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fluidigm cat 201194  (fluidigm)


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    fluidigm fluidigm cat 201194
    Fluidigm Cat 201194, supplied by fluidigm, used in various techniques. Bioz Stars score: 94/100, based on 64 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/cell+id+cisplatin+fluidigm+cat/Cell-ID+Cisplatin-194Pt/pm40280123-315-8-8
    Average 94 stars, based on 64 article reviews
    fluidigm cat 201194 - by Bioz Stars, 2026-10
    94/100 stars

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    Related Articles

    Polymerase Chain Reaction:

    Article Title: Single-cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment
    Article Snippet: SEQC is available on https://github.com/ambrosejcarr/seqc.git and Biscuit is available on https://github.com/sandhya212/BISCUIT_SingleCell_IMM_ICML_2016 . table ft1 table-wrap mode="anchored" t5 REAGENT or RESOURCE SOURCE IDENTIFIER Biological Samples Breast carcinoma Fresh operative tissue samples at MSKCC N/A Normal breast tissue Fresh operative tissue samples at MSKCC N/A Lymph node Fresh operative tissue samples at MSKCC N/A Peripheral blood Patient venipuncture at MSKCC N/A Antibodies anti-CD45 ab Biolegend RRID:AB_2566372 DAPI Stain Calbiochem SCR_014366 anti-Foxp3 ab Thermo Fisher RRID:AB_1834364 anti-CD3 ab Biolegend RRID:AB_1575008 anti-CD4 ab Biolegend RRID:AB_571945 anti-CD16 ab Biolegend RRID:AB_314207 anti-CD56 ab BD Biosciences RRID:AB_396853 anti-CD8 ab Biolegend RRID:AB_528885 anti-CD19 ab Biolegend RRID:AB_2562015 anti-CD11b ab Biolegend RRID:AB_2563395 anti-CD45 Y89 Fluidigm RRID:AB_2261851 anti-CD235ab BioLegend RRID:AB_314620 anti-CD61 BioLegend RRID:AB_1227584 anti-CD196/CCR6 Pr141 Fluidigm Cat:3141014A anti-CD19 142Nd Fluidigm RRID:AB_2651155 anti-CD278/ICOS 143Nd Fluidigm Cat:3143025B anti-CD270 144Nd Fluidigm Cat:3144022B anti-CD4 145Nd Fluidigm RRID:AB_2661789 anti-CD8a 146Nd Fluidigm Cat:3146001B anti-CD11c 147Sm Fluidigm RRID:AB_2687850 anti-CD14 148Nd Fluidigm Cat:3148010B anti-CD127 149Sm Fluidigm RRID:AB_2661792 anti-TIGIT eBioscience Cat:16-9500-82 anti-CD123 151Eu Fluidigm RRID:AB_2661794 anti-CD95/Fas 152Sm Fluidigm Cat:3152017B anti-CD45RA 153Eu Fluidigm Cat:3153001B anti-TIM3 154Sm Fluidigm Cat:3154010B anti-CD39 BioLegend RRID:AB_940438 anti-CD274/PD-L1 156Gd Fluidigm Cat: 3156026B anti-CD27 158Gd Fluidigm Cat: 3158010B anti-CD357/GITR 159Tb Fluidigm Cat: 3159020B anti-CD28 160Gd Fluidigm Cat: 3160003B anti-CD152/CTLA4 161Dy Fluidigm Cat: 3161004B anti-FoxP3 162Dy Fluidigm RRID:AB_2687650 anti-CD33 163Dy Fluidigm RRID:AB_2687857 anti-CD45RO 164Dy Fluidigm Cat: 3164007B anti-CD223/LAG3 165Ho Fluidigm RRID:AB_2687859 anti-Ki67 BD RRID:AB_396287 anti-CD197/CCR7 167Er Fluidigm Cat:3167009A anti-CD154/CD40L 168Er Fluidigm Cat: 3170011B anti-CD25 169Tm Fluidigm RRID:AB_2661806 anti-CD3 170Er Fluidigm RRID:AB_2661807 anti-CD226 171Tb Fluidigm Cat: 3171013B anti-CD38 172Yb Fluidigm Cat: 3172007B anti-CD137/4–1BB 173Yb Fluidigm Cat: 3173015B anti-CD279/PD-1 174Yb Fluidigm Cat: 3174020B anti-CD194/CCR4 175Lu Fluidigm Cat: 3175021A anti-CD56 176Yb Fluidigm RRID:AB_2661813 anti-CD11b 209Bi Fluidigm Cat: 3209003B Critical Commercial Assays inDrop platform Custom-built droplet microfluidics platform; Klein et al., 2015 ; Zilionis et al., 2017 . .. N/A Microfluidic chips and consumables Droplet Genomics https://dropletgenomics.com Chromium Single Cell 5’ Library and Bead Kit 10× Genomics cat no. 1000014 HiSeq 2500 Illumina at MSKCC N/A NEBNext mRNA Second Strand Synthesis Module NEB cat no. E6111S HiScribe T7 High Yield RNA Synthesis Kit NEB cat no. E2040S Kapa 2× HiFi HotStart PCR mix Kapa Biosystems cat no. KK2601 CyTOF2 Fluidigm N/A CyTOF2 Supersampler & Sample Chiller Victorian Airship & Scientific Apparatus N/A Indium(III) Chloride Sigma Cat: 203440 Maxpar X8 Antibody Labeling Kit 150Nd Fluidigm Cat: 201150A Maxpar X8 Antibody Labeling Kit 155Gd Fluidigm Cat: 201155A Maxpar X8 Antibody Labeling Kit 166Er Fluidigm Cat: 201166A Cell-ID 20-Plex Pd Barcoding Kit Fluidigm Cat: 201060 Cell-ID Intercalator-Ir Fluidigm Cat: 201192 Cell-ID Cisplatin Fluidigm Cat: 201064 FoxP3 Transcription Factor Fix/Perm eBiosciences Cat: 00-5523-00 TruStain FcX BioLegend Cat: 422302 Deposited Data inDrop single-cell RNA-seq dataset GEO Accession numbers {"type":"entrez-geo","attrs":{"text":"GSE114727","term_id":"114727"}} GSE114727 , {"type":"entrez-geo","attrs":{"text":"GSE114725","term_id":"114725"}} GSE114725 10× paired single-cell TCR and RNA-seq dataset GEO Accession numbers {"type":"entrez-geo","attrs":{"text":"GSE114727","term_id":"114727"}} GSE114727 , {"type":"entrez-geo","attrs":{"text":"GSE114724","term_id":"114724"}} GSE114724 CyTOF dataset Flow Repository https://flowrepository.org/id/FR-FCM-ZYJP Software and Algorithms SEQC This paper https://github.com/ambrosejcarr/seqc.git Biscuit This paper and Prabhkaran et al., 2016 . https://github.com/sandhya212/BISCUIT_SingleCell_IMM_ICML_2016 t-SNE van der Maaten and Hinton, 2008 . https://lvdmaaten.github.io/software/ PhenoGraph Levine et al., 2015 . https://github.com/jacoblevine/PhenoGraph Diffusion maps Coifman et al., 2005 . http://www.math.jhu.edu/~mauro/#tab_DiffusionGeom FACSDiva BD Biosciences RRID:SCR_001456 FlowJo BD Biosciences RRID:SCR_008520 https://www.flowjo.com/ FastQC Andrews, 2010. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ STAR 2.5.3a Dobin et al., 2013. https://github.com/alexdobin/STAR Edittag Faircloth and Glenn, 2012. https://github.com/faircloth-lab/edittag Cell Ranger 2.1.1 10× Genomics https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest Loupe Cell Browser 10× Genomics https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest#loupetab CyTOF cell debarcoder Zunder et al., 2015. https://github.com/nolanlab/single-cell-debarcoder CyTOF Bead Normalization Finck et al., 2013. https://github.com/nolanlab/bead-normalization/ Open in a separate window KEY RESOURCES TABLE ..

    Antibody Labeling:

    Article Title: Single-cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment
    Article Snippet: SEQC is available on https://github.com/ambrosejcarr/seqc.git and Biscuit is available on https://github.com/sandhya212/BISCUIT_SingleCell_IMM_ICML_2016 . table ft1 table-wrap mode="anchored" t5 REAGENT or RESOURCE SOURCE IDENTIFIER Biological Samples Breast carcinoma Fresh operative tissue samples at MSKCC N/A Normal breast tissue Fresh operative tissue samples at MSKCC N/A Lymph node Fresh operative tissue samples at MSKCC N/A Peripheral blood Patient venipuncture at MSKCC N/A Antibodies anti-CD45 ab Biolegend RRID:AB_2566372 DAPI Stain Calbiochem SCR_014366 anti-Foxp3 ab Thermo Fisher RRID:AB_1834364 anti-CD3 ab Biolegend RRID:AB_1575008 anti-CD4 ab Biolegend RRID:AB_571945 anti-CD16 ab Biolegend RRID:AB_314207 anti-CD56 ab BD Biosciences RRID:AB_396853 anti-CD8 ab Biolegend RRID:AB_528885 anti-CD19 ab Biolegend RRID:AB_2562015 anti-CD11b ab Biolegend RRID:AB_2563395 anti-CD45 Y89 Fluidigm RRID:AB_2261851 anti-CD235ab BioLegend RRID:AB_314620 anti-CD61 BioLegend RRID:AB_1227584 anti-CD196/CCR6 Pr141 Fluidigm Cat:3141014A anti-CD19 142Nd Fluidigm RRID:AB_2651155 anti-CD278/ICOS 143Nd Fluidigm Cat:3143025B anti-CD270 144Nd Fluidigm Cat:3144022B anti-CD4 145Nd Fluidigm RRID:AB_2661789 anti-CD8a 146Nd Fluidigm Cat:3146001B anti-CD11c 147Sm Fluidigm RRID:AB_2687850 anti-CD14 148Nd Fluidigm Cat:3148010B anti-CD127 149Sm Fluidigm RRID:AB_2661792 anti-TIGIT eBioscience Cat:16-9500-82 anti-CD123 151Eu Fluidigm RRID:AB_2661794 anti-CD95/Fas 152Sm Fluidigm Cat:3152017B anti-CD45RA 153Eu Fluidigm Cat:3153001B anti-TIM3 154Sm Fluidigm Cat:3154010B anti-CD39 BioLegend RRID:AB_940438 anti-CD274/PD-L1 156Gd Fluidigm Cat: 3156026B anti-CD27 158Gd Fluidigm Cat: 3158010B anti-CD357/GITR 159Tb Fluidigm Cat: 3159020B anti-CD28 160Gd Fluidigm Cat: 3160003B anti-CD152/CTLA4 161Dy Fluidigm Cat: 3161004B anti-FoxP3 162Dy Fluidigm RRID:AB_2687650 anti-CD33 163Dy Fluidigm RRID:AB_2687857 anti-CD45RO 164Dy Fluidigm Cat: 3164007B anti-CD223/LAG3 165Ho Fluidigm RRID:AB_2687859 anti-Ki67 BD RRID:AB_396287 anti-CD197/CCR7 167Er Fluidigm Cat:3167009A anti-CD154/CD40L 168Er Fluidigm Cat: 3170011B anti-CD25 169Tm Fluidigm RRID:AB_2661806 anti-CD3 170Er Fluidigm RRID:AB_2661807 anti-CD226 171Tb Fluidigm Cat: 3171013B anti-CD38 172Yb Fluidigm Cat: 3172007B anti-CD137/4–1BB 173Yb Fluidigm Cat: 3173015B anti-CD279/PD-1 174Yb Fluidigm Cat: 3174020B anti-CD194/CCR4 175Lu Fluidigm Cat: 3175021A anti-CD56 176Yb Fluidigm RRID:AB_2661813 anti-CD11b 209Bi Fluidigm Cat: 3209003B Critical Commercial Assays inDrop platform Custom-built droplet microfluidics platform; Klein et al., 2015 ; Zilionis et al., 2017 . .. N/A Microfluidic chips and consumables Droplet Genomics https://dropletgenomics.com Chromium Single Cell 5’ Library and Bead Kit 10× Genomics cat no. 1000014 HiSeq 2500 Illumina at MSKCC N/A NEBNext mRNA Second Strand Synthesis Module NEB cat no. E6111S HiScribe T7 High Yield RNA Synthesis Kit NEB cat no. E2040S Kapa 2× HiFi HotStart PCR mix Kapa Biosystems cat no. KK2601 CyTOF2 Fluidigm N/A CyTOF2 Supersampler & Sample Chiller Victorian Airship & Scientific Apparatus N/A Indium(III) Chloride Sigma Cat: 203440 Maxpar X8 Antibody Labeling Kit 150Nd Fluidigm Cat: 201150A Maxpar X8 Antibody Labeling Kit 155Gd Fluidigm Cat: 201155A Maxpar X8 Antibody Labeling Kit 166Er Fluidigm Cat: 201166A Cell-ID 20-Plex Pd Barcoding Kit Fluidigm Cat: 201060 Cell-ID Intercalator-Ir Fluidigm Cat: 201192 Cell-ID Cisplatin Fluidigm Cat: 201064 FoxP3 Transcription Factor Fix/Perm eBiosciences Cat: 00-5523-00 TruStain FcX BioLegend Cat: 422302 Deposited Data inDrop single-cell RNA-seq dataset GEO Accession numbers {"type":"entrez-geo","attrs":{"text":"GSE114727","term_id":"114727"}} GSE114727 , {"type":"entrez-geo","attrs":{"text":"GSE114725","term_id":"114725"}} GSE114725 10× paired single-cell TCR and RNA-seq dataset GEO Accession numbers {"type":"entrez-geo","attrs":{"text":"GSE114727","term_id":"114727"}} GSE114727 , {"type":"entrez-geo","attrs":{"text":"GSE114724","term_id":"114724"}} GSE114724 CyTOF dataset Flow Repository https://flowrepository.org/id/FR-FCM-ZYJP Software and Algorithms SEQC This paper https://github.com/ambrosejcarr/seqc.git Biscuit This paper and Prabhkaran et al., 2016 . https://github.com/sandhya212/BISCUIT_SingleCell_IMM_ICML_2016 t-SNE van der Maaten and Hinton, 2008 . https://lvdmaaten.github.io/software/ PhenoGraph Levine et al., 2015 . https://github.com/jacoblevine/PhenoGraph Diffusion maps Coifman et al., 2005 . http://www.math.jhu.edu/~mauro/#tab_DiffusionGeom FACSDiva BD Biosciences RRID:SCR_001456 FlowJo BD Biosciences RRID:SCR_008520 https://www.flowjo.com/ FastQC Andrews, 2010. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ STAR 2.5.3a Dobin et al., 2013. https://github.com/alexdobin/STAR Edittag Faircloth and Glenn, 2012. https://github.com/faircloth-lab/edittag Cell Ranger 2.1.1 10× Genomics https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest Loupe Cell Browser 10× Genomics https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest#loupetab CyTOF cell debarcoder Zunder et al., 2015. https://github.com/nolanlab/single-cell-debarcoder CyTOF Bead Normalization Finck et al., 2013. https://github.com/nolanlab/bead-normalization/ Open in a separate window KEY RESOURCES TABLE ..

    RNA Sequencing:

    Article Title: Single-cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment
    Article Snippet: SEQC is available on https://github.com/ambrosejcarr/seqc.git and Biscuit is available on https://github.com/sandhya212/BISCUIT_SingleCell_IMM_ICML_2016 . table ft1 table-wrap mode="anchored" t5 REAGENT or RESOURCE SOURCE IDENTIFIER Biological Samples Breast carcinoma Fresh operative tissue samples at MSKCC N/A Normal breast tissue Fresh operative tissue samples at MSKCC N/A Lymph node Fresh operative tissue samples at MSKCC N/A Peripheral blood Patient venipuncture at MSKCC N/A Antibodies anti-CD45 ab Biolegend RRID:AB_2566372 DAPI Stain Calbiochem SCR_014366 anti-Foxp3 ab Thermo Fisher RRID:AB_1834364 anti-CD3 ab Biolegend RRID:AB_1575008 anti-CD4 ab Biolegend RRID:AB_571945 anti-CD16 ab Biolegend RRID:AB_314207 anti-CD56 ab BD Biosciences RRID:AB_396853 anti-CD8 ab Biolegend RRID:AB_528885 anti-CD19 ab Biolegend RRID:AB_2562015 anti-CD11b ab Biolegend RRID:AB_2563395 anti-CD45 Y89 Fluidigm RRID:AB_2261851 anti-CD235ab BioLegend RRID:AB_314620 anti-CD61 BioLegend RRID:AB_1227584 anti-CD196/CCR6 Pr141 Fluidigm Cat:3141014A anti-CD19 142Nd Fluidigm RRID:AB_2651155 anti-CD278/ICOS 143Nd Fluidigm Cat:3143025B anti-CD270 144Nd Fluidigm Cat:3144022B anti-CD4 145Nd Fluidigm RRID:AB_2661789 anti-CD8a 146Nd Fluidigm Cat:3146001B anti-CD11c 147Sm Fluidigm RRID:AB_2687850 anti-CD14 148Nd Fluidigm Cat:3148010B anti-CD127 149Sm Fluidigm RRID:AB_2661792 anti-TIGIT eBioscience Cat:16-9500-82 anti-CD123 151Eu Fluidigm RRID:AB_2661794 anti-CD95/Fas 152Sm Fluidigm Cat:3152017B anti-CD45RA 153Eu Fluidigm Cat:3153001B anti-TIM3 154Sm Fluidigm Cat:3154010B anti-CD39 BioLegend RRID:AB_940438 anti-CD274/PD-L1 156Gd Fluidigm Cat: 3156026B anti-CD27 158Gd Fluidigm Cat: 3158010B anti-CD357/GITR 159Tb Fluidigm Cat: 3159020B anti-CD28 160Gd Fluidigm Cat: 3160003B anti-CD152/CTLA4 161Dy Fluidigm Cat: 3161004B anti-FoxP3 162Dy Fluidigm RRID:AB_2687650 anti-CD33 163Dy Fluidigm RRID:AB_2687857 anti-CD45RO 164Dy Fluidigm Cat: 3164007B anti-CD223/LAG3 165Ho Fluidigm RRID:AB_2687859 anti-Ki67 BD RRID:AB_396287 anti-CD197/CCR7 167Er Fluidigm Cat:3167009A anti-CD154/CD40L 168Er Fluidigm Cat: 3170011B anti-CD25 169Tm Fluidigm RRID:AB_2661806 anti-CD3 170Er Fluidigm RRID:AB_2661807 anti-CD226 171Tb Fluidigm Cat: 3171013B anti-CD38 172Yb Fluidigm Cat: 3172007B anti-CD137/4–1BB 173Yb Fluidigm Cat: 3173015B anti-CD279/PD-1 174Yb Fluidigm Cat: 3174020B anti-CD194/CCR4 175Lu Fluidigm Cat: 3175021A anti-CD56 176Yb Fluidigm RRID:AB_2661813 anti-CD11b 209Bi Fluidigm Cat: 3209003B Critical Commercial Assays inDrop platform Custom-built droplet microfluidics platform; Klein et al., 2015 ; Zilionis et al., 2017 . .. N/A Microfluidic chips and consumables Droplet Genomics https://dropletgenomics.com Chromium Single Cell 5’ Library and Bead Kit 10× Genomics cat no. 1000014 HiSeq 2500 Illumina at MSKCC N/A NEBNext mRNA Second Strand Synthesis Module NEB cat no. E6111S HiScribe T7 High Yield RNA Synthesis Kit NEB cat no. E2040S Kapa 2× HiFi HotStart PCR mix Kapa Biosystems cat no. KK2601 CyTOF2 Fluidigm N/A CyTOF2 Supersampler & Sample Chiller Victorian Airship & Scientific Apparatus N/A Indium(III) Chloride Sigma Cat: 203440 Maxpar X8 Antibody Labeling Kit 150Nd Fluidigm Cat: 201150A Maxpar X8 Antibody Labeling Kit 155Gd Fluidigm Cat: 201155A Maxpar X8 Antibody Labeling Kit 166Er Fluidigm Cat: 201166A Cell-ID 20-Plex Pd Barcoding Kit Fluidigm Cat: 201060 Cell-ID Intercalator-Ir Fluidigm Cat: 201192 Cell-ID Cisplatin Fluidigm Cat: 201064 FoxP3 Transcription Factor Fix/Perm eBiosciences Cat: 00-5523-00 TruStain FcX BioLegend Cat: 422302 Deposited Data inDrop single-cell RNA-seq dataset GEO Accession numbers {"type":"entrez-geo","attrs":{"text":"GSE114727","term_id":"114727"}} GSE114727 , {"type":"entrez-geo","attrs":{"text":"GSE114725","term_id":"114725"}} GSE114725 10× paired single-cell TCR and RNA-seq dataset GEO Accession numbers {"type":"entrez-geo","attrs":{"text":"GSE114727","term_id":"114727"}} GSE114727 , {"type":"entrez-geo","attrs":{"text":"GSE114724","term_id":"114724"}} GSE114724 CyTOF dataset Flow Repository https://flowrepository.org/id/FR-FCM-ZYJP Software and Algorithms SEQC This paper https://github.com/ambrosejcarr/seqc.git Biscuit This paper and Prabhkaran et al., 2016 . https://github.com/sandhya212/BISCUIT_SingleCell_IMM_ICML_2016 t-SNE van der Maaten and Hinton, 2008 . https://lvdmaaten.github.io/software/ PhenoGraph Levine et al., 2015 . https://github.com/jacoblevine/PhenoGraph Diffusion maps Coifman et al., 2005 . http://www.math.jhu.edu/~mauro/#tab_DiffusionGeom FACSDiva BD Biosciences RRID:SCR_001456 FlowJo BD Biosciences RRID:SCR_008520 https://www.flowjo.com/ FastQC Andrews, 2010. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ STAR 2.5.3a Dobin et al., 2013. https://github.com/alexdobin/STAR Edittag Faircloth and Glenn, 2012. https://github.com/faircloth-lab/edittag Cell Ranger 2.1.1 10× Genomics https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest Loupe Cell Browser 10× Genomics https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest#loupetab CyTOF cell debarcoder Zunder et al., 2015. https://github.com/nolanlab/single-cell-debarcoder CyTOF Bead Normalization Finck et al., 2013. https://github.com/nolanlab/bead-normalization/ Open in a separate window KEY RESOURCES TABLE ..

    Software:

    Article Title: Single-cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment
    Article Snippet: SEQC is available on https://github.com/ambrosejcarr/seqc.git and Biscuit is available on https://github.com/sandhya212/BISCUIT_SingleCell_IMM_ICML_2016 . table ft1 table-wrap mode="anchored" t5 REAGENT or RESOURCE SOURCE IDENTIFIER Biological Samples Breast carcinoma Fresh operative tissue samples at MSKCC N/A Normal breast tissue Fresh operative tissue samples at MSKCC N/A Lymph node Fresh operative tissue samples at MSKCC N/A Peripheral blood Patient venipuncture at MSKCC N/A Antibodies anti-CD45 ab Biolegend RRID:AB_2566372 DAPI Stain Calbiochem SCR_014366 anti-Foxp3 ab Thermo Fisher RRID:AB_1834364 anti-CD3 ab Biolegend RRID:AB_1575008 anti-CD4 ab Biolegend RRID:AB_571945 anti-CD16 ab Biolegend RRID:AB_314207 anti-CD56 ab BD Biosciences RRID:AB_396853 anti-CD8 ab Biolegend RRID:AB_528885 anti-CD19 ab Biolegend RRID:AB_2562015 anti-CD11b ab Biolegend RRID:AB_2563395 anti-CD45 Y89 Fluidigm RRID:AB_2261851 anti-CD235ab BioLegend RRID:AB_314620 anti-CD61 BioLegend RRID:AB_1227584 anti-CD196/CCR6 Pr141 Fluidigm Cat:3141014A anti-CD19 142Nd Fluidigm RRID:AB_2651155 anti-CD278/ICOS 143Nd Fluidigm Cat:3143025B anti-CD270 144Nd Fluidigm Cat:3144022B anti-CD4 145Nd Fluidigm RRID:AB_2661789 anti-CD8a 146Nd Fluidigm Cat:3146001B anti-CD11c 147Sm Fluidigm RRID:AB_2687850 anti-CD14 148Nd Fluidigm Cat:3148010B anti-CD127 149Sm Fluidigm RRID:AB_2661792 anti-TIGIT eBioscience Cat:16-9500-82 anti-CD123 151Eu Fluidigm RRID:AB_2661794 anti-CD95/Fas 152Sm Fluidigm Cat:3152017B anti-CD45RA 153Eu Fluidigm Cat:3153001B anti-TIM3 154Sm Fluidigm Cat:3154010B anti-CD39 BioLegend RRID:AB_940438 anti-CD274/PD-L1 156Gd Fluidigm Cat: 3156026B anti-CD27 158Gd Fluidigm Cat: 3158010B anti-CD357/GITR 159Tb Fluidigm Cat: 3159020B anti-CD28 160Gd Fluidigm Cat: 3160003B anti-CD152/CTLA4 161Dy Fluidigm Cat: 3161004B anti-FoxP3 162Dy Fluidigm RRID:AB_2687650 anti-CD33 163Dy Fluidigm RRID:AB_2687857 anti-CD45RO 164Dy Fluidigm Cat: 3164007B anti-CD223/LAG3 165Ho Fluidigm RRID:AB_2687859 anti-Ki67 BD RRID:AB_396287 anti-CD197/CCR7 167Er Fluidigm Cat:3167009A anti-CD154/CD40L 168Er Fluidigm Cat: 3170011B anti-CD25 169Tm Fluidigm RRID:AB_2661806 anti-CD3 170Er Fluidigm RRID:AB_2661807 anti-CD226 171Tb Fluidigm Cat: 3171013B anti-CD38 172Yb Fluidigm Cat: 3172007B anti-CD137/4–1BB 173Yb Fluidigm Cat: 3173015B anti-CD279/PD-1 174Yb Fluidigm Cat: 3174020B anti-CD194/CCR4 175Lu Fluidigm Cat: 3175021A anti-CD56 176Yb Fluidigm RRID:AB_2661813 anti-CD11b 209Bi Fluidigm Cat: 3209003B Critical Commercial Assays inDrop platform Custom-built droplet microfluidics platform; Klein et al., 2015 ; Zilionis et al., 2017 . .. N/A Microfluidic chips and consumables Droplet Genomics https://dropletgenomics.com Chromium Single Cell 5’ Library and Bead Kit 10× Genomics cat no. 1000014 HiSeq 2500 Illumina at MSKCC N/A NEBNext mRNA Second Strand Synthesis Module NEB cat no. E6111S HiScribe T7 High Yield RNA Synthesis Kit NEB cat no. E2040S Kapa 2× HiFi HotStart PCR mix Kapa Biosystems cat no. KK2601 CyTOF2 Fluidigm N/A CyTOF2 Supersampler & Sample Chiller Victorian Airship & Scientific Apparatus N/A Indium(III) Chloride Sigma Cat: 203440 Maxpar X8 Antibody Labeling Kit 150Nd Fluidigm Cat: 201150A Maxpar X8 Antibody Labeling Kit 155Gd Fluidigm Cat: 201155A Maxpar X8 Antibody Labeling Kit 166Er Fluidigm Cat: 201166A Cell-ID 20-Plex Pd Barcoding Kit Fluidigm Cat: 201060 Cell-ID Intercalator-Ir Fluidigm Cat: 201192 Cell-ID Cisplatin Fluidigm Cat: 201064 FoxP3 Transcription Factor Fix/Perm eBiosciences Cat: 00-5523-00 TruStain FcX BioLegend Cat: 422302 Deposited Data inDrop single-cell RNA-seq dataset GEO Accession numbers {"type":"entrez-geo","attrs":{"text":"GSE114727","term_id":"114727"}} GSE114727 , {"type":"entrez-geo","attrs":{"text":"GSE114725","term_id":"114725"}} GSE114725 10× paired single-cell TCR and RNA-seq dataset GEO Accession numbers {"type":"entrez-geo","attrs":{"text":"GSE114727","term_id":"114727"}} GSE114727 , {"type":"entrez-geo","attrs":{"text":"GSE114724","term_id":"114724"}} GSE114724 CyTOF dataset Flow Repository https://flowrepository.org/id/FR-FCM-ZYJP Software and Algorithms SEQC This paper https://github.com/ambrosejcarr/seqc.git Biscuit This paper and Prabhkaran et al., 2016 . https://github.com/sandhya212/BISCUIT_SingleCell_IMM_ICML_2016 t-SNE van der Maaten and Hinton, 2008 . https://lvdmaaten.github.io/software/ PhenoGraph Levine et al., 2015 . https://github.com/jacoblevine/PhenoGraph Diffusion maps Coifman et al., 2005 . http://www.math.jhu.edu/~mauro/#tab_DiffusionGeom FACSDiva BD Biosciences RRID:SCR_001456 FlowJo BD Biosciences RRID:SCR_008520 https://www.flowjo.com/ FastQC Andrews, 2010. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ STAR 2.5.3a Dobin et al., 2013. https://github.com/alexdobin/STAR Edittag Faircloth and Glenn, 2012. https://github.com/faircloth-lab/edittag Cell Ranger 2.1.1 10× Genomics https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest Loupe Cell Browser 10× Genomics https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest#loupetab CyTOF cell debarcoder Zunder et al., 2015. https://github.com/nolanlab/single-cell-debarcoder CyTOF Bead Normalization Finck et al., 2013. https://github.com/nolanlab/bead-normalization/ Open in a separate window KEY RESOURCES TABLE ..

    Diffusion-based Assay:

    Article Title: Single-cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment
    Article Snippet: SEQC is available on https://github.com/ambrosejcarr/seqc.git and Biscuit is available on https://github.com/sandhya212/BISCUIT_SingleCell_IMM_ICML_2016 . table ft1 table-wrap mode="anchored" t5 REAGENT or RESOURCE SOURCE IDENTIFIER Biological Samples Breast carcinoma Fresh operative tissue samples at MSKCC N/A Normal breast tissue Fresh operative tissue samples at MSKCC N/A Lymph node Fresh operative tissue samples at MSKCC N/A Peripheral blood Patient venipuncture at MSKCC N/A Antibodies anti-CD45 ab Biolegend RRID:AB_2566372 DAPI Stain Calbiochem SCR_014366 anti-Foxp3 ab Thermo Fisher RRID:AB_1834364 anti-CD3 ab Biolegend RRID:AB_1575008 anti-CD4 ab Biolegend RRID:AB_571945 anti-CD16 ab Biolegend RRID:AB_314207 anti-CD56 ab BD Biosciences RRID:AB_396853 anti-CD8 ab Biolegend RRID:AB_528885 anti-CD19 ab Biolegend RRID:AB_2562015 anti-CD11b ab Biolegend RRID:AB_2563395 anti-CD45 Y89 Fluidigm RRID:AB_2261851 anti-CD235ab BioLegend RRID:AB_314620 anti-CD61 BioLegend RRID:AB_1227584 anti-CD196/CCR6 Pr141 Fluidigm Cat:3141014A anti-CD19 142Nd Fluidigm RRID:AB_2651155 anti-CD278/ICOS 143Nd Fluidigm Cat:3143025B anti-CD270 144Nd Fluidigm Cat:3144022B anti-CD4 145Nd Fluidigm RRID:AB_2661789 anti-CD8a 146Nd Fluidigm Cat:3146001B anti-CD11c 147Sm Fluidigm RRID:AB_2687850 anti-CD14 148Nd Fluidigm Cat:3148010B anti-CD127 149Sm Fluidigm RRID:AB_2661792 anti-TIGIT eBioscience Cat:16-9500-82 anti-CD123 151Eu Fluidigm RRID:AB_2661794 anti-CD95/Fas 152Sm Fluidigm Cat:3152017B anti-CD45RA 153Eu Fluidigm Cat:3153001B anti-TIM3 154Sm Fluidigm Cat:3154010B anti-CD39 BioLegend RRID:AB_940438 anti-CD274/PD-L1 156Gd Fluidigm Cat: 3156026B anti-CD27 158Gd Fluidigm Cat: 3158010B anti-CD357/GITR 159Tb Fluidigm Cat: 3159020B anti-CD28 160Gd Fluidigm Cat: 3160003B anti-CD152/CTLA4 161Dy Fluidigm Cat: 3161004B anti-FoxP3 162Dy Fluidigm RRID:AB_2687650 anti-CD33 163Dy Fluidigm RRID:AB_2687857 anti-CD45RO 164Dy Fluidigm Cat: 3164007B anti-CD223/LAG3 165Ho Fluidigm RRID:AB_2687859 anti-Ki67 BD RRID:AB_396287 anti-CD197/CCR7 167Er Fluidigm Cat:3167009A anti-CD154/CD40L 168Er Fluidigm Cat: 3170011B anti-CD25 169Tm Fluidigm RRID:AB_2661806 anti-CD3 170Er Fluidigm RRID:AB_2661807 anti-CD226 171Tb Fluidigm Cat: 3171013B anti-CD38 172Yb Fluidigm Cat: 3172007B anti-CD137/4–1BB 173Yb Fluidigm Cat: 3173015B anti-CD279/PD-1 174Yb Fluidigm Cat: 3174020B anti-CD194/CCR4 175Lu Fluidigm Cat: 3175021A anti-CD56 176Yb Fluidigm RRID:AB_2661813 anti-CD11b 209Bi Fluidigm Cat: 3209003B Critical Commercial Assays inDrop platform Custom-built droplet microfluidics platform; Klein et al., 2015 ; Zilionis et al., 2017 . .. N/A Microfluidic chips and consumables Droplet Genomics https://dropletgenomics.com Chromium Single Cell 5’ Library and Bead Kit 10× Genomics cat no. 1000014 HiSeq 2500 Illumina at MSKCC N/A NEBNext mRNA Second Strand Synthesis Module NEB cat no. E6111S HiScribe T7 High Yield RNA Synthesis Kit NEB cat no. E2040S Kapa 2× HiFi HotStart PCR mix Kapa Biosystems cat no. KK2601 CyTOF2 Fluidigm N/A CyTOF2 Supersampler & Sample Chiller Victorian Airship & Scientific Apparatus N/A Indium(III) Chloride Sigma Cat: 203440 Maxpar X8 Antibody Labeling Kit 150Nd Fluidigm Cat: 201150A Maxpar X8 Antibody Labeling Kit 155Gd Fluidigm Cat: 201155A Maxpar X8 Antibody Labeling Kit 166Er Fluidigm Cat: 201166A Cell-ID 20-Plex Pd Barcoding Kit Fluidigm Cat: 201060 Cell-ID Intercalator-Ir Fluidigm Cat: 201192 Cell-ID Cisplatin Fluidigm Cat: 201064 FoxP3 Transcription Factor Fix/Perm eBiosciences Cat: 00-5523-00 TruStain FcX BioLegend Cat: 422302 Deposited Data inDrop single-cell RNA-seq dataset GEO Accession numbers {"type":"entrez-geo","attrs":{"text":"GSE114727","term_id":"114727"}} GSE114727 , {"type":"entrez-geo","attrs":{"text":"GSE114725","term_id":"114725"}} GSE114725 10× paired single-cell TCR and RNA-seq dataset GEO Accession numbers {"type":"entrez-geo","attrs":{"text":"GSE114727","term_id":"114727"}} GSE114727 , {"type":"entrez-geo","attrs":{"text":"GSE114724","term_id":"114724"}} GSE114724 CyTOF dataset Flow Repository https://flowrepository.org/id/FR-FCM-ZYJP Software and Algorithms SEQC This paper https://github.com/ambrosejcarr/seqc.git Biscuit This paper and Prabhkaran et al., 2016 . https://github.com/sandhya212/BISCUIT_SingleCell_IMM_ICML_2016 t-SNE van der Maaten and Hinton, 2008 . https://lvdmaaten.github.io/software/ PhenoGraph Levine et al., 2015 . https://github.com/jacoblevine/PhenoGraph Diffusion maps Coifman et al., 2005 . http://www.math.jhu.edu/~mauro/#tab_DiffusionGeom FACSDiva BD Biosciences RRID:SCR_001456 FlowJo BD Biosciences RRID:SCR_008520 https://www.flowjo.com/ FastQC Andrews, 2010. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ STAR 2.5.3a Dobin et al., 2013. https://github.com/alexdobin/STAR Edittag Faircloth and Glenn, 2012. https://github.com/faircloth-lab/edittag Cell Ranger 2.1.1 10× Genomics https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest Loupe Cell Browser 10× Genomics https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest#loupetab CyTOF cell debarcoder Zunder et al., 2015. https://github.com/nolanlab/single-cell-debarcoder CyTOF Bead Normalization Finck et al., 2013. https://github.com/nolanlab/bead-normalization/ Open in a separate window KEY RESOURCES TABLE ..



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