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. 2023 Feb 28;4(3):100956. doi: 10.1016/j.xcrm.2023.100956
REAGENT or RESOURCE SOURCE IDENTIFIER
Biological samples
Organ samples for scRNA-seq and Histological analysis This paper Supplementary file
sera from SLE patients for measurement of the UR proteins 44 Supplementary file
Critical commercial assays
Luminex Assay for protein Bio-techne (R&D) Custom code: LXSAHM-17 Lot number: L143454
EILSA for TGFB1 Bio-techne (R&D) Catalog: DB100C
Deposited data
scRNA-seq data of CIA mouse This paper GEO: GSE206659
bulk-RNA data of treated UC patients 45 GEO: GSE92415
bulk-RNA data of treated CD patients 46 GEO: GSE52746
bulk-RNA of AD patients 47 GEO: GSE16161
bulk-RNA of AD patients 48 GEO: GSE32924
bulk-RNA of CD patients 49 GEO: GSE16879
bulk-RNA of CD patients 50 GEO: GSE179285
bulk-RNA of CD patients 51 GEO: GSE75214
bulk-RNA of JM patients 52 GEO: GSE148810
bulk-RNA of LN patients 52 GEO: GSE32591
bulk-RNA of PSO patients 53 GEO: GSE14905
bulk-RNA of PSO patients 54 GEO: GSE181318
bulk-RNA of RA patients 55 GEO: GSE1919
bulk-RNA of RA patients 56 GEO: GSE55235
bulk-RNA of lupus patients 57 GEO: GSE112943
bulk-RNA of SLE patients 52 GEO: GSE148810
bulk-RNA of lupus patients 58,59,60,61,62 GEO: GSE81071
bulk-RNA of SS patients 63 GEO: GSE176510
bulk-RNA of SS patients 64,65 GEO: GSE40568
bulk-RNA of SSc patients 66 GEO: GSE81292
bulk-RNA of SSc patients 67 GEO: GSE95065
bulk-RNA of T1D patients 68 GEO: GSE66413
bulk-RNA of UC patients 69 GEO: GSE11223
bulk-RNA of UC patients 50 GEO: GSE179285
bulk-RNA of UC patients 51 GEO: GSE75214
Experimental models: Organisms/strains
model organism: mouse model of arthritis Mouse: DBA1/J Jordbruksverket (Stockholm, Sweden) and GemPharmatech Co., Ltd. (Nanjing, China) N/A
Software and algorithms
Full analysis pipeline This paper https://github.com/SDTC-CPMed/multi-organ_DigiTwin.
MONOCLE 70 http://monocle-bio.sourceforge.net/.
James Nemesh, McCarrol’s lab Drop-seq Core Computational Protocol v1.0.1 http://mccarrolllab.com http://mccarrolllab.co
Drop-Seq tools v1.12 http://mccarrolllab.com http://mccarrolllab.com
bcl2fastq v2.19.1 https://emea.support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html https://emea.support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html
Picard software v2.9.0 71 https://github.com/broadinstitute/picard.
STAR software v2.5.3 72 http://code.google.com/p/rna-star/.
2019SingleR v1.0.6 73 https://github.com/dviraran/SingleR.
Deep count autoencoder (DCA) v0.2.3 74 https://github.com/theislab/dca.
Seurat v3.1.2 75 https://cran.r-project.org/web/packages/Seurat/index.html.
scVI v0.7.1 76 https://github.com/romain-lopez/scVI-reproducibility.
NicheNet v1.0.0 12 https://github.com/saeyslab/nichenetr
Ingenuity Pathway Analysis vQ1 2021 and vQ4 2020 77 https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/analysis-and-visualization/qiagen-ipa/
rstatix v0.7.0 https://CRAN.R-project.org/package=rstatix https://CRAN.R-project.org/package=rstatix.
GEO2R 78 https://www.ncbi.nlm.nih.gov/geo/geo2r/
missForest v1.5 79,80 https://CRAN.R-project.org/package=missForest
MASS v7.3-54 81 https://cran.r-project.org/web/packages/MASS/index.html.
DHARMa v0.4.5 82 https://cran.r-project.org/web/packages/DHARMa/index.html.
stats v4.0.4 https://rdrr.io/r/stats/stats-package.html https://rdrr.io/r/stats/stats-package.html
Other
The indexed reference GRCm38 (June 2017, Ensembl) https://www.ensembl.org/index.html https://www.ensembl.org/index.html
Ensembl genes GRCh38.p13, Downloaded June 6, 2020 http://www.ensembl.org/biomart/martview http://www.ensembl.org/biomart/martview
GWAS-associated genes downloaded from DisGeNET (data downloaded on February 9, 2021) https://www.disgenet.org/ https://www.disgenet.org/