benostendorf / ostendorf_etal_2022

Code for Ostendorf et al., Nature, 2022

APOE in COVID-19

This repository contains the code to reproduce all figures from the manuscript

Common human genetic variants of APOE impact murine COVID-19 mortality, Nature, 2022

Benjamin N. Ostendorf†, Mira A. Patel, Jana Bilanovic, H.-Heinrich Hoffmann, Sebastian E. Carrasco, Charles M. Rice, Sohail F. Tavazoie†

†Correspondence: [e-mail], [e-mail]

doi: 10.1038/s41586-022-05344-2

Overview

Figures	Code file	R markdown output
- Fig1 - ED Fig 1	Fig_01/Fig_01.Rmd	Fig_01/Fig_01.md
- Fig2 - ED Fig 2	Fig_02/Fig_02.Rmd	Fig_02/Fig_02.md
- Fig 3b-c, - ED Fig 3f-o	Fig_03/RNAseq/01_RNAseq.Rmd	Fig_03/RNAseq/01_RNAseq.md
- ED Fig 3b-c	Fig_03/RNAseq/02_RNAseq.Rmd	Fig_03/RNAseq/02_RNAseq.md
- ED Fig 3d-e	Fig_03/RNAseq/03_RNAseq.Rmd	Fig_03/RNAseq/03_RNAseq.md
- Fig3d - Fig3i - ED Fig 4b - ED Fig 4d-f	Fig_03/Fig_03d_03i.Rmd	Fig_03/Fig_03d_03i.md
- Fig 3e-g - ED Fig 5 - ED Fig 6	Fig_03/scRNAseq/Fig_03_scRNAseq.Rmd	Fig_03/scRNAseq/Fig_03_scRNAseq.md
- ED Fig 3p	Fig_03/ED_Fig_03p.Rmd	Fig_03/ED_Fig_03p.md
- Fig 4 - ED Fig 7 - ED Fig 8	Fig_04/Fig_04.Rmd	Fig_04/Fig_04.md

GEO upload for bulk RNA-seq (GSE184289)

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE184289

GEO upload for scRNA-seq (GSE199498)

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE199498