Journal: Cell chemical biology

Article Title: Time variant SRC kinase activation determines endothelial permeability response

doi: 10.1016/j.chembiol.2019.04.007

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: The following reagents were used: Protein G-coupled agarose beads (Millipore, cat. no. IP04–1.5ML), Rapamycin (LC Laboratories, cat. no. R5000) Leupeptin hemisulfate (Gold Biotechnology, cat. no. L-010–5), and Aprotinin (Gold Biotechnology, cat. no. A-655–25), Pierce™ BCA Protein Assay Kit (Thermo Fisher, cat. no. 23225), Fluorescein isothiocyanate-dextra (Sigma-Aldrich cat. no. 46944), D- erythro -sphingosine-1-phosphate (Avanti Polar Lipids, cat. no. 860492), 1-NA-PP1 (1-Naphthyl-PP1) (Cayman, cat. no. 10954), Human Alpha Thrombin (Factor IIa) (Enzyme Research Laboratories, cat. no. HT1002a), Fluorescein isothiocyanate-avidin (Invitrogen, cat. no. 43–4411), gelatin (Sigma-Aldrich cat. no. G2500), Salmon Sperm DNA Solution (Thermo Fisher cat. no. 15632011), Saracatinib (Santa Cruz, cat. no. sc-364607), 2X Laemmli Buffer (Bio Rad 1610737), and donkey serum (Jackson ImmunoResearch, cat. no. 017–000-121).

Techniques: Recombinant, Plasmid Preparation, Software

Journal: Cell reports

Article Title: Integrated genomic and proteomic analyses identify stimulus-dependent molecular changes associated with distinct modes of skeletal muscle atrophy

doi: 10.1016/j.celrep.2021.109971

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Rabbit anti-alpha- tubulin (11H10) , Cell Signaling Technologies , 2125S; RRID:AB_2619646.

Techniques: Recombinant, SYBR Green Assay, Membrane, Electron Microscopy, Bicinchoninic Acid Protein Assay, Cell Based Assay, Reverse Transcription, Muscles, Gene Expression, Control, Mass Spectrometry, Software

Journal: STAR Protocols

Article Title: Cloning BRD4 long isoform into overexpression vectors for stable overexpression of BRD4-L in mammalian cells

doi: 10.1016/j.xpro.2022.101785

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Article Snippet: Download the appropriate sequences. a. Download the Reference Sequence for Homo sapiens bromodomain containing 4 (BRD4), transcript variant long, mRNA (GenBank: NM_058243.3) from the NCBI’s website, using the GenBank data base ( BRD4-L RefSeq ). b. Download the sequence for LentiV_Blast (Addgene, cat# 111887) from Addgene’s website ( LentiV_Blast ).

Techniques: Virus, Recombinant, Cloning, Gel Extraction, Plasmid Preparation, Sequencing, Over Expression, Expressing, Software, Imaging

Journal: Developmental cell

Article Title: SUPPRESSING MITOCHONDRIAL RESPIRATION IS CRITICAL FOR HYPOXIA TOLERANCE IN THE FETAL GROWTH PLATE

doi: 10.1016/j.devcel.2019.04.029

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Rabbit polyclonal anti LDHA , Cell Signaling Technology , Cat# 2012, RRID:AB_2137173.

Techniques: Virus, Luciferase, Plasmid Preparation, Recombinant, Saline, Reverse Transcription, SYBR Green Assay, Protease Inhibitor, Bicinchoninic Acid Protein Assay, Marker, Western Blot, Stripping, In Situ, Imaging, Live Cell Imaging, Membrane, Cell Based Assay, Software

Journal: Developmental cell

Article Title: SUPPRESSING MITOCHONDRIAL RESPIRATION IS CRITICAL FOR HYPOXIA TOLERANCE IN THE FETAL GROWTH PLATE

doi: 10.1016/j.devcel.2019.04.029

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Article Snippet: Rabbit polyclonal anti Caspase-3 , Cell Signaling Technology , Cat# 9662, RRID: AB_331439.

Techniques: Virus, Luciferase, Plasmid Preparation, Recombinant, Saline, Reverse Transcription, SYBR Green Assay, Protease Inhibitor, Bicinchoninic Acid Protein Assay, Marker, Western Blot, Stripping, In Situ, Imaging, Live Cell Imaging, Membrane, Cell Based Assay, Software

Journal: Cellular and Molecular Life Sciences: CMLS

Article Title: RAB23 facilitates clathrin-coated nascent vesicle formation at the plasma membrane and modulates cell signaling

doi: 10.1007/s00018-025-05694-w

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Article Snippet: GFP-Trap based co-immunoprecipitation was performed using GFP-Trap A agarose beads (iST GFP-Trap Test Kit, Kit for AP-MS sample preparation of GFP-fusion proteins, Chromotek; gtak-iST-8,).

Techniques: Marker, Recombinant, Lysis, Blocking Assay, Protease Inhibitor, Transfection, Bicinchoninic Acid Protein Assay, Derivative Assay, Plasmid Preparation, Software, Imaging

Journal: Developmental cell

Article Title: SUPPRESSING MITOCHONDRIAL RESPIRATION IS CRITICAL FOR HYPOXIA TOLERANCE IN THE FETAL GROWTH PLATE

doi: 10.1016/j.devcel.2019.04.029

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Reverse transcription of mRNA was performed using Omniscript Reverse Transcriptase (Qiagen) as the manufacturer’s protocol recommended.

Techniques: Luciferase, Plasmid Preparation, Recombinant, SYBR Green Assay, Protease Inhibitor, Bicinchoninic Acid Protein Assay, Marker, Western Blot, Stripping, In Situ, Imaging, Live Cell Imaging, Cell Based Assay, Software

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