Journal: Cell

Article Title: Single-Cell Analysis of Crohn’s Disease Lesions Identifies a Pathogenic Cellular Module Associated with Resistance to Anti-TNF Therapy

doi: 10.1016/j.cell.2019.08.008

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Surgeries were performed by the Department of Colorectal Surgery at Mount Sinai Hospital N/A Chemicals, Peptides, and Recombinant Proteins Collagenase, Type IV, Clostridium histolyticum Sigma-Aldrich Cat#: C5138 Deoxyribonuclease I Sigma-Aldrich Cat#: DN25 Ficoll-Paque PLUS GE Healthcare Cat#: 17144003 Rh103 intercalator Fluidigm Cat#: 201103A 0.125uM Ir intercalator Fluidigm Cat#: 201192A HEPES 1M Fisher Scientific Cat#: MT25060CI Penicillin/Streptomycin (10,000 U/mL) Fisher Scientific Cat#: 15-140-163 0.5 m EDTA, pH 8.0 Corning Cat#: 46-034-CI Critical Commercial Assays Dead Cell Removal Kit Miltenyi Biotec Cat#: 130-090-101 Cytofix/Cytoperm BD Biosciences Cat#: 51-2090KZ Perm/Wash BD Biosciences Cat#: 51-2091KZ Chromium Single Cell 3 ′ Library & Gel Bead Kit v2, 16 rxns 10x Genomics Cat#: PN-120237 Chromium Single Cell A Chip Kit, 48 rxns 10x Genomics Cat#: PN-120236 Chromium i7 Multiplex Kit, 96 rxns 10x Genomics Cat#: PN-120262 Deposited Data Single cell RNaseq data GEO GEO: GSE134809 RNaseq data RISK cohort GEO GEO: GSE134881 Software and Algorithms Cytobank Mountain View https://cytobank.org/ QuPath 0.1.3 Bankhead et al., 2017 https://qupath.github.io/ Fiji - ImageJ 1.52 h Schindelin et al., 2012 https://imagej.net/Fiji/Downloads Trakem2 Cardona et al., 2012 https://imagej.net/TrakEM2 CellRanger Version 2.0 Version 2.0 10x Genomics https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest GraphPad Prism version 7.0 GraphPad Software https://www.graphpad.com/scientific-software/prism/ R R Development Core Team, 2008 http://www.R-project.org Tglkmeans (R-package) 0.1.3 Amos Tanay Lab https://bitbucket.org/tanaylab/tglkmeans scDissector (R-package) 1.0 Ephraim Kenigsberg Lab https://github.com/effiken/scDissector Seriation (R-package) 1.2.7 CRAN https://github.com/mhahsler/seriation XPS (R-package) 1.44.0 Bioconductor https://bioconductor.org/packages/release/bioc/html/xps.html TopHat2 2.0.13 CCB, Johns Hopkins University https://ccb.jhu.edu/software/tophat/index.shtml Cufflinks 2.1.1 Cole Trapnell Lab http://cole-trapnell-lab.github.io/cufflinks/ R code for clustering and analyses This study https://github.com/effiken/martin_et_al_cell_2019 Other Surgical biopsy forceps Endochoice MAKO Cat#: DBC-206-40 Open in a separate window KEY RESOURCES TABLE Identification of a cellular module called GIMATS in a subset of CD patients The GIMATS module refers to IgG PCs, inf.

Techniques: Recombinant, Multiplex Assay, Software

Journal: Cell

Article Title: Single-Cell Analysis of Crohn’s Disease Lesions Identifies a Pathogenic Cellular Module Associated with Resistance to Anti-TNF Therapy

doi: 10.1016/j.cell.2019.08.008

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Surgeries were performed by the Department of Colorectal Surgery at Mount Sinai Hospital N/A Chemicals, Peptides, and Recombinant Proteins Collagenase, Type IV, Clostridium histolyticum Sigma-Aldrich Cat#: C5138 Deoxyribonuclease I Sigma-Aldrich Cat#: DN25 Ficoll-Paque PLUS GE Healthcare Cat#: 17144003 Rh103 intercalator Fluidigm Cat#: 201103A 0.125uM Ir intercalator Fluidigm Cat#: 201192A HEPES 1M Fisher Scientific Cat#: MT25060CI Penicillin/Streptomycin (10,000 U/mL) Fisher Scientific Cat#: 15-140-163 0.5 m EDTA, pH 8.0 Corning Cat#: 46-034-CI Critical Commercial Assays Dead Cell Removal Kit Miltenyi Biotec Cat#: 130-090-101 Cytofix/Cytoperm BD Biosciences Cat#: 51-2090KZ Perm/Wash BD Biosciences Cat#: 51-2091KZ Chromium Single Cell 3 ′ Library & Gel Bead Kit v2, 16 rxns 10x Genomics Cat#: PN-120237 Chromium Single Cell A Chip Kit, 48 rxns 10x Genomics Cat#: PN-120236 Chromium i7 Multiplex Kit, 96 rxns 10x Genomics Cat#: PN-120262 Deposited Data Single cell RNaseq data GEO GEO: GSE134809 RNaseq data RISK cohort GEO GEO: GSE134881 Software and Algorithms Cytobank Mountain View https://cytobank.org/ QuPath 0.1.3 Bankhead et al., 2017 https://qupath.github.io/ Fiji - ImageJ 1.52 h Schindelin et al., 2012 https://imagej.net/Fiji/Downloads Trakem2 Cardona et al., 2012 https://imagej.net/TrakEM2 CellRanger Version 2.0 Version 2.0 10x Genomics https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest GraphPad Prism version 7.0 GraphPad Software https://www.graphpad.com/scientific-software/prism/ R R Development Core Team, 2008 http://www.R-project.org Tglkmeans (R-package) 0.1.3 Amos Tanay Lab https://bitbucket.org/tanaylab/tglkmeans scDissector (R-package) 1.0 Ephraim Kenigsberg Lab https://github.com/effiken/scDissector Seriation (R-package) 1.2.7 CRAN https://github.com/mhahsler/seriation XPS (R-package) 1.44.0 Bioconductor https://bioconductor.org/packages/release/bioc/html/xps.html TopHat2 2.0.13 CCB, Johns Hopkins University https://ccb.jhu.edu/software/tophat/index.shtml Cufflinks 2.1.1 Cole Trapnell Lab http://cole-trapnell-lab.github.io/cufflinks/ R code for clustering and analyses This study https://github.com/effiken/martin_et_al_cell_2019 Other Surgical biopsy forceps Endochoice MAKO Cat#: DBC-206-40 Open in a separate window KEY RESOURCES TABLE Identification of a cellular module called GIMATS in a subset of CD patients The GIMATS module refers to IgG PCs, inf.

Techniques: Recombinant, Multiplex Assay, Software

Journal: Cell

Article Title: Single-Cell Analysis of Crohn’s Disease Lesions Identifies a Pathogenic Cellular Module Associated with Resistance to Anti-TNF Therapy

doi: 10.1016/j.cell.2019.08.008

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Surgeries were performed by the Department of Colorectal Surgery at Mount Sinai Hospital N/A Chemicals, Peptides, and Recombinant Proteins Collagenase, Type IV, Clostridium histolyticum Sigma-Aldrich Cat#: C5138 Deoxyribonuclease I Sigma-Aldrich Cat#: DN25 Ficoll-Paque PLUS GE Healthcare Cat#: 17144003 Rh103 intercalator Fluidigm Cat#: 201103A 0.125uM Ir intercalator Fluidigm Cat#: 201192A HEPES 1M Fisher Scientific Cat#: MT25060CI Penicillin/Streptomycin (10,000 U/mL) Fisher Scientific Cat#: 15-140-163 0.5 m EDTA, pH 8.0 Corning Cat#: 46-034-CI Critical Commercial Assays Dead Cell Removal Kit Miltenyi Biotec Cat#: 130-090-101 Cytofix/Cytoperm BD Biosciences Cat#: 51-2090KZ Perm/Wash BD Biosciences Cat#: 51-2091KZ Chromium Single Cell 3 ′ Library & Gel Bead Kit v2, 16 rxns 10x Genomics Cat#: PN-120237 Chromium Single Cell A Chip Kit, 48 rxns 10x Genomics Cat#: PN-120236 Chromium i7 Multiplex Kit, 96 rxns 10x Genomics Cat#: PN-120262 Deposited Data Single cell RNaseq data GEO GEO: GSE134809 RNaseq data RISK cohort GEO GEO: GSE134881 Software and Algorithms Cytobank Mountain View https://cytobank.org/ QuPath 0.1.3 Bankhead et al., 2017 https://qupath.github.io/ Fiji - ImageJ 1.52 h Schindelin et al., 2012 https://imagej.net/Fiji/Downloads Trakem2 Cardona et al., 2012 https://imagej.net/TrakEM2 CellRanger Version 2.0 Version 2.0 10x Genomics https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest GraphPad Prism version 7.0 GraphPad Software https://www.graphpad.com/scientific-software/prism/ R R Development Core Team, 2008 http://www.R-project.org Tglkmeans (R-package) 0.1.3 Amos Tanay Lab https://bitbucket.org/tanaylab/tglkmeans scDissector (R-package) 1.0 Ephraim Kenigsberg Lab https://github.com/effiken/scDissector Seriation (R-package) 1.2.7 CRAN https://github.com/mhahsler/seriation XPS (R-package) 1.44.0 Bioconductor https://bioconductor.org/packages/release/bioc/html/xps.html TopHat2 2.0.13 CCB, Johns Hopkins University https://ccb.jhu.edu/software/tophat/index.shtml Cufflinks 2.1.1 Cole Trapnell Lab http://cole-trapnell-lab.github.io/cufflinks/ R code for clustering and analyses This study https://github.com/effiken/martin_et_al_cell_2019 Other Surgical biopsy forceps Endochoice MAKO Cat#: DBC-206-40 Open in a separate window KEY RESOURCES TABLE Identification of a cellular module called GIMATS in a subset of CD patients The GIMATS module refers to IgG PCs, inf.

Techniques: Recombinant, Multiplex Assay, Software

Journal: Cell

Article Title: Single-Cell Analysis of Crohn’s Disease Lesions Identifies a Pathogenic Cellular Module Associated with Resistance to Anti-TNF Therapy

doi: 10.1016/j.cell.2019.08.008

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Surgeries were performed by the Department of Colorectal Surgery at Mount Sinai Hospital N/A Chemicals, Peptides, and Recombinant Proteins Collagenase, Type IV, Clostridium histolyticum Sigma-Aldrich Cat#: C5138 Deoxyribonuclease I Sigma-Aldrich Cat#: DN25 Ficoll-Paque PLUS GE Healthcare Cat#: 17144003 Rh103 intercalator Fluidigm Cat#: 201103A 0.125uM Ir intercalator Fluidigm Cat#: 201192A HEPES 1M Fisher Scientific Cat#: MT25060CI Penicillin/Streptomycin (10,000 U/mL) Fisher Scientific Cat#: 15-140-163 0.5 m EDTA, pH 8.0 Corning Cat#: 46-034-CI Critical Commercial Assays Dead Cell Removal Kit Miltenyi Biotec Cat#: 130-090-101 Cytofix/Cytoperm BD Biosciences Cat#: 51-2090KZ Perm/Wash BD Biosciences Cat#: 51-2091KZ Chromium Single Cell 3 ′ Library & Gel Bead Kit v2, 16 rxns 10x Genomics Cat#: PN-120237 Chromium Single Cell A Chip Kit, 48 rxns 10x Genomics Cat#: PN-120236 Chromium i7 Multiplex Kit, 96 rxns 10x Genomics Cat#: PN-120262 Deposited Data Single cell RNaseq data GEO GEO: GSE134809 RNaseq data RISK cohort GEO GEO: GSE134881 Software and Algorithms Cytobank Mountain View https://cytobank.org/ QuPath 0.1.3 Bankhead et al., 2017 https://qupath.github.io/ Fiji - ImageJ 1.52 h Schindelin et al., 2012 https://imagej.net/Fiji/Downloads Trakem2 Cardona et al., 2012 https://imagej.net/TrakEM2 CellRanger Version 2.0 Version 2.0 10x Genomics https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest GraphPad Prism version 7.0 GraphPad Software https://www.graphpad.com/scientific-software/prism/ R R Development Core Team, 2008 http://www.R-project.org Tglkmeans (R-package) 0.1.3 Amos Tanay Lab https://bitbucket.org/tanaylab/tglkmeans scDissector (R-package) 1.0 Ephraim Kenigsberg Lab https://github.com/effiken/scDissector Seriation (R-package) 1.2.7 CRAN https://github.com/mhahsler/seriation XPS (R-package) 1.44.0 Bioconductor https://bioconductor.org/packages/release/bioc/html/xps.html TopHat2 2.0.13 CCB, Johns Hopkins University https://ccb.jhu.edu/software/tophat/index.shtml Cufflinks 2.1.1 Cole Trapnell Lab http://cole-trapnell-lab.github.io/cufflinks/ R code for clustering and analyses This study https://github.com/effiken/martin_et_al_cell_2019 Other Surgical biopsy forceps Endochoice MAKO Cat#: DBC-206-40 Open in a separate window KEY RESOURCES TABLE Identification of a cellular module called GIMATS in a subset of CD patients The GIMATS module refers to IgG PCs, inf.

Techniques: Recombinant, Multiplex Assay, Software

Journal: Cell

Article Title: Single-Cell Analysis of Crohn’s Disease Lesions Identifies a Pathogenic Cellular Module Associated with Resistance to Anti-TNF Therapy

doi: 10.1016/j.cell.2019.08.008

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Surgeries were performed by the Department of Colorectal Surgery at Mount Sinai Hospital N/A Chemicals, Peptides, and Recombinant Proteins Collagenase, Type IV, Clostridium histolyticum Sigma-Aldrich Cat#: C5138 Deoxyribonuclease I Sigma-Aldrich Cat#: DN25 Ficoll-Paque PLUS GE Healthcare Cat#: 17144003 Rh103 intercalator Fluidigm Cat#: 201103A 0.125uM Ir intercalator Fluidigm Cat#: 201192A HEPES 1M Fisher Scientific Cat#: MT25060CI Penicillin/Streptomycin (10,000 U/mL) Fisher Scientific Cat#: 15-140-163 0.5 m EDTA, pH 8.0 Corning Cat#: 46-034-CI Critical Commercial Assays Dead Cell Removal Kit Miltenyi Biotec Cat#: 130-090-101 Cytofix/Cytoperm BD Biosciences Cat#: 51-2090KZ Perm/Wash BD Biosciences Cat#: 51-2091KZ Chromium Single Cell 3 ′ Library & Gel Bead Kit v2, 16 rxns 10x Genomics Cat#: PN-120237 Chromium Single Cell A Chip Kit, 48 rxns 10x Genomics Cat#: PN-120236 Chromium i7 Multiplex Kit, 96 rxns 10x Genomics Cat#: PN-120262 Deposited Data Single cell RNaseq data GEO GEO: GSE134809 RNaseq data RISK cohort GEO GEO: GSE134881 Software and Algorithms Cytobank Mountain View https://cytobank.org/ QuPath 0.1.3 Bankhead et al., 2017 https://qupath.github.io/ Fiji - ImageJ 1.52 h Schindelin et al., 2012 https://imagej.net/Fiji/Downloads Trakem2 Cardona et al., 2012 https://imagej.net/TrakEM2 CellRanger Version 2.0 Version 2.0 10x Genomics https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest GraphPad Prism version 7.0 GraphPad Software https://www.graphpad.com/scientific-software/prism/ R R Development Core Team, 2008 http://www.R-project.org Tglkmeans (R-package) 0.1.3 Amos Tanay Lab https://bitbucket.org/tanaylab/tglkmeans scDissector (R-package) 1.0 Ephraim Kenigsberg Lab https://github.com/effiken/scDissector Seriation (R-package) 1.2.7 CRAN https://github.com/mhahsler/seriation XPS (R-package) 1.44.0 Bioconductor https://bioconductor.org/packages/release/bioc/html/xps.html TopHat2 2.0.13 CCB, Johns Hopkins University https://ccb.jhu.edu/software/tophat/index.shtml Cufflinks 2.1.1 Cole Trapnell Lab http://cole-trapnell-lab.github.io/cufflinks/ R code for clustering and analyses This study https://github.com/effiken/martin_et_al_cell_2019 Other Surgical biopsy forceps Endochoice MAKO Cat#: DBC-206-40 Open in a separate window KEY RESOURCES TABLE Identification of a cellular module called GIMATS in a subset of CD patients The GIMATS module refers to IgG PCs, inf.

Techniques: Recombinant, Multiplex Assay, Software

Journal: Cell

Article Title: Single-Cell Analysis of Crohn’s Disease Lesions Identifies a Pathogenic Cellular Module Associated with Resistance to Anti-TNF Therapy

doi: 10.1016/j.cell.2019.08.008

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Surgeries were performed by the Department of Colorectal Surgery at Mount Sinai Hospital N/A Chemicals, Peptides, and Recombinant Proteins Collagenase, Type IV, Clostridium histolyticum Sigma-Aldrich Cat#: C5138 Deoxyribonuclease I Sigma-Aldrich Cat#: DN25 Ficoll-Paque PLUS GE Healthcare Cat#: 17144003 Rh103 intercalator Fluidigm Cat#: 201103A 0.125uM Ir intercalator Fluidigm Cat#: 201192A HEPES 1M Fisher Scientific Cat#: MT25060CI Penicillin/Streptomycin (10,000 U/mL) Fisher Scientific Cat#: 15-140-163 0.5 m EDTA, pH 8.0 Corning Cat#: 46-034-CI Critical Commercial Assays Dead Cell Removal Kit Miltenyi Biotec Cat#: 130-090-101 Cytofix/Cytoperm BD Biosciences Cat#: 51-2090KZ Perm/Wash BD Biosciences Cat#: 51-2091KZ Chromium Single Cell 3 ′ Library & Gel Bead Kit v2, 16 rxns 10x Genomics Cat#: PN-120237 Chromium Single Cell A Chip Kit, 48 rxns 10x Genomics Cat#: PN-120236 Chromium i7 Multiplex Kit, 96 rxns 10x Genomics Cat#: PN-120262 Deposited Data Single cell RNaseq data GEO GEO: GSE134809 RNaseq data RISK cohort GEO GEO: GSE134881 Software and Algorithms Cytobank Mountain View https://cytobank.org/ QuPath 0.1.3 Bankhead et al., 2017 https://qupath.github.io/ Fiji - ImageJ 1.52 h Schindelin et al., 2012 https://imagej.net/Fiji/Downloads Trakem2 Cardona et al., 2012 https://imagej.net/TrakEM2 CellRanger Version 2.0 Version 2.0 10x Genomics https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest GraphPad Prism version 7.0 GraphPad Software https://www.graphpad.com/scientific-software/prism/ R R Development Core Team, 2008 http://www.R-project.org Tglkmeans (R-package) 0.1.3 Amos Tanay Lab https://bitbucket.org/tanaylab/tglkmeans scDissector (R-package) 1.0 Ephraim Kenigsberg Lab https://github.com/effiken/scDissector Seriation (R-package) 1.2.7 CRAN https://github.com/mhahsler/seriation XPS (R-package) 1.44.0 Bioconductor https://bioconductor.org/packages/release/bioc/html/xps.html TopHat2 2.0.13 CCB, Johns Hopkins University https://ccb.jhu.edu/software/tophat/index.shtml Cufflinks 2.1.1 Cole Trapnell Lab http://cole-trapnell-lab.github.io/cufflinks/ R code for clustering and analyses This study https://github.com/effiken/martin_et_al_cell_2019 Other Surgical biopsy forceps Endochoice MAKO Cat#: DBC-206-40 Open in a separate window KEY RESOURCES TABLE Identification of a cellular module called GIMATS in a subset of CD patients The GIMATS module refers to IgG PCs, inf.

Techniques: Recombinant, Multiplex Assay, Software

Journal: Cell

Article Title: Single-Cell Analysis of Crohn’s Disease Lesions Identifies a Pathogenic Cellular Module Associated with Resistance to Anti-TNF Therapy

doi: 10.1016/j.cell.2019.08.008

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Surgeries were performed by the Department of Colorectal Surgery at Mount Sinai Hospital N/A Chemicals, Peptides, and Recombinant Proteins Collagenase, Type IV, Clostridium histolyticum Sigma-Aldrich Cat#: C5138 Deoxyribonuclease I Sigma-Aldrich Cat#: DN25 Ficoll-Paque PLUS GE Healthcare Cat#: 17144003 Rh103 intercalator Fluidigm Cat#: 201103A 0.125uM Ir intercalator Fluidigm Cat#: 201192A HEPES 1M Fisher Scientific Cat#: MT25060CI Penicillin/Streptomycin (10,000 U/mL) Fisher Scientific Cat#: 15-140-163 0.5 m EDTA, pH 8.0 Corning Cat#: 46-034-CI Critical Commercial Assays Dead Cell Removal Kit Miltenyi Biotec Cat#: 130-090-101 Cytofix/Cytoperm BD Biosciences Cat#: 51-2090KZ Perm/Wash BD Biosciences Cat#: 51-2091KZ Chromium Single Cell 3 ′ Library & Gel Bead Kit v2, 16 rxns 10x Genomics Cat#: PN-120237 Chromium Single Cell A Chip Kit, 48 rxns 10x Genomics Cat#: PN-120236 Chromium i7 Multiplex Kit, 96 rxns 10x Genomics Cat#: PN-120262 Deposited Data Single cell RNaseq data GEO GEO: GSE134809 RNaseq data RISK cohort GEO GEO: GSE134881 Software and Algorithms Cytobank Mountain View https://cytobank.org/ QuPath 0.1.3 Bankhead et al., 2017 https://qupath.github.io/ Fiji - ImageJ 1.52 h Schindelin et al., 2012 https://imagej.net/Fiji/Downloads Trakem2 Cardona et al., 2012 https://imagej.net/TrakEM2 CellRanger Version 2.0 Version 2.0 10x Genomics https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest GraphPad Prism version 7.0 GraphPad Software https://www.graphpad.com/scientific-software/prism/ R R Development Core Team, 2008 http://www.R-project.org Tglkmeans (R-package) 0.1.3 Amos Tanay Lab https://bitbucket.org/tanaylab/tglkmeans scDissector (R-package) 1.0 Ephraim Kenigsberg Lab https://github.com/effiken/scDissector Seriation (R-package) 1.2.7 CRAN https://github.com/mhahsler/seriation XPS (R-package) 1.44.0 Bioconductor https://bioconductor.org/packages/release/bioc/html/xps.html TopHat2 2.0.13 CCB, Johns Hopkins University https://ccb.jhu.edu/software/tophat/index.shtml Cufflinks 2.1.1 Cole Trapnell Lab http://cole-trapnell-lab.github.io/cufflinks/ R code for clustering and analyses This study https://github.com/effiken/martin_et_al_cell_2019 Other Surgical biopsy forceps Endochoice MAKO Cat#: DBC-206-40 Open in a separate window KEY RESOURCES TABLE Identification of a cellular module called GIMATS in a subset of CD patients The GIMATS module refers to IgG PCs, inf.

Techniques: Recombinant, Multiplex Assay, Software