Analysis of host transcriptome entropy during an infection to predict disease outcome

Dataset 1 (RNAseq) - Defne
Host: Mouse (10 strains with different susceptibility to Ebola)
Infection: Ebola Virus
Tissue: Spleen and Liver
Timepoints: 1, 3, 5 days post infection
Differential expression: EBOV infected vs mock infected
GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE130629
Study: https://www.sciencedirect.com/science/article/pii/S2211124720300358#bib45

Dataset 2 (RNAseq) - Nabil & Jakob
Host: Human (174 patients, including convalescent, acute recovered, acute fatal)
Infection: Ebola Virus
Tissue: Blood Timepoints: -
Differential expression: EBOV infected vs convalescent
BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA352396
Study: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1137-3

Dataset 3 (microarray) - Jakob
Host: Human (including no dengue, dengue fever, and dengue hemorrhagic fever)
Infection: Dengue fever
Tissue: Blood Timepoints: -
Differential expression: DF or DHF vs no Dengue
GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18090
GEO has raw data as CEL files in Supplemental
Study: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0007892

Dataset 4 (microarray)
Host: Mouse (multiple strains of mice and spn, with different infection outcomes)
Infection: S. pneumoniae
Tissue: Lung Timepoints: -
Differential expression: Infected vs mock infected
GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE61459
GEO has raw data as CEL files in Supplemental
Study: https://iai.asm.org/content/84/4/894.long

Datasets with TREATMENT outcome

Dataset 5 (RNAseq) - Defne
Host: Human (treatment outcome included: cured vs not cured)
Infection: M. tuberculosis
Tissue: Sputum Timepoints: 1 wk, 4 wk, 24 wk post treatment
Differential expression: Infected vs avg control (healthy) samples
GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE89403
Raw counts included as supplemental file on GEO
Study: https://www.sciencedirect.com/science/article/pii/S1472979217301889

Dataset 6 (microarray)
Host: Human (treatment outcome included: cured vs not cured)
Infection: Borrelia burgdorferi (Lyme disease)
Tissue: Blood Timepoints: 1 month and 6 months post treatment
Differential expression: Infected vs avg control (healthy) samples
GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE145974
GEO has raw data as CEL files in Supplemental
Study: https://mbio.asm.org/content/11/2/e00047-20.long

Dataset7 (microarray)
Host: Human (undergoing IFN therapy. Relapse vs no relapse info available)
Infection: Hepatitis C virus
Tissue: Blood Timepoints: -
Differential expression: Infected vs avg control (healthy) samples
GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59312
GEO has raw data as CEL files in Supplemental
Study: http://jvi.asm.org/cgi/pmidlookup?view=long&pmid=25100847