Dataset for the article: Single-cell profiling of lncRNA expression during Ebola virus infection in rhesus macaques

Santus, Luisa, Sopena-Rios, Maria, García-Pérez, Raquel, Lin, Aaron E., Adams, Gordon C., Barnes, Kayla, Siddle, Katherine J., Wohl, Shirlee, Reverter, Ferran, Rinn, John L., Bennett, Richard S., Hensley, Lisa E., Sabeti, Pardis C. and Melé, Marta (2023) Dataset for the article: Single-cell profiling of lncRNA expression during Ebola virus infection in rhesus macaques. [Data Collection]

Summary

Data availability:

The sequencing data generated in this study have been deposited in the NCBI Gene Expression Omnibus (GEO) database under accession code GSE192447. The publicly available whole blood bulk short-read RNA-Seq data from healthy samples and samples infected with Makona Ebola Virus data used in this study are available in the NCBI Gene Expression Omnibus (GEO) database under accession code GSE115785. The single-cell RNA-Seq data used in this study are available in the NCBI Gene Expression Omnibus (GEO) database under accession code GSE158390. Raw Seurat Objects for both single-cell datasets used in this study are available at Zenodo. The full co-expression network file is also provided (https://doi.org/10.5281/zenodo.7997135). The reference genome of EBOV used in this study is available in the GenBank database under accession code KU182905.1. The assembly and reference genome of Macaca Mulatta used in this study are available in the Ensembl database (Mmul_10) (https://ftp.ensembl.org/pub/release-100/fasta/macaca_mulatta/dna/Macaca_mulatta.Mmul_10.dna.toplevel.fa.gz, https://ftp.ensembl.org/pub/release-100/gtf/macaca_mulatta/Macaca_mulatta.Mmul_10.100.gtf.gz). The assembly and reference genome of human used in this study are available in the Gencode database (release_23) (https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_23/gencode.v23.annotation.gtf.gz, https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_23/GRCh38.primary_assembly.genome.fa.gz). Source data are provided with this paper.

Code availability:

The code used for this study is available at: https://github.com/Mele-Lab/2023_SingleCellEbolaLncRNAs_NatComms.