Aug 10, 2022

Public workspace2021 Featured Protocols

This collection is a draft, published without a DOI.
  • protocols.io team1
  • 1protocols.io
Lenny Teytelman
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Collection Citation: protocols.io team 2022. 2021 Featured Protocols. protocols.io https://protocols.io/view/2021-featured-protocols-bvann2de
License: This is an open access collection distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this collection and it's working
Created: May 25, 2021
Last Modified: August 10, 2022
Collection Integer ID: 50222
Abstract
This is a growing collection that includes all protocols that were featured in 2021 on our welcome page and on social media (Twitter, Facebook).

Every week, we feature 3 new protocols that are particularly fantastic examples of reproducible and detailed method sharing. (Please note that there are many weeks where we would love to highlight dozens of public protocols instead of three!)

Files
Protocol
Icon representing the file Analysis of protein structure using Molprobity
Name
Analysis of protein structure using Molprobity
Version 3
, James Madison University
Chris BerndsenJames Madison University
Protocol
Icon representing the file Homology modeling using Phyre2 for Biochemistry I
Name
Homology modeling using Phyre2 for Biochemistry I
Version 4
, James Madison University
Chris BerndsenJames Madison University
Protocol
Icon representing the file Assessing multiplex tiling PCR sequencing approaches for detecting genomic variants of SARS-CoV-2 in municipal wastewater
Name
Assessing multiplex tiling PCR sequencing approaches for detecting genomic variants of SARS-CoV-2 in municipal wastewater
Version 1
, University of British Columbia
Xuan LinUniversity of British Columbia
Protocol
Icon representing the file MarineSediment-BlueC-eDNA
Name
MarineSediment-BlueC-eDNA
Version 1
, Norwegian Institute for Water Research
Marc Anglès d'AuriacNorwegian Institute for Water Research
Protocol
Icon representing the file Concentration of viruses from sewage using HA filters
Name
Concentration of viruses from sewage using HA filters
Version 4
, University of Wisconsin - Milwaukee
McLellan LabUniversity of Wisconsin - Milwaukee
Protocol
Icon representing the file Structure-from-motion multi-view photogrammetry applied to linear-scan sediment cores images
Name
Structure-from-motion multi-view photogrammetry applied to linear-scan sediment cores images
Version 2
, Université Rouen Normandie
Kevin JacqUniversité Rouen Normandie
Protocol
Icon representing the file Biolayer Interferometry for DNA-Protein Interactions
Name
Biolayer Interferometry for DNA-Protein Interactions
Version 1
, Reinhardt University
John K BarrowsReinhardt University
Protocol
Icon representing the file Sample collection and eDNA extraction from Sterivex filter units
Name
Sample collection and eDNA extraction from Sterivex filter units
Version 1
, Institute for Environmental Research
Pedro InostrozaInstitute for Environmental Research
Protocol
Icon representing the file outlineR: Artefact Processing and Extraction Protocol
Name
ForkoutlineR: Artefact Processing and Extraction Protocol
Version 1
, Department of Archaeology and Heritage Studies, Aarhus University
David N MatzigDepartment of Archaeology and Heritage Studies, Aarhus University
Protocol
Icon representing the file Protocol for detection of Salmonella Typhi and Salmonella Paratyphi A in Produce
Name
Protocol for detection of Salmonella Typhi and Salmonella Paratyphi A in Produce
Version 1
,
etgrill
Protocol
Icon representing the file Mitogenome Assembly from NGS Genome Skimming Data
Name
Mitogenome Assembly from NGS Genome Skimming Data
Version 1
, UCSD - Scripps Institution of Oceanography
Avery S HileyUCSD - Scripps Institution of Oceanography
Protocol
Icon representing the file HyDrop-ATAC v1.0
Name
HyDrop-ATAC v1.0
Version 2
, Aerts Lab for Computational Biology
Florian De RopAerts Lab for Computational Biology
Protocol
Icon representing the file Carrier-assisted One-pot Sample Preparation for Targeted Proteomics Analysis of Small Numbers of Human Cells
Name
Carrier-assisted One-pot Sample Preparation for Targeted Proteomics Analysis of Small Numbers of Human Cells
Version 1
, City of Hope
Sandy BeshirCity of Hope
Protocol
Icon representing the file IMC STAINING FOR PARAFFIN SECTIONS
Name
IMC STAINING FOR PARAFFIN SECTIONS
Version 1
,
Lili Liang
Protocol
Icon representing the file Making E8 medium for ES/iPS culture
Name
Making E8 medium for ES/iPS culture
Version 1
,
Felix Kraus
Protocol
Icon representing the file Targeted Sequencing by Sanger to Recover Key Mutations in Illumina SARS-CoV-2 Whole-genome Sequences
Name
Targeted Sequencing by Sanger to Recover Key Mutations in Illumina SARS-CoV-2 Whole-genome Sequences
Version 1
, Kwazulu-Natal Research and Innovation Sequencing Platform
James Emmanuel SanKwazulu-Natal Research and Innovation Sequencing Platform
Protocol
Icon representing the file Human Pancreas Processing for Multiple Applications
Name
Human Pancreas Processing for Multiple Applications
Version 1
,
Carrie Romer
Protocol
Icon representing the file Modeling acute visceral pain in adult zebrafish
Name
Modeling acute visceral pain in adult zebrafish
Version 1
,
Denis Rosemberg
Protocol
Icon representing the file Spectral Flow Phenotyping of CD226 KO CD127- Tregs During Expansion
Name
Spectral Flow Phenotyping of CD226 KO CD127- Tregs During Expansion
Version 1
,
Matthew Brown
Protocol
Icon representing the file High molecular weight bacterial DNA extraction from field-collected fecal samples preserved in ethanol for long-read sequencing
Name
High molecular weight bacterial DNA extraction from field-collected fecal samples preserved in ethanol for long-read sequencing
Version 1
, Institut des Sciences de l'Evolution de Montpellier
Sophie TeulletInstitut des Sciences de l'Evolution de Montpellier
Protocol
Icon representing the file Accelerated High-Yield Generation of Limb-Innervating Motor Neurons from Human Stem Cells
Name
Accelerated High-Yield Generation of Limb-Innervating Motor Neurons from Human Stem Cells
Version 1
,
hendersa
Protocol
Icon representing the file Profiling metazoan transcription genome-wide with nucleotide resolution using NET-seq (native elongating transcript sequencing)
Name
Profiling metazoan transcription genome-wide with nucleotide resolution using NET-seq (native elongating transcript sequencing)
Version 1
,
Robert ietswaart
Protocol
Icon representing the file Fixation of HeLa-M cells expressing Halo and SNAP fusion proteins conjugated to ligands
Name
Fixation of HeLa-M cells expressing Halo and SNAP fusion proteins conjugated to ligands
Version 1
, Children's Hospital of Philadelphia
OLIVIA HARDINGChildren's Hospital of Philadelphia
Protocol
Icon representing the file Pristionchus Whole Genome Sequence Analysis
Name
Pristionchus Whole Genome Sequence Analysis
Version 1
, California State University, Northridge
Ray L HongCalifornia State University, Northridge
Protocol
Icon representing the file Bioluminescence-based Minimum Inhibitory Concentration (MIC) testing of fungal extracts against Mycobacterium marinum
Name
ForkBioluminescence-based Minimum Inhibitory Concentration (MIC) testing of fungal extracts against Mycobacterium marinum
Version 1
,
Alex Grey
Protocol
Icon representing the file How to create baseurl for OAI-PMH harvesting with OpenRefine
Name
ForkHow to create baseurl for OAI-PMH harvesting with OpenRefine
Version 1
,
Andrea Marchitelli
Protocol
Icon representing the file Deep cleaning COPAS
Name
Deep cleaning COPAS
Version 1
, MRC Laboratory of Medical Sciences
Bonnie EvansMRC Laboratory of Medical Sciences
Protocol
Icon representing the file A method for the temperature-controlled extraction of DNA from ancient bones
Name
A method for the temperature-controlled extraction of DNA from ancient bones
Version 1
, Max Planck Institute for Evolutionary Anthropology
Elena EsselMax Planck Institute for Evolutionary Anthropology
Protocol
Icon representing the file 3'-DGE High Throughput RNA Library Preparation
Name
3'-DGE High Throughput RNA Library Preparation
Version 2
, Harvard Medical School
Sarah BoswellHarvard Medical School
Protocol
Icon representing the file Pseudotyping lentiviral particles with SARS-CoV-2 Spike protein for neutralization assays
Name
Pseudotyping lentiviral particles with SARS-CoV-2 Spike protein for neutralization assays
Version 2
,
Kate Crawford
Protocol
Icon representing the file Keio Screen
Name
Keio Screen
Version 1
,
Saul Moore
Protocol
Icon representing the file Pseudomonas syringae seed infections
Name
Pseudomonas syringae seed infections
Version 1
, University of Glasgow
William RooneyUniversity of Glasgow
Protocol
Icon representing the file Extracting shape and size information from fungal spores
Name
Extracting shape and size information from fungal spores
Version 1
, Universität Kassel
Alexander OrdynetsUniversität Kassel
Protocol
Icon representing the file Optimized Derivation of Midbrain Dopaminergic Neurons from iPSCs for research application
Name
Optimized Derivation of Midbrain Dopaminergic Neurons from iPSCs for research application
Version 1
, German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
Elisangela BressanGerman Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
Protocol
Icon representing the file Prepare and run test on available dataset
Name
Prepare and run test on available dataset
Version 1
,
Alexey Zhuravlev
Protocol
Icon representing the file Chlamydomonas reinhardtii nuclear transformation by electroporation.
Name
Chlamydomonas reinhardtii nuclear transformation by electroporation.
Version 2
, Ronin Institute
Joao Vitor MolinoRonin Institute
Protocol
Icon representing the file Complete CO-Detection by IndEXing (CODEX) Protocol for FF and FFPE Tissues
Name
Complete CO-Detection by IndEXing (CODEX) Protocol for FF and FFPE Tissues
Version 1
, Broad Institute of MIT and Harvard
Sachi KrishnaBroad Institute of MIT and Harvard
Protocol
Icon representing the file Cytoplasmic pH measurements with pHluorin
Name
Cytoplasmic pH measurements with pHluorin
Version 1
,
Ekaterina Krasnopeeva
Protocol
Icon representing the file TaqMan Genotyping Assay for Detection of B.1.1.7 SARS-CoV-2
Name
TaqMan Genotyping Assay for Detection of B.1.1.7 SARS-CoV-2
Version 1
,
isaac.bell
Protocol
Icon representing the file Prestwick screen protocol
Name
ForkPrestwick screen protocol
Version 1
, Imperial College London
Thomas J O'BrienImperial College London
Protocol
Icon representing the file Daughter of Frankenstein protocol for nuclei isolation from fresh and frozen tissues using OptiPrep® continuous gradient
Name
Daughter of Frankenstein protocol for nuclei isolation from fresh and frozen tissues using OptiPrep® continuous gradient
Version 2
, University of Adelaide
Luciano G MartelottoUniversity of Adelaide
Protocol
Icon representing the file General Field Plot Sampling Protocol for DNA-based analyses (2018-2020)
Name
General Field Plot Sampling Protocol for DNA-based analyses (2018-2020)
Version 1
, Agriculture and Agri-food Canada
David EmdeAgriculture and Agri-food Canada
Protocol
Icon representing the file Processing of pediatric bronchoalveolar lavage samples for single cell analysis
Name
Processing of pediatric bronchoalveolar lavage samples for single cell analysis
Version 1
, Murdoch Children's Research Institute
Melanie R NeelandMurdoch Children's Research Institute
Protocol
Icon representing the file Full-UDG treated double-stranded ancient DNA library preparation for Illumina sequencing
Name
ForkFull-UDG treated double-stranded ancient DNA library preparation for Illumina sequencing
Version 1
, Max Planck Institute for Evolutionary Anthropology
James A Fellows YatesMax Planck Institute for Evolutionary Anthropology
Protocol
Icon representing the file Maintenance of Undifferentiated hiPSC Cultures and Differentiation to Cardiomyocytes on Glass Surfaces
Name
Maintenance of Undifferentiated hiPSC Cultures and Differentiation to Cardiomyocytes on Glass Surfaces
Version 1
,
Angelique Nelson
Protocol
Icon representing the file High-throughput Sars-CoV-2 detection from self-collected saline gargle samples
Name
High-throughput Sars-CoV-2 detection from self-collected saline gargle samples
Version 1
,
Karl Frontzek
Protocol
Icon representing the file Iodine staining of starch to determine amylose percentage
Name
Iodine staining of starch to determine amylose percentage
Version 1
, James Madison University
Chris BerndsenJames Madison University
Protocol
Icon representing the file Fluorescence Recovery after Photobleaching (FRAP)  in adult C. elegans nuclei
Name
Fluorescence Recovery after Photobleaching (FRAP)  in adult C. elegans nuclei
Version 1
, Harvard University
Laura BreimannHarvard University
Protocol
Icon representing the file Measure Effects of Manufacturing Variations of ENDS on coil Lifetime and Aerosol Generation
Name
Measure Effects of Manufacturing Variations of ENDS on coil Lifetime and Aerosol Generation
Version 1
, Rochester Institute of Technology
Qutaiba SalehRochester Institute of Technology
Protocol
Icon representing the file edX Learner and Course Analytics and Visualization Pipeline
Name
edX Learner and Course Analytics and Visualization Pipeline
Version 6
, Indiana University at Bloomington
Michael GindaIndiana University at Bloomington
Protocol
Icon representing the file Self Pollinating Tobacco
Name
Self Pollinating Tobacco
Version 1
, Realizing Increased Photosynthetic Efficiency (RIPE)
Lynn DoranRealizing Increased Photosynthetic Efficiency (RIPE)
Protocol
Icon representing the file Assembly Instructions for colosseum
Name
Assembly Instructions for colosseum
Version 2
,
Yeokyoung Kil
Protocol
Icon representing the file Fungal gene knockout with Agrobacterium tumefaciens using Gibson assembly
Name
Fungal gene knockout with Agrobacterium tumefaciens using Gibson assembly
Version 1
, Curtin University
Johannes Wolfram JWD DeblerCurtin University
Protocol
Icon representing the file Preparation of acute midbrain slices for patch-clamp recordings
Name
Preparation of acute midbrain slices for patch-clamp recordings
Version 3
, Sainsbury Wellcome Centre for Neural Circuits and Behaviour
Oriol PavonSainsbury Wellcome Centre for Neural Circuits and Behaviour
Protocol
Icon representing the file High-Molecular-Weight gDNA extraction protocol from moss gametophytes
Name
High-Molecular-Weight gDNA extraction protocol from moss gametophytes
Version 1
, University of California, Riverside
Lei ZhuUniversity of California, Riverside
Protocol
Icon representing the file Gold nanoparticle synthesis
Name
Gold nanoparticle synthesis
Version 1
, Technological University Dublin
James F CurtinTechnological University Dublin
Protocol
Icon representing the file Salmonella spp. detection and isolation
Name
Salmonella spp. detection and isolation
Version 1
, UNAM Mexico
Enrique DelgadoUNAM Mexico
Protocol
Icon representing the file Whole-genome sequencing of two human rhinovirus A types - A15 and A101
Name
Whole-genome sequencing of two human rhinovirus A types - A15 and A101
Version 1
, University of Glasgow
Martha LukaUniversity of Glasgow
Protocol
Icon representing the file ARTIC NEB Tagmentation protocol - high throughput whole genome sequencing of SARS-CoV-2.
Name
ARTIC NEB Tagmentation protocol - high throughput whole genome sequencing of SARS-CoV-2.
Version 1
, Chan Zuckerberg Biohub
Karan D BhattChan Zuckerberg Biohub
Protocol
Icon representing the file ‘Frankenstein’ protocol for nuclei isolation from fresh and frozen tissue for snRNAseq
Name
‘Frankenstein’ protocol for nuclei isolation from fresh and frozen tissue for snRNAseq
Version 3
, University of Adelaide
Luciano G MartelottoUniversity of Adelaide
Protocol
Icon representing the file Fish eDNA: DNA extraction from water samples filtered through Sterivex filter unit and preserved in buffer
Name
Fish eDNA: DNA extraction from water samples filtered through Sterivex filter unit and preserved in buffer
Version 1
, UMR CARRTEL
Cecile ChardonUMR CARRTEL
Protocol
Icon representing the file ANY-maze Protocol (Elevated Plus Maze) v6.2
Name
ANY-maze Protocol (Elevated Plus Maze) v6.2
Version 1
,
Cristina Corral
Protocol
Icon representing the file isolating human malaria parasites for RNA-sequencing at ultra-low densities
Name
isolating human malaria parasites for RNA-sequencing at ultra-low densities
Version 1
,
Wiebke Nahrendorf
Protocol
Icon representing the file SP3 (Single-Pot, Solid-Phase, Sample-Preperation) Protein Extraction for Dental Calculus
Name
SP3 (Single-Pot, Solid-Phase, Sample-Preperation) Protein Extraction for Dental Calculus
Version 1
, Max Planck Institute for the Science of Human History
Sandra HebestreitMax Planck Institute for the Science of Human History
Protocol
Icon representing the file Seek & Blastn Standard Operating Procedure
Name
Seek & Blastn Standard Operating Procedure
Version 1
,
Yasunori Park
Protocol
Icon representing the file Geometric Method for Estimating Coral Surface Area Using Image Analysis
Name
Geometric Method for Estimating Coral Surface Area Using Image Analysis
Version 1
, Oregon State University
Rowan MclachlanOregon State University
Protocol
Icon representing the file Navigating in UNIX
Name
Navigating in UNIX
Version 1
,
Anthony Underwood
Protocol
Icon representing the file RNA Extraction of SARS-CoV-2 from Wastewater
Name
RNA Extraction of SARS-CoV-2 from Wastewater
Version 1
, University of North Carolina at Charlotte
Nick StarkUniversity of North Carolina at Charlotte
Protocol
Icon representing the file Rapid Single-Pot Assembly of Modular Chromatin Proteins for Epigenetic Engineering
Name
Rapid Single-Pot Assembly of Modular Chromatin Proteins for Epigenetic Engineering
Version 1
, Wallace H. Coulter Department of Biomedical Engineering, Emory University, Atlanta, GA, USA
Karmella A HaynesWallace H. Coulter Department of Biomedical Engineering, Emory University, Atlanta, GA, USA
Protocol
Icon representing the file Anthoceros agrestis (hornwort) transformation v01
Name
Anthoceros agrestis (hornwort) transformation v01
Version 1
, University of Cambridge
Eftychis FrangedakisUniversity of Cambridge
Protocol
Icon representing the file Isolation of clean single-cell samples for physiological or molecular experiments (Radiolaria, Acantharia)
Name
Isolation of clean single-cell samples for physiological or molecular experiments (Radiolaria, Acantharia)
Version 2
, University of Arizona
Joost S MansourUniversity of Arizona
Protocol
Icon representing the file Using polyan: a Python package for modelling polysome profiles from ribosome density data
Name
Using polyan: a Python package for modelling polysome profiles from ribosome density data
Version 2
, University of Kent
Tobias von der HaarUniversity of Kent