Biological samples |
|
Whole blood preoperative samples |
Lukaszewski et al.23
|
06/Q1702/152; IRB00001756 |
Blood samples of patients infected with SARS-CoV-2 |
ESCAPE study |
2020-001039-29; NCT04339712
|
|
Chemicals, peptides, and recombinant proteins |
|
RNAlater |
ThermoFisher |
Cat#AM7021 |
|
Critical commercial assays |
|
RiboPure-Blood Kit |
ThermoFisher |
Cat#AM1928 |
TruSeq Stranded Total RNA with Ribo-Zero Globin kit |
Illumina |
Cat#20020613 |
High-Capacity cDNA Reverse Transcription Kit |
ThermoFisher |
Cat#4368813 |
TaqMan PreAmp Master Mix |
ThermoFisher |
Cat#4488593 |
|
Deposited data |
|
Raw and processed RNA sequencing data of preoperative samples |
This paper |
GEO: GSE208581
|
Raw and processed RNA sequencing data of COVID-19 samples |
This paper |
GEO: GSE208587
|
Human reference genome GRCh38.99 |
Genome Reference Consortium |
www.ensembl.org |
|
Software and algorithms |
|
Original code |
This paper |
Zenodo (https://doi.org/10.5281/zenodo.10835070) & GitHub (https://github.com/thisisalbert/preoperative_sepsis_risk) |
GEO2RNAseq (v 0.100.3) |
Seelbinder et al.50
|
https://hub.docker.com/r/xentrics/geo2rnaseq |
FastQC (v0.11.8) |
Babraham Institute - Babraham Bioinformatics |
https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
Trimmomatic (v0.39) |
The Usadel Lab |
https://github.com/usadellab/Trimmomatic |
SortMeRNA (v2.1b) |
Bonsai Bioinformatics |
https://bioinfo.univ-lille.fr/sortmerna/ |
HiSAT2 (v2.1.0) |
The Daehwan Kim Lab |
https://daehwankimlab.github.io/hisat2/ |
DESeq2 (v1.26) |
Love et al.51
|
https://bioconductor.org/packages/DESeq2/ |
edgeR (v3.28.1) |
Robinson et al.52
|
https://bioconductor.org/packages/edgeR/ |
ComplexHeatmap (v2.4.3) |
Gu et al.53
|
https://www.bioconductor.org/packages/ComplexHeatmap/ |
VennDiagram (v1.6.20) |
Chen et al.54
|
https://cran.r-project.org/package=VennDiagram |
org.Hs.e.g.,.db (v3.11.4) |
Marc Carlson |
https://bioconductor.org/packages/org.Hs.eg.db/ |
clusterProfiler (v3.16.1) |
Yu et al.55
|
https://bioconductor.org/packages/clusterProfiler/ |
Cytoscape (v3.7.0) |
Shannon et al.56
|
https://cytoscape.org/ |
mice (v3.16.0) |
van Buuren et al. |
https://cran.r-project.org/package=mice |
ROSE (v0.0-4) |
Lunardon et al. |
https://cran.r-project.org/package=ROSE |
caret (ranger) (v6.0-94) |
Max Kuhn |
https://cran.r-project.org/package=caret |
Boruta (v8.0.0) |
Kursa et al.57
|
https://cran.r-project.org/package=Boruta |
R (v4.2.3) |
Ross Ihaka and Robert Gentleman |
https://www.r-project.org/ |