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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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Github ssh keys Resource Report Resource Website |
Ken Youens-Clark | DOI:10.17504/protocols.io.fskbncw | MetaFunc Course | University of Arizona | 1 | 2016 | Ken Youens-Clark 2016. Github ssh keys. protocols.io https://dx.doi.org/10.17504/protocols.io.fskbncw | 2021-04-15 09:14:26 | ||||
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Nuclei Isolation from Human Frozen Liver Resource Report Resource Website |
Sanjay Subramanian, Stacey Huppert | DOI:10.17504/protocols.io.bhpej5je | This protocol is used to isolate human liver nuclei from frozen samples in an effort to facilitate human nuclei extraction for use in single nuclear RNA sequencing and single cell ATAC sequencing without the need for fresh samples. This approach enables the ability to acquire signatures from all cell types, even those from fibrotic liver samples. A brief fixation step is included in order to preserve nuclear membrane integrity and prevent nuclear leakage. This protocol has been tested and works in frozen human liver samples weighing approximately 1 gram stored in cryopreservation medium. Single nuclear RNA seqencing was run using the 10x Chromium system.This project was supported in part by NIH P30 DK078392 (Gene Analysis Core) of the Digestive Diseases Research Core Center in Cincinnati, R01DK107553, and the Cincinnati Pediatric Cell Atlas Center funded by Cincinnati Children’s Research Foundation to Stacey S. Huppert | [Division of Gastroenterology, Hepatology & Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States], [Division of Gastroenterology, Hepatology & Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States] | 1 | 2020 | Sanjay Subramanian, Stacey Huppert 2020. Nuclei Isolation from Human Frozen Liver. protocols.io https://dx.doi.org/10.17504/protocols.io.bhpej5je | 2021-04-15 09:14:27 | ||||
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EDTA disodium salt dihydrate Resource Report Resource Website |
James Thornton | DOI:10.17504/protocols.io.dbm2k5 | VERVE Net, Sullivan Lab | For use in DNase I Treatment protocol for DNase inactivation. | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2015 | James Thornton 2015. EDTA disodium salt dihydrate. protocols.io https://dx.doi.org/10.17504/protocols.io.dbm2k5 | 2021-04-15 09:14:34 | |||
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Fresh 4% Paraformaldehyde in PBS Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bezijf4e | BICCN, Allen Institute for Brain Science | Freshly prepared 4% Paraformaldehyde in PBS is used to fix adult and developing mouse brains during the transcardial perfusion process, as well as for immersion fixation. This solution can be used for no more than one week post-preparation date.Note: Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Award Number U19MH114830. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. | Allen Institute | 1 | 2020 | Allen Institute for Brain Science 2020. Fresh 4% Paraformaldehyde in PBS. protocols.io https://dx.doi.org/10.17504/protocols.io.bezijf4e | 2021-04-15 09:14:28 | |||
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Non-radioactive phosphorylation with T4 PNK 3' phosphatase minus Resource Report Resource Website |
New England Biolabs | DOI:10.17504/protocols.io.cp2vqd | New England Biolabs (NEB) | Protocol for non-radioactive phosphorylation with T4 PNK 3' phosphatase minus. | New England Biolabs | https://www.neb.com/protocols/1/01/01/non-radioactive-phosphorylation-with-t4-pnk-or-pnk3-phosphatase-minus | 1 | 2015 | New England Biolabs 2015. Non-radioactive phosphorylation with T4 PNK 3' phosphatase minus. protocols.io https://dx.doi.org/10.17504/protocols.io.cp2vqd | 2021-04-15 09:14:35 | ||
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Water Sampling onto Filters for Nucleic Acids Sequencing Resource Report Resource Website |
Melissa Duhaime, Morgan Lindback, Rachel Cable | DOI:10.17504/protocols.io.jegcjbw | Duhaime Lab, Biosphere2 Ocean, ELA Microplastics Team | This protocol will guide you through the process of filter water using a serial filtration approach to generate filters with microbial biomass. Later, nucleic acids will be extracted from these filters. | University of Michigan - Ann Arbor, University of Michigan - Ann Arbor, University of Michigan - Ann Arbor | 1 | 2019 | Melissa Duhaime, Morgan Lindback, Rachel Cable 2019. Water Sampling onto Filters for Nucleic Acids Sequencing. protocols.io https://dx.doi.org/10.17504/protocols.io.jegcjbw | 2021-04-15 09:14:28 | |||
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PCLS Whole Mounts Resource Report Resource Website |
Morrisey Lab | LungMap2 Consortium | University of Pennsylvania | 1 | 2021 | Morrisey Lab 2021. PCLS Whole Mounts. protocols.io https:// | 2021-04-15 09:14:35 | |||||
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DPP4 Resource Report Resource Website |
thananda | DOI:10.17504/protocols.io.brvtm66n | Navamindradhiraj University | 1 | 2021 | thananda 2021. DPP4. protocols.io https://dx.doi.org/10.17504/protocols.io.brvtm66n | 2021-04-15 09:14:27 | |||||
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Oyster Shell Processing Protocol Resource Report Resource Website |
Benjamin Walther | DOI:10.17504/protocols.io.bbd7ii9n | This protocol describes the procedure for sectioning oyster shells, micromilling to extract carbonate powder, and an overview of analyses at the UC Davis Stable Isotope Facility to obtain carbon and oxygen stable isotope ratios of shell carbonate. | Texas A&M University - Corpus Christi | 1 | 2020 | Benjamin Walther 2020. Oyster Shell Processing Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bbd7ii9n | 2021-04-15 09:14:32 | ||||
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Make LB agar plates to grown bacteria without antibiotic selection. Resource Report Resource Website |
Cancer Research UK / Wellcome Gurdon Institute media kitchen | DOI:10.17504/protocols.io.3nvgme6 | Make LB agar plates to grown bacteria without antibiotic selection. | Cancer Research UK / Wellcome Gurdon Institute | 1 | 2019 | Cancer Research UK / Wellcome Gurdon Institute media kitchen 2019. Make LB agar plates to grown bacteria without antibiotic selection.. protocols.io https://dx.doi.org/10.17504/protocols.io.3nvgme6 | 2021-04-15 09:14:33 | ||||
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Phenol/chloroform genomic DNA extraction-1.5 ml Eppendorf tube. Resource Report Resource Website |
Daniel Richter | DOI:10.17504/protocols.io.inzcdf6 | Ecology of Marine Plankton (ECOMAP) team - Roscoff, Protist Research to Optimize Tools in Genetics (PROT-G) | Richter, Daniel J and Fozouni, Parinaz and Eisen, Michael and King, Nicole. Gene family innovation, conservation and loss on the animal stem lineage. 2018;7:e34226 https://doi.org/10.7554/eLife.34226 | King Lab, University of California Berkeley. | https://elifesciences.org/articles/34226 | 1 | 2017 | Daniel Richter 2017. Phenol/chloroform genomic DNA extraction-1.5 ml Eppendorf tube.. protocols.io https://dx.doi.org/10.17504/protocols.io.inzcdf6 | 2021-04-15 09:14:26 | ||
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LC-MS/MS Label-Free Proteomic Data Analysis Parameters Resource Report Resource Website |
Danielle Gutierrez, Jamie Allen, Zach Jenkins, Jeff Spraggins | DOI:10.17504/protocols.io.bfshjnb6 | VU Biomolecular Multimodal Imaging Center, Human BioMolecular Atlas Program (HuBMAP) Method Development Community | List of parameters and settings for searching label free proteomic data in MaxQuant version 1.6.7. | Vanderbilt University, Vanderbilt University, Vanderbilt University, Vanderbilt University | 2 | 2020 | Danielle Gutierrez, Jamie Allen, Zach Jenkins, Jeff Spraggins 2020. LC-MS/MS Label-Free Proteomic Data Analysis Parameters. protocols.io https://dx.doi.org/10.17504/protocols.io.bfshjnb6 | 2021-04-15 09:14:26 | |||
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RAPID RNA Extraction Resource Report Resource Website |
Noah Toppings | DOI:10.17504/protocols.io.bkp8kvrw | XPRIZE Rapid Covid Testing | University of Calgary | 1 | 2020 | Noah Toppings 2020. RAPID RNA Extraction. protocols.io https://dx.doi.org/10.17504/protocols.io.bkp8kvrw | 2021-04-15 09:14:33 | ||||
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U Mass - Albumin Resource Report Resource Website |
Jason Kim | DOI:10.17504/protocols.io.xprfmm6 | Mouse Metabolic Phenotyping Centers | This experiment involves a spectrophotometric measurement using Roche Cobas Clinical Chemistry Analyzer. Albumin is a major circulating protein in body. | University of Massachusetts | https://mmpc.org/shared/document.aspx?id=179&docType=Protocol | 1 | 2019 | Jason Kim 2019. U Mass - Albumin. protocols.io https://dx.doi.org/10.17504/protocols.io.xprfmm6 | 2021-04-15 09:14:26 | ||
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Isolation of mitochondria from Diplonema papillatum Resource Report Resource Website |
Matus Valach | DOI:10.17504/protocols.io.pkydkxw | Université de Montréal, Montreal, Quebec, Canada | 2 | 2019 | Matus Valach 2019. Isolation of mitochondria from Diplonema papillatum. protocols.io https://dx.doi.org/10.17504/protocols.io.pkydkxw | 2021-04-15 09:14:33 | |||||
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MethylC-seq using EZ DNA Methylation-Gold Bisulfite and Accel-NGS DNA Library Kits Resource Report Resource Website |
Diep Ganguly, Steven Eichten | DOI:10.17504/protocols.io.p88drzw | Pogson Genomics Group, EBL_ANU | Protocol to use ACCEL-NGS® METHYL-SEQ DNA LIBRARY KIT (NGS Prep with Bisulfite-Converted DNA Capability; Cat. No. DL-ILMMS-12/48) to perform MethylC-sequencing in Arabidopsis.Code used to analyse raw sequencing data can be found: Please see https://github.com/dtrain16/NGS-scripts/tree/master/MethylC. | Australian National University, Australian National University | 1 | 2018 | Diep Ganguly, Steven Eichten 2018. MethylC-seq using EZ DNA Methylation-Gold Bisulfite and Accel-NGS DNA Library Kits. protocols.io https://dx.doi.org/10.17504/protocols.io.p88drzw | 2021-04-15 09:14:26 | |||
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Cell DIVE™ Platform | Slide Clearing and Antigen Retrieval Resource Report Resource Website |
Liz McDonough, Chrystal Chadwick, Fiona Ginty, Christine Surrette, Anup Sood | DOI:10.17504/protocols.io.bpwumpew | Human BioMolecular Atlas Program (HuBMAP) Method Development Community, GE Research | The purpose of this protocol is to manually deparaffinize and rehydrate slides for the Cell DIVE™ Platform. | GE Research, GE Research, GE Research, GE Research, GE Research | 1 | 2020 | Liz McDonough, Chrystal Chadwick, Fiona Ginty, Christine Surrette, Anup Sood 2020. Cell DIVE™ Platform | Slide Clearing and Antigen Retrieval. protocols.io https://dx.doi.org/10.17504/protocols.io.bpwumpew | 2021-04-15 09:14:33 | |||
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Protocol for Bacterial Heterotrophic Production Resource Report Resource Website |
Jed Fuhrman | DOI:10.17504/protocols.io.dmd425 | VERVE Net, Fuhrman Lab | Fuhrman Lab | 1 | 2015 | Jed Fuhrman 2015. Protocol for Bacterial Heterotrophic Production. protocols.io https://dx.doi.org/10.17504/protocols.io.dmd425 | 2021-04-15 09:14:33 | ||||
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Protocol to immunostain Gastruloids (LSCB, EPFL) Resource Report Resource Website |
Stefano Vianello, Mehmet Girgin, Giuliana Rossi, Matthias Lutolf | DOI:10.17504/protocols.io.7tzhnp6 | Standard protocol used for immunostaining Gastruloids (aggregates of mouse embryonic stem cells) in the Lutolf Lab, EPFL.For a published protocol on how to generate Gastruloids, see: | Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences (SV) and School of Engineering (STI), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland, Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences (SV) and School of Engineering (STI), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland, Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences (SV) and School of Engineering (STI), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland, Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences (SV) and School of Engineering (STI), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland, and Institute of Chemical Sciences and Engineering, School of Basic Science (SB), EPFL, Lausanne, Switzerland | 1 | 2020 | Stefano Vianello, Mehmet Girgin, Giuliana Rossi, Matthias Lutolf 2020. Protocol to immunostain Gastruloids (LSCB, EPFL). protocols.io https://dx.doi.org/10.17504/protocols.io.7tzhnp6 | 2021-04-15 09:14:33 | ||||
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Miniprep Protocol (QIAGEN) Resource Report Resource Website |
Aditya Mohan | DOI:10.17504/protocols.io.8ibhuan | Johns Hopkins University | 1 | 2019 | Aditya Mohan 2019. Miniprep Protocol (QIAGEN). protocols.io https://dx.doi.org/10.17504/protocols.io.8ibhuan | 2021-04-15 09:14:33 |
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