV. | 73 | Bulk RNA-Seq | Cell line |
| [ERP124749](ERP124749_multiqc_report.html) | RNA-seq of SARS-CoV-2-infected human primary hepatocyte-derived spheroids upon interferon a2 and baricitinib treatment | 12 | Bulk RNA-Seq | Cell line |
| [SRP256166](SRP256166_multiqc_report.html) | Modeling SARS-Cov-2 Infection in Human Airway Epithelium Organoids Transcriptome | 8 | Bulk RNA-Seq | Cell line |
| [SRP258687](SRP258687_multiqc_report.html) | Bulk RNA sequencing of SARS-CoV and SARS-CoV-2 infected human intestinal organoids | 22 | Bulk RNA-Seq | Cell line |
| [SRP265388](SRP265388_multiqc_report.html) | Experimental and natural evidence of SARS-CoV-2 infection-induced activation of type I interferon responses | 36 | Bulk RNA-Seq | Cell line |
| [SRP266130](SRP266130_multiqc_report.html) | Cardiomyocytes Infected by SARS-CoV-2 Recruit Cardiotoxic Macrophages [bulk RNA-seq dataset) | 18 | Bulk RNA-Seq | Cell line |
| [SRP269721](SRP269721_multiqc_report.html) | SARS-CoV-2 infection and replication in human fetal and pediatric gastric organoids | 18 | Bulk RNA-Seq | Cell line |
| [SRP271173](SRP271173_multiqc_report.html) | Targeting heparan sulfate proteoglycan-assisted endocytosis as a COVID-19 therapeutic option | 15 | Bulk RNA-Seq | Cell line |
| [SRP272808](SRP272808_multiqc_report.html) | A human disease model of SARS-CoV-2-induced lung injury and immune responses with a microengineered organ chip | 12 | Bulk RNA-Seq | Cell line |
| [SRP273808](SRP273808_multiqc_report.html) | Identification of Drugs Blocking SARS-CoV-2 Infection using hPSC-derived Lung and Colonic Organoids | 18 | Bulk RNA-Seq | Cell line |
| [SRP273970](SRP273970_multiqc_report.html) | SARS-CoV-2 infection is effectively treated and prevented by EIDD-2801 | 26 | Bulk RNA-Seq | Cell line |
| [SRP278486](SRP278486_multiqc_report.html) | RNA-Sequencing of intestinal eithelial and endothelial cells upon SARS-CoV-2 infection on a intestine chip | 12 | Bulk RNA-Seq | Cell line |
| [SRP278618](SRP278618_multiqc_report.html) | SARS-CoV2 infection of iPSC-derived cardiac cells predicts novel cytopathic features in COVID-19 patients | 40 | Bulk RNA-Seq | Cell line |
| [SRP283940](SRP283940_multiqc_report.html) | Human primary brain microvascular endothelial cells transcriptome with/without SARS-CoV-2 infection | 6 | Bulk RNA-Seq | Cell line |
| [SRP285334](SRP285334_multiqc_report.html) | SARS-CoV-2 suppresses mRNA splicing, translation, and protein trafficking in a multipronged mechanism to evade host defenses | 19 | Bulk RNA-Seq | Cell line |
| [SRP285394](SRP285394_multiqc_report.html) | SARS-CoV-2 suppresses mRNA splicing, translation, and protein trafficking in a multipronged mechanism to evade host defenses | 73 | Bulk RNA-Seq | Cell line |
| [SRP286174](SRP286174_multiqc_report.html) | Nonstructural protein 1 of SARS-CoV-2 is a potent pathogenicity factor redirecting host protein synthesis machinery toward viral RNA | 12 | Bulk RNA-Seq | Cell line |
| [SRP286660](SRP286660_multiqc_report.html) | SARS-CoV-2 infected cells present HLA-I peptides from canonical and out-of-frame ORFs | 16 | Bulk RNA-Seq | Cell line |
| [SRP286669](SRP286669_multiqc_report.html) | iPSC-derived Human Intestinal Organoids are permissive to SARS-CoV-2 infection | 24 | Bulk RNA-Seq | Cell line |
| [SRP286805](SRP286805_multiqc_report.html) | A genome-wide RNAi screen to identify human factors essential for SARS-CoV-2 infection | 6 | Bulk RNA-Seq | Cell line |
| [SRP292198](SRP292198_multiqc_report.html) | SARS-CoV-2 on hESC-derived peripheral neurons | 4 | Bulk RNA-Seq | Cell line |
| [SRP294125](SRP294125_multiqc_report.html) | Infection of human Nasal Epithelial Cells with SARS-CoV-2 and a 382-nt deletion isolate lacking ORF8 reveals similar viral kinetics and host transcriptional profiles | 41 | Bulk RNA-Seq | Cell line |
| [SRP295094](SRP295094_multiqc_report.html) | SARS-CoV-2 utilizes a multipronged strategy to suppress host protein synthesis | 42 | Bulk RNA-Seq | Cell line |
| [SRP295561](SRP295561_multiqc_report.html) | Immune transcriptomes of highly exposed SARS-CoV-2 asymptomatic seropositive versus seronegative individuals from the Ischgl community | 104 | Bulk RNA-Seq | Cell line |
| [SRP295687](SRP295687_multiqc_report.html) | Role of Top1 and Genome structure in SARS-CoV-2 infection [RNA-Seq human] | 72 | Bulk RNA-Seq | Cell line |
| [SRP295706](SRP295706_multiqc_report.html) | A novel cell culture system modeling the SARS-CoV-2 life cycle | 2 | Bulk RNA-Seq | Cell line |
| [SRP296566](SRP296566_multiqc_report.html) | SARS-CoV-2 infects human pluripotent stem cell-derived cardiomyocytes, impairing electrical and mechanical function | 48 | Bulk RNA-Seq | Cell line |
| [SRP297170](SRP297170_multiqc_report.html) | Clofazimine is a broad-spectrum coronavirus inhibitor that antagonizes SARS-CoV-2 replication in primary human cell culture and hamsters | 39 | Bulk RNA-Seq | Cell line |
| [SRP302575](SRP302575_multiqc_report.html) | Adult Stem Cell-derived Complete Lung Organoid Models Emulate Lung Disease in COVID-19 | 33 | Bulk RNA-Seq | Cell line |
| [SRP303317](SRP303317_multiqc_report.html) | Virus-induced senescence is a central pathogenic principle and therapeutic target in COVID-19 disease | 25 | Bulk RNA-Seq | Cell line |
| [SRP307098](SRP307098_multiqc_report.html) | m6A modification in SARS-CoV-2 virus regulates host cell innate immune response | 16 | Bulk RNA-Seq | Cell line |
| [SRP308020](SRP308020_multiqc_report.html) | SARS-CoV-2 spike protein interacts with and activates TLR4 | 6 | Bulk RNA-Seq | Cell line |
| [SRP311379](SRP311379_multiqc_report.html) | hPSC-derived cells to model Macrophage-mediated inflammation in COVID19 Hearts | 23 | Bulk RNA-Seq | Cell line |
| [SRP311694](SRP311694_multiqc_report.html) | RNA-Seq Quantitative Analysis of the regulation of SARS-CoV-2 infection on autophagy and apoptosis related gene transcriptome in infected cells | 4 | Bulk RNA-Seq | Cell line |
| [SRP312603](SRP312603_multiqc_report.html) | Comparative Transcriptomic and Molecular Pathway Analyses of HL-CZ Human Pro-Monocytic Cells Expressing SARS-CoV-2 Spike S1, S2, NP, NSP15 and NSP16 Genes | 21 | Bulk RNA-Seq | Cell line |
| [SRP319696](SRP319696_multiqc_report.html) | Switching of OAS1 splicing isoforms mitigates SARS-CoV-2 infection | 6 | Bulk RNA-Seq | Cell line |
| [SRP324059](SRP324059_multiqc_report.html) | Viral and host transcriptomes in SARS-CoV-2 infected human lung cells | 42 | Bulk RNA-Seq | Cell line |
| [SRP325484](SRP325484_multiqc_report.html) | Severe COVID-19 is Characterized by an Impaired Type I Interferon Response and Elevated Levels of Arginase Producing Granulocytic Myeloid Derived Suppressor Cells | 16 | Bulk RNA-Seq | Cell line |
| [SRP325675](SRP325675_multiqc_report.html) | SARS-CoV-2 infected and uninfected VeroE6 and A549-ACE2: Bemcentinib and liposome treatments | 70 | Bulk RNA-Seq | Cell line |
| [SRP326251](SRP326251_multiqc_report.html) | Mapping the 3D genome and epigenome in SARS-CoV-2 infected human cells | 47 | Bulk RNA-Seq | Cell line |
| [SRP327322](SRP327322_multiqc_report.html) | Transcriptome analysis of PBMCs reveals distinct immune response in the asymptomatic and re-detectable positive COVID-19 patients | 70 | Bulk RNA-Seq | Cell line |
## Other datasets