id float64 1.55k 110k ⌀ | title stringlengths 1 256 ⌀ | template_id float64 0 6 ⌀ | doi stringlengths 39 49 ⌀ | url stringlengths 40 92 ⌀ | authors stringlengths 1 933 ⌀ | protocol_text stringlengths 34 1.08M | steps_list stringlengths 2 269k |
|---|---|---|---|---|---|---|---|
47,856 | Samples preparation of human plasma for proteomic assay and LC-MS analysis | 1 | dx.doi.org/10.17504/protocols.io.bsyqnfvw | https://www.protocols.io/view/samples-preparation-of-human-plasma-for-proteomic-bsyqnfvw | Arthur T. Kopylov, Alexander A Stepanov, Kristina A Malsagova, Anna L Kaysheva, Tatiana Butkova, Natalia Zakharova, Georgy Kostyuk, Artem Elmuratov | TITLE: Samples preparation of human plasma for proteomic assay and LC-MS analysis
AUTHORS: Arthur T. Kopylov, Alexander A Stepanov, Kristina A Malsagova, Anna L Kaysheva, Tatiana Butkova, Natalia Zakharova, Georgy Kostyuk, Artem Elmuratov
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The proprie... | ["[Samples Handling for Proteome Analysis]\nBlood samples were collected for participating subjects in the morning between 08 am to 10 am in EDTA-2K+ vacuum tubes (Becton Dickinson; Franklin Lakes, NJ, USA). Totally, up to 8 mL of blood was withdrawn from each subject. Tubes were gently mixed end-over-end (approximatel... |
70,293 | Deriving steps per mm for an LVE system | 5 | dx.doi.org/10.17504/protocols.io.ewov1o8jplr2/v1 | https://www.protocols.io/view/deriving-steps-per-mm-for-an-lve-system-cgvvtw66 | Robert B Jess, Jonathan Widdowson, Feihu Zhao, Christopher Wright | TITLE: Deriving steps per mm for an LVE system
AUTHORS: Robert B Jess, Jonathan Widdowson, Feihu Zhao, Christopher Wright
[DESCRIPTION]
Modification of off-the-shelf fused filament fabrication (FFF) 3D printers with a syringe pump, used as a large volume extruder (LVE) is a common method for the creation of low-cost l... | ["[Take measurements] Take the following measurements:", "[Deriving the revolutions per mm] The ratio between the syringe and the Bowden tube can be calculated as follows:\n\n \nWhere is the distance travelled by the syringe plunger, is the resultant distance the gel travels through the bowden tube, is the intern... |
65,108 | 10000x DNA gel stain: User protocol | 4 | null | https://www.protocols.io/view/10000x-dna-gel-stain-user-protocol-cbtusnnw | Stephane Fadanka, Nadine Mowoh | TITLE: 10000x DNA gel stain: User protocol
AUTHORS: Stephane Fadanka, Nadine Mowoh
[DESCRIPTION]
Beneficial Bio DNA Gel Stain is a conventional nucleic acid staining reagent made of Thiazole Orange dye and DMSO. The DNA gel stain compares favorably to common staining methods, in that it is sensitive, excitable wit... | ["[User protocol] Preparing a 0.0013 mg/mL final concentration of DNA gel stain in agarose gel for electrophoresis from a 13mg/ml stock\n\nPrepare a 1x TBE buffer from a 10x stock by diluting 10 mLof the 10x TBE buffer stock into 90 mLof distilled water.\nPrepare a 1% agarose gel by dissolving0.25 g of Agarose into 25 ... |
57,758 | isolation and extraction of plant nuclei in plug | 4 | dx.doi.org/10.17504/protocols.io.6qpvr6632vmk/v1 | https://www.protocols.io/view/isolation-and-extraction-of-plant-nuclei-in-plug-b4m6qu9e | Karine Labadie, Benoît Vacherie | TITLE: isolation and extraction of plant nuclei in plug
AUTHORS: Karine Labadie, Benoît Vacherie
[DESCRIPTION]
Method for isolation and extraction of plant cell nuclei.
Protocol for obtaining UHMW DNA (> 150kb) allowing the production of optical cards with Bionano technology.
[GUIDELINES]
Never use a vortex in ord... | ["[preparation of reagents] NIB Buffer : 200 ml : freshly prepared\n \nAdjust the Ph to 9.4 then filter at 0.22 µm", "[preparation of reagents] NIBT Buffer : 160 ml", "[preparation of reagents] NIBTM Buffer : 40 ml", "[preparation of reagents] Lysis Buffer : Can be stored for 1 year at RT.", "[Nuclei isolation] Putti... |
null | null | null | dx.doi.org/10.17504/protocols.io.smfec3n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The different kinds of stained histological sections are widely used to detect and observe physiological and pathological changes in various tissues.</p>
[BEFORE_START]
<p>Bouin's fixative was formulated by saturated solution of picric acid (75 ml), 40% aqueous formaldehyde ... | [] |
109,320 | SOP52v1_TGD_IIDP-HIGISampleProcessing_Public | 4 | null | https://www.protocols.io/view/sop52v1-tgd-iidp-higisampleprocessing-public-dnzg5f3w | Varsha Rajesh, Swaraj Thaman | TITLE: SOP52v1_TGD_IIDP-HIGISampleProcessing_Public
AUTHORS: Varsha Rajesh, Swaraj Thaman
[DESCRIPTION]
This protocol details the workflow to process pancreatic tissues (received from the Integrated Islet Distribution Program's distribution centers) for genotyping at the Translational Genomics of Diabetes Lab at Stanf... | ["[Receiving Samples] When acinar samples are received from the various isolation centers, match what is physically sent with sample info list sent with package and make sure all samples are accounted for. Take note of the condition of the samples.", "[Receiving Samples] Let isolation center know samples were received ... |
31,081 | SPARC - Analysis of multiplexed bead data using MPLEX software | 1 | dx.doi.org/10.17504/protocols.io.81wgbpym1vpk/v1 | https://www.protocols.io/view/sparc-analysis-of-multiplexed-bead-data-using-mple-bakhict6 | J Paul Robinson | TITLE: SPARC - Analysis of multiplexed bead data using MPLEX software
AUTHORS: J Paul Robinson
[DESCRIPTION]
This protocol describes the process of achieving analysis of multiplexed bead data that was collected by flow cytometry and analyzed using the MPLEX software.
[GUIDELINES]
These assays are frequently run as "h... | ["Transfer all the data frills from the flow cytometer to the appropriate computer directory", "This directory must be available to the MPLEX software. The MPLEX software requires a license file to be placed in the same directory as the EXE file before the software will operate. The software is only available to academ... |
null | null | null | dx.doi.org/10.17504/protocols.io.rmvd466 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Ancient DNA work was performed in the specialized ancient DNA (aDNA) facilities of the Department of Genetics, University of Szeged, Hungary with strict clean-room conditions. In order to authenticate the results, we considered the latest recommendations of (Llamas et al. 201... | [] |
40,865 | Financing and Insurance (Part 12 of Phase 3 study of Vaccine Candidate for COVID-19) | 1 | dx.doi.org/10.17504/protocols.io.bj59kq96 | https://www.protocols.io/view/financing-and-insurance-part-12-of-phase-3-study-o-bj59kq96 | Chris Ockenhouse, Chris Gast, Renee Holt, Jorge Flores | TITLE: Financing and Insurance (Part 12 of Phase 3 study of Vaccine Candidate for COVID-19)
AUTHORS: Chris Ockenhouse, Chris Gast, Renee Holt, Jorge Flores
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This is Part 12 of "Phase 3 randomized, double-blinded, placebo-controlled trial to evalua... | [] |
27,919 | Dental Calculus Field-Sampling Protocol (Warinner Version) | 1 | dx.doi.org/10.17504/protocols.io.7hphj5n | https://www.protocols.io/view/dental-calculus-field-sampling-protocol-warinner-v-7hphj5n | Christina Warinner, Irina Velsko, James Fellows Yates | TITLE: Dental Calculus Field-Sampling Protocol (Warinner Version)
AUTHORS: Christina Warinner, Irina Velsko, James Fellows Yates
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describes how to sample dental calculus from individual teeth for biomolecular analysis. The primary us... | ["[Workstation Preparation]\nPut on two pairs of gloves\nReplacement The outer layer will be replace after each sampling.", "[Sampling Preparation]\nFill in your metadata sheet with corresponding tubes IDs.", "[Sampling Preparation]\nConstruct a foil bowl as in the picture. The purpose of the bowl is to catch any calcu... |
86,501 | U54 SCENT Olink® Target 96 | 1 | null | https://www.protocols.io/view/u54-scent-olink-target-96-cyqdxvs6 | andrew.nixon, Chris Brady | TITLE: U54 SCENT Olink® Target 96
AUTHORS: andrew.nixon, Chris Brady
[DESCRIPTION]
This protocol outlines the sample preparation and running of the Olink 96 panel
[STEPS]
SECTION: Preparation
1. Aliquoting and Day of Preparation
For Aliquoting of EDTA plasma samples:
Thaw all EDTA plasma samples in a -4°C refrigera... | ["[Preparation] Aliquoting and Day of Preparation \n\nFor Aliquoting of EDTA plasma samples:\nThaw all EDTA plasma samples in a -4°C refrigerator until ready to use.\nKeep Samples in a chilled rack whenever possible.\nMatch your parent tubes (Original tubes shipped) with a prelabelled 2mL\nclarification tube.\nVortex a... |
51,619 | Carrier-assisted One-pot Sample Preparation for Targeted Proteomics Analysis of Small Numbers of Human Cells | 4 | dx.doi.org/10.17504/protocols.io.bwnbpdan | https://www.protocols.io/view/carrier-assisted-one-pot-sample-preparation-for-ta-bwnbpdan | Kendall Martin, Tong Zhang, William B. Chrisler, Fillmore L. Thomas, Wei-Jun Qian, Tujin Shi | TITLE: Carrier-assisted One-pot Sample Preparation for Targeted Proteomics Analysis of Small Numbers of Human Cells
AUTHORS: Kendall Martin, Tong Zhang, William B. Chrisler, Fillmore L. Thomas, Wei-Jun Qian, Tujin Shi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Protein analysis... | ["[PROCEDURE]\nPretreatment of PCR tubes", "[PROCEDURE]\nAdd of nonhuman (e.g., Shewanella oneidensis)cell lysate digests at to PCR tubes. Incubate at room temperature for overnight to coat PCR tube surface.\n100 µl", "[PROCEDURE]\nRemove the cell lysate digests by pipetting, rinse PCR tubes with HPLC-grade water for... |
82,159 | 7.2: Taxon Group: Crustacea - Peracarida | 1 | dx.doi.org/10.17504/protocols.io.n92ldp4n8l5b/v1 | https://www.protocols.io/view/7-2-taxon-group-crustacea-peracarida-cugpwtvn | Chris Fletcher, Paul Clark, Miranda Lowe, Lauren Hughes, Inez Januszczak | TITLE: 7.2: Taxon Group: Crustacea - Peracarida
AUTHORS: Chris Fletcher, Paul Clark, Miranda Lowe, Lauren Hughes, Inez Januszczak
[DESCRIPTION]
This is part of the collection "DToL Taxon-specific Standard Operating Procedures (SOPs) for Marine Metazoa", lead by the Other Metazoa Working Group. The SOP collection conta... | [] |
20,570 | Double picking protocol for tracking | null | dx.doi.org/10.17504/protocols.io.yb2fsqe | null | Priota Islam | TITLE: Double picking protocol for tracking
AUTHORS: Priota Islam
[STEPS]
?. [Imaging plates]
Prepare and pour low peptone NGM onto 35mm imaging plates Put them in the cold room for at least 2 days before use Seed imaging plates with 50ul of freshly made 1:10 solution (OP50:M9 solution) the day before recording Leave... | ["[Imaging plates]\nPrepare and pour low peptone NGM onto 35mm imaging plates Put them in the cold room for at least 2 days before use Seed imaging plates with 50ul of freshly made 1:10 solution (OP50:M9 solution) the day before recording Leave on bench to dry with lid on overnight", "[Day before recording]\nPick arou... |
36,111 | Minimal Event Distance Aneuploidy Lineage Tree (MEDALT) inference based on single cell copy number profile | null | dx.doi.org/10.17504/protocols.io.bfhpjj5n | https://www.protocols.io/view/minimal-event-distance-aneuploidy-lineage-tree-me-bfhpjj5n | Fang Wang, Qihan Wang, Vakul Mohanty, Shaoheng Liang, Jinzhuang Dou, Jincheng Han, Darlan Conterno Minussi, Ruli Gao, Li Ding, Nicholas Navin, Ken Chen | TITLE: Minimal Event Distance Aneuploidy Lineage Tree (MEDALT) inference based on single cell copy number profile
AUTHORS: Fang Wang, Qihan Wang, Vakul Mohanty, Shaoheng Liang, Jinzhuang Dou, Jincheng Han, Darlan Conterno Minussi, Ruli Gao, Li Ding, Nicholas Navin, Ken Chen
[DESCRIPTION]
<div class = "text-blocks"><d... | ["Install Python 2.7 and R 3.5Download MEDALT tool from https://github.com/KChen-lab/MEDALT.gitExtract input dataset", "Decompress gzipped files (MEDALT-1.0.tar.gz)", "Run the example data generated based on single cell DNA sequencing technology\nR packages (igraph, HelloRanges and DescTools) are loaded.\nThree text fi... |
34,616 | Transformation Protocol | 1 | dx.doi.org/10.17504/protocols.io.bd2yi8fw | https://www.protocols.io/view/transformation-protocol-bd2yi8fw | New England Biolabs | TITLE: Transformation Protocol
AUTHORS: New England Biolabs
[DESCRIPTION]
Quick Ligation products may be transformed by many different methods. The following protocol is recommended by New England Biolabs.
[STEPS]
1. Thaw competent cells on ice.
2. Chill approximately 5 ng (2 µL) in a 1.5 ml microcentrifuge tube.... | ["Thaw competent cells on ice.", "Chill approximately 5 ng (2 µL) in a 1.5 ml microcentrifuge tube.", "Add 50 µL to the DNA.", "Mix gently by pipetting up and down or flicking the tube 4–5 times to mix the cells and DNA. Do not vortex.", "Place the mixture on ice for 30 min. Do not mix.", "Heat shock at 42 °C for 30 s.... |
null | null | null | dx.doi.org/10.17504/protocols.io.jricm4e | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?. | [] |
22,276 | M9 Medium | 1 | dx.doi.org/10.17504/protocols.io.zzcf72w | https://www.protocols.io/view/m9-medium-zzcf72w | Fan Zhang, Jessica Weckhorst, Adrien Assie, Anastasia Khodakova, Mario Loeza Cabrera, Daniela Vidal, Christopher Ayoub, Buck Samuel | TITLE: M9 Medium
AUTHORS: Fan Zhang, Jessica Weckhorst, Adrien Assie, Anastasia Khodakova, Mario Loeza Cabrera, Daniela Vidal, Christopher Ayoub, Buck Samuel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>M9 Buffer recipe, transposed from the WormBook chapter: Maintenance of</span><span style... | ["Start with\n[water]", "of Na2HPO4 ()\n6 g", "of KH2PO4 ()\n3 g", "of NaCl ()\n5 g", "of MgSO4∙7H2O OR MgSO4\n0.25 g\n1 mL", "Adjust water to\n1000 mL", "Autoclave"] |
26,242 | REAGENTS AND SOLUTIONS (Support Protocol 7.2) | null | dx.doi.org/10.17504/protocols.io.5vag62e | null | Michael S. Fernandopulle, Ryan Prestil, Christopher Grunseich, Chao Wang, Li Gan, Michael E. Ward | TITLE: REAGENTS AND SOLUTIONS (Support Protocol 7.2)
AUTHORS: Michael S. Fernandopulle, Ryan Prestil, Christopher Grunseich, Chao Wang, Li Gan, Michael E. Ward
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-style:italic;font-weight:bold;">Primers</span></div><div class = "text-b... | [] |
40,906 | ELISA for measurement of platelet-activating factor (PAF) in serum. | 6 | dx.doi.org/10.17504/protocols.io.bj7ikrke | https://www.protocols.io/view/elisa-for-measurement-of-platelet-activating-fact-bj7ikrke | Angel Justiz-Vaillant, Belkis Ferrer-Cosme | TITLE: ELISA for measurement of platelet-activating factor (PAF) in serum.
AUTHORS: Angel Justiz-Vaillant, Belkis Ferrer-Cosme
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. An anti-human PAF coating antibody is adsorbed onto the microwells by incubation overnight at 4°C with carbonate-bicarbon... | ["An anti-human PAF coating antibody is adsorbed onto the microwells by incubation overnight at 4°C with carbonate-bicarbonate buffer.", "Add 50 µl of human serum or plasma. Human PAF present in the serum or plasma binds to antibodies adsorbed into the microwells.", "The microplate is blocked with 3% non-fat milk-PBS b... |
52,335 | Single-cell RNA sequencing | 4 | dx.doi.org/10.17504/protocols.io.bxcppivn | https://www.protocols.io/view/single-cell-rna-sequencing-bxcppivn | Klaus H. Kaestner Lab, Suzanne Shapira | TITLE: Single-cell RNA sequencing
AUTHORS: Klaus H. Kaestner Lab, Suzanne Shapira
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Single-cell RNA sequencing (scRNA-seq) allows for transcriptional profiling of individual cells within a heterogenous sample. This proto... | ["[Steps in pre-processing]\n1. Transfer handpicked islets (approximately 5,000 IEQs) into conical tube. 2. Add of 1xPBS w/o Ca2+, Mg2+ (Rockland, MB-008). Centrifuge for 2 min at RT, 180 xg. Aspirate the supernatant.3. Add of warm ( ) 0.05% Trypsin (Invitrogen, 25300054) to the islets. Pipette up and down with p100... |
52,512 | Candida tropicalis filamentation assay with fluconazole | 4 | dx.doi.org/10.17504/protocols.io.bxh8pj9w | https://www.protocols.io/view/candida-tropicalis-filamentation-assay-with-flucon-bxh8pj9w | Laboratorio de Microbiología Mr JORGE ENRIQUE PEREZ CARDENAS, Sebastian Hernandez | TITLE: Candida tropicalis filamentation assay with fluconazole
AUTHORS: Laboratorio de Microbiología Mr JORGE ENRIQUE PEREZ CARDENAS, Sebastian Hernandez
[DESCRIPTION]
This protocol was used to obtain enough quantity of RNA of a nonsusceptible strain of Candida tropicalis, with the goal to do a transcriptomic analys... | ["[RPMI PREPARATION] MEDIA PREPARATION", "[RPMI PREPARATION] Medium to inhibit filamentation (RPMI+NAC)\nRPMI1640: 10g\n3-[N-morpholino]propane sulfonic acid buffer (MOPS): 35 g\nN-acetyl glucosamine: 20 g\nDistilled water 500 ml\nAdjust pH at 7.0\nAdjust volume at 1000 ml\nEsterilize by filtration", "[RPMI PREPARATIO... |
37,913 | UABMC - PDX Passage Protocol | 1 | null | https://www.protocols.io/view/uabmc-pdx-passage-protocol-bg9zjz76 | Christopher Willey | TITLE: UABMC - PDX Passage Protocol
AUTHORS: Christopher Willey
[STEPS]
?. [TUMOR HARVEST]
.justify:after {
content: "";
display:inline-block;
width: 100%;
}
Select 1 to 2 mice that have tumors that measure no more than 8-10mm in greatest diameter, are not ulcerated and... | ["[TUMOR HARVEST]\n.justify:after {\n\t\t\t\t\t\t\t content: \"\";\n\t\t\t\t\t\t\t display:inline-block;\n\t\t\t\t\t\t\t width: 100%;\n\t\t\t\t\t\t\t }\n\t\t\t\t\t\t\tSelect 1 to 2 mice that have tumors that measure no more than 8-10mm in greatest diameter, are not ulcerated and appear to have grown in a cons... |
33,719 | Nuclei isolation from snap-frozen tendon tissue for single nucleus RNA Sequencing | 1 | dx.doi.org/10.17504/protocols.io.bc6xizfn | https://www.protocols.io/view/nuclei-isolation-from-snap-frozen-tendon-tissue-fo-bc6xizfn | Jolet Y Mimpen, Claudia Paul, Tendon Seed Network, Adam Cribbs, Sarah Snelling | TITLE: Nuclei isolation from snap-frozen tendon tissue for single nucleus RNA Sequencing
AUTHORS: Jolet Y Mimpen, Claudia Paul, Tendon Seed Network, Adam Cribbs, Sarah Snelling
[DESCRIPTION]
Next generation sequencing, especially single cell RNA Sequencing (scRNA-Seq) using enzymatic digestion, has revolutionised o... | ["[Preparation] If running the experiment beyond step 5, prepare the buffers:\nWe recommend making all the buffers fresh on the day.\n\nPrepare 2x Salts and Tris (ST) buffer. For 5 mL, mix:\n0.73 mL of 2M NaCl\n0.10 mL of 1M Tris-HCl pH 7.5\n0.01 mL of 1M CaCl2\n0.21 mL of 1M MgCl2\n3.95 mL sterile H2O\nMix well and s... |
99,895 | Coating Slides with Gelatin | 1 | dx.doi.org/10.17504/protocols.io.e6nvw9qm2gmk/v3 | https://www.protocols.io/view/coating-slides-with-gelatin-ddsx26fn | Allen Institute for Brain Science | TITLE: Coating Slides with Gelatin
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
The protocol describes how 1x3 glass microscope slides are coated with gelatin to improve adherence of fixed adult mouse brain sections or other tissue to slides.
Note: Research reported in this publication was supported by th... | [] |
107,483 | QUINT Workflow for Fluorescence | 4 | dx.doi.org/10.17504/protocols.io.4r3l22y6jl1y/v2 | https://www.protocols.io/view/quint-workflow-for-fluorescence-dk734zqn | Michael X. Henderson | TITLE: QUINT Workflow for Fluorescence
AUTHORS: Michael X. Henderson
[DESCRIPTION]
This protocol describes QUINT workflow for fluorescence. It was updated 9/17/2024. It is based on the published QUINT workflow established by Yates and colleagues (PMID: 31849633).
[GUIDELINES]
Purpose
The purpose of this workflow is ... | ["[QuPath Visualization/Segmentation] Open the QuPath application. Select ‘Create project’.", "[QuPath Visualization/Segmentation] Select your slide/stain folder within your QUINT Workflow project folder (i.e., slide24stain19).", "[QuPath Visualization/Segmentation] Select ‘Add images’ > ‘Choose files’. Navigate to the... |
40,852 | Preparation of horseradish peroxidase (HRP) conjugated Peptostreptococcal protein-L by the periodate method. | 6 | dx.doi.org/10.17504/protocols.io.bj5ukq6w | https://www.protocols.io/view/preparation-of-horseradish-peroxidase-hrp-conjugat-bj5ukq6w | Angel Justiz-Vaillant | TITLE: Preparation of horseradish peroxidase (HRP) conjugated Peptostreptococcal protein-L by the periodate method.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This reagent can be used in ELISA, Western blotting and Dot blot to detect antigens and antibodies. It ... | ["Horseradish peroxidase (500 µg in 50 µl NaCO3 , pH 9.6) is mixed with freshly made sodium periodate solution (1.71 mg/ml) followed by incubation in the dark for 2 h.", "Mix 500 µg of protein-L (SpL) with an equal amount (500 micrograms) of a mix of horseradish peroxidase-sodium periodate.", "The mixture is incubated ... |
67,833 | BASIC PROTOCOL 3: Population Single Nucleotide Variant Calling | 5 | dx.doi.org/10.17504/protocols.io.81wgb638nlpk/v1 | https://www.protocols.io/view/basic-protocol-3-population-single-nucleotide-vari-cegztbx6 | miriam.goldman , chunyu.zhao | TITLE: BASIC PROTOCOL 3: Population Single Nucleotide Variant Calling
AUTHORS: miriam.goldman , chunyu.zhao
[DESCRIPTION]
This protocol describes the SNV module of MIDAS2, which takes as input metagenomic sequencing reads from a set of samples and generates files with SNV genotypes for each sample for all detected ... | ["Perform species prescreening as described in Basic Protocol 1.", "Download MIDASDB as described in Basic Protocol 2.", "Execute the run_snps command for each sample.", "Prepare sample manifest file for merging pileup results across samples. We can use the same file list_of_samples.tsv generated by step 6 in Basic Pro... |
null | null | null | dx.doi.org/10.17504/protocols.io.hwib7ce | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The overall aim of this study is to examine whether oxytocin has a mechanistic effect on pain perception, physical functioning, and physiological and psychological arousal in individuals with chronic musculoskeletal neck and shoulder pain. This study involves receiving a one-... | [] |
34,900 | Viral Sequencing, from Gunk to Graph (Two-step, strand-switching) | null | dx.doi.org/10.17504/protocols.io.bebujanw | null | David Eccles | TITLE: Viral Sequencing, from Gunk to Graph (Two-step, strand-switching)
AUTHORS: David Eccles
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a fast "gunk to graph" protocol for analysing viral RNA from nasopharyngeal swabs. The approach involves swab lysis and inactivation at the point of ... | ["[Swab Lysis]\nPrepare a centrifuge tube with heated lysis buffer and a cellulose disc\n1.5 ml", "[Swab Lysis]\nAdd lysis / RNAse inactivation buffer (Twitter reference) to 1.5ml centrifuge tube:OR extraction buffer #2 (see paper):\n500 µl\n[Tris]\n[EDTA]\n[SDS]\n[NaCl]\n500 µl\n[guanidine hydrochloride]\n[Tris [pH ... |
101,191 | Modelling human neuronal catecholaminergic pigmentation in rodents recapitulates age-related multisystem neurodegenerative deficits | 0 | dx.doi.org/10.17504/protocols.io.4r3l2qq1ql1y/v1 | https://www.protocols.io/view/modelling-human-neuronal-catecholaminergic-pigment-de3f3gjn | Ariadna Laguna, Núria Peñuelas, Miquel Vila | TITLE: Modelling human neuronal catecholaminergic pigmentation in rodents recapitulates age-related multisystem neurodegenerative deficits
AUTHORS: Ariadna Laguna, Núria Peñuelas, Miquel Vila
[DESCRIPTION]
Methods used in the manuscript entitled "Modelling
human neuronal catecholaminergic pigmentation in rodents recap... | [] |
40,458 | INSIGHT: a population scale COVID-19 testing strategy combining point-of-care diagnosis with centralised high-throughput sequencing | 1 | null | https://www.protocols.io/view/insight-a-population-scale-covid-19-testing-strate-bjrikm4e | Qianxin Wu, Chenqu Suo, Tom Brown, Tengyao Wang, Sarah Teichmann, Andrew Bassett | TITLE: INSIGHT: a population scale COVID-19 testing strategy combining point-of-care diagnosis with centralised high-throughput sequencing
AUTHORS: Qianxin Wu, Chenqu Suo, Tom Brown, Tengyao Wang, Sarah Teichmann, Andrew Bassett
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">We present INSIGHT (... | ["Lysis of saliva samples\n\t\t\t\t\t\t\t .justify:after {\n\t\t\t\t\t\t\t content: \"\";\n\t\t\t\t\t\t\t display:inline-block;\n\t\t\t\t\t\t\t width: 100%;\n\t\t\t\t\t\t\t }\n\t\t\t\t\t\t\tMix crude saliva (commercial pooled human saliva from healthy individuals) at 1:1 ratio with QuickExtract DNA Extractio... |
44,914 | OG1RF lipid extraction protocol | 4 | null | https://www.protocols.io/view/og1rf-lipid-extraction-protocol-bp4smqwe | Elizabeth Fozo | TITLE: OG1RF lipid extraction protocol
AUTHORS: Elizabeth Fozo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = ":UNDERLINE;">Lipid Extraction for </span><span style = ":UNDERLINE;font-style:italic;">E. faecalis</span><span style = ":UNDERLINE;"> OG1RF</span></div></div>
[STEPS]
?. [St... | ["[Steps]\nInoculate 50mL of BHI at O.D. of 0.01 from overnight culture. Spike supplement at OD600 0.25. Incubate for 30 minutes and harvest cells. Spin at 2,739 G for 10 minutes.", "[Steps]\nWash twice in 25mL 1X PBS. Spin for 5 minutes at 3,000 rpm.", "[Steps]\nRe-suspend pellets in 1mL of PBS", "[Steps]\nAdd 100u... |
29,109 | Drawing ROIs in ITK-Snap | null | dx.doi.org/10.17504/protocols.io.8nvhve6 | null | Courtney Comrie | TITLE: Drawing ROIs in ITK-Snap
AUTHORS: Courtney Comrie
[STEPS]
?. [ Introduction]
This protocol will show you two different methods for drawing ROIs in ITK-SNAP. The first method will be drawing ROIs manually and the second method will show the automatic ROI with the snake tool.Note: The example in this protocol use... | ["[ Introduction]\nThis protocol will show you two different methods for drawing ROIs in ITK-SNAP. The first method will be drawing ROIs manually and the second method will show the automatic ROI with the snake tool.Note: The example in this protocol uses the Fornix Fimbria in a ferret brain as the ROI.", "[Manual ROIs... |
24,083 | Plant Infiltration for Mimulus in Planta Transformation | null | dx.doi.org/10.17504/protocols.io.3rtgm6n | null | Yaowu Yuan | TITLE: Plant Infiltration for Mimulus in Planta Transformation
AUTHORS: Yaowu Yuan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is part of a </span><a style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">collection for </span><span style = ":;font-... | ["Trim off mature buds from the plants.", "Gently peel back the leaves around the young buds.", "Spray the young buds 2-3 times with the Agro (spray right before they will be put in the vacuum).", "Vacuum infiltrate 1-2 plants at a time. pull a vacuum until 29 inches Hg, seal the vacuum andturn off the pump, wait 2 min... |
28,420 | Preparation of primary chicken embryo liver (CEL) cells | null | dx.doi.org/10.17504/protocols.io.7zchp2w | null | Norfitriah Mohamed Sohaimi, Mohd Hair Bejo, Abdul Rahman Omar, Aini Ideris, Nurulfiza Mat Isa | TITLE: Preparation of primary chicken embryo liver (CEL) cells
AUTHORS: Norfitriah Mohamed Sohaimi, Mohd Hair Bejo, Abdul Rahman Omar, Aini Ideris, Nurulfiza Mat Isa
[STEPS] | [] |
63,758 | Total ATP Level Determination | 4 | dx.doi.org/10.17504/protocols.io.6qpvr62w2vmk/v1 | https://www.protocols.io/view/total-atp-level-determination-cahnsb5e | mitsjoecohen | TITLE: Total ATP Level Determination
AUTHORS: mitsjoecohen
[DESCRIPTION]
Measuring the total ATP level of cells can provide important information about cell proliferation, differentiation, activation, and apoptosis.Creative Biogene introduces the Seahorse XF real-time ATP rate determination platform, which can simul... | [] |
18,579 | The heparin-binding proteome in normal pancreas and murine experimental acute pancreatitis | null | dx.doi.org/10.17504/protocols.io.wdtfa6n | null | Quentin M. Nunes, Dunhao Su, Phuong Thao Bui, Deborah M. Simpson, Philip J. Brownridge, Changye Sun, Yong Li, Zhang X, Wei Huang, Daniel J. Rigden, Robert J. Beynon, Robert Sutton, David G. Fernig | TITLE: The heparin-binding proteome in normal pancreas and murine experimental acute pancreatitis
AUTHORS: Quentin M. Nunes, Dunhao Su, Phuong Thao Bui, Deborah M. Simpson, Philip J. Brownridge, Changye Sun, Yong Li, Zhang X, Wei Huang, Daniel J. Rigden, Robert J. Beynon, Robert Sutton, David G. Fernig
[DESCRIPTION]
<... | ["[Heparin affinity chromatography]\nThe frozen murine plasma was defrosted on ice and centrifuged at 16,100 g for 10 min, at 4 ˚C.The resulting supernatant was diluted (1:8) in 75 mM NaCl, 6.85 mM Na2HPO4, 3.15 mM NaH2PO4, pH 7.2.The diluted supernatant was centrifuged at 5,000 g for 5 min.and the resulting supernatan... |
71,759 | Acclimation of in vitro grown individual lines of big sagebrush (Artemisia tridentata) to ex vitro conditions in support of genotype-by-environment experiments and restoration | 4 | dx.doi.org/10.17504/protocols.io.j8nlk4zpxg5r/v2 | https://www.protocols.io/view/acclimation-of-in-vitro-grown-individual-lines-of-cibpuamn | Peggy Martinez, Marcelo Serpe, Rachael Barron, Sven Buerki | TITLE: Acclimation of in vitro grown individual lines of big sagebrush (Artemisia tridentata) to ex vitro conditions in support of genotype-by-environment experiments and restoration
AUTHORS: Peggy Martinez, Marcelo Serpe, Rachael Barron, Sven Buerki
[DESCRIPTION]
The following protocol describes the ex vitro,... | ["[Prepare sandy soil with nutrient solution] Prepare sandy soil\n\nMix play sand and vermiculite to a 4:1 v/v (sand/vermiculite) in large plastic tub (hereafter referred to as sandy soil). If play sand is very dry, add enough DI water to moisten the sandy soil mixture.\n \n\n2. Tare PhytoCon vessel (946mL) on the bala... |
80,600 | DOT BLOT - DENGUE VIRUS | 1 | dx.doi.org/10.17504/protocols.io.bp2l696jdlqe/v1 | https://www.protocols.io/view/dot-blot-dengue-virus-csxywfpw | Delia Piedad Recalde-Reyes, Juliana Lopez Calderon | TITLE: DOT BLOT - DENGUE VIRUS
AUTHORS: Delia Piedad Recalde-Reyes, Juliana Lopez Calderon
[DESCRIPTION]
Es un inmunoensayo simple y rápido. Requiere la aplicación de una pequeña cantidad de muestra directamente sobre una membrana polivinilo PVDF, en la que se deposita antigeno total de DENV y posteriormente se expone... | ["Activación membrana de polivinilo \n\nPara realizar este paso es necesario sumergir la membrana de polivinilo poro 0,45μm en metanol absoluto durante 5 min.\n\nPosteriormente se retira y se deja secar a temperatura ambiente.", "Adición del antígeno total sobre la membrana (transferencia directa)\n\nEn la membrana de... |
38,268 | Sequence-Independent, Single-Primer Amplification of RNA viruses | 1 | dx.doi.org/10.17504/protocols.io.bhk4j4yw | https://www.protocols.io/view/sequence-independent-single-primer-amplification-o-bhk4j4yw | Gage Moreno, David O'connor | TITLE: Sequence-Independent, Single-Primer Amplification of RNA viruses
AUTHORS: Gage Moreno, David O'connor
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines the methods to perform unbiased direct metagenomic sequencing of nucleic acid extracts from cell-free fluids. This proto... | ["[Nucleic Acid Extraction]\nAdd 280µL cell-free liquid to 0.22µm centrifuge filter. Note: (add in 2x what you want to get out)", "[Nucleic Acid Extraction]\nCentrigue at 14,000 RPM for 5 minutes\nCentrifuge: 14000 33, 5 min", "[Nucleic Acid Extraction]\nTransfer 140µL of filtered sample to a new tube.", "[Nucleic Acid... |
null | null | null | dx.doi.org/10.17504/protocols.io.euhbet6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.p2wdqfe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The Sisbiota-mar photoquadrat survey aims to quantify the benthic cover of horizontal reef surfaces using photography and subsequent image analysis, in a manner that is directly comparable across geographies. Our survey method employs 2m<sup>2</sup> horizontal surfaces of ree... | [] |
71,082 | PCR cleanup and size selection with magnetic beads | 4 | dx.doi.org/10.17504/protocols.io.36wgqj45xvk5/v2 | https://www.protocols.io/view/pcr-cleanup-and-size-selection-with-magnetic-beads-chnit5ce | Dominik Buchner | TITLE: PCR cleanup and size selection with magnetic beads
AUTHORS: Dominik Buchner
[DESCRIPTION]
This protocol describes how to clean up PCR products or DNA extracts and perform a size selection with carboxylated-magnetic beads and a PEG-NaCl buffer. It can also be used for volume reduction of a sample or for buffer e... | ["Shake the cleanup solution until the beads are homogeneously resuspended", "Add 30 µL and 32 µL to a 250 µL U-bottom assay plate", "Add 10 µL of sample.", "To bind the DNA to the beads shake at", "Place the plate on a magnet to pellet the beads for 2 min", "Discard the supernatant by pipetting", "With the plate stil... |
41,015 | Fast and inexpensive protocols for consistent extraction of high quality DNA and RNA from challenging plant and fungal samples for high-throughput SNP genotyping and sequencing applications | 1 | null | https://www.protocols.io/view/fast-and-inexpensive-protocols-for-consistent-extr-bkaxksfn | Peter Inglis, Marilia de Castro R. Pappas, Lucileide V. Resende, Dario Grattapaglia | TITLE: Fast and inexpensive protocols for consistent extraction of high quality DNA and RNA from challenging plant and fungal samples for high-throughput SNP genotyping and sequencing applications
AUTHORS: Peter Inglis, Marilia de Castro R. Pappas, Lucileide V. Resende, Dario Grattapaglia
[DESCRIPTION]
<div class = "t... | ["[DNA Extraction Protocol]\nAdd an excess of sorbitol wash buffer to fill sample tubes containing macerated plant material to approximately ¾ capacity (0.9 – 1.5 ml, depending on tubes used). Cap tubes and shake in the bead mill, manually or using vortex. Inspect to confirm suspension of the powdered material and shak... |
null | null | null | dx.doi.org/10.17504/protocols.io.syfeftn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This staining was performed to detect fetuin-A in activated microglia. CD68 is a marker, that stains activated microglia, macrophages and monocytes. Fetuin-A and microglia were detected in paraffin sections (1 μm thickness) of formalin-fixed human brain tissue. CD68 was stain... | ["[Clear slides] Place slides in hybridization oven: 37°C overnight, then 1 hour at 65°C", "Deparaffination in xylene 3x20 minutes (different containers) on a shaker", "Rehydration in graded ethanol: 3x2 minutes in 100% ethanol, followed by 2x2 minutes in 96% ethanol and at last 2 minutes in 70% ethanol", "Wash in PBS ... |
30,501 | ELISA IL-10 | null | dx.doi.org/10.17504/protocols.io.92dh8a6 | null | Tamiris Silva | TITLE: ELISA IL-10
AUTHORS: Tamiris Silva
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">To evaluate the effects of photobiomodulation (PBM) on IL-10 expression in individuals with relapsing-remitting multiple sclerosis, a clinical trial was performed. Participants were randomized and then collect... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.s9aeh2e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocolo para preparação de pequenos artrópodes de cutícula pouco esclerotizada quando não há disponibilidade de secador de ponto crítico. Adaptado de:</p>
<p><a href="http://www.phorid.net/hmds.php" target="_blank" rel="noopener noreferrer">Brown, B.V. 1993.</a> A further c... | [] |
52,002 | NEBNext® ARTIC Protocols Collection | 2 | dx.doi.org/10.17504/protocols.io.bw2apgae | https://www.protocols.io/view/nebnext-artic-protocols-collection-bw2apgae | Isabel Gautreau | TITLE: NEBNext® ARTIC Protocols Collection
AUTHORS: Isabel Gautreau
[DESCRIPTION]
Express and Standard protocols for the NEBNext® ARTIC products (E7650, E7658, E7660, E7626) for SARS-CoV-2 sequencing.
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.nmtdc6n | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?. | [] |
78,968 | Expansion microscopy | 1 | dx.doi.org/10.17504/protocols.io.kqdg39n5qg25/v1 | https://www.protocols.io/view/expansion-microscopy-crcyv2xw | michela.deleidi, María José Pérez J., Hariam Raji, Pascale Baden, Federico Bertoli | TITLE: Expansion microscopy
AUTHORS: michela.deleidi, María José Pérez J., Hariam Raji, Pascale Baden, Federico Bertoli
[DESCRIPTION]
Expansion microscopy is a technique to visualize biological structures with higher spatial resolution than traditional microscopy methods.
[STEPS]
SECTION: Expansion microscopy
1.
... | ["[Expansion microscopy] Block cells with 10% (v/v) normal goat serum (NGS) in 0.1% (v/v) Triton X-100 in PBS and incubate it with primary antibodies in blocking solution .", "[Expansion microscopy] After a 3-h incubation with the corresponding secondary antibody (Alexa Fluor, Invitrogen), wash the samples and treat w... |
null | null | null | dx.doi.org/10.17504/protocols.io.cg5ty5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol is a group of the following 5 methods from the NEB website:<br />1. <a href="https://www.neb.com/protocols/2012/11/15/nebnext-end-prep-e7370" target="_blank">NEBNext End Prep </a> <br />2. <a href="https://www.neb.com/protocols/2012/11/15/adaptor-ligation-e737... | [] |
86,607 | U54 SCENT T/NK Immunosenescence Profiling Flow Cytometry Panel | 1 | dx.doi.org/10.17504/protocols.io.q26g7ppm9gwz/v1 | https://www.protocols.io/view/u54-scent-t-nk-immunosenescence-profiling-flow-cyt-cytpxwmn | Zachary R Healy, David Murdoch, Alicia Cooper-Volkheimer | TITLE: U54 SCENT T/NK Immunosenescence Profiling Flow Cytometry Panel
AUTHORS: Zachary R Healy, David Murdoch, Alicia Cooper-Volkheimer
[DESCRIPTION]
This protocol describes the T/NK Immunosenescence Profiling Flow Cytometry Panel
[STEPS]
SECTION: FBS Aliquot Prep
1. FBS (hiFBS): Gemini Bio Products Cat #100-106 1L
P... | ["[FBS Aliquot Prep] FBS (hiFBS): Gemini Bio Products Cat #100-106 1L\nPrepare FBS Aliquots:", "[FBS Aliquot Prep] Thaw heat-inactivated FBS (hiFBS):\nThaw a 500mL Bottle of FBS at 4°C. This may require more than overnight so the 500mL Bottle may be removed 2 or 3 days prior to use. Do not leave the FBS at room tempera... |
60,610 | Counting kidneys | 4 | dx.doi.org/10.17504/protocols.io.6qpvr6k4pvmk/v1 | https://www.protocols.io/view/counting-kidneys-b7farjie | Gabriel J Barrero, Abraham Palmer, Oksana Polesskaya | TITLE: Counting kidneys
AUTHORS: Gabriel J Barrero, Abraham Palmer, Oksana Polesskaya
[DESCRIPTION]
Dissecting and counting kidneys in rats.
[STEPS]
1. Rats are euthanized as per IACUC guidelines
Spray fur with ethanol. Pick up skin above the sternum, and make a cut through skin and muscle layers.
Don’t cut the ch... | ["Rats are euthanized as per IACUC guidelines\nSpray fur with ethanol. Pick up skin above the sternum, and make a cut through skin and muscle layers.\nDon’t cut the chest cavity (don’t go above the diaphragm).", "Cut skin and muscles from the sternum down to the lower belly. Mostly you will see liver and colon.", "Lift... |
33,856 | snATAC-Seq on 10x ChromiumTM platform for fresh, frozen and cryopreserved material: my notes from the lab (UPDATED VERSION) | null | dx.doi.org/10.17504/protocols.io.bda8i2hw | null | Luciano Martelotto | TITLE: snATAC-Seq on 10x ChromiumTM platform for fresh, frozen and cryopreserved material: my notes from the lab (UPDATED VERSION)
AUTHORS: Luciano Martelotto
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left"><span>-Here, I will </span><span style = "fo... | ["[snATAC-Seq]\nSort as many nuclei as possible into a round-bottom 96-well plate well containing of ice-cold ATAC Wash Buffer-Dig.\nIdeally, perform the following steps WHILE the RT reaction is RUNNING. See Frankenstein protocol for nuclei prep. The steps below assumes the nuclei input for snATAC is relatively low.\n... |
51,908 | Total Nucleic Acids Extraction from Soil | 1 | dx.doi.org/10.17504/protocols.io.bwxcpfiw | https://www.protocols.io/view/total-nucleic-acids-extraction-from-soil-bwxcpfiw | Roey Angel, Eva Petrova, Ana Lara-Rodriguez | TITLE: Total Nucleic Acids Extraction from Soil
AUTHORS: Roey Angel, Eva Petrova, Ana Lara-Rodriguez
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The following protocol is intended for the simultaneous extraction of DNA and RNA (total nucleic acids, or TNA) from various soil and sediment sa... | ["[Solutions for TNA extraction]\nPrepare the following solutions for TNA extractionUse clean and preferably baked glassware (make sure all non-glass components can withstand the high temperatures).", "[Solutions for TNA extraction]\nOne of the following phosphate buffers:Phosphate buffer ( , )Dissolve the salts in ... |
43,797 | Test document | 3 | null | https://www.protocols.io/view/test-document-bnzvmf66 | Lenny Teytelman | TITLE: Test document
AUTHORS: Lenny Teytelman
[STEPS] | [] |
8,538 | Gas chromatochraphic detection of Sesquiterpenoids in Dodecane using Perkin Elmer GC 580 | null | dx.doi.org/10.17504/protocols.io.kj2cuqe | null | Dennis Dienst, João Rodrigues, Pia Lindberg | TITLE: Gas chromatochraphic detection of Sesquiterpenoids in Dodecane using Perkin Elmer GC 580
AUTHORS: Dennis Dienst, João Rodrigues, Pia Lindberg
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This is a quick guide for routine quantitative analysis of sesquiterpenoids in dodecane using an ... | ["[Prepare autosampler ]\nGeneral Setup fill two wash bottles w/ each 3 mL Dodecane (solvent)place bottles into 'wash' positions 1 & 2 of autosampler platformplace emtpy wash bottles into 'waste' positions 1 & 2 place GC vials (max. 108) into corresponding positions of autosampler platformFor sample preparation check ... |
null | null | null | dx.doi.org/10.17504/protocols.io.e3cbgiw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Precision Count Beads™ are designed for counting the absolute number of cells in a complex mix population and other particles by flow cytometry. Precision Count Beads™ are excited by a variety of lasers including violet (405nm), blue (488nm), yellow/green (562nm), and red (63... | [] |
81,476 | SmartSPIM setup and alignment | 1 | dx.doi.org/10.17504/protocols.io.5jyl8jyb7g2w/v1 | https://www.protocols.io/view/smartspim-setup-and-alignment-cttcwniw | John Rohde | TITLE: SmartSPIM setup and alignment
AUTHORS: John Rohde
[DESCRIPTION]
Setting-up and aligning the SmartSPIM light sheet microscope is required before acquiring each dataset. The instrument is capable of imaging whole, cleared, delipidated mouse brains. It utilizes two illumination paths, corresponding to each hemisph... | ["[Hardware set-up] Turn on the instrument BEFORE starting the acquisition software:", "[Software set-up] Restarting or starting the software: if the software is open from a previous acquisition, close the software and reopen it to begin an acquisition. In rare cases, the software may be frozen, and you may need to use... |
93,204 | Targeted optogenetic stimulations | 1 | dx.doi.org/10.17504/protocols.io.5jyl8pxz6g2w/v1 | https://www.protocols.io/view/targeted-optogenetic-stimulations-c69uzh6w | Mai-Anh Vu, mwhowe | TITLE: Targeted optogenetic stimulations
AUTHORS: Mai-Anh Vu, mwhowe
[DESCRIPTION]
We have developed a new micro-fiber array approach capable of chronically measuring and optogenetically manipulating local dynamics across over 100 targeted locations simultaneously in head-fixed and freely moving mice, enabling investi... | ["[Targeted optogenetic stimulations] To couple light into individual optical fibers in our array for targeted optogenetic manipulations, simultaneously with imaging, we integrated a programmable digital mirror device (DMD, Mightex Polygon1000 Pattern Illuminator DSI-K3-L20) into the light path of our imaging microscop... |
79,581 | WC Medium | 1 | null | https://www.protocols.io/view/wc-medium-crx5v7q6 | Richard Wilander Lambrecht | TITLE: WC Medium
AUTHORS: Richard Wilander Lambrecht
[DESCRIPTION]
WC Medium modified from Guillard and Lorenzen (1972)
[STEPS]
SECTION: Medium preparation (for 1L of WC)
2. Weigh 0,115 g of TES Buffer (C6H15NO6S) and add it to a volumetric flask with almost 1L of MilliQ water
SECTION: Medium preparation (for 1L of W... | ["[Medium preparation (for 1L of WC)] Weigh 0,115 g of TES Buffer (C6H15NO6S) and add it to a volumetric flask with almost 1L of MilliQ water", "[Medium preparation (for 1L of WC)] Add 1 mL of each of the stock solutions A to G to the medium preparation bottle.", "[Medium preparation (for 1L of WC)] Complete the volume... |
35,963 | AAU-nCoV-2019_Tailed_Long_Amplicon_Sequncing | null | dx.doi.org/10.17504/protocols.io.bfc3jiyn | https://www.protocols.io/view/aau-ncov-2019-tailed-long-amplicon-sequncing-bfc3jiyn | Emil Aarre Sorensen, Søren M. Karst, Simon Knutsson | TITLE: AAU-nCoV-2019_Tailed_Long_Amplicon_Sequncing
AUTHORS: Emil Aarre Sorensen, Søren M. Karst, Simon Knutsson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the preparation of long read amplicon libraries of nCoV-2019 for sequencing with the Oxford Nanopore MinION platfor... | ["[Section 1: Preparations]\nCreate journal Create a journal with associated unique journal number (CJXXX) inculding metadata for the samples to be processed.Metadata must include reference to a sample registration journal and a sample overview of the samples to be processed. For reference see SOP for setting up journa... |
null | null | null | dx.doi.org/10.17504/protocols.io.kdxcs7n | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.r6vd9e6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?. | ["We systematically searched Medline via PubMed, Embase, CNKI and the Cochrane Library Center Register to identify randomized controlled trials up to March 2018. English and Chinese were imposed in the search strategy. The following subject headings and keywords were used for each electronic databases: “(((2-(Diethylam... |
54,887 | Clinical characterization of a cohort of patients under treatment for systemic lupus erythematosus in Colombia | 1 | dx.doi.org/10.17504/protocols.io.bzufp6tn | https://www.protocols.io/view/clinical-characterization-of-a-cohort-of-patients-bzufp6tn | Jorge Machado Alba | TITLE: Clinical characterization of a cohort of patients under treatment for systemic lupus erythematosus in Colombia
AUTHORS: Jorge Machado Alba
[DESCRIPTION]
Introduction/objectives:
To describe the clinical characteristics and health care resource utilization in a Colombian systemic lupus erythematosus (SLE... | [] |
63,432 | Huuman CBD Gummies Help You Recovering Over Your Own Life! | 3 | dx.doi.org/10.17504/protocols.io.kxygxz2pkv8j/v1 | https://www.protocols.io/view/huuman-cbd-gummies-help-you-recovering-over-your-o-b97gr9jw | Huuman CBD Gummies | TITLE: Huuman CBD Gummies Help You Recovering Over Your Own Life!
AUTHORS: Huuman CBD Gummies
[DESCRIPTION]
https://www.bulbapp.com/rimasid818/portfolio
[STEPS] | [] |
85,658 | Immunohistochemistry (using floating section) | 4 | dx.doi.org/10.17504/protocols.io.6qpvr36yovmk/v1 | https://www.protocols.io/view/immunohistochemistry-using-floating-section-cxv2xn8e | Tae-Un Han, Ellen Sidransky | TITLE: Immunohistochemistry (using floating section)
AUTHORS: Tae-Un Han, Ellen Sidransky
[DESCRIPTION]
- This is an immunohistochemistry protocol used for evaluation of pathology in mouse brain.
- We successfully detected Gfap, Iba1, CD68, TH and alpha-Syn and phospho S129 alpha synuclein protein expression using t... | ["Mount floating sections onto slides and dry for 30 min (<45 min), While section drying, PAP pen drawing line and dry 5 min.", "PBS rehydrate 10 min, Wash with PBS for 5 min three times.", "Blocking sol 500 µL, incubate 60 min at Room temperature.", "Replace buffer to primary antibody sol, incubate 10 min at 4 °C.", ... |
28,163 | Neuropathy Phentoyping Protocols - Nerve Conduction Velocity | null | dx.doi.org/10.17504/protocols.io.7rbhm2n | null | Eva Feldman | TITLE: Neuropathy Phentoyping Protocols - Nerve Conduction Velocity
AUTHORS: Eva Feldman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block"><span style = "font-weight:bold;">Phenotyping of Rodents for the Presence of Diabe... | ["[Settings:]\nMotor tests: • Duration .02 ms. • Range 25 Ma. • Low frequency filter 1 Hz. • High frequency filter 10 kHz. • Sensitivity 1 mV. • Time 2 ms/div.Sensory test: • Duration .02 ms. • Range 25 mA. • Low frequency filter 1 Hz. • High frequency filter 10 kHz. • Sensitivity 50 µV. • Time 2 ms/div.", "[Procedure:... |
68,340 | Extraction of meiofauna and meioflora from aquatic environmental samples | 4 | null | https://www.protocols.io/view/extraction-of-meiofauna-and-meioflora-from-aquatic-ceyutfww | Daisuke Shimada | TITLE: Extraction of meiofauna and meioflora from aquatic environmental samples
AUTHORS: Daisuke Shimada
[DESCRIPTION]
Meiofauna and microalgae are benthic communities of small animals and algae, respectively, that can pass through a 1-mm sieve but are retained in a 32-µm sieve. This simplified protocol collects meiof... | ["[Sampling] Collect substrates (sediments, seagrasses, seaweeds, sessile animals, etc.) by hand or by using sampling devices.", "[Filtration] Transfer 100–500 ml of substrate into a bucket and wash the substrate well with approximately 10 times volume of tap water. If the substrate is mud, reduce the substrate vo... |
88,812 | Carver et al, Aged Brain Spatial Profiling - Tissue Processing | 1 | dx.doi.org/10.17504/protocols.io.kqdg3x841g25/v2 | https://www.protocols.io/view/carver-et-al-aged-brain-spatial-profiling-tissue-p-c2ykyfuw | Chase Carver | TITLE: Carver et al, Aged Brain Spatial Profiling - Tissue Processing
AUTHORS: Chase Carver
[DESCRIPTION]
This protocol provides the steps for mouse brain tissue processing and preparation for use in immunohistochemistry and spatial -omic techniques used in Carver et al., "Senescent- and disease-associated microglia ... | ["[Perfusion] Euthanize mouse with intraperitoneal injection of 32.5mg/ml pentobarbital", "[Perfusion] Perfuse transcardially with ice-cold PBS", "Bisect the two hemispheres of the brain", "[Brain Processing] Decapitate mouse and extract brain from skull", "[Perfusion] Extract blood via inferior vena cava with a syring... |
40,931 | ELISA for quantification of human C6 in serum or plasma. | 6 | dx.doi.org/10.17504/protocols.io.bj8bkrsn | https://www.protocols.io/view/elisa-for-quantification-of-human-c6-in-serum-or-bj8bkrsn | Angel Justiz-Vaillant, Belkis Ferrer-Cosme | TITLE: ELISA for quantification of human C6 in serum or plasma.
AUTHORS: Angel Justiz-Vaillant, Belkis Ferrer-Cosme
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. An anti-human C6 coating antibody is adsorbed onto the microwells by incubation overnight at 4°C with carbonate-bicarbonate buffer.
?... | ["An anti-human C6 coating antibody is adsorbed onto the microwells by incubation overnight at 4°C with carbonate-bicarbonate buffer.", "Add 50 µl of human serum or plasma. Human C6 present in the serum or plasma binds to antibodies adsorbed into the microwells.", "The microplate is blocked with 3% non-fat milk-PBS buf... |
28,670 | PCR (Toehold) Fragment Protocol for a 25ul reaction | null | dx.doi.org/10.17504/protocols.io.786hrze | null | Janet Standeven | TITLE: PCR (Toehold) Fragment Protocol for a 25ul reaction
AUTHORS: Janet Standeven
[STEPS]
?. Pipette all reaction agents into pcr tube
?. put pcr tube in thermal cycler and set the annealing temperature to 55 degrees celsius
?. Annealing temperatures vary depending on DNA
?. Set elongation time to 30 seconds
?. 1 mi... | ["Pipette all reaction agents into pcr tube", "put pcr tube in thermal cycler and set the annealing temperature to 55 degrees celsius", "Annealing temperatures vary depending on DNA", "Set elongation time to 30 seconds", "1 min/2kb for Q5 High Fidelity → may vary"] |
30,704 | Immunoprecipitation Protocol | null | dx.doi.org/10.17504/protocols.io.98qh9vw | null | Sam Li | TITLE: Immunoprecipitation Protocol
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Immunoprecipitation is a procedure by which proteins or peptides that react specifically with an antibody are removed from solution and examined for quantity or physical characteristics. Immunoprecipi... | ["[Preparation of antibody-protein A, G, A/G agarose beads:]\nWash protein A, G, A/G agarose beads with cell lysis buffer by pulsing in a microcentrifuge tube (two minutes at 5,000 rpm). Aspirate and discard supernatant. Wash the beads three times with cell lysis buffer.", "[Preparation of antibody-protein A, G, A/G ag... |
96,913 | Neuronal co-culture | 0 | dx.doi.org/10.17504/protocols.io.dm6gpze38lzp/v1 | https://www.protocols.io/view/neuronal-co-culture-davr2e56 | Nisha Mohd Rafiq, Pietro De Camilli | TITLE: Neuronal co-culture
AUTHORS: Nisha Mohd Rafiq, Pietro De Camilli
[DESCRIPTION]
This protocol describes the co-culturing of iPSC-derived dopaminergic (DA) neurons and iPSC-derived medium spiny neurons (MSNs) in a microfluidic compartmentalization device.
[STEPS]
SECTION: Neuronal co-culture device set-up
1.
... | ["[Neuronal co-culture device set-up] Coat chambers with 200 µL per well with 0.1 1524 Poly-L-Ornithine (PLO) in PBS.", "[Neuronal co-culture device set-up] Incubate plates overnight at 37 °C.", "[Neuronal co-culture device set-up] Wash the chambers thrice with PBS.", "[Neuronal co-culture device set-up] Coat chambers ... |
26,538 | U Mass - Transverse Aortic Constriction | null | dx.doi.org/10.17504/protocols.io.56ig9ce | null | Mark Kelly, Timothy P. Fitzgibbons | TITLE: U Mass - Transverse Aortic Constriction
AUTHORS: Mark Kelly, Timothy P. Fitzgibbons
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">
This is a Mouse model of Transverse aortic constriction (TAC). A commonly used ... | ["Expected procedure duration:20-40 minutes", "Adequacy or depth of anesthesia is monitored by:Respiratory Rate and Toe Pinch", "Frequency of anesthesia depth assessment:At the start of surgical procedure, a toe or ear pinch can be used to assess the depth of anesthesia. Visual monitoring should be performed thought-ou... |
80,064 | Image Registration of MALDI IMS to Microscopy | 1 | dx.doi.org/10.17504/protocols.io.5qpvor6xxv4o/v1 | https://www.protocols.io/view/image-registration-of-maldi-ims-to-microscopy-cse8wbhw | Nathan Heath Patterson, Jamie Allen, Angela Kruse, allison.b.esselman, ellie.l.pingry, Danielle Gutierrez, Jeff Spraggins | TITLE: Image Registration of MALDI IMS to Microscopy
AUTHORS: Nathan Heath Patterson, Jamie Allen, Angela Kruse, allison.b.esselman, ellie.l.pingry, Danielle Gutierrez, Jeff Spraggins
[DESCRIPTION]
Scope:
To process to register MALDI IMS images to different types of microscopy images using IMS MicroLink and WSIREG.
... | ["Install Napari with IMS MicroLink plugin using https://github.com/NHPatterson/napari-imsmicrolink", "Install the WSIREG plugin with Napari https://github.com/NHPatterson/wsireg", "When complete, all images will be sampled in the same coordinates as the IMS pixel map.", "Use MicroLink to align laser ablation marks fro... |
40,374 | MPAPASS - Gating flow cytometry multiplex data | 1 | dx.doi.org/10.17504/protocols.io.bjnwkmfe | https://www.protocols.io/view/mpapass-gating-flow-cytometry-multiplex-data-bjnwkmfe | Joshua Welsh, Sean Cook, Jennifer Jones | TITLE: MPAPASS - Gating flow cytometry multiplex data
AUTHORS: Joshua Welsh, Sean Cook, Jennifer Jones
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is collection contains the protocols required for each step in the mpapass software pipeline for performing stitched multiplex analysis. This is... | ["[Gating the Bead Populations]\nDouble-click on any of the samples in order to bring up a scatter plot. Change the parameters of the scatter plot to FSC-A and SSC-A channels and gate around the single events using a rectangular gate.", "[Importing the Files into FlowJo]\nImport the desired files into the FlowJo worksp... |
54,099 | BPHL SARS-CoV-2 Tiled Amplicon Illumina Sequencing | 4 | dx.doi.org/10.17504/protocols.io.by3tpynn | https://www.protocols.io/view/bphl-sars-cov-2-tiled-amplicon-illumina-sequencing-by3tpynn | Jason Blanton | TITLE: BPHL SARS-CoV-2 Tiled Amplicon Illumina Sequencing
AUTHORS: Jason Blanton
[DESCRIPTION]
This protocol details the Florida Department of Health's Bureau of Public Health Laboratories' (BPHL) wet lab portion of our SARS-CoV-2 next generation sequencing workflow. The method is a tiled amplicon approach using ART... | ["[RNA Extraction] Extract RNA from positive COVID-19 clinical specimens with the KingFisher Flex instrument using the Applied Biosystems™MagMAX™ Viral/Pathogen II (MVP II) Nucleic Acid Isolation Kit and its associated protocol.", "[cDNA Generation] cDNA from RNA (from any extraction method) is produced using with t... |
50,054 | Titan Clear Labs SARS-CoV-2 Strain Characterization Workflow for the Terra Platform | 5 | null | https://www.protocols.io/view/titan-clear-labs-sars-cov-2-strain-characterizatio-bu5eny3e | Frank J Ambrosio, Jill V Hagey, Kevin Libuit, Technical Outreach and Assistance for States Team | TITLE: Titan Clear Labs SARS-CoV-2 Strain Characterization Workflow for the Terra Platform
AUTHORS: Frank J Ambrosio, Jill V Hagey, Kevin Libuit, Technical Outreach and Assistance for States Team
[DESCRIPTION]
The Titan_ClearLabs workflow is a part of the Public Health Viral Genomics Titan series for SARS-CoV-2 geno... | ["[Setup Terra and Google Cloud Accounts]", "[Import Titan Clear Labs workflow from Dockstore] Importing the Titan Workflow from Dockstore to the User Workspace\n\nThe Titan Clear Labs workflow is hosted in the Theiagen Dockstore (https://dockstore.org/) repository and has to be imported into the user's Terra Workspace... |
40,761 | ELISA for quantification of IL-1 in human serum. | 6 | dx.doi.org/10.17504/protocols.io.bj2zkqf6 | https://www.protocols.io/view/elisa-for-quantification-of-il-1-in-human-serum-bj2zkqf6 | Angel Justiz-Vaillant | TITLE: ELISA for quantification of IL-1 in human serum.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Interleukins (IL) are a type of cytokine first thought to be expressed by leukocytes alone but have later been found to be produced by many other body cells.... | ["An anti-human IL-1 coating antibody is adsorbed onto microwells by incubation overnight at 4°C.", "Add 50 µl of human serum. Human IL-1 present in the serum sample binds to antibodies adsorbed to the microwells.", "The microplate is blocked with 3% non-fat milk-PBS buffer and later wasth o remove unbound proteins.",... |
59,052 | Western Blot | 4 | dx.doi.org/10.17504/protocols.io.b5wkq7cw | https://www.protocols.io/view/western-blot-b5wkq7cw | Haley Geertsma | TITLE: Western Blot
AUTHORS: Haley Geertsma
[DESCRIPTION]
This protocol is used to western blot proteins-of-interest.
[STEPS]
1. Add 4X Laemmli buffer to protein samples and incubate at 95oC for 7 minutes.
2. Load samples into 12% polyacrylamide gel and run in running buffer at 80-100V for 60-120 minutes.
3. Transf... | ["Add 4X Laemmli buffer to protein samples and incubate at 95oC for 7 minutes.", "Load samples into 12% polyacrylamide gel and run in running buffer at 80-100V for 60-120 minutes.", "Transfer gel to 0.2μm nitrocellulose membrane at 350mA for 60 minutes at 4oC.", "Wash membrane with 1X TBS-T then block in 10% milk for 3... |
48,982 | How to expose existing R code as a web service | 5 | null | https://www.protocols.io/view/how-to-expose-existing-r-code-as-a-web-service-bt3wnqpe | Sonia García-Ruiz | TITLE: How to expose existing R code as a web service
AUTHORS: Sonia García-Ruiz
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol shows how to expose any existing R method as a web service. The code shown here has been used as part of the development of the CoExp Web Application <... | ["First, we install the R package Plumber. To install the latest stable version from CRAN, we can type the following R command:install.packages(\"plumber\")", "The next step will consist of creating the API specification to expose our R methods of interest. In this case, we are going to expose the method 'CoExpNets::ge... |
35,799 | Redirected lysis (P815 functional assay) | 1 | dx.doi.org/10.17504/protocols.io.14egn8jzyg5d/v1 | https://www.protocols.io/view/redirected-lysis-p815-functional-assay-be7xjhpn | Philippa R Kennedy | TITLE: Redirected lysis (P815 functional assay)
AUTHORS: Philippa R Kennedy
[DESCRIPTION]
In order to test the function of specific activating receptors on the surface of human natural killer (NK) cells, 1) mouse antibodies that cross-link those human receptors and 2) mouse cell line P815 that has Fc receptors to gath... | ["Optional: Label specific cell subsets prior to this assay with Cell Trace Violet (CTV) according to the manufacturer's instructions to examine the behavior of a particular cell subset.", "One hour after the addition of anti-CD107a, cells are given monensin (GolgiStop Cat. No. 554724, BD Biosciences) and brefeldin A (... |
85,929 | mCherry-YIPF4 Immunoprecipitation V2 | 4 | dx.doi.org/10.17504/protocols.io.8epv5xj9ng1b/v1 | https://www.protocols.io/view/mcherry-yipf4-immunoprecipitation-v2-cx6hxrb6 | Kelsey Hickey, Sharan Sharan Swarup, Harper JW | TITLE: mCherry-YIPF4 Immunoprecipitation V2
AUTHORS: Kelsey Hickey, Sharan Sharan Swarup, Harper JW
[DESCRIPTION]
This protocol is for immunoprecipitating an mcherry tagged Golgi protein- YIPF4, and probing for ATG8 interactions.
[STEPS]
SECTION: HEK293 YIPF4 KO Creation
1. Maintain HEK293 cells in Dulbecco’ Modifie... | ["[HEK293 YIPF4 KO Creation] Maintain HEK293 cells in Dulbecco’ Modifies Eagles Medium (DMEM) with 10% fetal bovine serum and optional 1x penicillin-streptomycin.", "[HEK293 YIPF4 KO Creation] Individual clones were subjected to immunoblotting with anti-YIPF4 (Sino Biological 202844-T46), clones lacking the relevant pr... |
33,945 | Washing a MinION flowcell | null | dx.doi.org/10.17504/protocols.io.bddzi276 | null | Kirstyn Brunker | TITLE: Washing a MinION flowcell
AUTHORS: Kirstyn Brunker
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details the steps required to wash a MInION flowcell using Oxford Nanopore's Flowcell Wash kit (EXP-WSH003). The kit contains a DNase I to digest the previous library and unblock p... | ["Place the tube of Wash Solution A on ice. Do not vortex the tube.\nSolution A contains DNase I, which is especially sensitive to physical denaturation. Mixing should only be carried out by gently inverting the tube.", "Thaw one tube of Wash Solution B at room temperature. Mix thoroughly by vortexing, spin down briefl... |
41,022 | Addressing Social Determinants of Health in Linkage-to-Care Interventions for Hepatitis C: A systematic review | 1 | dx.doi.org/10.17504/protocols.io.bka6kshe | https://www.protocols.io/view/addressing-social-determinants-of-health-in-linkag-bka6kshe | Hasheemah Afaneh , Gabrielle Gonzalez, Olivia Sugarman, Edward Trapido, Susanne Straif-Bourgeois, Evrim Oral, Ashley Wennerstrom | TITLE: Addressing Social Determinants of Health in Linkage-to-Care Interventions for Hepatitis C: A systematic review
AUTHORS: Hasheemah Afaneh , Gabrielle Gonzalez, Olivia Sugarman, Edward Trapido, Susanne Straif-Bourgeois, Evrim Oral, Ashley Wennerstrom
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-bl... | ["[Objective]\nWhat social determinants of health do Hepatitis C Linkage-to-Care interventions address?", "[Methods]\nThis section will include the methods and guidelines by which the systematic review will be conducted.", "Inclusion CriteriaA) Peer-reviewed articlesB) Published between 2010-2020C) Limited to the Unite... |
null | null | null | dx.doi.org/10.17504/protocols.io.rq5d5y6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?. | ["Dilute the mitochondrial into 0.4ug/uL with distilled water", "Add 5uL of diluted mitochondria to 73uL of distilled water and incubate for 1 minute", "Prepare buffer mix= 100uL of potassium phosphate buffer (0.5M, pH 7.5), 60uL of fatty acid free BSA (50mg/mL), 30uL of KCN (10mM), and 10uL of NADH (10mM)", "Add 20uL ... |
28,262 | Glycerol Stock | null | dx.doi.org/10.17504/protocols.io.7uehnte | null | Alba Balletbó, Sebastiaan Kuiper | TITLE: Glycerol Stock
AUTHORS: Alba Balletbó, Sebastiaan Kuiper
[STEPS]
?. Take of overnight culture and add it to a sterile Cryotube.
700 µl
?. Add of sterile solution and invert 2-3 times.
300 µl
[Glycerol]
?. Place the glycerol stock in -80ºC until needed again.
?. Grow desired culture overnight in to media.... | ["Take of overnight culture and add it to a sterile Cryotube.\n700 µl", "Add of sterile solution and invert 2-3 times.\n300 µl\n[Glycerol]", "Place the glycerol stock in -80ºC until needed again.", "Grow desired culture overnight in to media. Note: Other desired media can also be used, such as M9 minimal medi... |
null | null | null | dx.doi.org/10.17504/protocols.io.k88czzw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The intention of this protocol is to isolate high molecular weight DNA. This means you should avoid any pipetting without using a wide-bore or cut off pipette tip, vortexing, mixer shakers or anything else which generate a velocity gradient which may shear the DNA. In additio... | [] |
47,530 | WU sn-prep Protocol for Solid Tumors - snRNA protocol v2.7 | 4 | dx.doi.org/10.17504/protocols.io.261ge4w2wv47/v1 | https://www.protocols.io/view/wu-sn-prep-protocol-for-solid-tumors-snrna-protoco-bsnindce | Wagma Caravan, Reyka Jayasinghe, Nataly Naser Al Deen | TITLE: WU sn-prep Protocol for Solid Tumors - snRNA protocol v2.7
AUTHORS: Wagma Caravan, Reyka Jayasinghe, Nataly Naser Al Deen
[DESCRIPTION]
WU sn-prep Protocol for Solid Tumors -snRNA protocol v2.7
[STEPS]
SECTION: Reagents and Tools
1.
1x Lysis buffer (2mL):
10mM Tris-HCl (pH 7.4) (Thermo; 15567027), 20 uL
10... | ["[Reagents and Tools] 1x Lysis buffer (2mL):\n10mM Tris-HCl (pH 7.4) (Thermo; 15567027), 20 uL\n10mM NaCl (Thermo; AM9759), 4 uL\n3 mM MgCl2 (Thermo; AM9530G), 6 uL\nNP-40 substitute (Sigma, 74385-1L), 2 uL\n1 M DTT (Sigma, 646563), 2 uL\nNuclease Free Water (Invitrogen, AM9937), 1.966 mL", "[Reagents and Tools] Lysis... |
96,359 | HuBMAP Donor Selection Criteria for Inclusion in the UCSD TTD | 0 | dx.doi.org/10.17504/protocols.io.n92ldmomol5b/v1 | https://www.protocols.io/view/hubmap-donor-selection-criteria-for-inclusion-in-t-dacf2atn | Sheng Zhong, Wenxin Zhao, Xingzhao Wen | TITLE: HuBMAP Donor Selection Criteria for Inclusion in the UCSD TTD
AUTHORS: Sheng Zhong, Wenxin Zhao, Xingzhao Wen
[DESCRIPTION]
This document outlines the inclusion and exclusion criteria for donors of brain tissues in the Human BioMolecular Atlas Program (HuBMAP).
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.fdgbi3w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Salt solution used in preparation of minimal medium for <em>Chlamydomonas reinhardtii.</em></p>
<p> </p>
<p>Source:</p>
<p>Sueoka, N. (1960) <em>Proc. Natl. Acad. Sci. USA</em> <strong>46</strong>, 83-91.</p>
<p>http://www.chlamycollection.org/Sueoka.html</p>
[STEPS]
?.
?. ... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.q5wdy7e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>A protocol for isolation single cells from human skeletal muscle. The isolated single cells can be used for scRANseq.</p>
[STEPS] | [] |
94,076 | One-dimensional SDS-PAGE (9-18% TGX gel) | 1 | dx.doi.org/10.17504/protocols.io.5jyl8pz27g2w/v1 | https://www.protocols.io/view/one-dimensional-sds-page-9-18-tgx-gel-c744zqyw | Sigrid Verhelst | TITLE: One-dimensional SDS-PAGE (9-18% TGX gel)
AUTHORS: Sigrid Verhelst
[DESCRIPTION]
Protocol for one-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) on a 9-18% TGX gel for visualization and quantification of histone proteins.
[STEPS]
SECTION: Sample preparation
1. Dry samples (equ... | ["[Sample preparation] Dry samples (equal to 400.000 cells)", "[Sample preparation] Resuspend samples in 10µl laemmli-buffer", "[Sample preparation] Add 1µl β-mercaptoethanol to each sample", "[Sample preparation] Vortex and spin down", "[Sample preparation] Incubate for 7 minutes at 95°C in a thermoshaker", "[Sample p... |
null | null | null | dx.doi.org/10.17504/protocols.io.dez3f5 | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<strong>Zobell plates (1 L)</strong><br />15 g sea salts<br />1 g yeast extract<br />5 g peptone<br />fill to 1 L qH<sub>2</sub>O<br />14 g agar<br /><br /><strong>MLB (1 L)</strong><br />15 g sea salts<br />0.5 g yeast extract<br />0.5 g peptone<br />0.5 g casamino acids<br />3 ... | [] |
52,462 | FindingNemo Extraction 1: Phenol-based Method | 1 | dx.doi.org/10.17504/protocols.io.bxgnpjve | https://www.protocols.io/view/findingnemo-extraction-1-phenol-based-method-bxgnpjve | Inswasti Cahyani, John Tyson, Nadine Holmes, Josh Quick, Nicholas Loman, Matthew Loose | TITLE: FindingNemo Extraction 1: Phenol-based Method
AUTHORS: Inswasti Cahyani, John Tyson, Nadine Holmes, Josh Quick, Nicholas Loman, Matthew Loose
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a sub-protocol designed to extract/isolate ultra-high molecular weight (UHMW) DNA to obtain ult... | ["[UHMW DNA Extraction]\nThis protocol is a scaled-down and modified version of the “Ultra-long read sequencing protocol for RAD004 V.3” by Josh Quick (https://dx.doi.org/10.17504/protocols.io.mrxc57n).\nElution volume is adjusted for downstream application of preparing ultra-long DNA library following the new ONT prot... |
56,689 | Bogus Data Acquisition Protocol III | 1 | null | https://www.protocols.io/view/bogus-data-acquisition-protocol-iii-b3krqkv6 | Abby Moore | TITLE: Bogus Data Acquisition Protocol III
AUTHORS: Abby Moore
[DESCRIPTION]
The purpose of this protocol is to demo protocol development.
[BEFORE_START]
Know before you start.
[GUIDELINES]
My guidelines.
[STEPS]
2. I'll display an image using embed code retrieved from Box.
3. I'll show a command usi... | ["I'll display an image using embed code retrieved from Box.", "I'll show a command using the Command component:", "Bogus Data Acquisition Protocol IBefore starting, you need to run a test using the following protocol. I referred to this protocol using a hyperlink: Bogus Data Acquisition Protocol I."] |
56,096 | USDA-ARS potato genetics lab drone data collection protocol | 1 | null | https://www.protocols.io/view/usda-ars-potato-genetics-lab-drone-data-collection-b2z8qf9w | Max J Feldman | TITLE: USDA-ARS potato genetics lab drone data collection protocol
AUTHORS: Max J Feldman
[DESCRIPTION]
This protocol describes the steps performed to collect multispectral data from field experiments using a small unmanned aerial system (sUAS). Our group uses a MicaSense 10-band multispectral camera system (MicaSense... | ["[Before flying] Upon arriving at the field site, place the ground control point (GCP) indicators in their proper location. Generally, four ground control points are placed around the perimeter of the target field. We use a set of two flags (each a different color) to denote the location GCPs should be placed at.", "[... |
28,096 | Nucleofector Protocol for Dinoflagellates using Lonza’s 4D-Nucleofector X Unit | null | dx.doi.org/10.17504/protocols.io.7n8hmhw | null | Senjie Lin, Huan Zhang, Brittany Sprecher | TITLE: Nucleofector Protocol for Dinoflagellates using Lonza’s 4D-Nucleofector X Unit
AUTHORS: Senjie Lin, Huan Zhang, Brittany Sprecher
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is intended to work for many dinoflagellates but focusses on the method used to successfully tr... | ["Harvest dinoflagellate cells using centrifugation. Determine the lowest centrifuge speed and shortest time at which you can achieve both a good pellet with minimal damage to your species. Karlodinium veneficum CCMP1975 should be cultured as reported (Zhang et al. 2008) and spun at 1500 g for 2 minutes in 1.5mL tubes.... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.