Journal: Cell

Article Title: Single-cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment

doi: 10.1016/j.cell.2018.05.060

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: 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

Techniques: Staining, Antibody Labeling, Software, Diffusion-based Assay

Journal: Cell

Article Title: Single-cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment

doi: 10.1016/j.cell.2018.05.060

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: 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

Techniques: Staining, Antibody Labeling, Software, Diffusion-based Assay

Journal: OncoTargets and therapy

Article Title: Noninvasive monitoring of the genetic evolution of EGFR -mutant non-small-cell lung cancer by analyzing circulating tumor DNA during combination chemotherapy with gefitinib and pemetrexed or S-1

doi: 10.2147/OTT.S105976

Figure Lengend Snippet: EGFR mutation detected by digital PCR and serum HGF levels

Article Snippet: Fluidigm 48.770 Digital-Array based digital PCR was carried out as described previously (Fluidigm, San Francisco, CA, USA).

Techniques: Mutagenesis, Digital PCR

Journal: OncoTargets and therapy

Article Title: Noninvasive monitoring of the genetic evolution of EGFR -mutant non-small-cell lung cancer by analyzing circulating tumor DNA during combination chemotherapy with gefitinib and pemetrexed or S-1

doi: 10.2147/OTT.S105976

Figure Lengend Snippet: PFS and the timing of second digital PCR. Abbreviations: G, gefitinib; HGF, hepatocyte growth factor; mo, months; PEM, pemetrexed; PCR, polymerase chain reaction; PFS, progression-free survival.

Article Snippet: Fluidigm 48.770 Digital-Array based digital PCR was carried out as described previously (Fluidigm, San Francisco, CA, USA).

Techniques: Digital PCR, Polymerase Chain Reaction