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| Name | Authors | DOI | Group |
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Mitochondrial oxygen consumption Resource Report Resource Website |
Wen Aw | 10.17504/protocols.io.rrud56w | Cage Studies | Aw WC, Towarnicki SG, Melvin RG, Youngson NA, Garvin MR, Hu Y, Nielsen S, Thomas T, Pickford R, Bustamante S, Vila-Sanjurjo A, Smyth GK, Ballard JWO (2018) Genotype to phenotype: Diet-by-mitochondrial DNA haplotype interactions drive metabolic flexibility and organismal fitness. PLoS Genet 14(11): e1007735. doi: 10.1371/journal.pgen.1007735 | [email protected] | https://doi.org/10.1371/journal.pgen.1007735 | 1 | 2018 | Wen Aw 2018. Mitochondrial oxygen consumption. protocols.io dx.doi.org/10.17504/protocols.io.rrud56w | 2021-03-29 03:10:57 | ||
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Isolation and isotopic labeling of bacteria Resource Report Resource Website |
Ramon Terrado | 10.17504/protocols.io.eyzbfx6 | Caron Lab - Protistan Ecology | This protocol describes how to isolate bacteria in order to label its biomass using 13C-glucose and 15N-ammonia. The first steps aim to isolate candidate bacteria that are able of growing on the chosen substrates for isotopic labeling.The protocol was applied to the isolation of bacetria from freshwater algal cultures, although it can be applied to natural samples.The M9 media used in the protocol is based on the media from Marley, Lu and Bracken (2001).References:Marley, J., Lu, M., & Bracken, C. (2001). A method for efficient isotopic labeling of recombinant proteins. Journal of Biomolecular Nmr, 20(1), 71–75. | University of Southern California (USC) | 1 | 2016 | Ramon Terrado 2016. Isolation and isotopic labeling of bacteria. protocols.io dx.doi.org/10.17504/protocols.io.eyzbfx6 | 2021-03-29 03:10:57 | |||
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Squalene Quantification using Nile Red Staining (M4455 Version) Resource Report Resource Website |
Sebastian Triesch | 10.17504/protocols.io.y6vfze6 | M4455 - Synthetische Biologie und Biotechnologie | This protocol is under development and for teaching purposes only!Nile Red is a fluorescent dye that stains selectively hydrophobic substances. We assume that squalene accumulates in the cell membrane or in lipid vesicles where it can be stained by the dye. | Institute for Synthetic Microbiology, HHU Düsseldorf | 1 | 2019 | Sebastian Triesch 2019. Squalene Quantification using Nile Red Staining (M4455 Version). protocols.io dx.doi.org/10.17504/protocols.io.y6vfze6 | 2021-03-29 03:10:57 | |||
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Plate Reader experiment Resource Report Resource Website |
Anna Behle | 10.17504/protocols.io.kx5cxq6 | Axmann Lab | This protocol covers the inoculation, cultivation, IPTG-induction and plate reader measurement of E. coli BL21 strains carrying constructs with various toehold switch devices from Green et al., 2014. | Institute for Synthetic Microbiology | 1 | 2017 | Anna Behle 2017. Plate Reader experiment. protocols.io dx.doi.org/10.17504/protocols.io.kx5cxq6 | 2021-03-29 03:10:57 | |||
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Determination of infectious lentiviral titers with GFP-encoding lentivirus Resource Report Resource Website |
Susanna C. Concilio | 10.17504/protocols.io.bcbsisne | Concilio SC, Zhekova HR, Noskov SY, Russell SJ (2020) Inter-species variation in monovalent anion substrate selectivity and inhibitor sensitivity in the sodium iodide symporter (NIS). PLoS ONE 15(2): e0229085. doi: 10.1371/journal.pone.0229085 | Department of Molecular Medicine, Mayo Clinic | https://doi.org/10.1371/journal.pone.0229085 | 1 | 2020 | Susanna C. Concilio 2020. Determination of infectious lentiviral titers with GFP-encoding lentivirus. protocols.io dx.doi.org/10.17504/protocols.io.bcbsisne | 2021-03-29 03:10:57 | |||
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Poly-d lysine coating slides Resource Report Resource Website |
Grace Burgin | 10.17504/protocols.io.32cgqaw | coating standard blank slides with poly-d lysine to increase adhesion of tissue | Regev Lab | 1 | 2019 | Grace Burgin 2019. Poly-d lysine coating slides. protocols.io dx.doi.org/10.17504/protocols.io.32cgqaw | 2021-03-29 03:10:54 | ||||
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RNA Imaging with MERFISH - Design of Oligonucleotide Probes Resource Report Resource Website |
Jeffrey R. Moffitt, Xiaowei Zhuang | 10.17504/protocols.io.menc3de | Human Cell Atlas Method Development Community, Neurodegeneration Method Development Community | The first step in any MERFISH experiment is the design of the oligonucleotide probes that will be used to label individual RNA species. In our current implementation of MERFISH, each oligonucleotide encoding probe consists of three basic components as illustrated in Figure 2. The first region is a 30-nt targeting region that is complementary to a portion of the sequence of the RNA to which it is designed to bind. The second region is a set of sequences that are called readout sequences, which were designed to be complementary and hence only bind to MERFISH readout probes and not other nucleic acid in the cell. Finally, the third region is a set of priming regions used in the construction of these probes, which will be discussed in detail in Probe Construction. In addition to the nucleotide sequences for each of these components, a codebook —the specific set of binary barcodes that will be used and their association with different RNA species of interest—must also be designed. In this section, we provide protocols to design these sequences and to build a codebook. Example code to perform these steps can be found at http://zhuang.harvard.edu/merfish/ . | Harvard University, Cambridge, Massachusetts, Harvard University, Cambridge, Massachusetts | https://www.ncbi.nlm.nih.gov/pubmed/27241748 | 1 | 2018 | Jeffrey R. Moffitt, Xiaowei Zhuang 2018. RNA Imaging with MERFISH - Design of Oligonucleotide Probes. protocols.io dx.doi.org/10.17504/protocols.io.menc3de | 2021-03-29 03:10:58 | ||
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Chromatin Immunoprecipitation (ChIP) Assay Protocol Resource Report Resource Website |
Kelsey Knight | 10.17504/protocols.io.tj7ekrn | BioLegend | Reagents - Basic cell culture media: respective to the cell line used and experimental design Distilled water: Invitrogen® UltraPure™ Distilled Water (catalog number 19977015) or equivalent product from other vendor.Highthroughput (HT) Pro A or G 96 well plate or Spin Column (Chromatrap® HT ChIP-qPCR kit; catalog number 500161 or 500162 or 500163)96-well collection plate: USA scientific® TempPlate non-skirted 96-well PCR plate natural (catalog number 1402-9596) or equivalent product from other vendor.QIAquick™ PCR purification kit (Qiagen®; catalog number 28104) or equivalent product from other vendor.Hypotonic Buffer (Chromatrap® HT ChIP-qPCR kit; catalog number 500161 or 500162 or 500163)Digestion Buffer (Chromatrap® HT ChIP-qPCR kit; catalog number 500161 or 500162 or 500163)Lysis Buffer (Chromatrap® HT ChIP-qPCR kit; catalog number 500161 or 500162 or 500163)Column Conditioning Buffer (Chromatrap® HT ChIP-qPCR kit; catalog number 500161 or 500162 or 500163)Wash Buffer 1 (Chromatrap® HT ChIP-qPCR kit; catalog number 500161 or 500162 or 500163)Wash Buffer 2 (Chromatrap® HT ChIP-qPCR kit; catalog number 500161 or 500162 or 500163)Wash Buffer 3 (Chromatrap® HT ChIP-qPCR kit; catalog number 500161 or 500162 or 500163)Elution Buffer (Chromatrap® HT ChIP-qPCR kit; catalog number 500161 or 500162 or 500163)5M NaCl: dissolve 292g of NaCl in 800mL of H2O. Adjust the volume to 1L with H2O.1M NaHCO3: dissolve 12.6g of NaHCO3 in 100 mL of H2O. Adjust the volume to 150 mL with H2O.Protease Inhibitor Cocktail (PIC): Cell signaling Technology® (catalog number 5871) or equivalent product from other vendor.Proteinase K: Qiagen® (catalog number 19133) or equivalent product from other vendor.Proteinase K stop solution: 100mM Phenylmethylsulfonyl fluoride (PMSF). Weigh 1.742g PMSF (Sigma-Aldrich®, catalog number 10837091001) and add DMSO (Sigma-Aldrich®, catalog number D2650) to a final volume of 100mL. Dissolve completely.PBS: HyClone™ Phosphate Buffered Saline (1X) (catalog number SH30256.01) or equivalent product from other vendor.Formaldehyde: VWR® 37% w/w aqueous solution (catalog number 97064-604) or equivalent product from other vendor.0.65M Glycine: Dissolve 488g of glycine into 1L of H2O to make 6.5M glycine (10X). Dilute with PBS to make 1X before each experiment. Micrococcal Nuclease: Cell Signaling Technologies® (catalog number 10011S) or equivalent product from other vendor.1.3-1.5% Agarose gel: dissolve 1.3-1.5g of agarose powder into 100mL of TAE buffer by microwave heating. Visualize DNA under UV light by adding appropriate amount of Ethidium Bromide, or use an equivalent method.Add appropriate amount of Ethidium Bromide to cooled down gel solution to visualize DNA under UV light.0.5M EDTA: Dissolve 186.1g EDTA into 700mL of H2O. Adjust the volume to 1L with H2O.100bp ladder: NEB® (catalog number N0467S) or equivalent product from other vendor.Materials -Heat blockRotatorCentrifugeMicrocentrifuge37ºC incubatorNanodropSonicatorUV light imagerRocking platform | BioLegend | http://www.biolegend.com/media_assets/support_protocol/ChIP_Assay_Technical_Protocol_v8.pdf | 3 | 2018 | Kelsey Knight 2018. Chromatin Immunoprecipitation (ChIP) Assay Protocol. protocols.io dx.doi.org/10.17504/protocols.io.tj7ekrn | 2021-03-29 03:10:58 | ||
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Phagocytosis Bead Conjugation Resource Report Resource Website |
Andrew Crowley | 10.17504/protocols.io.4cygsxw | Ackerman Lab | Protocols for the amine coupling of fluorescent microspheres with antigen or capture reagent for opsonization and phagocytosisQuantity as written: approx. 1 x 108 under typical yields (enough for 400 phagocytosis wells under standard protocol) | Dartmouth College, Ackerman Lab | 2 | 2019 | Andrew Crowley 2019. Phagocytosis Bead Conjugation. protocols.io dx.doi.org/10.17504/protocols.io.4cygsxw | 2021-03-29 03:10:58 | |||
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TissueCyte Specimen Embedding Acrylamide Coembedding Resource Report Resource Website |
Allen Institute for Brain Science | 10.17504/protocols.io.bf65jrg6 | BICCN, Allen Institute for Brain Science | This protocol describes the preparation of a fixed mouse brain specimen bonded to an agarose block for blockface imaging and sectioning using the TissueCyte 1000 system.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 | 4 | 2020 | Allen Institute for Brain Science 2020. TissueCyte Specimen Embedding Acrylamide Coembedding. protocols.io dx.doi.org/10.17504/protocols.io.bf65jrg6 | 2021-03-29 03:10:57 | |||
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Phage stock preparation Resource Report Resource Website |
Marijn Ceelen | 10.17504/protocols.io.7kthkwn | iGEM Wageningen 2019 | A protocol for phage lambda and phage T7 phage stock preparation | Wageningen University | 1 | 2019 | Marijn Ceelen 2019. Phage stock preparation. protocols.io dx.doi.org/10.17504/protocols.io.7kthkwn | 2021-03-29 03:11:03 | |||
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DNA Extraction for college laboratory setting Resource Report Resource Website |
James M. Burnette III, Susan R. Wessler | 10.17504/protocols.io.dwu7ev | Genetics | This protocol is based on one described by Li et al. (2010) and has been modified to work in a college laboratory setting. The protocol is from:James M. Burnette III andSusan R. Wessler (2013) Transposing from the Laboratory to the Classroom to Generate Authentic Research Experiences for UndergraduatesGenetics193:367-375; doi:10.1534/genetics.112.147355Students need approximately 1.5 hours to extract DNA from up to five samples and the protocol can be carried out over several class periods by stopping at steps 6 and 9. Please see the full manuscript for additional details. | , | http://www.genetics.org/content/193/2/367.full | 1 | 2015 | James M. Burnette III, Susan R. Wessler 2015. DNA Extraction for college laboratory setting. protocols.io dx.doi.org/10.17504/protocols.io.dwu7ev | 2021-03-29 03:11:03 | ||
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Euplotes crassus transformation using Lipofectamine 2000 as vehicle Resource Report Resource Website |
RACHELE CESARONI | 10.17504/protocols.io.g5aby2e | Protist Research to Optimize Tools in Genetics (PROT-G) | University of Bern, Institute of Biology | 4 | 2017 | RACHELE CESARONI 2017. Euplotes crassus transformation using Lipofectamine 2000 as vehicle. protocols.io dx.doi.org/10.17504/protocols.io.g5aby2e | 2021-03-29 03:11:02 | ||||
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Phenol-based RNA extraction from polycarbonate filters Resource Report Resource Website |
Robbie M. Martin, Steven W. Wilhelm | 10.17504/protocols.io.bivuke6w | The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs) | This protocol is an acid-phenol-based method for extracting RNA from samples collected onto polycarbonate filters. Bead-beating is included to increase yields from difficult to lyse cells, for example, in some species of cyanobacteria. We have used it successfully in RNA-sequencing projects involving lab cultures of cyanobacteria and from freshwater and marine environmental samples. | University of Tennessee, Knoxville, University of Tennessee, Knoxville | 1 | 2020 | Robbie M. Martin, Steven W. Wilhelm 2020. Phenol-based RNA extraction from polycarbonate filters. protocols.io dx.doi.org/10.17504/protocols.io.bivuke6w | 2021-03-29 03:11:03 | |||
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Protein interaction analysis of KaiC3 with various Kai homologs via yeast two-hybrid experiments (Growth Assay) Resource Report Resource Website |
Anika Wiegard, Christin Köbler, Katsuaki Oyama, Anja K. Dörrich, Chihiro Azai, Kazuki Terauchi, Annegret Wilde, Ilka Maria Axmann | 10.17504/protocols.io.wcnfave | CyanoWorld | This protocol can be used to investigate protein-protein interaction via yeast two-hybrid experiments. It describes the yeast-two hybrid method relying on the activity of the histidine-synthetase. If the proteins interact, the yeast cells are able to grow on selective medium without histidine. | Karolinska Institutet, Department of Cell and Molecular Biology, Stockholm, Sweden, Institute of Biology III, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany, Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan, Institute for Microbiology and Molecular Biology, Justus-Liebig University, 35392 Giessen, Germany, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan, Institute of Biology III, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany, Institute for Synthetic Microbiology, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Duesseldorf, 40225 Duesseldorf, Germany | 1 | 2019 | Anika Wiegard, Christin Köbler, Katsuaki Oyama, Anja K. Dörrich, Chihiro Azai, Kazuki Terauchi, Annegret Wilde, Ilka Maria Axmann 2019. Protein interaction analysis of KaiC3 with various Kai homologs via yeast two-hybrid experiments (Growth Assay). protocols.io dx.doi.org/10.17504/protocols.io.wcnfave | 2021-03-29 03:10:59 | |||
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Bimanual Interference Experimental Paradigm Resource Report Resource Website |
Rini Varghese, Jasmine Ma, James Gordon, Robert L Sainburg, Carolee J Winstein | 10.17504/protocols.io.7r3hm8n | Successful bimanual coordination is accomplished by overcoming a variety of cognitive, perceptual and neuromotor constraints, e.g. higher-order representation of task goals, visual perceptual demands, attention demands, task demands (i.e., speed, accuracy) and sensorimotor integration. Sensorimotor interference in planning, executing and correcting bilateral movements especially arise when the hands are required to accomplish two independent or disparate goals. In this study, we describe the experimental paradigm to study sensorimotor interference during performance of a planar reaching task, in which the experimental condition consists of the two hands moving to two visually cued targets at separate distances (spatially asymmetric). Whereas the control conditions consisted of same-size movements performed unimanually with each limb and bimanually to symmetric targets. The paradigm is a modification of a previously conceptualized model task paradigm (e.g. 1-5) to study interference in discrete bilateral movements, wherein the two limbs are tasked with accomplishing asymmetric movement goals. However, our study paradigm involved important modifications to task design such as absence of online visual feedback (so as to test fairly rapid preprogrammed movements) and task instructions which emphasized speed and accuracy but not interlimb synchrony. The study aims: 1) to characterize sensorimotor interference in discrete bilateral reaching movements in young adults, and subsequently, 2) to determine the influence of the side of stroke on such sensorimotor interference. The experimental paradigm was conducted using the KineReach kinematic data collection system and accompanying software (Sainburg, Pennsylvania State University). MATLAB code to generate session and target files for this experiment are included in this protocol. Details of data processing and analysis will be published in the primary papers and code will be made available thereafter.References:1. Kelso (1979)2. Marteniuk (1984)3. Swinnen (1991)4. Diedrichsen (2006)5. Blich (2011) | University of Southern California, University of Southern California, University of Southern California, Pennsylvania State University, University of Southern California | 1 | 2020 | Rini Varghese, Jasmine Ma, James Gordon, Robert L Sainburg, Carolee J Winstein 2020. Bimanual Interference Experimental Paradigm. protocols.io dx.doi.org/10.17504/protocols.io.7r3hm8n | 2021-03-29 03:10:59 | ||||
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Injectable autologous platelet-rich plasma for regenerative medicine in donkeys Resource Report Resource Website |
Adolfo Maria TAMBELLA, Evelina SERRI, Fulvio LAUS, Anna Rita ATTILI | 10.17504/protocols.io.ncbdasn | A step-by-step procedure for autologous platelet-rich plasma production was developed for topical percutaneous injection in donkeys.This protocol was used in the following publication:Faillace V, Tambella AM, Fratini M, Paggi E, Dini F, Laus F. Use of autologous platelet-rich plasma for a delayed consolidation of a tibial fracture in a young donkey. The Journal of Veterinary Medical Science, 79(3), 2017: 618-622. (ISSN: 0916-7250) (DOI: 10.1292/jvms.16-0400)https://doi.org/10.1292/jvms.16-0400https://www.jstage.jst.go.jp/article/jvms/79/3/79_16-0400/_pdf/-char/en | School of Biosciences and Veterinary Medicine, University of Camerino, Matelica, MC, Italy, School of Biosciences and Veterinary Medicine, University of Camerino, Matelica, MC, Italy, School of Biosciences and Veterinary Medicine, University of Camerino, Matelica, MC, Italy, School of Biosciences and Veterinary Medicine, University of Camerino, Matelica, MC, Italy | https://doi.org/10.1292/jvms.16-0400 | 1 | 2018 | Adolfo Maria TAMBELLA, Evelina SERRI, Fulvio LAUS, Anna Rita ATTILI 2018. Injectable autologous platelet-rich plasma for regenerative medicine in donkeys. protocols.io dx.doi.org/10.17504/protocols.io.ncbdasn | 2021-03-29 03:10:59 | |||
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U Michigan - Intra-Epidermal Fiber Density Resource Report Resource Website |
Eva L. Feldman | 10.17504/protocols.io.563g9gn | Mouse Metabolic Phenotyping Centers | Intra-epidermal nerve fiber density (IENFD) is used as a tool to assess small fiber neuropathy. | RRID:AB_2210497 | University of Michigan - Ann Arbor | https://mmpc.org/shared/document.aspx?id=319&docType=Protocol | 2 | 2019 | Eva L. Feldman 2019. U Michigan - Intra-Epidermal Fiber Density. protocols.io dx.doi.org/10.17504/protocols.io.563g9gn | 2021-03-29 03:10:59 | |
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Immunoblot analyses for investigating SpLA binding to purified mammalian and avian immunoglobulins. Resource Report Resource Website |
Angel Justiz-Vaillant | 10.17504/protocols.io.bjq7kmzn | University of the West Indies, [email protected] | University of the West Indies St. Augustine | 1 | 2020 | Angel Justiz-Vaillant 2020. Immunoblot analyses for investigating SpLA binding to purified mammalian and avian immunoglobulins.. protocols.io dx.doi.org/10.17504/protocols.io.bjq7kmzn | 2021-03-29 03:10:59 | ||||
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Extraction of RNA from Wastewater Primary Solids Using a Direct Extraction Method for Downstream SARS-CoV-2 RNA Quantification Resource Report Resource Website |
Stephanie Loeb, Katy Graham, Marlene Wolfe, Krista Wigginton, Alexandria Boehm | 10.17504/protocols.io.bi6skhee | Coronavirus Method Development Community, Wastewater-based epidemiology working group | OverviewThis SOP describes pre-analytical procedures to be followed for the isolation and identification of SARS-CoV-2 RNA in primary settled solids samples from wastewater treatment plants. This protocal should be paired with our digital PCR protocal. The protocol follows the approximate workflow:Separate and aliquot sample (~4 hrs)Spike with BCoV (~1 hr)Extract RNA (~ 12 hours total, may be split into 2-3 steps/days)Inhibitor removal (~1 hr)Biosafety ConcernsConcentration and extraction procedures that utilize raw samples must adhere to strict Biosafety Level 2+ procedures. These procedures should be performed in a dedicated room. Downstream products may be handled using standard laboratory safety guidelines. This protocol was developed by Stephanie Loeb, Katy Graham, Marlene Wolfe, Krista Wigginton, and Alexandria Boehm at Stanford University and University of Michigan. | Stanford University, Stanford University, Stanford University, University of Michigan, Stanford University | 1 | 2020 | Stephanie Loeb, Katy Graham, Marlene Wolfe, Krista Wigginton, Alexandria Boehm 2020. Extraction of RNA from Wastewater Primary Solids Using a Direct Extraction Method for Downstream SARS-CoV-2 RNA Quantification. protocols.io dx.doi.org/10.17504/protocols.io.bi6skhee | 2021-03-29 03:11:00 |
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