| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| CD4 | Biolegend | Cat#300541; RRID: AB_2562809 |
| CD20 | Biolegend | Cat#302343; RRID: AB_2562816 |
| CD16 | Biolegend | Cat#302051; RRID: AB_2562814 |
| CD123 | Biolegend | Cat#306002; RRID: AB_314576 |
| CD69 | Biolegend | Cat#310939; RRID: AB_2562827 |
| CD14 | Biolegend | Cat#301843; RRID: AB_2562813 |
| CCR6 | Biolegend | Cat#353402; RRID: AB_10918625 |
| CCR4 | Biolegend | Cat#131202; RRID: AB_1227524 |
| CD8 | Biolegend | Cat#301053; RRID: AB_2562810 |
| CD62L | Biolegend | Cat#304802; RRID: AB_314462 |
| IL-10R | Biolegend | Cat#308802; RRID: AB_314734 |
| CD138 | Fluidigm | Cat#3150012B; RRID: AB_2756417 |
| CD56 | BD | Cat#559043; RRID: AB_397180 |
| CCR2 | Biolegend | Cat#357202; RRID: AB_2561851 |
| Adalimumab | AbbVie | Humira 40mg injection |
| CCR9 | Biolegend | Cat#358902; RRID: AB_2562298 |
| CD19 | Biolegend | Cat#302247; RRID: AB_2562815 |
| CD45RO | Biolegend | Cat#304239; RRID: AB_2563752 |
| CD38 | Biolegend | Cat#303535; RRID: AB_2562819 |
| CD25 | Fluidigm | Cat#3169003B; RRID: AB_2661806 |
| CD3 | Biolegend | Cat#300443; RRID: AB_2562808 |
| CD11b | Biolegend | Cat#301302; RRID: AB_314154 |
| CD45 | Biolegend | Cat#304045; RRID: AB_2562821 |
| TNFR2 | Biolegend | Cat#358402; RRID: AB_2562150 |
| CD103AE | Biolegend | Cat#350202; RRID: AB_10639864 |
| CXCR4 | Biolegend | Cat#306502; RRID: AB_314608 |
| TCRgd | Fluidigm | Cat#3152008B; RRID: AB_2687643 |
| IntegrinB7 | Biolegend | Cat#321202; RRID: AB_571975 |
| CD33 | eBioscience | Cat#14-0338-82; RRID: AB_467206 |
| CD45RA | Biolegend | Cat#304143; RRID: AB_2562822 |
| CD161 | Biolegend | Cat#339902; RRID: AB_1501090 |
| CD28 | Biolegend | Cat#302914; RRID: AB_314316 |
| CD66b | Biolegend | Cat#305102; RRID: AB_314494 |
| HLA-DR | Biolegend | Cat#307651; RRID: AB_2562826 |
| Infliximab | Janssen | Remicade 100mg |
| CD27 | Biolegend | Cat#302802; RRID: AB_314294 |
| CCR7 | Biolegend | Cat#353237; RRID: AB_2563726 |
| RAC1-Ser71 | Merck-Millipore | Cat#07–896; RRID: AB_612043 |
| IL-23R | R&D Systems | Cat#MAB14001; RRID: AB_2124779 |
| PAK 1/2/3 phospho T423 | Rockland | Cat#600-401-413; RRID: AB_2096533 |
| Integrin alpha 4 beta 7/LPAM-1 | R&D Systems | Cat#MAB10078; RRID: AB_827437 |
| Biological samples | ||
| Primary CD cohort: 24 Crohn’s disease (CD) patients who received IFX treatment. Includes 15 and 9 responding and non-responding patients respectively. samples were obtained at three time points: at baseline, before IFX treatment, and two and fourteen weeks post first treatment | the gastroenterology department of the Rambam Health Care Campus (RHCC) | N/A |
| Validation CD cohort: 29 CD patients from the RHCC, which were classified to 20 and 9 clinical responding and non-responding respectively patients | the gastroenterology department of the Rambam Health Care Campus (RHCC) | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| Fetal Bovine Serum | Biological Industries | Cat#04-121-1A |
| MaxPar Intercalator | Fluidigm Inc. | Cat#201192B |
| Formaldehyde | Thermo Scientific | Cat#28908 |
| PAXgene Blood RNA tubes | PreAnalytiX | Cat#762165 |
| Affymetrix Clariom S chips | Thermo Fisher Scientific | Cat#902927 |
| ProcartaPlex™ Immunoassay, | eBioscience | EPX450-12171-901 |
| UNI-SEPmaxi+ tubes | Novamed Ltd. | Cat#u-16 |
| DMSO | Sigma-Aldrich | Cat#D2650 |
| FCS | Biological industries | Cat#04-007-1A |
| PBS | Biological industries (Sartorius) | Cat#02-023-5A |
| Isopropyl alcohol | Sigma-Aldrich | Cat#I9030 |
| SmartTube | SMART TUBE Inc. | Cat#MTS1P |
| Mr. Frost® Freezing Container | ThermoFisher scientific | Cat#5100-0001 |
| RPMI 1640 | Biological industries (Sartorius) | Cat#01-100-1A |
| Pierce™ Universal Nuclease for Cell Lysis | Thermo Fisher Scientific | Cat#88700 |
| Cell-ID™ 20-Plex Pd Barcoding Kit | Standard Bio Tools | Cat#201060 |
| Chromium Next GEM Single Cell 3′ Library & Gel Bead Kit v3.1 | Illumina | Cat#PN-1000121 |
| Chromium Next GEM Chip G Single Cell Kit | Illumina | Cat#PN-1000120 |
| NextSeq 500/550 High Output v2 Kit (75 cycles) | Illumina | Cat#FC-404-2005 |
| RNeasy mini kit | Qiagen | Cat#74104 |
| Sequences of qPCR primers are listed in Table S10 | Sigma-Aldrich | N/A |
| Maxima first strand cDNA synthesis kit | Thermo Fisher Scientific | Cat#K1672 |
| RNase free DNase set | Qiagen | Cat# 79254 |
| KAPA SYBR FAST qPCR Kit | Kapa Biosystems | Cat#KK4604 |
| Deposited data | ||
| Microarray raw data - blood - IFX responders and non-responders at baseline, 2w and 14w post first treatment | This study, Table S1 | GEO: GSE186963 |
| CyTOF data - blood - IFX responders and non-responders at baseline, 2w and 14w post first treatment | This study, Table S1 | FlowRepository: FR-FCM-Z4MQ |
| Luminex data - blood - IFX responders and non-responders at baseline, 2w and 14w post first treatment | This study, Table S1 | data directory, https://github.com/shenorrLabTRDF/Disruption_Networks |
| External reference expression data for construction of the IBD inflammatory axis | Planell N et al. 2017 | GSE94648 |
| single cell expression data- PBMCs of representative responder and non-responder at baseline | This study | SRA: PRJNA779701 |
| Rheumatoid arthritis public expression datasets for validation of the IFX predictive signatures | Tanino et al.14, Toonen et al.15, Mesko et al..16 |
GSE20690 GSE33377 GSE42296 |
| Software and algorithms | ||
| R | https://www.cran.r-project.org | v4.3.1 |
| R Studio | https://www.rstudio.com/ | N/A |
| Original code used to generate this study’s figures (R scripts) | This Study; https://github.com/shenorrLabTRDF/Disruption_Networks | N/A |
| Cytobank premium | https://www.cytobank.org | N/A |
| Cell Ranger | 10X Genomics | v4.0.0 |
| Biobase (R package) | https://bioconductor.org/packages/release/bioc/html/Biobase.html | v2.60.0 |
| oligoClasses (R package) | https://bioconductor.org/packages/release/bioc/html/oligoClasses.html | v1.62.0 |
| oligo (R package) | https://www.bioconductor.org/packages/release/bioc/html/oligo.html | v1.64.1 |
| pd.clariom.s.human (R package) | https://bioconductor.org/packages/release/data/annotation/html/pd.clariom.s.human.html | v3.14.1 |
| clariomshumantranscriptcluster.db (R package) | https://bioconductor.org/packages/release/data/annotation/html/clariomshumantranscriptcluster.db.html | v8.8.0 |
| affycoretools (R package) | https://www.bioconductor.org/packages/release/bioc/html/affycoretools.html | v1.72.0 |
| genefilter (R package) | https://bioconductor.org/packages/release/bioc/html/genefilter.html | v1.82.1 |
| sva (R package) | https://www.bioconductor.org/packages/release/bioc/html/sva.html | v3.48.0 |
| plyr (R package) | https://cran.r-project.org/web/packages/plyr/index.html | v1.8.8 |
| hgu133plus2.db (R package) | https://bioconductor.org/packages/release/data/annotation/html/hgu133plus2.db.html | v3.13.0 |
| citrus (R package) | https://github.com/nolanlab/citrus | v0.08 |
| ComplexHeatmap (R package) | https://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html | v2.16.0 |
| data.table (R package) | https://cran.r-project.org/web/packages/data.table/index.html | v1.14.8 |
| XLConnect (R package) | https://cran.r-project.org/web/packages/XLConnect/index.html | v1.0.7 |
| reshape2 (R package) | https://cran.r-project.org/web/packages/reshape2/index.html | v1.4.4 |
| foreach (R package) | https://cran.r-project.org/web/packages/foreach/index.html | v1.5.2 |
| doParallel (R package) | https://cran.r-project.org/web/packages/doParallel/index.html | v 1.0.17 |
| permute (R package) | https://cran.r-project.org/web/packages/permute/index.html | v0.9-7 |
| gridExtra (R package) | https://cran.r-project.org/web/packages/gridExtra/index.html | v2.3 |
| GEOquery (R package) | https://bioconductor.org/packages/release/bioc/html/GEOquery.html | v2.68.0 |
| org.Hs.e.g.,.db (R package) | https://bioconductor.org/packages/release/data/annotation/html/org.Hs.eg.db.html | v3.17.0 |
| limma (R package) | https://bioconductor.org/packages/release/bioc/html/limma.html | v3.56.2 |
| glmnet (R package) | https://cran.r-project.org/web/packages/glmnet/index.html | v4.1-7 |
| glmnetcr (R package) | https://cran.r-project.org/web/packages/glmnetcr/index.html | v1.0.6 |
| scales (R package) | https://cran.r-project.org/web/packages/scales/index.html | v1.2.1 |
| ggplot2 (R package) | https://cran.r-project.org/web/packages/ggplot2/index.html | v3.4.2 |
| ggpubr (R package) | https://cran.r-project.org/web/packages/ggpubr/index.html | v0.6.0 |
| ggrepel (R package) | https://cran.r-project.org/web/packages/ggrepel/index.html | v0.9.3 |
| dplyr (R package) | https://cran.r-project.org/web/packages/dplyr/index.html | v1.1.2 |
| gtools (R package) | https://cran.r-project.org/web/packages/gtools/index.html | v3.9.4 |
| rstatix (R package) | https://cran.r-project.org/web/packages/rstatix/index.html | v0.7.2 |
| VennDiagram (R package) | https://cran.r-project.org/web/packages/VennDiagram/index.html | v1.7.3 |
| Hmisc (R package) | https://cran.r-project.org/web/packages/Hmisc/index.html | v5.1-0 |
| CellMix (R package) | https://github.com/r-forge/cellmix/blob/master/pkg/CellMix | v1.5.1 |
| fgsea (R package) | https://bioconductor.org/packages/release/bioc/html/fgsea.html | v1.26.0 |
| ggbeeswarm (R package) | https://cran.r-project.org/web/packages/ggbeeswarm/index.html | v0.7.2 |
| gage (R package) | https://bioconductor.org/packages/release/bioc/html/gage.html | v2.50.0 |
| xbioc (R package) | https://rdrr.io/github/renozao/xbioc/ | v0.1.19 |
| omics (R package) | https://cran.r-project.org/web/packages/omics/index.html | v0.1-5 |
| AnnotationDbi (R package) | https://bioconductor.org/packages/release/bioc/html/AnnotationDbi.html | v1.62.2 |
| igraph (R package) | https://cran.r-project.org/web/packages/igraph/index.html | v1.5.1 |
| psych (R package) | https://cran.r-project.org/web/packages/psych/index.html | v2.3.6 |
| ggforce (R package) | https://cran.r-project.org/web/packages/ggforce/index.html | v0.4.1 |
| rlist (R package) | https://cran.r-project.org/web/packages/rlist/index.html | v0.4.6.2 |
| circlize (R package) | https://cran.r-project.org/web/packages/circlize/index.html | v0.4.15 |
| pROC (R package) | https://cran.r-project.org/web/packages/pROC/index.html | v1.18.4 |
| ROCR (R package) | https://cran.r-project.org/web/packages/ROCR/index.html | v1.0-11 |
| Seurat (R package) | https://cran.r-project.org/web/packages/Seurat/index.html | v4.3.0.1 |
| SingleR (R package) | https://bioconductor.org/packages/release/bioc/html/SingleR.html | v2.2.0 |
| MTGOsc (R package) | https://github.com/ne1s0n/MTGOsc | N/A |
| ReactomePA (R package) | https://bioconductor.org/packages/release/bioc/html/ReactomePA.html | v1.44.0 |
| clusterProfiler (R package) | https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html | v4.8.2 |
| caret (R package) | http://cran.nexr.com/web/packages/caret/index.html | v6.0-78 |
| nsROC (R package) | https://cran.r-project.org/web/packages/nsROC/index.html | v1.1 |
| RColorBrewer (R package) | https://cran.r-project.org/web/packages/RColorBrewer/index.html | v1.1-3 |
| huex10sttranscriptcluster.db (R package) | https://bioconductor.org/packages/release/data/annotation/html/huex10sttranscriptcluster.db.html | v8.8.0 |
| Other | ||
| CyTOF 1 | Fluidigm Inc. | N/A |
| CyTOF software | Fluidigm Inc. | N/A |
| Helios Mass Cytometer | Standard Bio Tools | N/A |
| 7300 Real-Time PCR System | AB Applied B1iosystems | N/A |
| Illumina NextSeq500 | Illumina | N/A |
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