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Authors: Ken Youens-Clark
Group: MetaFunc Course
Proper citation: Ken Youens-Clark 2016. Github ssh keys. protocols.io https://dx.doi.org/10.17504/protocols.io.fskbncw Copy
Authors: Sanjay Subramanian, Stacey Huppert
Summary: 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
Proper citation: Sanjay Subramanian, Stacey Huppert 2020. Nuclei Isolation from Human Frozen Liver. protocols.io https://dx.doi.org/10.17504/protocols.io.bhpej5je Copy
Authors: James Thornton
Group: VERVE Net, Sullivan Lab
Summary: For use in DNase I Treatment protocol for DNase inactivation.
Proper citation: James Thornton 2015. EDTA disodium salt dihydrate. protocols.io https://dx.doi.org/10.17504/protocols.io.dbm2k5 Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: 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.
Proper citation: Allen Institute for Brain Science 2020. Fresh 4% Paraformaldehyde in PBS. protocols.io https://dx.doi.org/10.17504/protocols.io.bezijf4e Copy
Authors: New England Biolabs
Group: New England Biolabs (NEB)
Summary: Protocol for non-radioactive phosphorylation with T4 PNK 3' phosphatase minus.
Proper citation: New England Biolabs 2015. Non-radioactive phosphorylation with T4 PNK 3' phosphatase minus. protocols.io https://dx.doi.org/10.17504/protocols.io.cp2vqd Copy
Authors: Melissa Duhaime, Morgan Lindback, Rachel Cable
Group: Duhaime Lab, Biosphere2 Ocean, ELA Microplastics Team
Summary: 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.
Proper citation: 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 Copy
Authors: Morrisey Lab
Group: LungMap2 Consortium
Proper citation: Morrisey Lab 2021. PCLS Whole Mounts. protocols.io https:// Copy
Authors: thananda
Proper citation: thananda 2021. DPP4. protocols.io https://dx.doi.org/10.17504/protocols.io.brvtm66n Copy
Authors: Benjamin Walther
Summary: 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.
Proper citation: Benjamin Walther 2020. Oyster Shell Processing Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bbd7ii9n Copy
Authors: Cancer Research UK / Wellcome Gurdon Institute media kitchen
Summary: Make LB agar plates to grown bacteria without antibiotic selection.
Proper citation: 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 Copy
Authors: Daniel Richter
Group: Ecology of Marine Plankton (ECOMAP) team - Roscoff, Protist Research to Optimize Tools in Genetics (PROT-G)
Proper citation: Daniel Richter 2017. Phenol/chloroform genomic DNA extraction-1.5 ml Eppendorf tube.. protocols.io https://dx.doi.org/10.17504/protocols.io.inzcdf6 Copy
Authors: Danielle Gutierrez, Jamie Allen, Zach Jenkins, Jeff Spraggins
Group: VU Biomolecular Multimodal Imaging Center, Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: List of parameters and settings for searching label free proteomic data in MaxQuant version 1.6.7.
Proper citation: 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 Copy
Authors: Noah Toppings
Group: XPRIZE Rapid Covid Testing
Proper citation: Noah Toppings 2020. RAPID RNA Extraction. protocols.io https://dx.doi.org/10.17504/protocols.io.bkp8kvrw Copy
Authors: Jason Kim
Group: Mouse Metabolic Phenotyping Centers
Summary:
This experiment involves a spectrophotometric measurement using Roche Cobas Clinical Chemistry Analyzer. Albumin is a major circulating protein in body.
Proper citation: Jason Kim 2019. U Mass - Albumin. protocols.io https://dx.doi.org/10.17504/protocols.io.xprfmm6 Copy
Authors: Matus Valach
Proper citation: Matus Valach 2019. Isolation of mitochondria from Diplonema papillatum. protocols.io https://dx.doi.org/10.17504/protocols.io.pkydkxw Copy
Authors: Diep Ganguly, Steven Eichten
Group: Pogson Genomics Group, EBL_ANU
Summary: 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.
Proper citation: 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 Copy
Authors: Liz McDonough, Chrystal Chadwick, Fiona Ginty, Christine Surrette, Anup Sood
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community, GE Research
Summary: The purpose of this protocol is to manually deparaffinize and rehydrate slides for the Cell DIVE™ Platform.
Proper citation: 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 Copy
Authors: Jed Fuhrman
Group: VERVE Net, Fuhrman Lab
Proper citation: Jed Fuhrman 2015. Protocol for Bacterial Heterotrophic Production. protocols.io https://dx.doi.org/10.17504/protocols.io.dmd425 Copy
Authors: Stefano Vianello, Mehmet Girgin, Giuliana Rossi, Matthias Lutolf
Summary: 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:
Proper citation: 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 Copy
Authors: Aditya Mohan
Proper citation: Aditya Mohan 2019. Miniprep Protocol (QIAGEN). protocols.io https://dx.doi.org/10.17504/protocols.io.8ibhuan Copy
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