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. 2024 Sep 3;5(9):101712. doi: 10.1016/j.xcrm.2024.101712
REAGENT or RESOURCE SOURCE IDENTIFIER
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/