other:Article Title: Combinatorial Single-Cell Analyses of Granulocyte-Monocyte Progenitor Heterogeneity Reveals an Early Uni-potent Neutrophil Progenitor.
Article Snippet: Koeffler (Kyme et al., 2012) Software and Algorithms GraphPad Prism 7 GraphPad Software http://www.graphpad.com FlowJo 10 TreeStar http://flowjo.com/ t-SNE (Van Der Maaten and Hinton, 2008) https://cran.r-project.org/web/packages/ Rtsne/index.html edgeR (Robinson et al., 2010) https://bioconductor.org/packages/ release/bioc/html/edgeR.html pheatmap R package https://cran.r-project.org/web/packages/ pheatmap/index.html Enrichr (Chen et al., 2013) http://amp.pharm.mssm.edu/Enrichr/ Monocle 2 (Qiu et al., 2017) http://cole-trapnell-lab.github.io/monocle- release/docs/ Seurat v3 (Stuart et al., 2019) https://github.com/satijalab/seurat UMAP (McInnes et al., 2018) https://umap-learn.readthedocs.io/en/ latest/ SVM regression used in InfinityFlow The R foundation https://cran.r-project.org/web/ packages/e1071/ R 3.6 The R foundation https://www.r-project.org/
Article Title: Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Biomart Version 92 Ensembl RRID: SCR_002344; https://www.ensembl.org/ biomart/martview/ pROC Version 1.12.1 CRAN https://cran.r-project.org/web/packages/ pROC/index.html clusterProfiler Version 3.8.1 R Bioconductor https://github.com/GuangchuangYu/ clusterProfiler Destiny Version 2.10.2 R Bioconductor https://www.helmholtz-muenchen.de/icb/ destiny FastQC (v0.10.1) Babraham Bioinformatics RRID: SCR_014583; http://www.bioinformatics. babraham.ac.uk/projects/fastqc/ FeatureCounts (v1.5.0) Source Forge RRID: SCR_012919; http://subread. sourceforge.net HISAT (v2.0.3b) Kim et al., 2015 RRID: SCR_015530; https://ccb.jhu.edu/ software/hisat/index.shtml MultiQC (v0.7) Ewels et al., 2016 RRID: SCR_014982; http://multiqc.info NMF (v0.20.6) CRAN https://cran.r-project.org/web/packages/NMF/ index.html Picard Tools (v2.3.0) Github RRID: SCR_006525; http://broadinstitute. github.io/picard/ RUVSeq (v1.8.0) Github RRID: SCR_006263; https://github.com/drisso/ RUVSeq scater (v1.2.0) Github RRID: SCR_015954; https://github.com/ davismcc/scater Skewer Github RRID: SCR_001151; https://github.com/ relipmoc/skewer RTsne CRAN RRID: SCR_016342; https://cran.r-project.org/ web/packages/Rtsne/index.html WGCNA (v1.51) CRAN RRID: SCR_003302; https://cran.r-project.org/ web/packages/WGCNA/index.html RandomForest Version 4.6 CRAN RRID: SCR_015718; https://cran.r-project.org/ web/packages/randomForest/index.html Other ACD HybEZ Hybridization System (220v) ACD Europe SRL Cat#310013 Hg38 reference genome UCSC http://hgdownload.cse.ucsc.edu/goldenPath/ hg38/bigZips/ Mm10 reference genome UCSC http://hgdownload.cse.ucsc.edu/goldenPath/ mm10/bigZips/
Multiplex Assay:Article Title: Combinatorial Single-Cell Analyses of Granulocyte-Monocyte Progenitor Heterogeneity Reveals an Early Uni-potent Neutrophil Progenitor.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER EQ Four Element Calibration Beads Fluidigm Cat# 201078 Human G-CSF (Neupogen) Amgen Cat# 100696800 MethoCult M3234 Stem Cell Technologies Cat# 03234 StemSpan SFEM II Stem Cell Technologies Cat# 09655 Critical Commercial Assays ERCC RNA Spike-In Mix Thermo Fisher Cat# 4456740 MILLIPLEX MAP Mouse Cytokine/Chemokine Magnetic Bead Panel - Premixed 32 Plex - Immunology Multiplex Assay Merck Cat# MCYTMAG-70K-PX32 LEGENDScreen Human Kit Biolegend Cat# 700007 LEGENDScreen Mouse Kit Biolegend Cat# 70000 Arcturus PicoPure RNA isolation kit Thermo Fisher Cat# KIT0214 Deposited Data Bulk RNA-seq of myeloid progenitor populations This paper GEO: GSE151682 Smart-Seq2 Single-cell Dataset of myeloid precursors This paper GEO: GSE151630 Tabula Muris BM 10x single-cell RNA-seq dataset (Schaum et al., 2018) GEO: GSE109774 Single-cell RNA-seq of BM GMPs (Olsson et al., 2016) GEO: GSE70240 Experimental Models: Organisms/Strains Mouse: C57BL/6J The Jackson Laboratory Stock No: 000664 Mouse: Rosa26mT/mG: STOCK Gt(ROSA)26Sortm4(ACTB-tdTomato,-EGFP)Luo/J The Jackson Laboratory Stock No: 007676 Mouse: Fucci-S/G2/M (#474) RIKEN BRC, Ibaraki, Japan Stock No: RBRC02704 Mouse: C57BL/6-Tg(UBC-GFP)30Scha/J; UBI-GFP The Jackson Laboratory Stock No: 04353 Mouse: B6.SJL-Ptprca Pepcb/BoyJ; B6 Cd45.1 The Jackson Laboratory Stock No: 002014 Mouse: Cebpe / H.P. .. Koeffler (Kyme et al., 2012) Software and Algorithms GraphPad Prism 7 GraphPad Software http://www.graphpad.com FlowJo 10 TreeStar http://flowjo.com/ t-SNE (Van Der Maaten and Hinton, 2008) https://cran.r-project.org/web/packages/ Rtsne/index.html edgeR (Robinson et al., 2010) https://bioconductor.org/packages/ release/bioc/html/edgeR.html pheatmap R package https://cran.r-project.org/web/packages/ pheatmap/index.html Enrichr (Chen et al., 2013) http://amp.pharm.mssm.edu/Enrichr/ Monocle 2 (Qiu et al., 2017) http://cole-trapnell-lab.github.io/monocle- release/docs/ Seurat v3 (Stuart et al., 2019) https://github.com/satijalab/seurat UMAP (McInnes et al., 2018) https://umap-learn.readthedocs.io/en/ latest/ SVM regression used in InfinityFlow The R foundation https://cran.r-project.org/web/ packages/e1071/ R 3.6 The R foundation https://www.r-project.org/
Isolation:Article Title: Combinatorial Single-Cell Analyses of Granulocyte-Monocyte Progenitor Heterogeneity Reveals an Early Uni-potent Neutrophil Progenitor.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER EQ Four Element Calibration Beads Fluidigm Cat# 201078 Human G-CSF (Neupogen) Amgen Cat# 100696800 MethoCult M3234 Stem Cell Technologies Cat# 03234 StemSpan SFEM II Stem Cell Technologies Cat# 09655 Critical Commercial Assays ERCC RNA Spike-In Mix Thermo Fisher Cat# 4456740 MILLIPLEX MAP Mouse Cytokine/Chemokine Magnetic Bead Panel - Premixed 32 Plex - Immunology Multiplex Assay Merck Cat# MCYTMAG-70K-PX32 LEGENDScreen Human Kit Biolegend Cat# 700007 LEGENDScreen Mouse Kit Biolegend Cat# 70000 Arcturus PicoPure RNA isolation kit Thermo Fisher Cat# KIT0214 Deposited Data Bulk RNA-seq of myeloid progenitor populations This paper GEO: GSE151682 Smart-Seq2 Single-cell Dataset of myeloid precursors This paper GEO: GSE151630 Tabula Muris BM 10x single-cell RNA-seq dataset (Schaum et al., 2018) GEO: GSE109774 Single-cell RNA-seq of BM GMPs (Olsson et al., 2016) GEO: GSE70240 Experimental Models: Organisms/Strains Mouse: C57BL/6J The Jackson Laboratory Stock No: 000664 Mouse: Rosa26mT/mG: STOCK Gt(ROSA)26Sortm4(ACTB-tdTomato,-EGFP)Luo/J The Jackson Laboratory Stock No: 007676 Mouse: Fucci-S/G2/M (#474) RIKEN BRC, Ibaraki, Japan Stock No: RBRC02704 Mouse: C57BL/6-Tg(UBC-GFP)30Scha/J; UBI-GFP The Jackson Laboratory Stock No: 04353 Mouse: B6.SJL-Ptprca Pepcb/BoyJ; B6 Cd45.1 The Jackson Laboratory Stock No: 002014 Mouse: Cebpe / H.P. .. Koeffler (Kyme et al., 2012) Software and Algorithms GraphPad Prism 7 GraphPad Software http://www.graphpad.com FlowJo 10 TreeStar http://flowjo.com/ t-SNE (Van Der Maaten and Hinton, 2008) https://cran.r-project.org/web/packages/ Rtsne/index.html edgeR (Robinson et al., 2010) https://bioconductor.org/packages/ release/bioc/html/edgeR.html pheatmap R package https://cran.r-project.org/web/packages/ pheatmap/index.html Enrichr (Chen et al., 2013) http://amp.pharm.mssm.edu/Enrichr/ Monocle 2 (Qiu et al., 2017) http://cole-trapnell-lab.github.io/monocle- release/docs/ Seurat v3 (Stuart et al., 2019) https://github.com/satijalab/seurat UMAP (McInnes et al., 2018) https://umap-learn.readthedocs.io/en/ latest/ SVM regression used in InfinityFlow The R foundation https://cran.r-project.org/web/ packages/e1071/ R 3.6 The R foundation https://www.r-project.org/
RNA Sequencing:Article Title: Combinatorial Single-Cell Analyses of Granulocyte-Monocyte Progenitor Heterogeneity Reveals an Early Uni-potent Neutrophil Progenitor.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER EQ Four Element Calibration Beads Fluidigm Cat# 201078 Human G-CSF (Neupogen) Amgen Cat# 100696800 MethoCult M3234 Stem Cell Technologies Cat# 03234 StemSpan SFEM II Stem Cell Technologies Cat# 09655 Critical Commercial Assays ERCC RNA Spike-In Mix Thermo Fisher Cat# 4456740 MILLIPLEX MAP Mouse Cytokine/Chemokine Magnetic Bead Panel - Premixed 32 Plex - Immunology Multiplex Assay Merck Cat# MCYTMAG-70K-PX32 LEGENDScreen Human Kit Biolegend Cat# 700007 LEGENDScreen Mouse Kit Biolegend Cat# 70000 Arcturus PicoPure RNA isolation kit Thermo Fisher Cat# KIT0214 Deposited Data Bulk RNA-seq of myeloid progenitor populations This paper GEO: GSE151682 Smart-Seq2 Single-cell Dataset of myeloid precursors This paper GEO: GSE151630 Tabula Muris BM 10x single-cell RNA-seq dataset (Schaum et al., 2018) GEO: GSE109774 Single-cell RNA-seq of BM GMPs (Olsson et al., 2016) GEO: GSE70240 Experimental Models: Organisms/Strains Mouse: C57BL/6J The Jackson Laboratory Stock No: 000664 Mouse: Rosa26mT/mG: STOCK Gt(ROSA)26Sortm4(ACTB-tdTomato,-EGFP)Luo/J The Jackson Laboratory Stock No: 007676 Mouse: Fucci-S/G2/M (#474) RIKEN BRC, Ibaraki, Japan Stock No: RBRC02704 Mouse: C57BL/6-Tg(UBC-GFP)30Scha/J; UBI-GFP The Jackson Laboratory Stock No: 04353 Mouse: B6.SJL-Ptprca Pepcb/BoyJ; B6 Cd45.1 The Jackson Laboratory Stock No: 002014 Mouse: Cebpe / H.P. .. Koeffler (Kyme et al., 2012) Software and Algorithms GraphPad Prism 7 GraphPad Software http://www.graphpad.com FlowJo 10 TreeStar http://flowjo.com/ t-SNE (Van Der Maaten and Hinton, 2008) https://cran.r-project.org/web/packages/ Rtsne/index.html edgeR (Robinson et al., 2010) https://bioconductor.org/packages/ release/bioc/html/edgeR.html pheatmap R package https://cran.r-project.org/web/packages/ pheatmap/index.html Enrichr (Chen et al., 2013) http://amp.pharm.mssm.edu/Enrichr/ Monocle 2 (Qiu et al., 2017) http://cole-trapnell-lab.github.io/monocle- release/docs/ Seurat v3 (Stuart et al., 2019) https://github.com/satijalab/seurat UMAP (McInnes et al., 2018) https://umap-learn.readthedocs.io/en/ latest/ SVM regression used in InfinityFlow The R foundation https://cran.r-project.org/web/ packages/e1071/ R 3.6 The R foundation https://www.r-project.org/
Single Cell:Article Title: Combinatorial Single-Cell Analyses of Granulocyte-Monocyte Progenitor Heterogeneity Reveals an Early Uni-potent Neutrophil Progenitor.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER EQ Four Element Calibration Beads Fluidigm Cat# 201078 Human G-CSF (Neupogen) Amgen Cat# 100696800 MethoCult M3234 Stem Cell Technologies Cat# 03234 StemSpan SFEM II Stem Cell Technologies Cat# 09655 Critical Commercial Assays ERCC RNA Spike-In Mix Thermo Fisher Cat# 4456740 MILLIPLEX MAP Mouse Cytokine/Chemokine Magnetic Bead Panel - Premixed 32 Plex - Immunology Multiplex Assay Merck Cat# MCYTMAG-70K-PX32 LEGENDScreen Human Kit Biolegend Cat# 700007 LEGENDScreen Mouse Kit Biolegend Cat# 70000 Arcturus PicoPure RNA isolation kit Thermo Fisher Cat# KIT0214 Deposited Data Bulk RNA-seq of myeloid progenitor populations This paper GEO: GSE151682 Smart-Seq2 Single-cell Dataset of myeloid precursors This paper GEO: GSE151630 Tabula Muris BM 10x single-cell RNA-seq dataset (Schaum et al., 2018) GEO: GSE109774 Single-cell RNA-seq of BM GMPs (Olsson et al., 2016) GEO: GSE70240 Experimental Models: Organisms/Strains Mouse: C57BL/6J The Jackson Laboratory Stock No: 000664 Mouse: Rosa26mT/mG: STOCK Gt(ROSA)26Sortm4(ACTB-tdTomato,-EGFP)Luo/J The Jackson Laboratory Stock No: 007676 Mouse: Fucci-S/G2/M (#474) RIKEN BRC, Ibaraki, Japan Stock No: RBRC02704 Mouse: C57BL/6-Tg(UBC-GFP)30Scha/J; UBI-GFP The Jackson Laboratory Stock No: 04353 Mouse: B6.SJL-Ptprca Pepcb/BoyJ; B6 Cd45.1 The Jackson Laboratory Stock No: 002014 Mouse: Cebpe / H.P. .. Koeffler (Kyme et al., 2012) Software and Algorithms GraphPad Prism 7 GraphPad Software http://www.graphpad.com FlowJo 10 TreeStar http://flowjo.com/ t-SNE (Van Der Maaten and Hinton, 2008) https://cran.r-project.org/web/packages/ Rtsne/index.html edgeR (Robinson et al., 2010) https://bioconductor.org/packages/ release/bioc/html/edgeR.html pheatmap R package https://cran.r-project.org/web/packages/ pheatmap/index.html Enrichr (Chen et al., 2013) http://amp.pharm.mssm.edu/Enrichr/ Monocle 2 (Qiu et al., 2017) http://cole-trapnell-lab.github.io/monocle- release/docs/ Seurat v3 (Stuart et al., 2019) https://github.com/satijalab/seurat UMAP (McInnes et al., 2018) https://umap-learn.readthedocs.io/en/ latest/ SVM regression used in InfinityFlow The R foundation https://cran.r-project.org/web/ packages/e1071/ R 3.6 The R foundation https://www.r-project.org/
Article Title: Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Maxpar X8 Antibody Labeling Kit, 150Nd Fluidigm Cat#201150B Maxpar X8 Antibody Labeling Kit, 151Eu Fluidigm Cat#201151B Maxpar X8 Antibody Labeling Kit, 152Sm Fluidigm Cat#201152A Maxpar X8 Antibody Labeling Kit, 154Sm Fluidigm Cat#201154B Maxpar X8 Antibody Labeling Kit, 159Tb Fluidigm Cat#201159B Maxpar X8 Antibody Labeling Kit, 160Gd Fluidigm Cat#201160B Maxpar X8 Antibody Labeling Kit, 162Dy Fluidigm Cat#201162B Maxpar X8 Antibody Labeling Kit, 164Dy Fluidigm Cat#201164B Maxpar X8 Antibody Labeling Kit, 166Er Fluidigm Cat#201166B Maxpar X8 Antibody Labeling Kit, 167Er Fluidigm Cat#201167B Maxpar X8 Antibody Labeling Kit, 168Er Fluidigm Cat#201168B Maxpar X8 Antibody Labeling Kit, 169Tm Fluidigm Cat#201169B Maxpar X8 Antibody Labeling Kit, 172Yb Fluidigm Cat#201172B Maxpar X8 Antibody Labeling Kit, 173Yb Fluidigm Cat#201173B Maxpar X8 Antibody Labeling Kit, 175Lu Fluidigm Cat#201175B Maxpar X8 Antibody Labeling Kit, 176Yb Fluidigm Cat#201176B Biological Samples Human intestinal tissue biopsies University of Oxford Translational Gastroenterology Unit https://www.expmedndm.ox.ac.uk/ tgu/tgu-biobank-ibd-cohort Murine colon Epistem This study Chemicals, Peptides, and Recombinant Proteins 40,6-Diamidine-20-phenylindole dihydrochloride Sigma Aldrich Cat#10236276001 Dispase II, powder ThermoFisher Scientific Cat#17105041 Matrigel Basement Membrane Matrix Growth Factor Reduced (GFR) Phenol Red-Free LDEV-Free Corning Cat#356231 SB 431542 R&D Systems Cat#1614/10 Y-27632 dihydrochloride R&D Systems Cat#1254/10 CTS GlutaMAX-I Supplement ThermoFisher Scientific Cat#A1286001 N-2 Supplement (100X) ThermoFisher Scientific Cat#17502048 B-27 Supplement (50X), serum free ThermoFisher Scientific Cat#17504044 NICOTINAMIDE Sigma Aldrich Cat#N0636 Recombinant Human EGF PeproTech Cat#AF-100 Recombinant Human IL-6 R&D Systems Cat#206-IL-010 Recombinant Human LIGHT/TNFSF14 R&D Systems Cat#664-LI-025 A 83-01 R&D Systems Cat#2939/10 [LEU15]-Gastrin I HUMAN Sigma Aldrich Cat#G9145 Prostaglandin E2 Sigma Aldrich Cat#P0409 N-Acetylcysteine Sigma Aldrich Cat#A9165 Recombinant Human R-Spondin-1 PeproTech Cat#120-38 Recombinant Murine Noggin PeproTech Cat#250-38 2.5% Normal Goat Serum Vector Laboratories Cat#S-1012 ImmPRESS HRP Anti-Rabbit IgG (Peroxidase) Polymer Detection Kit, made in Goat Vector Laboratories Cat#MP-7451; RRID: AB_2631198 ImmPRESS HRP Anti-Mouse IgG (Peroxidase) Polymer Detection Kit, made in Goat Vector Laboratories Cat#MP-7452 (Continued on next page) e2 Cell 175, 372–386.e1–e11, October 4, 2018 .. REAGENT or RESOURCE SOURCE IDENTIFIER EQ Four Element Calibration Beads Fluidigm Cat201078 Cell-ID Intercalator-Ir Fluidigm Cat#201192A Deposited Data Single-cell RNaseq data This study GEO: GSE95459 Single-cell RNaseq data This study GEO: GSE114374 Experimental Models: Cell Lines L Wnt-3A (male) ATCC Cat#CRL-2647; RRID:CVCL_0635 RAW 264.7 (male) ATCC Cat#TIB71; RRID:CVCL_0493 Experimental Models: Organisms/Strains C57BL/6 male mice Envigo Laboratories RRID:IMSR_JAX:000664 Oligonucleotides LGR5 ThermoFisher Scientific Cat#Hs00969422_m1 OLFM4 ThermoFisher Scientific Cat#Hs00610344_m1 AXIN2 ThermoFisher Scientific Cat#Hs00610344_m1 NOTCH1 ThermoFisher Scientific Cat#Hs01062014_m1 ALDH1A1 ThermoFisher Scientific Cat#Hs00946916_m1 SOX9 ThermoFisher Scientific Cat#Hs00165814_m1 MSI1 ThermoFisher Scientific Cat#Hs01045894_m1 KRT20 ThermoFisher Scientific Cat#Hs00300643_m1 MUC2 ThermoFisher Scientific Cat#Hs03005103_g1 CDX2 ThermoFisher Scientific Cat#Hs01078080_m1 HPRT1 ThermoFisher Scientific Cat#Hs02800695_m1 GAPDH ThermoFisher Scientific Cat#Hs02786624_g1 RNAscope Probe - Hs-ADAMDEC1 ACD Europe SRL Cat#478471 RNAscope Probe - Hs-DCN ACD Europe SRL Cat#589521 RNAscope Probe - Hs-SLIT2 ACD Europe SRL Cat#466221 RNAscope Probe - Hs-CXCL12 ACD Europe SRL Cat#422991 RNAscope Probe - Hs-F3 ACD Europe SRL Cat#407611 RNAscope Probe - Hs-HSD17B2 ACD Europe SRL Cat#467271 RNAscope Probe - Hs-POSTN ACD Europe SRL Cat#409181 RNAscope Probe - Hs-FRZB ACD Europe SRL Cat#412391 RNAscope Probe - Hs-WNT5A ACD Europe SRL Cat#604921 RNAscope Probe - Hs-WNT5B ACD Europe SRL Cat#423041 RNAscope Probe - Hs-BMP2 ACD Europe SRL Cat#430641 RNAscope Probe - Hs-BMP5 ACD Europe SRL Cat#472461 RNAscope Probe - Hs-FDCSP ACD Europe SRL Cat#444231 Software and Algorithms ComBat sva Version 3.28.0 R Bioconductor RRID: SCR_012836; https://bioconductor.org/ packages/release/bioc/html/sva.html CellRanger Version 2.0 Version 2.1.1 10X Genomics https://support.10xgenomics.com/single-cell- gene-expression/software/downloads/latest Seurat Version 1.4.0.16 Version 2.3.0 R Bioconductor RRID: SCR_016341; https://www.satijalab.org/ seurat Scran Version 1.2.0 Version 1.6.9 R Bioconductor https://github.com/MarioniLab/scran Caret Version 6.0-80 CRAN https://cran.r-project.org/web/packages/ caret/index.html DMrW Version 0.4.1 CRAN https://cran.r-project.org/web/packages/ DMwR/index.html (Continued on next page) e4 Cell 175, 372–386.e1–e11, October 4, 2018 .. REAGENT or RESOURCE SOURCE IDENTIFIER Biomart Version 92 Ensembl RRID: SCR_002344; https://www.ensembl.org/ biomart/martview/ pROC Version 1.12.1 CRAN https://cran.r-project.org/web/packages/ pROC/index.html clusterProfiler Version 3.8.1 R Bioconductor https://github.com/GuangchuangYu/ clusterProfiler Destiny Version 2.10.2 R Bioconductor https://www.helmholtz-muenchen.de/icb/ destiny FastQC (v0.10.1) Babraham Bioinformatics RRID: SCR_014583; http://www.bioinformatics. babraham.ac.uk/projects/fastqc/ FeatureCounts (v1.5.0) Source Forge RRID: SCR_012919; http://subread. sourceforge.net HISAT (v2.0.3b) Kim et al., 2015 RRID: SCR_015530; https://ccb.jhu.edu/ software/hisat/index.shtml MultiQC (v0.7) Ewels et al., 2016 RRID: SCR_014982; http://multiqc.info NMF (v0.20.6) CRAN https://cran.r-project.org/web/packages/NMF/ index.html Picard Tools (v2.3.0) Github RRID: SCR_006525; http://broadinstitute. github.io/picard/ RUVSeq (v1.8.0) Github RRID: SCR_006263; https://github.com/drisso/ RUVSeq scater (v1.2.0) Github RRID: SCR_015954; https://github.com/ davismcc/scater Skewer Github RRID: SCR_001151; https://github.com/ relipmoc/skewer RTsne CRAN RRID: SCR_016342; https://cran.r-project.org/ web/packages/Rtsne/index.html WGCNA (v1.51) CRAN RRID: SCR_003302; https://cran.r-project.org/ web/packages/WGCNA/index.html RandomForest Version 4.6 CRAN RRID: SCR_015718; https://cran.r-project.org/ web/packages/randomForest/index.html Other ACD HybEZ Hybridization System (220v) ACD Europe SRL Cat#310013 Hg38 reference genome UCSC http://hgdownload.cse.ucsc.edu/goldenPath/ hg38/bigZips/ Mm10 reference genome UCSC http://hgdownload.cse.ucsc.edu/goldenPath/ mm10/bigZips/
RNA sequencing:Article Title: Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Maxpar X8 Antibody Labeling Kit, 150Nd Fluidigm Cat#201150B Maxpar X8 Antibody Labeling Kit, 151Eu Fluidigm Cat#201151B Maxpar X8 Antibody Labeling Kit, 152Sm Fluidigm Cat#201152A Maxpar X8 Antibody Labeling Kit, 154Sm Fluidigm Cat#201154B Maxpar X8 Antibody Labeling Kit, 159Tb Fluidigm Cat#201159B Maxpar X8 Antibody Labeling Kit, 160Gd Fluidigm Cat#201160B Maxpar X8 Antibody Labeling Kit, 162Dy Fluidigm Cat#201162B Maxpar X8 Antibody Labeling Kit, 164Dy Fluidigm Cat#201164B Maxpar X8 Antibody Labeling Kit, 166Er Fluidigm Cat#201166B Maxpar X8 Antibody Labeling Kit, 167Er Fluidigm Cat#201167B Maxpar X8 Antibody Labeling Kit, 168Er Fluidigm Cat#201168B Maxpar X8 Antibody Labeling Kit, 169Tm Fluidigm Cat#201169B Maxpar X8 Antibody Labeling Kit, 172Yb Fluidigm Cat#201172B Maxpar X8 Antibody Labeling Kit, 173Yb Fluidigm Cat#201173B Maxpar X8 Antibody Labeling Kit, 175Lu Fluidigm Cat#201175B Maxpar X8 Antibody Labeling Kit, 176Yb Fluidigm Cat#201176B Biological Samples Human intestinal tissue biopsies University of Oxford Translational Gastroenterology Unit https://www.expmedndm.ox.ac.uk/ tgu/tgu-biobank-ibd-cohort Murine colon Epistem This study Chemicals, Peptides, and Recombinant Proteins 40,6-Diamidine-20-phenylindole dihydrochloride Sigma Aldrich Cat#10236276001 Dispase II, powder ThermoFisher Scientific Cat#17105041 Matrigel Basement Membrane Matrix Growth Factor Reduced (GFR) Phenol Red-Free LDEV-Free Corning Cat#356231 SB 431542 R&D Systems Cat#1614/10 Y-27632 dihydrochloride R&D Systems Cat#1254/10 CTS GlutaMAX-I Supplement ThermoFisher Scientific Cat#A1286001 N-2 Supplement (100X) ThermoFisher Scientific Cat#17502048 B-27 Supplement (50X), serum free ThermoFisher Scientific Cat#17504044 NICOTINAMIDE Sigma Aldrich Cat#N0636 Recombinant Human EGF PeproTech Cat#AF-100 Recombinant Human IL-6 R&D Systems Cat#206-IL-010 Recombinant Human LIGHT/TNFSF14 R&D Systems Cat#664-LI-025 A 83-01 R&D Systems Cat#2939/10 [LEU15]-Gastrin I HUMAN Sigma Aldrich Cat#G9145 Prostaglandin E2 Sigma Aldrich Cat#P0409 N-Acetylcysteine Sigma Aldrich Cat#A9165 Recombinant Human R-Spondin-1 PeproTech Cat#120-38 Recombinant Murine Noggin PeproTech Cat#250-38 2.5% Normal Goat Serum Vector Laboratories Cat#S-1012 ImmPRESS HRP Anti-Rabbit IgG (Peroxidase) Polymer Detection Kit, made in Goat Vector Laboratories Cat#MP-7451; RRID: AB_2631198 ImmPRESS HRP Anti-Mouse IgG (Peroxidase) Polymer Detection Kit, made in Goat Vector Laboratories Cat#MP-7452 (Continued on next page) e2 Cell 175, 372–386.e1–e11, October 4, 2018 .. REAGENT or RESOURCE SOURCE IDENTIFIER EQ Four Element Calibration Beads Fluidigm Cat201078 Cell-ID Intercalator-Ir Fluidigm Cat#201192A Deposited Data Single-cell RNaseq data This study GEO: GSE95459 Single-cell RNaseq data This study GEO: GSE114374 Experimental Models: Cell Lines L Wnt-3A (male) ATCC Cat#CRL-2647; RRID:CVCL_0635 RAW 264.7 (male) ATCC Cat#TIB71; RRID:CVCL_0493 Experimental Models: Organisms/Strains C57BL/6 male mice Envigo Laboratories RRID:IMSR_JAX:000664 Oligonucleotides LGR5 ThermoFisher Scientific Cat#Hs00969422_m1 OLFM4 ThermoFisher Scientific Cat#Hs00610344_m1 AXIN2 ThermoFisher Scientific Cat#Hs00610344_m1 NOTCH1 ThermoFisher Scientific Cat#Hs01062014_m1 ALDH1A1 ThermoFisher Scientific Cat#Hs00946916_m1 SOX9 ThermoFisher Scientific Cat#Hs00165814_m1 MSI1 ThermoFisher Scientific Cat#Hs01045894_m1 KRT20 ThermoFisher Scientific Cat#Hs00300643_m1 MUC2 ThermoFisher Scientific Cat#Hs03005103_g1 CDX2 ThermoFisher Scientific Cat#Hs01078080_m1 HPRT1 ThermoFisher Scientific Cat#Hs02800695_m1 GAPDH ThermoFisher Scientific Cat#Hs02786624_g1 RNAscope Probe - Hs-ADAMDEC1 ACD Europe SRL Cat#478471 RNAscope Probe - Hs-DCN ACD Europe SRL Cat#589521 RNAscope Probe - Hs-SLIT2 ACD Europe SRL Cat#466221 RNAscope Probe - Hs-CXCL12 ACD Europe SRL Cat#422991 RNAscope Probe - Hs-F3 ACD Europe SRL Cat#407611 RNAscope Probe - Hs-HSD17B2 ACD Europe SRL Cat#467271 RNAscope Probe - Hs-POSTN ACD Europe SRL Cat#409181 RNAscope Probe - Hs-FRZB ACD Europe SRL Cat#412391 RNAscope Probe - Hs-WNT5A ACD Europe SRL Cat#604921 RNAscope Probe - Hs-WNT5B ACD Europe SRL Cat#423041 RNAscope Probe - Hs-BMP2 ACD Europe SRL Cat#430641 RNAscope Probe - Hs-BMP5 ACD Europe SRL Cat#472461 RNAscope Probe - Hs-FDCSP ACD Europe SRL Cat#444231 Software and Algorithms ComBat sva Version 3.28.0 R Bioconductor RRID: SCR_012836; https://bioconductor.org/ packages/release/bioc/html/sva.html CellRanger Version 2.0 Version 2.1.1 10X Genomics https://support.10xgenomics.com/single-cell- gene-expression/software/downloads/latest Seurat Version 1.4.0.16 Version 2.3.0 R Bioconductor RRID: SCR_016341; https://www.satijalab.org/ seurat Scran Version 1.2.0 Version 1.6.9 R Bioconductor https://github.com/MarioniLab/scran Caret Version 6.0-80 CRAN https://cran.r-project.org/web/packages/ caret/index.html DMrW Version 0.4.1 CRAN https://cran.r-project.org/web/packages/ DMwR/index.html (Continued on next page) e4 Cell 175, 372–386.e1–e11, October 4, 2018 .. REAGENT or RESOURCE SOURCE IDENTIFIER Biomart Version 92 Ensembl RRID: SCR_002344; https://www.ensembl.org/ biomart/martview/ pROC Version 1.12.1 CRAN https://cran.r-project.org/web/packages/ pROC/index.html clusterProfiler Version 3.8.1 R Bioconductor https://github.com/GuangchuangYu/ clusterProfiler Destiny Version 2.10.2 R Bioconductor https://www.helmholtz-muenchen.de/icb/ destiny FastQC (v0.10.1) Babraham Bioinformatics RRID: SCR_014583; http://www.bioinformatics. babraham.ac.uk/projects/fastqc/ FeatureCounts (v1.5.0) Source Forge RRID: SCR_012919; http://subread. sourceforge.net HISAT (v2.0.3b) Kim et al., 2015 RRID: SCR_015530; https://ccb.jhu.edu/ software/hisat/index.shtml MultiQC (v0.7) Ewels et al., 2016 RRID: SCR_014982; http://multiqc.info NMF (v0.20.6) CRAN https://cran.r-project.org/web/packages/NMF/ index.html Picard Tools (v2.3.0) Github RRID: SCR_006525; http://broadinstitute. github.io/picard/ RUVSeq (v1.8.0) Github RRID: SCR_006263; https://github.com/drisso/ RUVSeq scater (v1.2.0) Github RRID: SCR_015954; https://github.com/ davismcc/scater Skewer Github RRID: SCR_001151; https://github.com/ relipmoc/skewer RTsne CRAN RRID: SCR_016342; https://cran.r-project.org/ web/packages/Rtsne/index.html WGCNA (v1.51) CRAN RRID: SCR_003302; https://cran.r-project.org/ web/packages/WGCNA/index.html RandomForest Version 4.6 CRAN RRID: SCR_015718; https://cran.r-project.org/ web/packages/randomForest/index.html Other ACD HybEZ Hybridization System (220v) ACD Europe SRL Cat#310013 Hg38 reference genome UCSC http://hgdownload.cse.ucsc.edu/goldenPath/ hg38/bigZips/ Mm10 reference genome UCSC http://hgdownload.cse.ucsc.edu/goldenPath/ mm10/bigZips/
RNAscope:Article Title: Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Maxpar X8 Antibody Labeling Kit, 150Nd Fluidigm Cat#201150B Maxpar X8 Antibody Labeling Kit, 151Eu Fluidigm Cat#201151B Maxpar X8 Antibody Labeling Kit, 152Sm Fluidigm Cat#201152A Maxpar X8 Antibody Labeling Kit, 154Sm Fluidigm Cat#201154B Maxpar X8 Antibody Labeling Kit, 159Tb Fluidigm Cat#201159B Maxpar X8 Antibody Labeling Kit, 160Gd Fluidigm Cat#201160B Maxpar X8 Antibody Labeling Kit, 162Dy Fluidigm Cat#201162B Maxpar X8 Antibody Labeling Kit, 164Dy Fluidigm Cat#201164B Maxpar X8 Antibody Labeling Kit, 166Er Fluidigm Cat#201166B Maxpar X8 Antibody Labeling Kit, 167Er Fluidigm Cat#201167B Maxpar X8 Antibody Labeling Kit, 168Er Fluidigm Cat#201168B Maxpar X8 Antibody Labeling Kit, 169Tm Fluidigm Cat#201169B Maxpar X8 Antibody Labeling Kit, 172Yb Fluidigm Cat#201172B Maxpar X8 Antibody Labeling Kit, 173Yb Fluidigm Cat#201173B Maxpar X8 Antibody Labeling Kit, 175Lu Fluidigm Cat#201175B Maxpar X8 Antibody Labeling Kit, 176Yb Fluidigm Cat#201176B Biological Samples Human intestinal tissue biopsies University of Oxford Translational Gastroenterology Unit https://www.expmedndm.ox.ac.uk/ tgu/tgu-biobank-ibd-cohort Murine colon Epistem This study Chemicals, Peptides, and Recombinant Proteins 40,6-Diamidine-20-phenylindole dihydrochloride Sigma Aldrich Cat#10236276001 Dispase II, powder ThermoFisher Scientific Cat#17105041 Matrigel Basement Membrane Matrix Growth Factor Reduced (GFR) Phenol Red-Free LDEV-Free Corning Cat#356231 SB 431542 R&D Systems Cat#1614/10 Y-27632 dihydrochloride R&D Systems Cat#1254/10 CTS GlutaMAX-I Supplement ThermoFisher Scientific Cat#A1286001 N-2 Supplement (100X) ThermoFisher Scientific Cat#17502048 B-27 Supplement (50X), serum free ThermoFisher Scientific Cat#17504044 NICOTINAMIDE Sigma Aldrich Cat#N0636 Recombinant Human EGF PeproTech Cat#AF-100 Recombinant Human IL-6 R&D Systems Cat#206-IL-010 Recombinant Human LIGHT/TNFSF14 R&D Systems Cat#664-LI-025 A 83-01 R&D Systems Cat#2939/10 [LEU15]-Gastrin I HUMAN Sigma Aldrich Cat#G9145 Prostaglandin E2 Sigma Aldrich Cat#P0409 N-Acetylcysteine Sigma Aldrich Cat#A9165 Recombinant Human R-Spondin-1 PeproTech Cat#120-38 Recombinant Murine Noggin PeproTech Cat#250-38 2.5% Normal Goat Serum Vector Laboratories Cat#S-1012 ImmPRESS HRP Anti-Rabbit IgG (Peroxidase) Polymer Detection Kit, made in Goat Vector Laboratories Cat#MP-7451; RRID: AB_2631198 ImmPRESS HRP Anti-Mouse IgG (Peroxidase) Polymer Detection Kit, made in Goat Vector Laboratories Cat#MP-7452 (Continued on next page) e2 Cell 175, 372–386.e1–e11, October 4, 2018 .. REAGENT or RESOURCE SOURCE IDENTIFIER EQ Four Element Calibration Beads Fluidigm Cat201078 Cell-ID Intercalator-Ir Fluidigm Cat#201192A Deposited Data Single-cell RNaseq data This study GEO: GSE95459 Single-cell RNaseq data This study GEO: GSE114374 Experimental Models: Cell Lines L Wnt-3A (male) ATCC Cat#CRL-2647; RRID:CVCL_0635 RAW 264.7 (male) ATCC Cat#TIB71; RRID:CVCL_0493 Experimental Models: Organisms/Strains C57BL/6 male mice Envigo Laboratories RRID:IMSR_JAX:000664 Oligonucleotides LGR5 ThermoFisher Scientific Cat#Hs00969422_m1 OLFM4 ThermoFisher Scientific Cat#Hs00610344_m1 AXIN2 ThermoFisher Scientific Cat#Hs00610344_m1 NOTCH1 ThermoFisher Scientific Cat#Hs01062014_m1 ALDH1A1 ThermoFisher Scientific Cat#Hs00946916_m1 SOX9 ThermoFisher Scientific Cat#Hs00165814_m1 MSI1 ThermoFisher Scientific Cat#Hs01045894_m1 KRT20 ThermoFisher Scientific Cat#Hs00300643_m1 MUC2 ThermoFisher Scientific Cat#Hs03005103_g1 CDX2 ThermoFisher Scientific Cat#Hs01078080_m1 HPRT1 ThermoFisher Scientific Cat#Hs02800695_m1 GAPDH ThermoFisher Scientific Cat#Hs02786624_g1 RNAscope Probe - Hs-ADAMDEC1 ACD Europe SRL Cat#478471 RNAscope Probe - Hs-DCN ACD Europe SRL Cat#589521 RNAscope Probe - Hs-SLIT2 ACD Europe SRL Cat#466221 RNAscope Probe - Hs-CXCL12 ACD Europe SRL Cat#422991 RNAscope Probe - Hs-F3 ACD Europe SRL Cat#407611 RNAscope Probe - Hs-HSD17B2 ACD Europe SRL Cat#467271 RNAscope Probe - Hs-POSTN ACD Europe SRL Cat#409181 RNAscope Probe - Hs-FRZB ACD Europe SRL Cat#412391 RNAscope Probe - Hs-WNT5A ACD Europe SRL Cat#604921 RNAscope Probe - Hs-WNT5B ACD Europe SRL Cat#423041 RNAscope Probe - Hs-BMP2 ACD Europe SRL Cat#430641 RNAscope Probe - Hs-BMP5 ACD Europe SRL Cat#472461 RNAscope Probe - Hs-FDCSP ACD Europe SRL Cat#444231 Software and Algorithms ComBat sva Version 3.28.0 R Bioconductor RRID: SCR_012836; https://bioconductor.org/ packages/release/bioc/html/sva.html CellRanger Version 2.0 Version 2.1.1 10X Genomics https://support.10xgenomics.com/single-cell- gene-expression/software/downloads/latest Seurat Version 1.4.0.16 Version 2.3.0 R Bioconductor RRID: SCR_016341; https://www.satijalab.org/ seurat Scran Version 1.2.0 Version 1.6.9 R Bioconductor https://github.com/MarioniLab/scran Caret Version 6.0-80 CRAN https://cran.r-project.org/web/packages/ caret/index.html DMrW Version 0.4.1 CRAN https://cran.r-project.org/web/packages/ DMwR/index.html (Continued on next page) e4 Cell 175, 372–386.e1–e11, October 4, 2018 .. REAGENT or RESOURCE SOURCE IDENTIFIER Biomart Version 92 Ensembl RRID: SCR_002344; https://www.ensembl.org/ biomart/martview/ pROC Version 1.12.1 CRAN https://cran.r-project.org/web/packages/ pROC/index.html clusterProfiler Version 3.8.1 R Bioconductor https://github.com/GuangchuangYu/ clusterProfiler Destiny Version 2.10.2 R Bioconductor https://www.helmholtz-muenchen.de/icb/ destiny FastQC (v0.10.1) Babraham Bioinformatics RRID: SCR_014583; http://www.bioinformatics. babraham.ac.uk/projects/fastqc/ FeatureCounts (v1.5.0) Source Forge RRID: SCR_012919; http://subread. sourceforge.net HISAT (v2.0.3b) Kim et al., 2015 RRID: SCR_015530; https://ccb.jhu.edu/ software/hisat/index.shtml MultiQC (v0.7) Ewels et al., 2016 RRID: SCR_014982; http://multiqc.info NMF (v0.20.6) CRAN https://cran.r-project.org/web/packages/NMF/ index.html Picard Tools (v2.3.0) Github RRID: SCR_006525; http://broadinstitute. github.io/picard/ RUVSeq (v1.8.0) Github RRID: SCR_006263; https://github.com/drisso/ RUVSeq scater (v1.2.0) Github RRID: SCR_015954; https://github.com/ davismcc/scater Skewer Github RRID: SCR_001151; https://github.com/ relipmoc/skewer RTsne CRAN RRID: SCR_016342; https://cran.r-project.org/ web/packages/Rtsne/index.html WGCNA (v1.51) CRAN RRID: SCR_003302; https://cran.r-project.org/ web/packages/WGCNA/index.html RandomForest Version 4.6 CRAN RRID: SCR_015718; https://cran.r-project.org/ web/packages/randomForest/index.html Other ACD HybEZ Hybridization System (220v) ACD Europe SRL Cat#310013 Hg38 reference genome UCSC http://hgdownload.cse.ucsc.edu/goldenPath/ hg38/bigZips/ Mm10 reference genome UCSC http://hgdownload.cse.ucsc.edu/goldenPath/ mm10/bigZips/
Software:Article Title: Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Maxpar X8 Antibody Labeling Kit, 150Nd Fluidigm Cat#201150B Maxpar X8 Antibody Labeling Kit, 151Eu Fluidigm Cat#201151B Maxpar X8 Antibody Labeling Kit, 152Sm Fluidigm Cat#201152A Maxpar X8 Antibody Labeling Kit, 154Sm Fluidigm Cat#201154B Maxpar X8 Antibody Labeling Kit, 159Tb Fluidigm Cat#201159B Maxpar X8 Antibody Labeling Kit, 160Gd Fluidigm Cat#201160B Maxpar X8 Antibody Labeling Kit, 162Dy Fluidigm Cat#201162B Maxpar X8 Antibody Labeling Kit, 164Dy Fluidigm Cat#201164B Maxpar X8 Antibody Labeling Kit, 166Er Fluidigm Cat#201166B Maxpar X8 Antibody Labeling Kit, 167Er Fluidigm Cat#201167B Maxpar X8 Antibody Labeling Kit, 168Er Fluidigm Cat#201168B Maxpar X8 Antibody Labeling Kit, 169Tm Fluidigm Cat#201169B Maxpar X8 Antibody Labeling Kit, 172Yb Fluidigm Cat#201172B Maxpar X8 Antibody Labeling Kit, 173Yb Fluidigm Cat#201173B Maxpar X8 Antibody Labeling Kit, 175Lu Fluidigm Cat#201175B Maxpar X8 Antibody Labeling Kit, 176Yb Fluidigm Cat#201176B Biological Samples Human intestinal tissue biopsies University of Oxford Translational Gastroenterology Unit https://www.expmedndm.ox.ac.uk/ tgu/tgu-biobank-ibd-cohort Murine colon Epistem This study Chemicals, Peptides, and Recombinant Proteins 40,6-Diamidine-20-phenylindole dihydrochloride Sigma Aldrich Cat#10236276001 Dispase II, powder ThermoFisher Scientific Cat#17105041 Matrigel Basement Membrane Matrix Growth Factor Reduced (GFR) Phenol Red-Free LDEV-Free Corning Cat#356231 SB 431542 R&D Systems Cat#1614/10 Y-27632 dihydrochloride R&D Systems Cat#1254/10 CTS GlutaMAX-I Supplement ThermoFisher Scientific Cat#A1286001 N-2 Supplement (100X) ThermoFisher Scientific Cat#17502048 B-27 Supplement (50X), serum free ThermoFisher Scientific Cat#17504044 NICOTINAMIDE Sigma Aldrich Cat#N0636 Recombinant Human EGF PeproTech Cat#AF-100 Recombinant Human IL-6 R&D Systems Cat#206-IL-010 Recombinant Human LIGHT/TNFSF14 R&D Systems Cat#664-LI-025 A 83-01 R&D Systems Cat#2939/10 [LEU15]-Gastrin I HUMAN Sigma Aldrich Cat#G9145 Prostaglandin E2 Sigma Aldrich Cat#P0409 N-Acetylcysteine Sigma Aldrich Cat#A9165 Recombinant Human R-Spondin-1 PeproTech Cat#120-38 Recombinant Murine Noggin PeproTech Cat#250-38 2.5% Normal Goat Serum Vector Laboratories Cat#S-1012 ImmPRESS HRP Anti-Rabbit IgG (Peroxidase) Polymer Detection Kit, made in Goat Vector Laboratories Cat#MP-7451; RRID: AB_2631198 ImmPRESS HRP Anti-Mouse IgG (Peroxidase) Polymer Detection Kit, made in Goat Vector Laboratories Cat#MP-7452 (Continued on next page) e2 Cell 175, 372–386.e1–e11, October 4, 2018 .. REAGENT or RESOURCE SOURCE IDENTIFIER EQ Four Element Calibration Beads Fluidigm Cat201078 Cell-ID Intercalator-Ir Fluidigm Cat#201192A Deposited Data Single-cell RNaseq data This study GEO: GSE95459 Single-cell RNaseq data This study GEO: GSE114374 Experimental Models: Cell Lines L Wnt-3A (male) ATCC Cat#CRL-2647; RRID:CVCL_0635 RAW 264.7 (male) ATCC Cat#TIB71; RRID:CVCL_0493 Experimental Models: Organisms/Strains C57BL/6 male mice Envigo Laboratories RRID:IMSR_JAX:000664 Oligonucleotides LGR5 ThermoFisher Scientific Cat#Hs00969422_m1 OLFM4 ThermoFisher Scientific Cat#Hs00610344_m1 AXIN2 ThermoFisher Scientific Cat#Hs00610344_m1 NOTCH1 ThermoFisher Scientific Cat#Hs01062014_m1 ALDH1A1 ThermoFisher Scientific Cat#Hs00946916_m1 SOX9 ThermoFisher Scientific Cat#Hs00165814_m1 MSI1 ThermoFisher Scientific Cat#Hs01045894_m1 KRT20 ThermoFisher Scientific Cat#Hs00300643_m1 MUC2 ThermoFisher Scientific Cat#Hs03005103_g1 CDX2 ThermoFisher Scientific Cat#Hs01078080_m1 HPRT1 ThermoFisher Scientific Cat#Hs02800695_m1 GAPDH ThermoFisher Scientific Cat#Hs02786624_g1 RNAscope Probe - Hs-ADAMDEC1 ACD Europe SRL Cat#478471 RNAscope Probe - Hs-DCN ACD Europe SRL Cat#589521 RNAscope Probe - Hs-SLIT2 ACD Europe SRL Cat#466221 RNAscope Probe - Hs-CXCL12 ACD Europe SRL Cat#422991 RNAscope Probe - Hs-F3 ACD Europe SRL Cat#407611 RNAscope Probe - Hs-HSD17B2 ACD Europe SRL Cat#467271 RNAscope Probe - Hs-POSTN ACD Europe SRL Cat#409181 RNAscope Probe - Hs-FRZB ACD Europe SRL Cat#412391 RNAscope Probe - Hs-WNT5A ACD Europe SRL Cat#604921 RNAscope Probe - Hs-WNT5B ACD Europe SRL Cat#423041 RNAscope Probe - Hs-BMP2 ACD Europe SRL Cat#430641 RNAscope Probe - Hs-BMP5 ACD Europe SRL Cat#472461 RNAscope Probe - Hs-FDCSP ACD Europe SRL Cat#444231 Software and Algorithms ComBat sva Version 3.28.0 R Bioconductor RRID: SCR_012836; https://bioconductor.org/ packages/release/bioc/html/sva.html CellRanger Version 2.0 Version 2.1.1 10X Genomics https://support.10xgenomics.com/single-cell- gene-expression/software/downloads/latest Seurat Version 1.4.0.16 Version 2.3.0 R Bioconductor RRID: SCR_016341; https://www.satijalab.org/ seurat Scran Version 1.2.0 Version 1.6.9 R Bioconductor https://github.com/MarioniLab/scran Caret Version 6.0-80 CRAN https://cran.r-project.org/web/packages/ caret/index.html DMrW Version 0.4.1 CRAN https://cran.r-project.org/web/packages/ DMwR/index.html (Continued on next page) e4 Cell 175, 372–386.e1–e11, October 4, 2018 .. REAGENT or RESOURCE SOURCE IDENTIFIER Biomart Version 92 Ensembl RRID: SCR_002344; https://www.ensembl.org/ biomart/martview/ pROC Version 1.12.1 CRAN https://cran.r-project.org/web/packages/ pROC/index.html clusterProfiler Version 3.8.1 R Bioconductor https://github.com/GuangchuangYu/ clusterProfiler Destiny Version 2.10.2 R Bioconductor https://www.helmholtz-muenchen.de/icb/ destiny FastQC (v0.10.1) Babraham Bioinformatics RRID: SCR_014583; http://www.bioinformatics. babraham.ac.uk/projects/fastqc/ FeatureCounts (v1.5.0) Source Forge RRID: SCR_012919; http://subread. sourceforge.net HISAT (v2.0.3b) Kim et al., 2015 RRID: SCR_015530; https://ccb.jhu.edu/ software/hisat/index.shtml MultiQC (v0.7) Ewels et al., 2016 RRID: SCR_014982; http://multiqc.info NMF (v0.20.6) CRAN https://cran.r-project.org/web/packages/NMF/ index.html Picard Tools (v2.3.0) Github RRID: SCR_006525; http://broadinstitute. github.io/picard/ RUVSeq (v1.8.0) Github RRID: SCR_006263; https://github.com/drisso/ RUVSeq scater (v1.2.0) Github RRID: SCR_015954; https://github.com/ davismcc/scater Skewer Github RRID: SCR_001151; https://github.com/ relipmoc/skewer RTsne CRAN RRID: SCR_016342; https://cran.r-project.org/ web/packages/Rtsne/index.html WGCNA (v1.51) CRAN RRID: SCR_003302; https://cran.r-project.org/ web/packages/WGCNA/index.html RandomForest Version 4.6 CRAN RRID: SCR_015718; https://cran.r-project.org/ web/packages/randomForest/index.html Other ACD HybEZ Hybridization System (220v) ACD Europe SRL Cat#310013 Hg38 reference genome UCSC http://hgdownload.cse.ucsc.edu/goldenPath/ hg38/bigZips/ Mm10 reference genome UCSC http://hgdownload.cse.ucsc.edu/goldenPath/ mm10/bigZips/
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