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 |
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51,928 | Modular automated bottom-up proteomic sample preparation for high-throughput applications | 2 | dx.doi.org/10.17504/protocols.io.bwxypfpw | https://www.protocols.io/view/modular-automated-bottom-up-proteomic-sample-prepa-bwxypfpw | Yan Chen, Nurgul Kaplan Lease, Jennifer Gin, Tad Ogorzalek, Paul D. Adams, Nathan Hillson, Christopher J Petzold | TITLE: Modular automated bottom-up proteomic sample preparation for high-throughput applications
AUTHORS: Yan Chen, Nurgul Kaplan Lease, Jennifer Gin, Tad Ogorzalek, Paul D. Adams, Nathan Hillson, Christopher J Petzold
[DESCRIPTION]
Manual proteomic sample preparation methods limit sample throughput and often lea... | [] |
99,036 | Combined RNAscope and immunohistochemistry labeling of fresh mouse midbrain tissue | 0 | dx.doi.org/10.17504/protocols.io.yxmvmek85g3p/v1 | https://www.protocols.io/view/combined-rnascope-and-immunohistochemistry-labelin-dcx42xqw | William S Conrad | TITLE: Combined RNAscope and immunohistochemistry labeling of fresh mouse midbrain tissue
AUTHORS: William S Conrad
[DESCRIPTION]
Here we describe labeling coronal sections of mouse substantia nigra (SNc) and ventral tegmental area
(VTA) for the gene Slc17a6 (VGLUT2) and virally-expressed histone-tagged GFP.
[BEFORE_... | ["[RNAscope assay] Turn on HybEZ™ Oven (ACD) and set to 40°C.", "[RNAscope assay] Warm probe in heat-bath for 10 minutes at 40°C, then cool to RT.", "[RNAscope assay] Drop C1 probe into autoclaved Eppendorf tube. Prepare about 150 µL per slide, assuming each slide contains 4 coronal mouse sections.", "[RNAscope assay] ... |
51,052 | Auger/Auspice/UShER: SARS-CoV-2 Cluster Detection Workflow for the Terra Platform | 5 | dx.doi.org/10.17504/protocols.io.bv4kn8uw | https://www.protocols.io/view/auger-auspice-usher-sars-cov-2-cluster-detection-w-bv4kn8uw | Anusha Ginni, Jill Hagey | TITLE: Auger/Auspice/UShER: SARS-CoV-2 Cluster Detection Workflow for the Terra Platform
AUTHORS: Anusha Ginni, Jill Hagey
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The Titan_Augur workflows was written to process concatenated assembly fasta data for SARS-CoV-2 Phylogenetics analysis and clus... | ["[Setup Terra and Google Cloud Accounts]\nThe Terra platform registration requires a Google account. If you have a Google account you can sign in using the Terra login page: https://app.terra.bio/ If you do not have Google email you can set up a Google account with a non-Google email. The steps to do this are describ... |
93,635 | Preparation of Cells for Volume Electron Microscopy using Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) | 4 | dx.doi.org/10.17504/protocols.io.n92ldmeq7l5b/v1 | https://www.protocols.io/view/preparation-of-cells-for-volume-electron-microscop-c7pbzmin | Jillian C Danne, Rachel Templin, Gediminas Gervinskas, Denis Korneev, Sergey Gorelick, Georg Ramm | TITLE: Preparation of Cells for Volume Electron Microscopy using Focused Ion Beam Scanning Electron Microscopy (FIB-SEM)
AUTHORS: Jillian C Danne, Rachel Templin, Gediminas Gervinskas, Denis Korneev, Sergey Gorelick, Georg Ramm
[DESCRIPTION]
Volume Electron Microscopy (vEM) allows for the three-dimensional imaging of ... | ["[Fixation] All fixation and processing steps must be performed in a fume hood wearing appropriate personal protective equipment (PPE). The Material Safety Data Sheet (MSDS) for each chemical must be read before commencing.\n\nAdherent cells grown in a well-plate or petri dish must be submerged in solution at all time... |
88,561 | Ultra-high resolution imaging of the cat spinal cord | 1 | dx.doi.org/10.17504/protocols.io.dm6gp3d68vzp/v1 | https://www.protocols.io/view/ultra-high-resolution-imaging-of-the-cat-spinal-co-c2qrydv6 | Lucy Liang, Elvira Pirondini, T Kevin Hitchens | TITLE: Ultra-high resolution imaging of the cat spinal cord
AUTHORS: Lucy Liang, Elvira Pirondini, T Kevin Hitchens
[DESCRIPTION]
Detailed description of steps to extract and prepared tissue samples to acquire ultra-high resolution images of the cat spinal cord.
[STEPS]
SECTION: Sample Preparation
1. Place the cat ... | ["[Sample Preparation] Place the cat specimen in a prone position and identify the desired spinal segments by counting the spinous processes.", "[Imaging Protocol] Perform high-resolution CT imaging (50-100 um resolution) on the sample to obtain good images of the vertebral column.", "[Imaging Protocol] Place the glass... |
76,391 | Museum DNA extraction | 4 | null | https://www.protocols.io/view/museum-dna-extraction-cnufvetn | Andie C Hall, Ben Price | TITLE: Museum DNA extraction
AUTHORS: Andie C Hall, Ben Price
[DESCRIPTION]
Modified from Korlevic et al 2021& Rohland et al 2018 for high throughput DNA extraction from historical specimens in natural history collections. Please cite these papers when using this method.
An in depth SOP by Korlevic can be found here:... | ["[buffer preparation] Lysis buffer C\n200mM Tris pH8, 25mM EDTA pH8, 0.05% Tween 20, 0.4mg/ml PK\n\nTo make 10 mL mix together: 7295 µL molecular grade water, 2000 µL 1M Tris pH8, \n500 µL 0.5M EDTA (pH 8), 200 µL Proteinase K (20mg/ml), and 5 µL Tween 20.\n\nThis is sufficient for 1 extraction plate of 95 samples and... |
88,169 | Purification of MBP-NAP1 | 4 | dx.doi.org/10.17504/protocols.io.ewov1q2ykgr2/v1 | https://www.protocols.io/view/purification-of-mbp-nap1-c2chyat6 | Elias Adriaenssens | TITLE: Purification of MBP-NAP1
AUTHORS: Elias Adriaenssens
[DESCRIPTION]
This protocol describes purification of MBP-TEV-NAP1 protein.
[STEPS]
SECTION: Purification of MBP-NAP1
1. To purify MBP-NAP1, gene-synthesize human NAP1 cDNA (by Genscript) and subclone into a pGEX-4T1 vector with an N-terminal MBP-tag. Follow... | ["[Purification of MBP-NAP1] To purify MBP-NAP1, gene-synthesize human NAP1 cDNA (by Genscript) and subclone into a pGEX-4T1 vector with an N-terminal MBP-tag. Follow it by a TEV cleavage site before wild-type NAP1 (RRID:Addgene_208871), NAP1 delta-NDP52 (S37K/A44E) (RRID:Addgene_208872), or NAP1 delta-TBK1 (L226Q/L233... |
55,928 | NCBI submission protocol for SARS-CoV-2 wastewater data: SRA, BioSample, and BioProject | 1 | dx.doi.org/10.17504/protocols.io.b2uyqexw | https://www.protocols.io/view/ncbi-submission-protocol-for-sars-cov-2-wastewater-b2uyqexw | Ruth Timme, Maria Balkey | TITLE: NCBI submission protocol for SARS-CoV-2 wastewater data: SRA, BioSample, and BioProject
AUTHORS: Ruth Timme, Maria Balkey
[DESCRIPTION]
PURPOSE:
This method was developed at the FDA’s Center for Food Safety and Applied Nutrition for GenomeTrakr’s pandemic response project, monitoring SARS-CoV-2 variants in ... | ["["Ingredients" to have in place before starting your submissions] Set up a new NCBI submission environment for your lab\n1.1: Create an NCBI user account\n1.2: Set up an NCBI submission user group for your lab\n1.4: Bookmark the link to your Submission Portal\n1.5. Identify or establish new BioProjects (det... |
81,665 | Retro-orbital injection of AAV in mice | 1 | dx.doi.org/10.17504/protocols.io.3byl4joy8lo5/v1 | https://www.protocols.io/view/retro-orbital-injection-of-aav-in-mice-cty9wpz6 | Miguel Chuapoco | TITLE: Retro-orbital injection of AAV in mice
AUTHORS: Miguel Chuapoco
[DESCRIPTION]
This protocol is following:
[GUIDELINES]
Please adhere to your institue IACUC guidelines of animal care.
[STEPS]
SECTION: Injection
1. Prepare either virus dilution with PBS prepare. Injection is up to 100 μL per mouse.
S... | ["[Injection] Prepare either virus dilution with PBS prepare. Injection is up to 100 μL per mouse.", "[Injection] Take one mouse from the cage into an induction chamber and start isoflurane at 3% with flow rate of ~1L/min", "[Injection] After the mouse has slow breathing (~1/s) move the mouse to a nose cone delivery of... |
76,001 | Plate Streaking | 1 | dx.doi.org/10.17504/protocols.io.dm6gpjw1jgzp/v2 | https://www.protocols.io/view/plate-streaking-cnf9vbr6 | Carlos Carlos Goller, Carly Sjogren | TITLE: Plate Streaking
AUTHORS: Carlos Carlos Goller, Carly Sjogren
[DESCRIPTION]
Overview and Goals
Streaking bacteria on agar plates allows scientists to obtain isolated colonies of bacteria. An isolated colony provides up to 10^8 bacteria cells that are genetically identical. This is why we call them clones or refe... | ["[Procedure for plate streaking] Obtain a fresh petri dish containing TSA media.", "[Procedure for plate streaking] Label the bottom of the plate (the side containing TSA media) keeping to the circumference (write on the edge, not in the center) with your bacterial isolate#, your Team#, your initials and today's date... |
null | null | null | dx.doi.org/10.17504/protocols.io.es2bege | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
For use in <a href="https://www.protocols.io/view/CviRI-Purification-From-XZ-6E-Virus-Infected-NC64A-er4bd8w" target="_blank">CviRI Purification From XZ-6E Virus Infected NC64A Chlorella</a>.
[STEPS]
?.
?.
?.
?. | [] |
87,796 | Synthesis of 1-(3-Chlorophenethyl)-3-cyclopentylpyrimidine-2,4,6-(1H,3H,5H)-trione | 6 | dx.doi.org/10.17504/protocols.io.bp2l6xd71lqe/v1 | https://www.protocols.io/view/synthesis-of-1-3-chlorophenethyl-3-cyclopentylpyri-czyux7ww | Carole JR Bataille, Katherine Brimblecombe, Stephanie J Cragg | TITLE: Synthesis of 1-(3-Chlorophenethyl)-3-cyclopentylpyrimidine-2,4,6-(1H,3H,5H)-trione
AUTHORS: Carole JR Bataille, Katherine Brimblecombe, Stephanie J Cragg
[DESCRIPTION]
1-(3-chlorophenethyl)-3-cyclopentylpyrimidine-2,4,6-(1H,3H,5H)-trione (8), is a potent and highly selective Ca(V)1.3 L-type calcium channel anta... | ["[Synthesis of 1-(3-Chlorophenethyl)-3-cyclopentylpyrimidine-2,4,6-(1H,3H,5H)-trione] Add 357 µL 2-(3-chlorophenyl)ethylamine (2.58 mmol, 1.0 eq.) to a solution of 290 mg of Cyclopentaneisocyanate (2.58 mmol, 1.0 eq.) in 10 mL of CH2Cl2.", "[Synthesis of 1-(3-Chlorophenethyl)-3-cyclopentylpyrimidine-2,4,6-(1H,3H,5H)-t... |
25,084 | RNA Isolation from Plant Tissue Protocol 2: McKenzie et al’s Qiagen hybrid method | null | dx.doi.org/10.17504/protocols.io.4q4gvyw | null | Donald J. MacKenzie, Morven A. McLean, Srima Mukerji, Margaret Green | TITLE: RNA Isolation from Plant Tissue Protocol 2: McKenzie et al’s Qiagen hybrid method
AUTHORS: Donald J. MacKenzie, Morven A. McLean, Srima Mukerji, Margaret Green
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Implemented by: Jim Leebens-Mack and Charlotte Carrigan</div><div class = "text-block... | ["Grind sample (up to ) in liquid nitrogen to a fine powder using a mortar and pestle.\n50 mg\nIncomplete grinding of the starting material will lead to reduced RNA yields.", "Add lysis buffer to a maximum of of tissue powder. Vortex vigorously.\n600 µl\n50 mg", "Add of 20% sarkosyl.\n60 µl\nFor samples with a high ... |
28,361 | MojoSort™ Mouse anti-APC Nanobeads Protocol | null | dx.doi.org/10.17504/protocols.io.7xhhpj6 | null | Sam Li | TITLE: MojoSort™ Mouse anti-APC Nanobeads Protocol
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Product description and procedure summary:</span><span> Target cells are positively selected or depleted by incubating the sample with an anti-human AP... | ["Prepare cells from your tissue of interest or blood without lysing erythrocytes.", "In the final wash of your sample preparation, resuspend the cells in MojoSort™ Buffer by adding up to 4 mL in a 5 mL (12 x 75 mm) polypropylene tube.Note: Keep MojoSort™ Buffer on ice throughout the procedure.", "Filter the cells with... |
null | null | null | dx.doi.org/10.17504/protocols.io.g9gbz3w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Centrifuge is a classification software used on whole genome shotgun (WGS) reads. It uses a reference database to determine what organisms are found in your sample. This protocol will show you how to access the data on CyVerse and walk you through some questions to help in th... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.mapc2dn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?. | [] |
29,303 | Plasmid: NK644 (pAct-mCherryCCTLL) | null | dx.doi.org/10.17504/protocols.io.8uxhwxn | null | David Booth, Nicole King, Heather Middleton | TITLE: Plasmid: NK644 (pAct-mCherryCCTLL)
AUTHORS: David Booth, Nicole King, Heather Middleton
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The attached file is the full sequence for a plasmid that uses gene regulatory elements from </span><span style = "font-style:italic;">S. rosetta </spa... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.h8ub9ww | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?. | [] |
97,109 | USDA LTAR Common Experiment measurement: Infiltration and percolation | 1 | dx.doi.org/10.17504/protocols.io.81wgbzd9ygpk/v1 | https://www.protocols.io/view/usda-ltar-common-experiment-measurement-infiltrati-da3v2gn6 | Amartya Saha | TITLE: USDA LTAR Common Experiment measurement: Infiltration and percolation
AUTHORS: Amartya Saha
[DESCRIPTION]
Infiltration refers to water entering the soil from precipitation, condensation, irrigation, and surface flow (runoff). It is typically used to quantify water arriving at the root zone of plants (example ap... | ["[Data collection] Measurement.\nThe amount of water collected is measured over a particular time interval of collection.", "[Data collection] Perform sampling periodically or follow an intense rain event (typically 2-3 cm of rainfall).", "[Data collection] Site Maintenance. \nLysimeters are typically installed underg... |
22,980 | iGEM Calibration Protocol - Flow Cytometry Fluorescence | null | dx.doi.org/10.17504/protocols.io.2pcgdiw | null | Jacob Beal, Cheryl Telmer, Richard Tennant, Paul Rutten | TITLE: iGEM Calibration Protocol - Flow Cytometry Fluorescence
AUTHORS: Jacob Beal, Cheryl Telmer, Richard Tennant, Paul Rutten
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol can be applied to any strain of cell that can be safely run through a flow cytometer. For clarity, we have wri... | ["[Acquisition of Data]\nPrepare and culture experimental samples, negative process control, and positive process control according to your desired experimental procedure.", "[Acquisition of Data]\nPrepare experimental samples, negative process control, and positive process control as needed for running through your fl... |
45,952 | Gibson protocol from RJ communications | 4 | null | https://www.protocols.io/view/gibson-protocol-from-rj-communications-bq48myzw | Elizabeth Fozo | TITLE: Gibson protocol from RJ communications
AUTHORS: Elizabeth Fozo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Gibson protocol </div></div>
[STEPS]
?. [Protocol from RJ and SH]
Perform vector and insert amplification using Q5 PCR
?. [Protocol from RJ and SH]
Determine which reactions had suc... | ["[Protocol from RJ and SH]\nPerform vector and insert amplification using Q5 PCR", "[Protocol from RJ and SH]\nDetermine which reactions had successful amplification via agarose gel electrophoresis, use the reaction with a strong/bright band and the lowest amount of starting template for the following steps.", "[Proto... |
44,734 | Analyzing SARS-CoV-2 Spike Protein Expression in E. coli | 1 | null | https://www.protocols.io/view/analyzing-sars-cov-2-spike-protein-expression-in-e-bpw6mphe | Harley King | TITLE: Analyzing SARS-CoV-2 Spike Protein Expression in E. coli
AUTHORS: Harley King
[STEPS]
?. Discuss preparation and expression of spike-SUMO fusion protein in E. coli.
?. Use Benchling to calculate sizes of spike-SUMO and RBD-SUMO.
?. Are the proteins from Step 2 seen on Coomassie stain of SDS-PAGE? | ["Discuss preparation and expression of spike-SUMO fusion protein in E. coli.", "Use Benchling to calculate sizes of spike-SUMO and RBD-SUMO.", "Are the proteins from Step 2 seen on Coomassie stain of SDS-PAGE?"] |
40,238 | Purification of PBMCs | 4 | dx.doi.org/10.17504/protocols.io.bjinkkde | https://www.protocols.io/view/purification-of-pbmcs-bjinkkde | Roser Vento-Tormo | TITLE: Purification of PBMCs
AUTHORS: Roser Vento-Tormo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details the steps and methods of PBMC purification</div></div>
[STEPS]
?. [Ficoll Density Gradient Centrifugation]
Bring Ficoll to .
0 Room temperature
?. [Ficoll Density Gradient C... | ["[Ficoll Density Gradient Centrifugation]\nBring Ficoll to .\n0 Room temperature", "[Ficoll Density Gradient Centrifugation]\nClean the blood tubes with 70% ethanol and transfer the blood to a 50mL tube in a BSL2 hood.", "[Ficoll Density Gradient Centrifugation]\nDilute blood 1:1 in PBS and mix carefully.", "[Ficoll D... |
83,294 | Size selection (Purification) | 1 | dx.doi.org/10.17504/protocols.io.x54v9pezzg3e/v1 | https://www.protocols.click/view/size-selection-purification-cvj6w4re | Tsu-Chun Hung, Yin-Tse Huang | TITLE: Size selection (Purification)
AUTHORS: Tsu-Chun Hung, Yin-Tse Huang
[DESCRIPTION]
Size selection (Purification)
[STEPS]
1. Calculate the amount of magnetic beads you need and DISTRIBUTE in a new 1.5 mL eppendorf tube (Mix the bottle VIGOROUSLY to make sure it's homogeneous).
For example, if you have 5 samples... | ["Calculate the amount of magnetic beads you need and DISTRIBUTE in a new 1.5 mL eppendorf tube (Mix the bottle VIGOROUSLY to make sure it's homogeneous).\n\nFor example, if you have 5 samples to clean up, distribute 49.5 μl in a new 1.5 mL eppendorf tube.\n SampleMagnetic beads needMagnetic beads need *1.119 μl9.9 μ... |
90,575 | Protocol to isolate and fix nuclei from flash frozen mouse heart for IGVF | 4 | null | https://www.protocols.io/view/protocol-to-isolate-and-fix-nuclei-from-flash-froz-c4ppyvmn | Elisabeth Rebboah | TITLE: Protocol to isolate and fix nuclei from flash frozen mouse heart for IGVF
AUTHORS: Elisabeth Rebboah
[DESCRIPTION]
This protocol describes isolation of nuclei from 10 week old mouse heart (tissue ID: 06) from 8 founder strains (B6J, AJ, 129S1J, NZOJ, WSBJ, NODJ, PWKJ, and CASTJ), preparation of a single nucleus... | ["[Setup] Coat SHARE-seq nuclei prep tubes with BSA. Fill 8 1.5 ml tubes with 1.5 ml 1% BSA in H2O and incubate for 30 minutes. After incubation, aspirate BSA solution and dry for 30 minutes. Store at 4C.", "[Setup] Label tubes.", "[Setup] Pre-chill centrifuge to 4C.", "[Setup] Prepare ice buckets.", "[Setup] Prepare 4... |
51,830 | SPARC_Duke_Grill_OT2-OD025340_VagusNerve_IHC_TH | 1 | dx.doi.org/10.17504/protocols.io.bwuwpexe | https://www.protocols.io/view/sparc-duke-grill-ot2-od025340-vagusnerve-ihc-th-bwuwpexe | J. Ashley Ezzell, Nicole A. Pelot, Kara A. Clissold, Warren M. Grill | TITLE: SPARC_Duke_Grill_OT2-OD025340_VagusNerve_IHC_TH
AUTHORS: J. Ashley Ezzell, Nicole A. Pelot, Kara A. Clissold, Warren M. Grill
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The protocol describes immunohistochemistry with anti-tyrosine hydroxylase, as it has been applied to cervical and abdo... | ["[Immunohistochemistry]\nBake slides with sections of paraffin-embedded vagus nerve overnight at 50oC and then cool overnight.", "[Immunohistochemistry]\nDeparaffinize the slides and hydrate them to distilled water: xylene (2x 6 min), 100% ethanol (5 min), 95% ethanol (4 min), 70% ethanol (3 min), deionized water (2x ... |
37,287 | Simple Banana Bread Recipe | null | null | https://www.protocols.io/view/simple-banana-bread-recipe-bgnfjvbn | Anita Bröllochs | TITLE: Simple Banana Bread Recipe
AUTHORS: Anita Bröllochs
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a simple 6-ingredients vegan banana bread recipe. </div></div>
[STEPS]
?. [Pre-heating oven]
Preheat the oven to .
350 °F
?. [Making the batter]
Add and into a medium-sized bowl.
[fl... | ["[Pre-heating oven]\nPreheat the oven to .\n350 °F", "[Making the batter]\nAdd and into a medium-sized bowl.\n[flour]\n[baking powder]", "[Making the batter]\nMix the dry ingredients well.", "[Making the batter]\nMash the bananas with a fork.", "[Making the batter]\nTransfer the mashed banana into another medium-siz... |
43,568 | Notebook-INTRO_BIO-INFORMATICS_1_Using sequences | 3 | null | https://www.protocols.io/view/notebook-intro-bio-informatics-1-using-sequences-bnsqmedw | , | TITLE: Notebook-INTRO_BIO-INFORMATICS_1_Using sequences
AUTHORS: ,
[STEPS] | [] |
103,176 | Protein interaction modeling | 0 | dx.doi.org/10.17504/protocols.io.5jyl8215rl2w/v1 | https://www.protocols.io/view/protein-interaction-modeling-dgzg3x3w | Shiyi Wang | TITLE: Protein interaction modeling
AUTHORS: Shiyi Wang
[DESCRIPTION]
Protein interaction modeling using Alphafold 2.0 Multimer
[STEPS]
1. **Structure Prediction in AlphaFold 2.0 Multimer** - Use full-length mouse Ezrin (UniProt ID: Q4KML7) and Atg7 (UniProt ID: Q9D906) for structure prediction. - Predict the structu... | ["**Structure Prediction in AlphaFold 2.0 Multimer** - Use full-length mouse Ezrin (UniProt ID: Q4KML7) and Atg7 (UniProt ID: Q9D906) for structure prediction. - Predict the structure of Ezrin in the open conformation: - Independently predict Ezrin N- and C-termini. - Thread them onto an open ERM hinge structure using ... |
67,835 | BASIC PROTOCOL 4: Pan-genome Copy Number Variant Calling | 5 | dx.doi.org/10.17504/protocols.io.n92ldzke7v5b/v1 | https://www.protocols.io/view/basic-protocol-4-pan-genome-copy-number-variant-ca-ceg3tbyn | miriam.goldman , chunyu.zhao | TITLE: BASIC PROTOCOL 4: Pan-genome Copy Number Variant Calling
AUTHORS: miriam.goldman , chunyu.zhao
[DESCRIPTION]
This protocol describes the CNV module of MIDAS2, which takes as input metagenomic sequencing reads from a set of samples and generates files with CNV genotypes for each sample for all detected specie... | ["Perform species prescreening as described in Basic Protocol 1.", "Download MIDASDB as described in Basic Protocol 2.", "Execute the run_genes command for each sample", "Prepare sample manifest file for merging purpose. We can use the same list_of_samples.tsv generated by step 6 in Basic Protocol 1.", "Upon the comple... |
51,869 | SARS-CoV-2 DNA library preparation using an adapted version of Illumina DNA prep protocol v.1.1 | 4 | dx.doi.org/10.17504/protocols.io.bwv5pe86 | https://www.protocols.io/view/sars-cov-2-dna-library-preparation-using-an-adapte-bwv5pe86 | Emmanuel Kagning Tsinda, Masahiro Sakamoto, Michiko Okamoto, Clyde Dapat, Mariko Saito, Mayuko Saito, Hitoshi Oshitani | TITLE: SARS-CoV-2 DNA library preparation using an adapted version of Illumina DNA prep protocol v.1.1
AUTHORS: Emmanuel Kagning Tsinda, Masahiro Sakamoto, Michiko Okamoto, Clyde Dapat, Mariko Saito, Mayuko Saito, Hitoshi Oshitani
[DESCRIPTION]
This protocol describes the steps to prepare DNA libraries from PCR ampl... | ["[Overview of the library prep workflow] Please make sure you review and understand this library preparation workflow.", "[DNA tagmentation] This step uses the Nextera Transposome to tagment genomic DNA. Tagmentation is a process that fragments DNA and then tags the fragmented DNA with adapter sequences in a single r... |
70,841 | BIND&MODIFY: Long-range single-molecule mapping of chromatin modification in eukaryotes. V.2 | 4 | dx.doi.org/10.17504/protocols.io.3byl4j7m8lo5/v1 | https://www.protocols.io/view/bind-amp-modify-long-range-single-molecule-mapping-chezt3f6 | Zhe Weng, Fengying Ruan, Weitian Chen, Zhichao Chen, Yeming Xie, Meng Luo, Chen Zhang, Zhe Xie, Chen Tan, Juan Wang, Yuxin Sun, Yitong Fang, Mei Guo, Hongqi Wang, Chong Tang | TITLE: BIND&MODIFY: Long-range single-molecule mapping of chromatin modification in eukaryotes. V.2
AUTHORS: Zhe Weng, Fengying Ruan, Weitian Chen, Zhichao Chen, Yeming Xie, Meng Luo, Chen Zhang, Zhe Xie, Chen Tan, Juan Wang, Yuxin Sun, Yitong Fang, Mei Guo, Hongqi Wang, Chong Tang
[DESCRIPTION]
Here we describe a... | ["[OVERVIEW] This protocol describes step-by-step guidelines for BIND&MODIFY method.\n\nProtocol v2. \n\nBIND&MODIFY method is based on the indirect labelling of DNA regions bound to the protein of interest (with antibody) using an engineered recombinant fusion protein, protein A-M.EcoGII (pA-M.EcoGII), whose methyltra... |
82,920 | Sample vitrification and cryo-EM data acquisition | 4 | dx.doi.org/10.17504/protocols.io.kqdg39rreg25/v1 | https://www.protocols.io/view/sample-vitrification-and-cryo-em-data-acquisition-cu8gwztw | Minghao Chen | TITLE: Sample vitrification and cryo-EM data acquisition
AUTHORS: Minghao Chen
[DESCRIPTION]
Sample vitrification and cryo-EM data acquisition
[STEPS]
SECTION: Sample vitrification
1. Glow-discharge the grids at 25 mA for 30 sec with PELCO easiGlow system (Ted Pella)
SECTION: Sample vitrification
2. Apply 3 μl of pr... | ["[Sample vitrification] Glow-discharge the grids at 25 mA for 30 sec with PELCO easiGlow system (Ted Pella)", "[Sample vitrification] Apply 3 μl of protein solution to the grid:\nQUANTIFOIL R1.2/1.3 mesh 300 (Electron Microscopy Sciences), or\nQUANTIFOIL R2/1 mesh 300 (Electron Microscopy Sciences)", "[Sample vitrific... |
62,852 | Mosquito vector surveillance, processing and storage | 1 | dx.doi.org/10.17504/protocols.io.eq2lyn13qvx9/v2 | https://www.protocols.io/view/mosquito-vector-surveillance-processing-and-storag-b9mcr42w | Tanya L Russell, Kyran Staunton, Thomas Burkot, Amanda Murphy | TITLE: Mosquito vector surveillance, processing and storage
AUTHORS: Tanya L Russell, Kyran Staunton, Thomas Burkot, Amanda Murphy
[DESCRIPTION]
The purpose of this Standard Operating Procedure (SOP) is to outline processes for the surveillance, processing and storage of mosquito samples in the field.
A detailed... | ["[Overview of surveillance procedures] Preparation for vector surveillance activities\n· Develop vector surveillance work plan, with required standard operating protocols.\n· Secure the require funding.\n· Gain required research or ethical approvals.\n· Perform a stock-take and then order required equipment and consum... |
76,515 | STLFR library construction for snake genomes | 4 | dx.doi.org/10.17504/protocols.io.n2bvj8z4xgk5/v1 | https://www.protocols.io/view/stlfr-library-construction-for-snake-genomes-cnybvfsn | Boyang Liu, Liangyu Cui, Zhangwen Deng, Yue Ma, Diancheng Yang, Yanan Gong, Yanchun Xu, Shuhui Yang, Song Huang | TITLE: STLFR library construction for snake genomes
AUTHORS: Boyang Liu, Liangyu Cui, Zhangwen Deng, Yue Ma, Diancheng Yang, Yanan Gong, Yanchun Xu, Shuhui Yang, Song Huang
[DESCRIPTION]
This protocol is used to clarify the process of stLFR library preparation for the sequencing of high-quality snake genomes.
[STEPS]... | ["Sample preparation\nRemove the long-fragment gDNA from 4 °C and store on ice.", "Transposon Insertion", "Transfer 10 ng long-fragment gDNA gently into a 0.2ml PCR tube. Without mixing, add Nuclease Free Water to a total volume of 36.8 µL. Collect and dispense long fragment DNA slowly (the process should take >10 s) e... |
null | null | null | dx.doi.org/10.17504/protocols.io.kbacsie | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Obesity can be induced by exposing mice to a western-type diet high in sugar and fat for 15 weeks. Control animals receive a standard fat diet for 15 weeks.</p>
[GUIDELINES]
<p><span lang="EN-US" style="margin: 0px; line-height: 107%; font-family: 'Calibri',sans-serif; font-... | [] |
17,658 | Fluorescence-based Thermal Shift Assay (TSA) | null | dx.doi.org/10.17504/protocols.io.vg2e3ye | null | PALOMA VARELA | TITLE: Fluorescence-based Thermal Shift Assay (TSA)
AUTHORS: PALOMA VARELA
[STEPS] | [] |
97,347 | Proteolytic Peptides from Conditioned Media Desalting with C18 Hydrophilic–Lipophilic Balance (HLB) Cartridges | 4 | dx.doi.org/10.17504/protocols.io.eq2lywdzpvx9/v1 | https://www.protocols.io/view/proteolytic-peptides-from-conditioned-media-desalt-dbbb2iin | Joanna Bons, J P Rose, M A Watson, B Schilling | TITLE: Proteolytic Peptides from Conditioned Media Desalting with C18 Hydrophilic–Lipophilic Balance (HLB) Cartridges
AUTHORS: Joanna Bons, J P Rose, M A Watson, B Schilling
[DESCRIPTION]
Desalting of proteolytic peptides from conditioned media elution using C18 Hydrophilic–Lipophilic Balance (HLB) Cartridges in pre... | ["Centrifuge the samples at 1,850 x g for 5 minutes at room temperature to pellet insoluble material.", "Desalt the samples using Oasis HLB solid-phase extraction cartridges placed on top of a vacuum manifold as follows:", "Condition each cartridge two times with 800 µL of the condition buffer (50% ACN, 0.2% FA).", "Eq... |
29,341 | TotalSeq™-B or -C with 10x Feature Barcoding Technology | null | dx.doi.org/10.17504/protocols.io.8v5hw86 | null | Sam Li | TITLE: TotalSeq™-B or -C with 10x Feature Barcoding Technology
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Buyer is solely responsible for determining whether Buyer has all intellectual property rights that are necessary for Buyer's intended uses of the BioLegend TotalSeq™ produc... | ["[I) Sample and Solutions Preparation]\nPrepare single cell suspension following a suitable protocolPrepare Dextran Sulfate solution: 1% w/v (10 mg/ml) Dextran Sulfate Sodium Salt in Nuclease-free Water", "[II) Cell labeling for 10x Genomics platforms]\nCarefully count all cells to ensure accurate quantitation.Make no... |
76,386 | Non-guided neural organoids differentiation | 4 | dx.doi.org/10.17504/protocols.io.e6nvwjo27lmk/v1 | https://www.protocols.io/view/non-guided-neural-organoids-differentiation-cnuavese | anita.adami | TITLE: Non-guided neural organoids differentiation
AUTHORS: anita.adami
[DESCRIPTION]
This protocol describes how to perform non-guided neural organoid differentiation
[STEPS]
SECTION: hiPSCs lines (LINC01876 KD)
1. To generate the human cerebral-like organoids we followed the protocol detailed in Johansson et al., 2... | ["[hiPSCs lines (LINC01876 KD)] To generate the human cerebral-like organoids we followed the protocol detailed in Johansson et al., 2022, based on the protocol published by Lancaster et al., 2013. \n\nWe used three hIPSC6-derived lines obtained by transduction and FACS sorting as described in detail in the protocol CR... |
20,070 | U Mass - Chronic drug delivery | null | dx.doi.org/10.17504/protocols.io.xuefnte | null | Jason Kim | TITLE: U Mass - Chronic drug delivery
AUTHORS: Jason Kim
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">A subcutaneous or intraperitoneal implantation of Alzet osmotic pump is used to chronically administer selected d... | ["Anesthetize mice with an intraperitoneal injection of ketamine (100 mg/kg body weight) and xylazine (10 mg/kg body weight).", "Shave hair at the incision site on the back.", "Make an incision (~0.5 cm) using sterilized scalpel between the scapulae.", "Subcutaneously insert an Alzet mouse osmotic pump containing drug ... |
null | null | null | dx.doi.org/10.17504/protocols.io.e3zbgp6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.gzqbx5w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Simple assay to see the effect of microcystin on yeast catalase activity. Important note is to handle solutions containing microcystin only with glassware (no plastic pipettes, microcystin sticks to plastic).</p>
[STEPS]
?.
?.
?.
?.
?. | [] |
90,730 | Rab7 Phosphorylation reaction | 4 | dx.doi.org/10.17504/protocols.io.261ged92wv47/v1 | https://www.protocols.io/view/rab7-phosphorylation-reaction-c4uiywue | Dan Tudorica | TITLE: Rab7 Phosphorylation reaction
AUTHORS: Dan Tudorica
[DESCRIPTION]
Phosphorylation of Rab7 at S72 using TBK1
[STEPS]
SECTION: Phosphorylation reaction
1. Mix phosphorylation reaction mixture. Combine 4 uM human Rab7 with 400 nM purified human strep-tagged TBK1 in a buffer consisting of 50 mM HEPES 7.5, 150 mM N... | ["[Phosphorylation reaction] Mix phosphorylation reaction mixture. Combine 4 uM human Rab7 with 400 nM purified human strep-tagged TBK1 in a buffer consisting of 50 mM HEPES 7.5, 150 mM NaCl, 10 mM MgCl2, and 200 uM ATP. Incubate at room temperature for 3 hours.", "[Phosphorylation reaction] Pass reaction mixture over ... |
93,845 | Rabies Virus Sequencing using Illumina- MiSeq | 4 | dx.doi.org/10.17504/protocols.io.ewov1qbrogr2/v1 | https://www.protocols.io/view/rabies-virus-sequencing-using-illumina-miseq-c7vvzn66 | Chakrakodi N Varun, Dhanya K, Ashwini M Ananda, Reeta Mani | TITLE: Rabies Virus Sequencing using Illumina- MiSeq
AUTHORS: Chakrakodi N Varun, Dhanya K, Ashwini M Ananda, Reeta Mani
[DESCRIPTION]
This Rabies whole genome sequencing protocol has been derived and modified from the Illumina COVIDSeq RUO sequencing pipeline. The protocol has been modified and optimised for sequenci... | ["[Samples and Extraction] Samples:\nThe following samples (human or animal sources) may be used for viral RNA extraction for Rabies lyssavirus.\n1. Brain Tissue or Nuchal skin: Homogenise the tissue by crushing a small piece in a sterile environment. Transfer the contents to a vial and vortex and spin down the sample.... |
92,816 | UV decontamination of materials | 3 | dx.doi.org/10.17504/protocols.io.5qpvo31y9v4o/v1 | https://www.protocols.io/view/uv-decontamination-of-materials-c6vqze5w | Elena Essel | TITLE: UV decontamination of materials
AUTHORS: Elena Essel
[DESCRIPTION]
Protocol for reducing DNA contamination on tubes, bottles, zip lock bags and other reaction vessels and containers used in the ancient DNA cleanroom by UV treatment.
[STEPS] | [] |
68,916 | DNA Extraction | 4 | dx.doi.org/10.17504/protocols.io.5qpvobjw7l4o/v1 | https://www.protocols.io/view/dna-extraction-cfiutkew | klaus.stark, Kira Julia Stanzick | TITLE: DNA Extraction
AUTHORS: klaus.stark, Kira Julia Stanzick
[DESCRIPTION]
DNA extraction from frozen blood clots is challenging. Here we applied QIAGEN Clotspin Baskets and the Gentra Puregene Blood Kit for DNA extraction from 5.5 ml whole blood without anticoagulating additives.
[STEPS]
SECTION: Blood clot prep... | ["[Blood clot preparation and red blood cell lysis] Frozen blood clots in 15 ml tubes were transferred from ‑20°C to a warming cabinet 55 °Cfor10 min and thereafter immediately placed on ice", "[Blood clot preparation and red blood cell lysis] The tube was inverted to loosen the clot. The blood clot was completely pour... |
96,794 | Protocol for Preparing Brain Samples for MUSIC | 0 | dx.doi.org/10.17504/protocols.io.x54v92e8ml3e/v1 | https://www.protocols.io/view/protocol-for-preparing-brain-samples-for-music-dar22d8e | Wenxin Zhao, Sheng Zhong | TITLE: Protocol for Preparing Brain Samples for MUSIC
AUTHORS: Wenxin Zhao, Sheng Zhong
[DESCRIPTION]
Here states the detailed procedure to prepare brain samples for MUSIC study.
[STEPS]
SECTION: Tissue pulverization and crosslinking
1. Cut a portion of post-mortem human brain frontal cortex sample on dry ice with he... | ["[Tissue pulverization and crosslinking] Cut a portion of post-mortem human brain frontal cortex sample on dry ice with heavy razor blades, and collect 50 mg of the sample in a 1.5 mL LoBind tube.", "[Nuclei isolation] Use Chromium Nuclei Isolation kit (10X genomics, 1000494) to isolate nuclei from crosslinked cortex ... |
50,519 | Expression and purification of Rab10 (1-181) stoichiometrically phosphorylated at Thr73 (the LRRK2 site) | 1 | dx.doi.org/10.17504/protocols.io.bvjxn4pn | https://www.protocols.io/view/expression-and-purification-of-rab10-1-181-stoichi-bvjxn4pn | Axel Knebel , Kerryn Berndsen, Pawel Lis, Dario Alessi | TITLE: Expression and purification of Rab10 (1-181) stoichiometrically phosphorylated at Thr73 (the LRRK2 site)
AUTHORS: Axel Knebel , Kerryn Berndsen, Pawel Lis, Dario Alessi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Rab10 (Uniprot: P61026), a membrane associated small GTPase, likely involve... | ["[Transformation of plasmid into competent bacteria]\nMix of pET28a 6HIS Thrombin Rab10 1-181 plasmid (around ) with - of the competent BL21(DE3) cells and incubate for .\n10 µl\n50 µl\n100 µl\non ice", "[Transformation of plasmid into competent bacteria]\nTransfer the vial to a heat block equilibrated at and leave... |
97,798 | Synthesis of Carbon Nanofibers by Electrospinning | 0 | dx.doi.org/10.17504/protocols.io.rm7vzjnr4lx1/v1 | https://www.protocols.io/view/synthesis-of-carbon-nanofibers-by-electrospinning-dbre2m3e | Bukola Adesanmi, Raphael D. Ayivi, Eric S McLamore, Sherine O. Obare | TITLE: Synthesis of Carbon Nanofibers by Electrospinning
AUTHORS: Bukola Adesanmi, Raphael D. Ayivi, Eric S McLamore, Sherine O. Obare
[DESCRIPTION]
This protocol describes the synthesis of aligned carbon nano fiber for adsorbent/photocatalyst in
environmental samples, electrochemical energy storage and other industri... | ["[Solution preparation] Step 1) Prepare 10% PAN working solutions (Timing: 24 hours)\nWeigh 3g of polyacrylonitrile and carefully combine in a flask with 27g of dimethyl formamide\n(DMF) under a chemical fume hood. \nPlace on magnetic stirrer within chemical hood (Figure 1)\nStir the mixture at 300 to 400rpm for 24 ho... |
null | null | null | dx.doi.org/10.17504/protocols.io.pcydixw | null | null | TITLE: No Title
AUTHORS:
[BEFORE_START]
<ol>
<li>Clean all surfaces and pipettors to remove DNA</li>
<li>Label Plates
<ul>
<li>Plate #1 – 1ml collection plate</li>
<li>Plate #2 – 1ml collection plate</li>
<li>Plate #3 – 1ml collection plate</li>
<li>Plate #4 – 1ml collection plate</li>
<li>Plate #5 – 2ml collection p... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.esnbede | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
For use in <a href="https://www.protocols.io/view/CviJI-Purification-From-IL-3A-Virus-Infected-NC64A-er3bd8n" target="_blank">CviJI Purification From IL-3A Virus Infected NC64A Chlorella</a>.
[STEPS]
?.
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.u3heyj6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Preparation of electrocompetent cells
Weinstock paper:
Matthew T Weinstock, Eric D Hesek,Christopher M Wilson, Daniel G Gibson
Vibrio natriegens as a fast-growing host for molecular biology
Nature Methods volume 13, pages 849–851 (2016)
To prepare the day before:
-LB I me... | [] |
53,979 | Preparation of Encoding Probes SOP005.v1.2 (PCR, In-vitro Transcription, Reverse Transcription and USER ENZYME Digest) | 4 | null | https://www.protocols.io/view/preparation-of-encoding-probes-sop005-v1-2-pcr-in-byx3pxqn | Rory Kruithoff, Douglas Shepherd | TITLE: Preparation of Encoding Probes SOP005.v1.2 (PCR, In-vitro Transcription, Reverse Transcription and USER ENZYME Digest)
AUTHORS: Rory Kruithoff, Douglas Shepherd
[DESCRIPTION]
Document Summary:This document, Preparation of Encoding Probes (SOP005), describes the p... | ["[Part 1 - PCR Amplification - Step 1: Prepare the PCR reaction] In a 1.7 mL Eppendorf tube, mix the following:\n- 40 µL ;\n- 2 µL ;\n- 2 µL ; \n- 1 µL ; \n- 355 µL ; \n- 400 µL .", "[Part 1 - PCR Amplification - Step 1: Prepare the PCR reaction] Aliquot 50 µL into 16 PCR tubes.", "[Part 1 - PCR Amplification -... |
91,934 | HyDrop-RNA v1.0 | 1 | dx.doi.org/10.17504/protocols.io.dm6gpwqjjlzp/v4 | https://www.protocols.io/view/hydrop-rna-v1-0-c5z6y79e | Florian De Rop, Suresh Poovathingal, Stein Aerts | TITLE: HyDrop-RNA v1.0
AUTHORS: Florian De Rop, Suresh Poovathingal, Stein Aerts
[DESCRIPTION]
Step-by-step protocol for performing HyDrop-RNA. The duration of each step assumes an experienced protocol user. For a first-time user, we recommend doubling the expected time for each step.
[STEPS]
SECTION: Microfluidics P... | ["[Microfluidics Preparation] Setting up the Microfluidic Framework\nThese steps need to happen in advance before the run can be started, as time between the preparation of the cell resuspension in RT mix and actual encapsulation needs to be minimised to preserve cell viability.", "[Microfluidics Preparation] Boot up ... |
29,644 | Protocol for the generation of axenic/bacteria-depleted Symbiodiniaceae cultures | null | dx.doi.org/10.17504/protocols.io.87khzkw | null | Rúben M Costa, Cátia Fidalgo, Anny Cárdenas, Jörg C. Frommlet, Christian Voolstra | TITLE: Protocol for the generation of axenic/bacteria-depleted Symbiodiniaceae cultures
AUTHORS: Rúben M Costa, Cátia Fidalgo, Anny Cárdenas, Jörg C. Frommlet, Christian Voolstra
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left"><span>This protocol prod... | ["[Culture Maintenance]\nPrepare artificial seawater (ASW) by mixing reagents in MilliQ water and adjusting the pH of the final volume to 8.0–8.2. Filter through 0.22 µm pore size filter. Alternatively, autoclave natural seawater and filter through 0.22 µm pore size filter (NSW).", "[Culture Maintenance]\nPrepare F/2 m... |
null | null | null | dx.doi.org/10.17504/protocols.io.katcsen | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Processing murine tissues into paraffin sections.</p>
[STEPS]
?.
?.
?.
?.
?.
?. | [] |
76,752 | Setting up Zotero and Google Drive for syncing reference libraries (PC) | 1 | null | https://www.protocols.io/view/setting-up-zotero-and-google-drive-for-syncing-ref-cn7qvhmw | Carie M. Frantz | TITLE: Setting up Zotero and Google Drive for syncing reference libraries (PC)
AUTHORS: Carie M. Frantz
[DESCRIPTION]
This protocol is useful if you wish to sync a LARGE reference library across multiple computers. It uses Zotero, which has built-in free syncing for up to 300 MB of files (roughly 50-100 papers). For l... | ["[Set up Google Drive syncing] Install Drive for desktop on both computers", "[Install and set up Zotero on Computer 1] Install Zotero desktop\n\nDefault installation settings are fine.", "[Install and set up Zotero on Computer 2] Repeat the steps above for your second computer\n\nIf you do not have a prior (e.g., Men... |
null | null | null | dx.doi.org/10.17504/protocols.io.u2veye6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Dyes are colored organic compounds that can dye fibers or other substrates to a certain color. They can be divided into the following categories: Acid Dyes, Azoic Dyes, Basic Dyes, Direct Dyes, Cationic Dyes, Disperse Dyes, Neutral Dyes, Pigments, Reactive Dyes, Solvent Dyes and... | [] |
69,725 | Quantitative analyses of the ultrastructural features of dopaminergic axon terminals. Protocol #1: Tissue preparation for electron microscopy | 1 | dx.doi.org/10.17504/protocols.io.j8nlkw55wl5r/v1 | https://www.protocols.io/view/quantitative-analyses-of-the-ultrastructural-featu-cgb5tsq6 | Natalie M Doig, Peter J Magill | TITLE: Quantitative analyses of the ultrastructural features of dopaminergic axon terminals. Protocol #1: Tissue preparation for electron microscopy
AUTHORS: Natalie M Doig, Peter J Magill
[DESCRIPTION]
The release of dopamine from axons is critical for normative brain function and behaviour. Impaired or otherwise in... | ["[Perfusion-Fixation] A successful perfusion is not only key to ensuring good ultrastructure of tissue when assessed in the electron microscope, but also is a requirement for successful sectioning, staining, and embedding. The following steps are written for an adult mouse but can be adapted for a rat (Lapper, S. R. &... |
48,163 | Transplanting Tobacco Seedlings in the Greenhouse | 4 | null | https://www.protocols.io/view/transplanting-tobacco-seedlings-in-the-greenhouse-btabnian | Lynn Doran | TITLE: Transplanting Tobacco Seedlings in the Greenhouse
AUTHORS: Lynn Doran
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for transplanting and growing tobacco seedlings in the UIUC RIPE greenhouse. Has been verified on Petite Havana and Samson cultivars. </div><div class = "text-block... | ["[Initial Transplant]\nSelect the appropriate pot size for transplanting. Typical pot sizes:If keeping all transplants or after making selections for final growout: Classic 400 PotIf making selections for final growout: 3\" x 3\" , 18 well planting flatIf preparing plugs for transplanting into the field: 1\" x 1\", 72... |
95,896 | Digging Test | 0 | dx.doi.org/10.17504/protocols.io.bp2l6xj3zlqe/v1 | https://www.protocols.io/view/digging-test-c9vyz67w | sdwalto, Jeffrey Kordower, Bryan_Killinger | TITLE: Digging Test
AUTHORS: sdwalto, Jeffrey Kordower, Bryan_Killinger
[DESCRIPTION]
Digging test optimized for mice. This is a test to assess olfaction impairment. The more olfactory impairment or deficits, the longer it will take to find the sweetened treat.
[GUIDELINES]
Note: If the treat was found within 5 min... | ["Fast mice overnight (Do not exceed 24 hours).", "Prepare a clean mouse cage filled with 3 cm of bedding.", "Prepare an appetitive stimulus of sweetened cereal. Cinnamon Toast Crunch was used here.", "Bury cereal piece 0.5 cm below the bedding along the perimeter of the cage.", "Monitor the mouse for 5 mins or until t... |
26,799 | Microbe isolation and taxonomic classification from environmental samples | 1 | dx.doi.org/10.17504/protocols.io.14egnx5eyl5d/v1 | https://www.protocols.io/view/microbe-isolation-and-taxonomic-classification-fro-6ephbdn | Yiheng Hu, Alexander Kirbis, Eric Kemen | TITLE: Microbe isolation and taxonomic classification from environmental samples
AUTHORS: Yiheng Hu, Alexander Kirbis, Eric Kemen
[DESCRIPTION]
Numerous studies on plant,animal, or insect-associated microorganisms have significantly impacted host, and the number of microbe strains collected from different sources is ... | ["[Sub-culturing] First round subculturing", "[Sub-culturing] Second round subculturing:", "[Colony PCR] Prepare buffer in each 96 well plate:\nFor bacteria use 40uL TE buffer, for fungi use 30uL 10% Chelex + 10uL TE buffer.", "[Sub-culturing] From the plate of initial streaking, try to pick single yeast or bacterial c... |
96,938 | DNA Barcoding Protocol for Arthropods | 4 | null | https://www.protocols.io/view/dna-barcoding-protocol-for-arthropods-dawi2fce | Valerie Warhol | TITLE: DNA Barcoding Protocol for Arthropods
AUTHORS: Valerie Warhol
[DESCRIPTION]
This is a basic protocol for doing extraction and amplification of DNA barcodes (COI) for arthropods (typically small insects or spiders).
[STEPS]
SECTION: Prepare sample and equipment
1. Make sure all instruments, such as forceps and ... | ["[Prepare sample and equipment] Make sure all instruments, such as forceps and pestle, are clean and sterile.", "[Lyse cells] Put sample in tube. Grind sample with pestle until broken up into tiny pieces.", "[Prepare sample and equipment] Prepare water bath at 65 °C.", "[Prepare sample and equipment] Dissect sample fr... |
75,930 | Production of Crude AAV Virus Extract | 1 | dx.doi.org/10.17504/protocols.io.yxmvmx7r9l3p/v4 | https://www.protocols.io/view/production-of-crude-aav-virus-extract-cnd2va8e | Allen Institute for Brain Science | TITLE: Production of Crude AAV Virus Extract
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
This protocol is used to produce crude preps of AAV of any serotype.
Note: Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Awa... | [] |
41,762 | A study of the layout planning of plant facility based on the timed Petri net and systematic layout planning | 1 | dx.doi.org/10.17504/protocols.io.bk2akyae | https://www.protocols.io/view/a-study-of-the-layout-planning-of-plant-facility-b-bk2akyae | Hanwen Liu, Hanwen Liu, Xiaobing Liu, Lin Lin, Yuqing Xu, Sardar Mn Islam | TITLE: A study of the layout planning of plant facility based on the timed Petri net and systematic layout planning
AUTHORS: Hanwen Liu, Hanwen Liu, Xiaobing Liu, Lin Lin, Yuqing Xu, Sardar Mn Islam
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A study of the layout planning of plant facility base... | [] |
90,141 | Village Nuclei Isolation With Optiprep | 4 | dx.doi.org/10.17504/protocols.io.n2bvj3dxblk5/v3 | https://www.protocols.io/view/village-nuclei-isolation-with-optiprep-c395yr86 | liv_spina, Tara McDonald, Nora Reed, Alyssa Lutservitz | TITLE: Village Nuclei Isolation With Optiprep
AUTHORS: liv_spina, Tara McDonald, Nora Reed, Alyssa Lutservitz
[DESCRIPTION]
Isolation of nuclei from fresh-frozen brain tissue from sets of multiple (typically 2-20) human donors for analysis as a “cell village” (Wells et al., PMID 36796362) in which nuclei from all dono... | ["[Before Starting] Gather Supplies\nScalpels\nGlass slides\n14 mL Dounce\n20 µm vacuum filter\nEppendorf tubes (1.5 mL and 5 mL)\nEppendorf or Rainin pipette tips\nDry ice\nMetal plate\nOCT (Optimal cutting temperature compound)\nRNAse free water\nCell counting supplies (LUNA-FL)\nOther Reagents:\nPBS\nBSA\nRNAse inhi... |
54,413 | Cleavage assay | 1 | null | https://www.protocols.io/view/cleavage-assay-bzdmp246 | Yuichiroh Ikagawa | TITLE: Cleavage assay
AUTHORS: Yuichiroh Ikagawa
[DESCRIPTION]
Cleavage assay to validate for Cas12a activity
[STEPS]
1. Thawed crRNA solution on ice.
2. Add the following solution to the tube and gently mix by pipetting.
If the crRNA or Cas12a solution was not added to the reaction as a negative control, the re... | ["Thawed crRNA solution on ice.", "Add the following solution to the tube and gently mix by pipetting.\n\n \nIf the crRNA or Cas12a solution was not added to the reaction as a negative control, the reaction buffer for it was added and the total volume was adjusted to 20 μl.", "Incubate the mixture at 37°C overnight.", ... |
48,601 | PHA4GE contextual metadata SOP | 1 | dx.doi.org/10.17504/protocols.io.btpznmp6 | https://www.protocols.io/view/pha4ge-contextual-metadata-sop-btpznmp6 | Emma Griffiths, Ruth Timme, Nabil-Fareed Alikhan, Duncan MacCannell | TITLE: PHA4GE contextual metadata SOP
AUTHORS: Emma Griffiths, Ruth Timme, Nabil-Fareed Alikhan, Duncan MacCannell
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Contextual data curation is a critical part of public health pathogen genomic surveillance, as well as the data stewardship and dat... | ["[Populating and Curating the Template]\nDownload the file containing the collection template and reference guide from the following link: https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification", "[Populating and Curating the Template]\nBefore you begin to curate your contextual data: Review your datas... |
69,139 | HTTM : Illumina library preparation | 4 | dx.doi.org/10.17504/protocols.io.n2bvj8oowgk5/v2 | https://www.protocols.io/view/httm-illumina-library-preparation-cfrttm6n | Antoine Champie | TITLE: HTTM : Illumina library preparation
AUTHORS: Antoine Champie
[DESCRIPTION]
Part of the HTTM protocol dedicated to the preparation of Illumina sequencing libraries.
[BEFORE_START]
All steps and master mixes need to be kept on ice as much as possible. Thermocyclers need to be cooled at 4C before inserting sampl... | ["[Libraries] Transfer 2.5µl of DNA from the DNA extraction plate to a new PCR plate.", "[Libraries] Prepare a fragmentation master mix with :", "[Libraries] Add 1 µL of the fragmentation master mix to each well.", "[Libraries] Incubate in a thermocycler with the following protocol : \n15 minat 37 °C\n30 minat 65 °C", ... |
66,806 | Quality control analysis for 10X snRNA-seq | 5 | dx.doi.org/10.17504/protocols.io.261genbqjg47/v1 | https://www.protocols.io/view/quality-control-analysis-for-10x-snrna-seq-cdgws3xe | Daniel Jacobsen, Dinh H Diep | TITLE: Quality control analysis for 10X snRNA-seq
AUTHORS: Daniel Jacobsen, Dinh H Diep
[DESCRIPTION]
Here we describe a computational protocol for performing quality control analysis on shallow sequencing data obtained from 10X snRNA-seq experiments. The workflow starts with raw MiSeq run folders and uses cellrange... | ["Install cellranger using instructions from https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/installation", "Install anaconda or miniconda Python distributions following given instructions.\nGet anaconda from here: https://www.anaconda.com/products/distribution , OR\nget miniconda ... |
null | null | null | dx.doi.org/10.17504/protocols.io.e3hbgj6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This procedure is optimized for the isolation of 10<sup>7</sup> to 2 x 10<sup>8</sup> cells per tube from human peripheral blood mononuclear cells (PBMCs). If working with fewer cells keep volumes as indicated for 10<sup>7</sup> cells. For best results, optimize the condition... | [] |
88,425 | JMN-MSMP Muscle Single Cell Isolation | 1 | dx.doi.org/10.17504/protocols.io.j8nlko8xxv5r/v2 | https://www.protocols.io/view/jmn-msmp-muscle-single-cell-isolation-c2khyct6 | ccherry | TITLE: JMN-MSMP Muscle Single Cell Isolation
AUTHORS: ccherry
[DESCRIPTION]
Single cell isolation from muscle
[STEPS]
SECTION: Single cell isolation
1. Tissue was finely diced in RPMI 1640 (Gibco) with 1.6 Wunsh U/mL Liberase TL (Roche Diagnostics) and 0.2 mgl/mL deoxyribonuclease I (Roche Diagnostics).
SECTION: Sing... | ["[Single cell isolation] Tissue was finely diced in RPMI 1640 (Gibco) with 1.6 Wunsh U/mL Liberase TL (Roche Diagnostics) and 0.2 mgl/mL deoxyribonuclease I (Roche Diagnostics).", "[Single cell isolation] Finely diced tissue was incubated at 37C for 45 minutes.", "[Single cell isolation] Digested tissues were ground s... |
84,681 | INJECTION MOLDING TECHNIQUE: CORRECTING THE DREADED "BLACK TRIANGLE". | 4 | dx.doi.org/10.17504/protocols.io.5qpvo35obv4o/v2 | https://www.protocols.click/view/injection-molding-technique-correcting-the-dreaded-cwxhxfj6 | Álvaro Ferrando Cascales DDS,PhD., Antonio Mendoza Rodriguez DDS,MSc., Rubén Agustín-Panadero DDS,MSc,PhD., José Amengual Lorenzo DDS,PhD., Salvatore Sauro, Raúl Ferrando Cascales DDS,MSc,PhD., Ronaldo Hirata DDS,MSc,PhD., David Clark DDS,MSc. | TITLE: INJECTION MOLDING TECHNIQUE: CORRECTING THE DREADED "BLACK TRIANGLE".
AUTHORS: Álvaro Ferrando Cascales DDS,PhD., Antonio Mendoza Rodriguez DDS,MSc., Rubén Agustín-Panadero DDS,MSc,PhD., José Amengual Lorenzo DDS,PhD., Salvatore Sauro, Raúl Ferrando Cascales DDS,MSc,PhD., Ronaldo Hirata DDS,MSc,PhD., Dav... | ["[Description of the technique] Pre-treatment analysis of the gingival embrasure area and selection of the corresponding bioclear black triangle (BT) matrix.", "[Description of the technique] Smoothing and relief of the interdental contact points.", "[Description of the technique] This second step consists of checking... |
null | null | null | dx.doi.org/10.17504/protocols.io.pybdpsn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?. | [] |
73,173 | Cell treatments for time-lapse experiments | 1 | dx.doi.org/10.17504/protocols.io.j8nlkw8bxl5r/v1 | https://www.protocols.io/view/cell-treatments-for-time-lapse-experiments-cjpvumn6 | Electra Brunialti, Alessandro Maria Villa, Paolo Ciana | TITLE: Cell treatments for time-lapse experiments
AUTHORS: Electra Brunialti, Alessandro Maria Villa, Paolo Ciana
[DESCRIPTION]
Cell treatments for time-lapse experiments.
[STEPS]
1. For the timelapse experiments, cell cultures were treated for 6 h with vehicle (water) or lipopolysaccharide (LPS) at the final concent... | ["For the timelapse experiments, cell cultures were treated for 6 h with vehicle (water) or lipopolysaccharide (LPS) at the final concentration of 10 µg/ml LPS O111:B4, (Cat. L2630, Merk) starting from a 0,5 mg/ml stock solution, and then subjected to timelapse microscopy for 2h. For the GCase inhibition, cells were tr... |
90,779 | ITS amplicon computational workflow | 5 | dx.doi.org/10.17504/protocols.io.q26g7pw63gwz/v1 | https://www.protocols.io/view/its-amplicon-computational-workflow-c4v3yw8n | Geoff Zahn | TITLE: ITS amplicon computational workflow
AUTHORS: Geoff Zahn
[DESCRIPTION]
Many research questions in plant science depend on surveys of the plant microbiome. When the questions depend on answering "who is there" rather than "what are they doing," the most cost-effective method for interrogating microbiomes is oft... | ["[Remove primers] The first step is to remove any PCR primers that may still be present on your reads. Often, sequencing centers remove these by default, but it's a good idea to check. The R script \"00_Remove_Primers.R\" walks you through this process. In short, you provide the PCR primers\nthat we used for generatin... |
73,532 | Pancreatic β cell-specific deletion of Helicase-like transcription factor (Hltf) activates the Hmgb1-Rage axis and granzyme A-mediated killing of pancreatic β cells resulting in neonatal lethality | 4 | dx.doi.org/10.17504/protocols.io.kxygx9yqdg8j/v1 | https://www.protocols.io/view/pancreatic-cell-specific-deletion-of-helicase-like-cj24uqgw | Gurvinder Kaur, Rebecca A. Helmer, Dalia Martinez-Marin, Souad R. Sennoune, Rachel L. Washburn, Raul Martinez-Zaguilan, Jannette M. Dufour, Beverly S. Chilton | TITLE: Pancreatic β cell-specific deletion of Helicase-like transcription factor (Hltf) activates the Hmgb1-Rage axis and granzyme A-mediated killing of pancreatic β cells resulting in neonatal lethality
AUTHORS: Gurvinder Kaur, Rebecca A. Helmer, Dalia Martinez-Marin, Souad R. Sennoune, Rachel L. Washburn, Raul Martin... | ["[Reagents and Kits] Infrared warming pads were from Kent Scientific (Torrington, CT). OneTouch Ultra Mini and OneTouch Ultra Mini Blue test strips for the measurement of blood sugar were from LifeScan (Malpitas, CA). MiniCollect® red top capillary blood collection system (Z serum Clot Activator 450470, Greiner Bio-On... |
75,098 | LEGACY01: ADVERSE EVENTS | 1 | null | https://www.protocols.io/view/legacy01-adverse-events-cmj2u4qe | Katrina M Pollock, Calliope Dendrou | TITLE: LEGACY01: ADVERSE EVENTS
AUTHORS: Katrina M Pollock, Calliope Dendrou
[DESCRIPTION]
This protocol details about adverse events in an experimental medicine study of seasonal influenza vaccination responses in Lymph nodE single-cell Genomics in AnCestrY (LEGACY01).
[GUIDELINES]
DEFINITIONS
Adverse Event (AE): a... | [] |
103,194 | Immunofluorescence Staining and Analysis of Astrocyte-Neuron Co-Cultures | 0 | dx.doi.org/10.17504/protocols.io.x54v923j4l3e/v1 | https://www.protocols.io/view/immunofluorescence-staining-and-analysis-of-astroc-dgz23x8e | Shiyi Wang | TITLE: Immunofluorescence Staining and Analysis of Astrocyte-Neuron Co-Cultures
AUTHORS: Shiyi Wang
[DESCRIPTION]
Immunofluorescence Staining and Analysis of Astrocyte-Neuron Co-Cultures
[STEPS]
1. **Fixation**
1.1. - Fix astrocyte-neuron co-cultures on glass coverslips on Day in Vitro 12 (DIV 12) with warm 4% paraf... | ["**Fixation**", "- Fix astrocyte-neuron co-cultures on glass coverslips on Day in Vitro 12 (DIV 12) with warm 4% paraformaldehyde (PFA) for 7 minutes.", "- Wash coverslips 3 times with phosphate-buffered saline (PBS).", "**Blocking**", "- Block coverslips in a blocking buffer containing 50% normal goat serum (NGS) and... |
63,909 | Details Eagle Hemp CBD Gummies Read Ingredients and Really Work? | 3 | dx.doi.org/10.17504/protocols.io.81wgb69j3lpk/v1 | https://www.protocols.io/view/details-eagle-hemp-cbd-gummies-read-ingredients-an-candsda6 | Eagle Hemp CBD Gummies | TITLE: Details Eagle Hemp CBD Gummies Read Ingredients and Really Work?
AUTHORS: Eagle Hemp CBD Gummies
[DESCRIPTION]
https://www.mercurynews.com/2022/03/29/eagle-hemp-cbd-gummies-reviews-website-scam-2022-eagle-hemp-cbd-gummies-shark-tank-fact-check/
[STEPS] | [] |
72,294 | Lysis of diatom bulk samples | 4 | dx.doi.org/10.17504/protocols.io.x54v9ddkpg3e/v1 | https://www.protocols.io/view/lysis-of-diatom-bulk-samples-ciueuete | Till Macher | TITLE: Lysis of diatom bulk samples
AUTHORS: Till Macher
[DESCRIPTION]
This protocol describes the steps of sample preparation and lysis before DNA extraction for the diatoms metabarcoding protocol of the LeeseLab. The protocol was established in the GeDNA project.
[GUIDELINES]
Reagents are potentially damaging to t... | ["[Sample concentration] Centrifuge 50 mL falcon tubes containing the diatom samples 4000 x g, 10 min", "[Sample concentration] Discard supernatant EtOH (can be poured from the falcon tube).", "[Sample concentration] Add 10 mL to each sample (in falcon tube). Vortex samples to elute pellets again.", "[Sample lysis] Pre... |
null | null | null | dx.doi.org/10.17504/protocols.io.ka9csh6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?. | [] |
26,891 | RNA Isolation | null | dx.doi.org/10.17504/protocols.io.6hjhb4n | null | Natalie Brown | TITLE: RNA Isolation
AUTHORS: Natalie Brown
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Real Time Polymerase Chain Reaction</div></div>
[STEPS]
?. ● Get plates, aspirate media
?. ● Add 2mL ice cold DPBS
?. ○ Aspirate DPBS
?. ● Add 500uL Trizol/well in chemical hood
?. ● Bring yellow tubes to ho... | ["●\tGet plates, aspirate media", "●\tAdd 2mL ice cold DPBS", "○\tAspirate DPBS", "●\tAdd 500uL Trizol/well in chemical hood", "●\tBring yellow tubes to hood, collect trizol and add to tubes", "●\tAdd 100uL chloroform to tubes", "○\thand shake 15s", "○\tPlace on ice 5min until see layers (aq/lipids/bottom)", "●\tSpin f... |
95,469 | eDNA extraction from water samples filtered through Sterivex filter units (NucleoMag DNA/RNA Water Kit - MACHEREY NAGEL). | 4 | dx.doi.org/10.17504/protocols.io.ewov1qpkpgr2/v1 | https://www.protocols.io/view/edna-extraction-from-water-samples-filtered-throug-c9gmz3u6 | Marine Vautier, Cecile Chardon, Cyrielle Galiegue, Isabelle Domaizon | TITLE: eDNA extraction from water samples filtered through Sterivex filter units (NucleoMag DNA/RNA Water Kit - MACHEREY NAGEL).
AUTHORS: Marine Vautier, Cecile Chardon, Cyrielle Galiegue, Isabelle Domaizon
[DESCRIPTION]
The objective of this protocol is the environmental DNA (eDNA) extraction from water samples filte... | ["[Material preparation] Preheat the incubator at 70 °C \n\nTo limit contamination of the kit buffers, it is recommended to aliquote them:\n- Into 50 mL tubes for C1, MWA2, MWA3 and MWA4\n- Into 2 mL tubes for NucleoMag B-Beads solution and DNase-free H2O\n\nTubes annotation \n- one 2 mL tube per sample for lysate coll... |
29,318 | Plant nuclei enrichment for chromatin capture-based Hi-C library protocols | null | dx.doi.org/10.17504/protocols.io.8vehw3e | null | Elena Hilario | TITLE: Plant nuclei enrichment for chromatin capture-based Hi-C library protocols
AUTHORS: Elena Hilario
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Chromatin capture-based protocols to produce Hi-C libraries start with a crude nuclei extract or a total cell extract. Either way, plants can be ch... | ["[Nuclei isolation]\nWeight 1-2 g of young leaves, either fresh or frozen.", "[Nuclei isolation]\nPre-cool the mortar and pestle by pouring liquid nitrogen to the rim of the mortar. Once the liquid nitrogen is evaporated, repeat the pre-cooling step.", "[Nuclei isolation]\nAdd the leaves to the mortar and pour liquid ... |
28,130 | Protein purification strep-tag on gravity column | null | dx.doi.org/10.17504/protocols.io.7qahmse | null | Cleo B. | TITLE: Protein purification strep-tag on gravity column
AUTHORS: Cleo B.
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protein purification of a protein with a strep-tag on a gravity column. </div></div>
[STEPS]
?. [Protein extraction]
Place post-induction culture from Protein expression using E... | ["[Protein extraction]\nPlace post-induction culture from Protein expression using E. coli strain BL21DE3 on ice", "[Protein extraction]\nCentrifuge culture at 5000xg for at\n4 °C", "[Protein extraction]\nThe pellet is resuspended in buffer W per cell culture containing one crushed cOmplete mini tablet.\n1 ml\n100 ml"... |
44,626 | 3.3 Molecular Assembly of GST Effector Proteins on Glutathione Beads | 4 | dx.doi.org/10.17504/protocols.io.bptsmnne | https://www.protocols.io/view/3-3-molecular-assembly-of-gst-effector-proteins-on-bptsmnne | Peter Simons, Virginie Bondu, Angela Wandinger-Ness, Tione Buranda | TITLE: 3.3 Molecular Assembly of GST Effector Proteins on Glutathione Beads
AUTHORS: Peter Simons, Virginie Bondu, Angela Wandinger-Ness, Tione Buranda
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Small, monomeric guanine triphosphate hydrolases (GTPases) are ubiquitous cellular integrators... | ["[3.3 Molecular Assembly of GST Effector Proteins on Glutathione Beads]\nBriefly, glutathione beads are mixed with the desired, purified GST-effector protein of desired concentration (Eq. 1), incubated with rotation at , collected by centrifugation, and resuspended in HPSMT buffer to 10,000 beads/μL. Beads are prepar... |
99,087 | RNA extraction from milk for HPAI surveillance | 0 | dx.doi.org/10.17504/protocols.io.n2bvjn6obgk5/v1 | https://www.protocols.io/view/rna-extraction-from-milk-for-hpai-surveillance-dczp2x5n | Andrew Lail, Will Vuyk, Isla Emmen, David O'Connor | TITLE: RNA extraction from milk for HPAI surveillance
AUTHORS: Andrew Lail, Will Vuyk, Isla Emmen, David O'Connor
[DESCRIPTION]
This is an RNA extraction method that isolates HPAI RNA segments from commercially-available milk samples. The protocol involves processing with a MagMax RNA extraction kit on a Kingfisher in... | ["[RNA extraction] Use the MagMax Wastewater Ultra x96 kit1 (or comparable magnetic bead isolation kit2-5) on the ThermoFisher Kingfisher Apex (or comparable instrument). For each sample, load 400 uL of pasteurized milk or heavy whipping cream into the binding plate.", "[RNA extraction] Elute in 50 uL of elution soluti... |
76,296 | Lagash Archaeological Survey and Recording System (LASRS) - Rectangular Survey Grid Creation with QGIS | 5 | dx.doi.org/10.17504/protocols.io.bp2l69r3klqe/v1 | https://www.protocols.io/view/lagash-archaeological-survey-and-recording-system-cnrgvd3w | Paul C. Zimmerman | TITLE: Lagash Archaeological Survey and Recording System (LASRS) - Rectangular Survey Grid Creation with QGIS
AUTHORS: Paul C. Zimmerman
[DESCRIPTION]
Tools available in the open-source GIS program QGIS can be used to create a rectangular grid for archaeological surveys within irregularly-shaped boundaries. This proto... | ["[Create Your QGIS Project] Launch QGIS and select the New Empty Project template.", "[Create Your QGIS Project] Click the project CRS button in the lower right of the window and select the appropriate EPSG with UTM coordinates for your survey.\n\n For most of Iraq, this will be WGS 84 / UTM zone 38N (EPSG:32638).", "... |
72,720 | DengueSeq: A pan-serotype whole genome amplicon sequencing protocol for dengue virus | 4 | dx.doi.org/10.17504/protocols.io.kqdg39xxeg25/v1 | https://www.protocols.io/view/dengueseq-a-pan-serotype-whole-genome-amplicon-seq-ci9quh5w | Chantal Vogels, Chrispin Chaguza, Mallery I Breban, Afeez Sodeinde, Emma Taylor-Salmon, Abigail J. Porzucek, Nathan D Grubaugh | TITLE: DengueSeq: A pan-serotype whole genome amplicon sequencing protocol for dengue virus
AUTHORS: Chantal Vogels, Chrispin Chaguza, Mallery I Breban, Afeez Sodeinde, Emma Taylor-Salmon, Abigail J. Porzucek, Nathan D Grubaugh
[DESCRIPTION]
Background
Amplicon-based sequencing (PrimalSeq) was developed in response to... | ["[Prepare Working Primer Solutions] Briefly centrifuge all primers", "[cDNA Synthesis] Prepare the following reagents:", "[Amplicon Generation] Prepare the following reagents:", "[Amplicon Tagmentation and Cleanup] Prepare the following reagents:", "[Amplify Tagmented Amplicons] Prepare the following reagents:", "[Poo... |
47,885 | U-251MG Spheroid generation using low attachment plate method protocol | 1 | dx.doi.org/10.17504/protocols.io.bszmnf46 | https://www.protocols.io/view/u-251mg-spheroid-generation-using-low-attachment-p-bszmnf46 | Lara Carroll, Brijesh Tiwari, James Curtin, Janith Wanigasekara | TITLE: U-251MG Spheroid generation using low attachment plate method protocol
AUTHORS: Lara Carroll, Brijesh Tiwari, James Curtin, Janith Wanigasekara
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>3D cell culture is a process used to grow cells </span><span style = "font-style:italic;">in vi... | ["Prepare U-251MG single cell suspension at the desired seeding concentration. Cells can be from freshly prepared culture or from frozen vials in liquid nitrogen. Frozen vials can be immediately thawed using 37°C waterbath and maintained in Nunclon Delta T25 cell culture flask with complete medium (Dulbecco's Modified ... |
79,636 | Biofilm growth with starch treatment | 1 | dx.doi.org/10.17504/protocols.io.eq2lypqzelx9/v2 | https://www.protocols.io/view/biofilm-growth-with-starch-treatment-crzuv76w | Bjørn Peare Bartholdy, a.g.henry | TITLE: Biofilm growth with starch treatment
AUTHORS: Bjørn Peare Bartholdy, a.g.henry
[DESCRIPTION]
This is the main protocol to grow a calcifying oral biofilm model with starch treatments. It uses a 24 deepwell plate with the accompanying lid as substratum (polypropylene). The protocol takes 25 days to run, with dai... | ["[Saliva collection] Saliva donors rinse their mouth with water for 30 seconds.", "[Saliva collection] Stimulate saliva production by chewing tasteless gum or parafilm.", "[Saliva collection] Collect the saliva by spitting into 50 ml plastic centrifuge tubes.", "[Saliva collection] Make a 2-fold dilution of saliva in ... |
20,276 | Colorimetric Iron Quantification Assay | null | dx.doi.org/10.17504/protocols.io.x2ufqew | null | Natalie Rubio | TITLE: Colorimetric Iron Quantification Assay
AUTHORS: Natalie Rubio
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Measures iron from 0.4 - 20 nmol/83366) to quantify the levels of iron in cell culture and meat samples. Iron dissociates from its carrier protein in the presence of acidic buff... | ["[Prepare the reagents from the Iron Assay Kit.]\n1. Equilibrate the iron standard, iron assay buffer and iron reducer to room temperature. 2. Thaw the iron probe and then keep on ice during the duration of the assay.", "[Prepare the standard curve.]\n1. Dilute 10 μL of iron standard in 990 μL of distilled water to pr... |
98,141 | 3,3-Diaminobenzidine Tetrahydrochloride (DAB) Immunohistochemistry on Mouse Brain Tissue Sections | 0 | dx.doi.org/10.17504/protocols.io.3byl497zjgo5/v1 | https://www.protocols.io/view/3-3-diaminobenzidine-tetrahydrochloride-dab-immuno-db352qq6 | madalynn.erb Erb | TITLE: 3,3-Diaminobenzidine Tetrahydrochloride (DAB) Immunohistochemistry on Mouse Brain Tissue Sections
AUTHORS: madalynn.erb Erb
[DESCRIPTION]
This protocol details the staining for free floating mouse brain sections.
[STEPS]
SECTION: Day 1
1. Staining protocol for 35μm free floating mouse brain sections.
SECTION: ... | ["[Day 1] Staining protocol for 35μm free floating mouse brain sections.", "[Day 1] Staining is performed in glass staining dishes (Pyrex 36754-60) using 8-section staining nets (Ted Pella 36154-64) .", "[Day 1] Gently rock the plates during the washing and incubation steps.", "[Day 1] Wash sections: 3 times (5 min per... |
18,054 | Antibody & Antigen | null | dx.doi.org/10.17504/protocols.io.vvee63e | null | bello smitu | TITLE: Antibody & Antigen
AUTHORS: bello smitu
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left">Definition:</div></div><div class = "text-block"><div class = "justify" style = "text-align:left">Antigen </div></div><div class = "text-block"><div class =... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.crvv65 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol can be used to add As to the blunt-ends of DNA fragments that have been amplified using a high-fidelity polymerase (such as Q5® High Fidelity DNA Polymerase).
[STEPS]
?.
?.
?. | [] |
66,713 | Wonder Leaf CBD Oil [Supplement] | 1 | dx.doi.org/10.17504/protocols.io.dm6gpbkk1lzp/v1 | https://www.protocols.io/view/wonder-leaf-cbd-oil-supplement-cddzs276 | wondercbdaid | TITLE: Wonder Leaf CBD Oil [Supplement]
AUTHORS: wondercbdaid
[DESCRIPTION]
Wonder Leaf CBD Oilis a non-psychoactive recipe which is arranged with maryjane which is isolated from the normally accumulated hemp plant. The condition has a combination of supportive benefits and outfits you with getting through easing fr... | [] |
28,848 | Making LB agar plates | null | dx.doi.org/10.17504/protocols.io.8eqhtdw | null | Priota Islam | TITLE: Making LB agar plates
AUTHORS: Priota Islam
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Luria broth (LB) is a nutrient-rich media commonly used to culture bacteria in the lab. The addition of agar to LB results in the formation of a gel that bacteria can grow on, as they are unable to dig... | ["Purchase LB Agar from the media kitchen and autoclave it to meltContent of LB Agar:\n37 g pre-mixed powder consisting of:- 5 g peptone- 10 g peptone from casein- 10 g sodium chloride- 10 g g agar-agar1 L Sterile H2O", "If the bacteria have a specific antibiotic resistance then add 1000x of that antibiotic to the melt... |
95,925 | LENTIVIRAL TITRATION FOR EARLY POST- MITOTIC DOPAMINERGIC NEURONS | 0 | null | https://www.protocols.io/view/lentiviral-titration-for-early-post-mitotic-dopami-c9wvz7e6 | Renuka Ravi Gupta, Nona Farbehi, hendersa, Vikram Khurana, Gist Croft, Lorenz Studer, Joseph Powell | TITLE: LENTIVIRAL TITRATION FOR EARLY POST- MITOTIC DOPAMINERGIC NEURONS
AUTHORS: Renuka Ravi Gupta, Nona Farbehi, hendersa, Vikram Khurana, Gist Croft, Lorenz Studer, Joseph Powell
[DESCRIPTION]
iPSCs- derived neurons are particularly challenging cells for genetic screening. Hence we develop a protocol for lentiviral... | ["[Day -1: Coating wells with Poly - L ornithine(PO)] Coat 500 ul per well in a 48-well plate with 15 ug/ml PO in DPBS.", "[Day -1: Coating wells with Poly - L ornithine(PO)] Incubate the plate overnight at 37ºC with 5% CO2 and 20.9% O2.", "[Day 0: Coating wells with Laminin and Fibronectin] Thaw Fibronectin and Lamini... |
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