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| Name | Authors | DOI | Group |
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Single-cell mapping of lineage and identity via CellTagging Resource Report Resource Website |
Brent A. Biddy, Wenjun Kong, Kenji Kamimoto, Chuner Guo, Sarah Waye, Tao Sun, Samantha Morris | DOI:10.17504/protocols.io.xu6fnze | Single-cell technologies are offering unprecedented insight into complex biology, revealing the behavior of rare cell populations that are typically masked in bulk population analyses. One current limitation of single-cell approaches is that lineage relationships are lost as a result of cell processing, restricting interpretations of the data collected. Elegant computational approaches have been developed in an effort to infer these missing observations, but it remains a challenge to reconstruct true reprogramming trajectories using these tools. Although sophisticated lineage tracing solutions to connect cell history with fate are emerging, these protocols are either not compatible with high-throughput scRNA-seq, or require genome editing strategies that are not readily deployed in some systems. Here, our protocol describes a single-cell resolution clonal tracking approach, ‘CellTagging’, based on combinatorial cell indexing, permitting the parallel capture of lineage information and cell identity. CellTagging integrates with high-throughput single-cell RNA-sequencing, where iterative rounds of cell labeling enable the construction of multi-level lineage trees. This straightforward lentiviral-labeling approach can be applied to an array of cell biological applications to simultaneously profile lineage and identity, at single-cell resolution. | Department of Developmental Biology; Department of Genetics; Center of Regenerative Medicine. Washington University School of Medicine in St. Louis. 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA., Department of Developmental Biology; Department of Genetics; Center of Regenerative Medicine. Washington University School of Medicine in St. Louis. 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA., Department of Developmental Biology; Department of Genetics; Center of Regenerative Medicine. Washington University School of Medicine in St. Louis. 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA., Department of Developmental Biology; Department of Genetics; Center of Regenerative Medicine. Washington University School of Medicine in St. Louis. 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA., Department of Developmental Biology; Department of Genetics; Center of Regenerative Medicine. Washington University School of Medicine in St. Louis. 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA., Department of Developmental Biology; Department of Genetics; Center of Regenerative Medicine. Washington University School of Medicine in St. Louis. 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA., Department of Developmental Biology; Department of Genetics; Center of Regenerative Medicine. Washington University School of Medicine in St. Louis. 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA. | 6 | 2019 | Brent A. Biddy, Wenjun Kong, Kenji Kamimoto, Chuner Guo, Sarah Waye, Tao Sun, Samantha Morris 2019. Single-cell mapping of lineage and identity via CellTagging. protocols.io https://dx.doi.org/10.17504/protocols.io.xu6fnze | 2021-04-15 09:15:49 | ||||
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Mammalian Cell Nucleus Staining Resource Report Resource Website |
Kenneth Schackart, Kattika Kaarj | DOI:10.17504/protocols.io.xswfnfe | 481b Laboratory | Introductory protocol for cell nucelus staining using and imaging. This protocol uses Invitrogen™ NucBlue™ LiveReady Probes™. | University of Arizona, University of Arizona | 1 | 2019 | Kenneth Schackart, Kattika Kaarj 2019. Mammalian Cell Nucleus Staining. protocols.io https://dx.doi.org/10.17504/protocols.io.xswfnfe | 2021-04-15 09:15:29 | |||
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Genotype with Quant Studio™ 12K Flex protocol Resource Report Resource Website |
Na Wang, Chuan Wang, Xi'an Fu, Gongqi Yu, Zhenhua Yue, Tingting Liu | DOI:10.17504/protocols.io.pvbdn2n | Wang N, Wang Z, Wang C, Fu X, Yu G, Yue Z, Liu T, Zhang H, Li L, Chen M, Wang H, Niu G, Liu D, Zhang M, Xu Y, Zhang Y, Li J, Li Z, You J, Chu T, Li F, Liu D, Liu H, Zhang F (2018) Prediction of leprosy in the Chinese population based on a weighted genetic risk score. PLoS Negl Trop Dis 12(9): e0006789. doi: 10.1371/journal.pntd.0006789 | Shandong Provincial Hospital for Skin Diseases, Shandong University, Shandong Provincial Hospital for Skin Diseases, Shandong Provincial Hospital for Skin Diseases, Shandong Provincial Hospital for Skin Diseases, Shandong Provincial Hospital for Skin Diseases, Shandong Provincial Hospital for Skin Diseases | https://doi.org/10.1371/journal.pntd.0006789 | 1 | 2018 | Na Wang, Chuan Wang, Xi'an Fu, Gongqi Yu, Zhenhua Yue, Tingting Liu 2018. Genotype with Quant Studio™ 12K Flex protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.pvbdn2n | 2021-04-15 09:15:29 | |||
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1. Sample_prep_WB Resource Report Resource Website |
Elizabeth Fozo | In-house protocol | 1 | 2020 | Elizabeth Fozo 2020. 1. Sample_prep_WB. protocols.io https:// | 2021-04-15 09:15:26 | ||||||
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PCR Using Q5U Hot Start High-Fidelity DNA Polymerase (NEB #M0515): Amplification of bisulfite-converted, deaminated, or damaged DNA (Including FFPE DNA) Resource Report Resource Website |
New England Biolabs | DOI:10.17504/protocols.io.7sdhna6 | New England Biolabs (NEB) | Q5U Hot Start High-Fidelity DNA Polymerase is a modified version of Q5®High-Fidelity DNA Polymerase, a novel thermostable DNA polymerase that possesses 3′ to 5′ exonuclease activity, and is fused to a processivity-enhancing Sso7d domain. Q5U contains a mutation in the uracil-binding pocket that enables the ability to read and amplify templates containing uracil and inosine bases. | New England Biolabs | https://www.neb.com/protocols/2019/07/02/pcr-using-q5u-hot-start-high-fidelity-dna-polymerase-neb-m0515 | 1 | 2020 | New England Biolabs 2020. PCR Using Q5U Hot Start High-Fidelity DNA Polymerase (NEB #M0515): Amplification of bisulfite-converted, deaminated, or damaged DNA (Including FFPE DNA). protocols.io https://dx.doi.org/10.17504/protocols.io.7sdhna6 | 2021-04-15 09:15:28 | ||
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Natural Transformation of Campylobacter jejuni Resource Report Resource Website |
Jessica Sacher | DOI:10.17504/protocols.io.magc2bw | Irons J, Sacher JC, Szymanski CM, Downs DM, Cj1388 Is a RidA Homolog and Is Required for Flagella Biosynthesis and/or Function in . Frontiers in Microbiology doi: 10.3389/fmicb.2019.02058 | University of Alberta | https://doi.org/10.3389/fmicb.2019.02058 | 2 | 2017 | Jessica Sacher 2017. Natural Transformation of Campylobacter jejuni. protocols.io https://dx.doi.org/10.17504/protocols.io.magc2bw | 2021-04-15 09:15:49 | |||
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Phytoplankton sinking rates through time-resolved fluorescence plate spectroscopy Resource Report Resource Website |
Catherine C. Bannon, Douglas A. Campbell | DOI:10.17504/protocols.io.jqzcmx6 | We established a method for parallel, large scale analysis of multiple phytoplankton sinking rates through top-view monitoring of chlorophyll a fluorescence in microtitre well plates. We verified the method through experimental analysis of known factors that influence sinking rates, including exponential versus stationary growth phase in species of different cell sizes; Thalassiosira pseudonana CCMP1335, chain-forming Skeletonema marinoi RO5A and Coscinodiscus radiatus CCMP312. We fit decay curves to an algebraic transform of the decrease in fluorescence signal as cells sank away from the fluorometer detector, and then used minimal mechanistic assumptions to extract a sinking rate (m d-1) using an RStudio script, SinkWORX. | Mount Allison University, Mount Allison University | https://www.dropbox.com/sh/w03c2nt97rjk990/AACyg_nJrl75ztT9s6A89zT-a?dl=0 | 1 | 2017 | Catherine C. Bannon, Douglas A. Campbell 2017. Phytoplankton sinking rates through time-resolved fluorescence plate spectroscopy. protocols.io https://dx.doi.org/10.17504/protocols.io.jqzcmx6 | 2021-04-15 09:15:28 | |||
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PMN- 06 - Culture of Human PMN - TNF-α production Resource Report Resource Website |
Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino | DOI:10.17504/protocols.io.bkrakv2e | Published work using this protocol:- A Novel Standardized Cannabis sativa L. Extract and Its Constituent Cannabidiol Inhibit Human Polymorphonuclear Leukocyte Functions. Mabou Tagne A, Marino F, Legnaro M, Luini A, Pacchetti B, Cosentino M.Int J Mol Sci. 2019 Apr 13;20(8):1833. doi: 10.3390/ijms20081833 | Center for Research in Medical Pharmacology, University of Insubria (Varese, Italy), Center for Research in Medical Pharmacology, University of Insubria (Varese, Italy), Center for Research in Medical Pharmacology, University of Insubria (Varese, Italy), Center for Research in Medical Pharmacology, University of Insubria (Varese, Italy), Center for Research in Medical Pharmacology, University of Insubria (Varese, Italy), Center for Research in Medical Pharmacology, University of Insubria (Varese, Italy), Center for Research in Medical Pharmacology, University of Insubria (Varese, Italy) | 1 | 2020 | Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino 2020. PMN- 06 - Culture of Human PMN - TNF-α production. protocols.io https://dx.doi.org/10.17504/protocols.io.bkrakv2e | 2021-04-15 09:15:28 | ||||
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SPARC Retrograde Neuroanatomical Tracing of Phrenic Motor Neurons Using Intrapleural Injections of Cholera Toxin B Fragment Resource Report Resource Website |
Latoya Allen, Marissa Ciesla, Yasin Seven, Elisa Gonzalez-Rothi, Gordon Pool | DOI:10.17504/protocols.io.2kpgcvn | SPARC | This protocol describes the procedure for retrogradely labeling bilateral phrenic motor neuron pools in the cervical spinal cord using intrapleural injections of cholera toxin B fragment | University of Florida, University of Florida, University of Florida, University of Florida, University of Florida | 1 | 2019 | Latoya Allen, Marissa Ciesla, Yasin Seven, Elisa Gonzalez-Rothi, Gordon Pool 2019. SPARC Retrograde Neuroanatomical Tracing of Phrenic Motor Neurons Using Intrapleural Injections of Cholera Toxin B Fragment. protocols.io https://dx.doi.org/10.17504/protocols.io.2kpgcvn | 2021-04-15 09:15:28 | |||
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Overlap extension PCR Resource Report Resource Website |
Anna Behle | DOI:10.17504/protocols.io.psndnde | Axmann Lab, CyanoWorld, iGEM Duesseldorf 2018 | Linear assembly of PCR fragments.Can be used to quickly and efficiently fuse promoters, terminators, fusion proteins etc. without time-consuming sub-cloning steps. | Institute for Synthetic Microbiology | 1 | 2019 | Anna Behle 2019. Overlap extension PCR. protocols.io https://dx.doi.org/10.17504/protocols.io.psndnde | 2021-04-15 09:15:28 | |||
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IgG expression and purification Resource Report Resource Website |
Bei Wang, Wen-Hsin Sandy Lee, Helen Huang, Patricia Ng, Eve Ngoh, Chia Yin Lee, Hwee Ching Tan, Rabiatul Adawiyah, Mun Kuen Soh, Frannie Teo, Yvonne Yeap, Yuanyu Hu, Cheng-I Wang | DOI:10.17504/protocols.io.bitvken6 | Coronavirus Method Development Community | Singapore Immunology Network, A*STAR, Singapore, Singapore Immunology Network, A*STAR, Singapore, Singapore Immunology Network, A*STAR, Singapore, Singapore Immunology Network, A*STAR, Singapore, Singapore Immunology Network, A*STAR, Singapore, Singapore Immunology Network, A*STAR, Singapore, Singapore Immunology Network, A*STAR, Singapore, Singapore Immunology Network, A*STAR, Singapore, Singapore Immunology Network, A*STAR, Singapore, Singapore Immunology Network, A*STAR, Singapore, Singapore Immunology Network, A*STAR, Singapore, Singapore Immunology Network, A*STAR, Singapore, Singapore Immunology Network, A*STAR, Singapore | 1 | 2020 | Bei Wang, Wen-Hsin Sandy Lee, Helen Huang, Patricia Ng, Eve Ngoh, Chia Yin Lee, Hwee Ching Tan, Rabiatul Adawiyah, Mun Kuen Soh, Frannie Teo, Yvonne Yeap, Yuanyu Hu, Cheng-I Wang 2020. IgG expression and purification. protocols.io https://dx.doi.org/10.17504/protocols.io.bitvken6 | 2021-04-15 09:15:49 | ||||
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UC Davis - High fat diet feeding Resource Report Resource Website |
Kristin Evans | DOI:10.17504/protocols.io.xfmfjk6 | Mouse Metabolic Phenotyping Centers | SummaryA high-fat diet of varying composition and percent fat is administered to induce obesity in mice. High-fat diet induced obesity is causally associated with insulin resistance and type 2 diabetes. Diets will be provided in consultation with the investigator needs. This service applies to specialized feeding for vendor supplied animals being supplied out of the UC Davis vendor approved barrier facility. |
RRID:IMSR_JAX:000664 RRID:IMSR_CRL:27 RRID:IMSR_TAC:b6 |
University of California, Davis | https://mmpc.org/shared/document.aspx?id=266&docType=Protocol | 1 | 2019 | Kristin Evans 2019. UC Davis - High fat diet feeding. protocols.io https://dx.doi.org/10.17504/protocols.io.xfmfjk6 | 2021-04-15 09:15:26 | |
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Selective protection and labelling of arginine/lysine side chains in HBSs of proteins Resource Report Resource Website |
Phuong Thao Bui, Quentin Nunes, Yong Li, David G.Fernig | DOI:10.17504/protocols.io.wq6fdze | Interactions between heparan sulfate proteoglycans and the partner proteins regulate many aspects of cell functions, however, their binding properties are still equivocal. Developed eight years ago was a method for selective labelling of lysine residues in the heparin binding sites of Fibroblast Growth Factors (FGFs). The labelling of arginine residues is far more challenging, due to the multiple reaction products between a dicarbonyl and a guanidino group. | University of Liverpool, University of Liverpool, University of Liverpool, University of Liverpool | 3 | 2019 | Phuong Thao Bui, Quentin Nunes, Yong Li, David G.Fernig 2019. Selective protection and labelling of arginine/lysine side chains in HBSs of proteins. protocols.io https://dx.doi.org/10.17504/protocols.io.wq6fdze | 2021-04-15 09:15:26 | ||||
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Make LB agar medium Resource Report Resource Website |
Gurdon Institute mediak | DOI:10.17504/protocols.io.55zg876 | Make LB agar medium. | Wellcome Trust / Cancer Research UK Gurdon Institute | 2 | 2019 | Gurdon Institute mediak 2019. Make LB agar medium. protocols.io https://dx.doi.org/10.17504/protocols.io.55zg876 | 2021-04-15 09:15:28 | ||||
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Phalloidin Immunofluorescence Staining Resource Report Resource Website |
Dania Villarnovo | DOI:10.17504/protocols.io.rd8d29w | Cornell University | 1 | 2018 | Dania Villarnovo 2018. Phalloidin Immunofluorescence Staining. protocols.io https://dx.doi.org/10.17504/protocols.io.rd8d29w | 2021-04-15 09:15:28 | |||||
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Validation of Selected RNA Extraction Method Resource Report Resource Website |
Ariel Cerda, Catalina Ibarra-Henriquez, Valentina Sebastian, Grace Armijo, Liliana Lamig, Carolina Miranda, Marcela Lagos, Sandra Solari, Ana María Guzmán, Teresa Quiroga, Susan Hitschfeld, Eleodoro Riveras, Marcela Ferres, Rodrigo A. Gutiérrez, Patricia García, Aniela Wozniak | Coronavirus Method Development Community, Reclone.org (The Reagent Collaboration Network) | FONDAP Center for Genome Regulation. Millennium Institute for Integrative Biology (iBio), Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile, FONDAP Center for Genome Regulation. Millennium Institute for Integrative Biology (iBio), Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile, Laboratorio de Microbiología. Servicio de laboratorios Clínicos. Red de Salud UC-CHRISTUS, FONDAP Center for Genome Regulation. Millennium Institute for Integrative Biology (iBio), Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile, FONDAP Center for Genome Regulation. Millennium Institute for Integrative Biology (iBio), Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile, Laboratorio de Microbiología. Servicio de laboratorios Clínicos. Red de Salud UC-CHRISTUS, Departamento de Laboratorios Clínicos. Escuela de Medicina. Facultad de Medicina. Pontificia Universidad Católica de chile, Departamento de Laboratorios Clínicos. Escuela de Medicina. Facultad de Medicina. Pontificia Universidad Católica de chile, Departamento de Laboratorios Clínicos. Escuela de Medicina. Facultad de Medicina. Pontificia Universidad Católica de chile, Departamento de Laboratorios Clínicos. Escuela de Medicina. Facultad de Medicina. Pontificia Universidad Católica de chile, FONDAP Center for Genome Regulation. Millennium Institute for Integrative Biology (iBio), Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile, FONDAP Center for Genome Regulation. Millennium Institute for Integrative Biology (iBio), Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile, Departamento de Laboratorios Clínicos. Escuela de Medicina. Facultad de Medicina. Pontificia Universidad Católica de chile, FONDAP Center for Genome Regulation. Millennium Institute for Integrative Biology (iBio), Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile, Departamento de Laboratorios Clínicos. Escuela de Medicina. Facultad de Medicina. Pontificia Universidad Católica de chile, Departamento de Laboratorios Clínicos. Escuela de Medicina. Facultad de Medicina. Pontificia Universidad Católica de chile | https://doi.org/10.1101/2020.05.07.083048 | 1 | 2020 | Ariel Cerda, Catalina Ibarra-Henriquez, Valentina Sebastian, Grace Armijo, Liliana Lamig, Carolina Miranda, Marcela Lagos, Sandra Solari, Ana María Guzmán, Teresa Quiroga, Susan Hitschfeld, Eleodoro Riveras, Marcela Ferres, Rodrigo A. Gutiérrez, Patricia García, Aniela Wozniak 2020. Validation of Selected RNA Extraction Method. protocols.io https:// | 2021-04-15 09:15:26 | ||||
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Environmental DNA (eDNA) COI metabarcoding Illumina MiSeq NGS PCR Protocol Resource Report Resource Website |
Collin Closek, Anni Djurhuus, Katie Pitz, Ryan Kelly, Reiko Michisaki, Kristine Walz, Hilary Starks, Francisco Chavez, Alexandria Boehm, Mya Breitbart | DOI:10.17504/protocols.io.mwnc7de | MBON eDNA | This protocol is aimed at amplifying the cytochrome c oxidase subunit I (COI) mitochondrial gene in eukaryotes. The primers (forward: mlCOIintF, reverse: HCO2198) utilized in this protocol are based on the primers utilized in Leray et al. 2013 (forward) and Folmer et al. 1994 (reverse).Amplicons generated using this protocol can then be sequenced using the Illumina platform.Primers used:Fluidigm CS1+mlCOIinfFFluidigm CS2+HCO2198Secondary COI PCR primersPE1-BC-CS1PE2-BC-CS2 | Center for Ocean Solutions, Stanford University, CA, University of South Florida, College of Marine Science, St Petersburg, FL, Monterey Bay Aquarium Research Institute, Moss Landing, CA, University of Washington, Seattle, WA, Monterey Bay Aquarium Research Institute, Moss Landing, CA, Monterey Bay Aquarium Research Institute, Moss Landing, CA, Center for Ocean Solutions, Stanford University, CA, Monterey Bay Aquarium Research Institute, Moss Landing, CA, Center for Ocean Solutions, Stanford University, CA, University of South Florida, College of Marine Science, St Petersburg, FL | 1 | 2018 | Collin Closek, Anni Djurhuus, Katie Pitz, Ryan Kelly, Reiko Michisaki, Kristine Walz, Hilary Starks, Francisco Chavez, Alexandria Boehm, Mya Breitbart 2018. Environmental DNA (eDNA) COI metabarcoding Illumina MiSeq NGS PCR Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.mwnc7de | 2021-04-15 09:15:28 | |||
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NEBNext Ultra II Ligation Module (NEB # E7595) for NEBNext Ultra II End Repair/dA Tailing Module (NEB #E7546) Resource Report Resource Website |
New England Biolabs, Menna Teffera | DOI:10.17504/protocols.io.4nqgvdw | This module is part of the Ultra™ II workflow, and is optimized for use with the NEBNext®Ultra II End Repair/dA-Tailing Module (NEB #E7546), for Illumina®-compatible library construction.The NEBNext Ultra II Ligation Module is optimized for use with the NEBNext Ultra II End Repair/dA-Tailing Module (NEB #E7546) or the NEBNext Ultra II FS DNA Module (NEB #E7810). | New England Biolabs, New England Biolabs | https://www.neb.com/-/media/catalog/datacards-or-manuals/manuale7595.pdf?rev=6d5ae698cf394a27864e788e6056e8d8 | 1 | 2019 | New England Biolabs, Menna Teffera 2019. NEBNext Ultra II Ligation Module (NEB # E7595) for NEBNext Ultra II End Repair/dA Tailing Module (NEB #E7546). protocols.io https://dx.doi.org/10.17504/protocols.io.4nqgvdw | 2021-04-15 09:15:26 | |||
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PCR HSP60 - 96 well plate Resource Report Resource Website |
Sarah Hessen-Schmidt | DOI:10.17504/protocols.io.fbebije | University of Southern California | 1 | 2016 | Sarah Hessen-Schmidt 2016. PCR HSP60 - 96 well plate. protocols.io https://dx.doi.org/10.17504/protocols.io.fbebije | 2021-04-15 09:15:26 | |||||
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GEP analysis of BM CD34+/lin- cells of patients with CML Resource Report Resource Website |
Alessandra Trojani | DOI:10.17504/protocols.io.yncfvaw | Trojani A, Pungolino E, Molin AD, Lodola M, Rossi G, D’Adda M, Perego A, Elena C, Turrini M, Borin L, Bucelli C, Malato S, Carraro MC, Spina F, Latargia ML, Artale S, Spedini P, Anghilieri M, Camillo BD, Baruzzo G, Canal GD, Iurlo A, Morra E, Cairoli R (2019) Nilotinib interferes with cell cycle, ABC transporters and JAK-STAT signaling pathway in CD34+/lin- cells of patients with chronic phase chronic myeloid leukemia after 12 months of treatment. PLoS ONE 14(7): e0218444. doi: 10.1371/journal.pone.0218444 | ASST Grande Ospedale Metropolitano Niguarda, Milano, Italy | https://doi.org/10.1371/journal.pone.0218444 | 1 | 2019 | Alessandra Trojani 2019. GEP analysis of BM CD34+/lin- cells of patients with CML. protocols.io https://dx.doi.org/10.17504/protocols.io.yncfvaw | 2021-04-15 09:15:28 |
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