REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti-human CD16-FITC (3G8)	Beckman Coulter	RRID: AB_2848116
Anti-human HLA DR-PE (immu-357)	Beckman Coulter	RRID: AB_131284
Anti-human CD14-ECD (RM052)	Beckman Coulter	RRID: AB_130853
Anti-human CD4-Pe-Cy5.5 (13B8.2)	Beckman Coulter	Cat#B16491; RRID: NA
Anti-human CD56-APC (N901)	Beckman Coulter	RRID: AB_130791
Anti-human CD8-APC-AF700 (B9.11)	Beckman Coulter	RRID: AB_2750854
Anti-human CD19-APC-AF750 (J3-119)	Beckman Coulter	RRID: AB_2833030
Anti-human CD3-PB (UCHT1)	Beckman Coulter	RRID: AB_2728095
Anti-human CD45-KO (J33)	Beckman Coulter	RRID: AB_2833027
Anti-human CD25-Pe-Cy7 (M-A251)	BD Biosciences	RRID: AB_396847
Anti-human IgD-FITC (IADB6)	Southern Biotech	RRID: AB_2687521
Anti-human IgM-PE (SA-DA4)	Beckman Coulter	Cat#B30657; RRID: NA
Anti-human CD3-ECD (UCHT1)	Beckman Coulter	RRID: 31,622420
Anti-human CD27-PE-Cy5.5 (1A4CD27)	Beckman Coulter	Cat#B21444; RRID: NA
Anti-human CD38-PE-Cy7 (LS198-4-3)	Beckman Coulter	Cat#B49198; RRID: NA
Anti-human CD24-APC (ALB9)	Beckman Coulter	Cat#A87785; RRID: NA
Anti-human CD5-APC-AF700 (BL1a)	Beckman Coulter	Cat#A78835; RRID: NA
Anti-human CD20-PB (B9E9)	Beckman Coulter	RRID: AB_2833030
Biological samples
RNA isolated from whole blood of COVID-19 ICU patients	This paper	Radboud University Medical Center, Department of Intensive Care Medicine
Chemicals, peptides, and recombinant proteins
SuperScript II	invitrogen	18,064–014
Critical commercial assays
PAXgene Blood RNA Tubes	Qiagen	762,165
Milliplex Luminex cytokine assay	Merck Millipore	HCYTOMAG-60K
PAXgene Blood miRNA kit	Qiagen/BD	763,134
TruSeq® Stranded Total RNA Library Prep Globin	Illumina	20,020,613
RNA ScreenTape	Agilent Technologies	5067–5576
RNA ScreenTape Sample Buffer	Agilent Technologies	5067–5577
RNA ScreenTape Ladder	Agilent Technologies	5067–5578
High Sensitivity D1000 ScreenTape	Agilent Technologies	5067–5584
High Sensitivity D1000 Reagents	Agilent Technologies	5067–5585
Deposited data
Raw data (Cohort 1)	This paper	EGA-ID: EGAS00001005735
Raw data (Cohort 2)	Warnat-Herresthal et al., 2021	EGA-ID: EGAD00001006231
Processed data (Cohort 3)	Bergamaschi et al., 2021	https://www.covid19cellatlas.org/patient/citiid/
Human reference genome, gencode build 33	GENCODE consortium	https://www.gencodegenes.org/human/release_33.html
Software and algorithms
Paper analysis code	This paper	https://github.com/amitfrish/COVIDRecoveryCode
STAR 2.7.3a	Dobin et al., 2013	https://github.com/alexdobin/STAR
Samtools 1.9	Li et al., 2009	https://www.htslib.org
TimeAx	Frishberg et al., 2021 (biorXiv)	https://doi.org/10.1101/2021.11.17.468952
R	R Core Team, 2015	N/A
Diffcor	Fukushima et al. 2013	https://cran.r-project.org/web/packages/diffcor/index.html
Sva	Leek et al. 2012	https://bioconductor.org/packages/release/bioc/html/sva.html
scBio	Frishberg et al. 2019	https://cran.r-project.org/web/packages/scBio//index.html
NMF	Gaujoux et al. 2010	https://cran.r-project.org/web/packages/NMF/index.html
Kaluza 2.1	Beckman Coulter	https://www.mybeckman.nl/flow-cytometry/software/kaluza
Other
DxH 500 Hematology Analyzer	Beckman Coulter	https://www.beckmancoulter.com/en/products/hematology/dxh-500
Navios Flowcytometer 10C/3L	Beckman Coulter	Cat# A52103
Freedom Evo 200	Tecan	11,321,226
NANODROP II	GC biotech BV	N/A
TAdvanced 96SG	analytikjena	846-2-070-241
TapeStation 4200	Agilent	G2991A
NovaSeq 6000	Illumina	N/A