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 |
|---|---|---|---|---|---|---|---|
80,758 | Organelle Tag Introduction in Mouse Embryonic Fibroblasts (MEFs) | 4 | dx.doi.org/10.17504/protocols.io.6qpvr456bgmk/v1 | https://www.protocols.io/view/organelle-tag-introduction-in-mouse-embryonic-fibr-cs4wwgxe | Matthew Taylor, Francesca Tonelli, Dario R Alessi | TITLE: Organelle Tag Introduction in Mouse Embryonic Fibroblasts (MEFs)
AUTHORS: Matthew Taylor, Francesca Tonelli, Dario R Alessi
[DESCRIPTION]
We describe here a method to generate MEFs stably expressing a lysosome localized TMEM192-3×HA fusion protein (“LysoTag”), or a Golgi localized TMEM115-3×HA fusion protein (“... | ["[1.1 Packaging the SV40 large T antigen plasmid into a Retrovirus system] 1.1.1) Grow HEK293FT cells to 60% confluency in Growth media in a 10 cm Petri Dish.", "[1.1 Packaging the SV40 large T antigen plasmid into a Retrovirus system] 1.1.2) Prepare a transfection mix in a sterile 1.5ml Eppendorf tube, containing:\n3... |
96,376 | Metagenomic library plates | 0 | dx.doi.org/10.17504/protocols.io.5jyl8p328g2w/v1 | https://www.protocols.io/view/metagenomic-library-plates-dacy2axw | Bonnie Evans | TITLE: Metagenomic library plates
AUTHORS: Bonnie Evans
[DESCRIPTION]
Arraying Canadian MetaMicroBiome Library (Neufeld et al. 2011) clones into multi-well plates for screening.
[BEFORE_START]
Make up 30% glycerol in sterile water and autoclave.
[STEPS]
SECTION: Plate pooled library sample
1. Prepare tetracycline L... | ["[Plate pooled library sample] Prepare tetracycline LB agar plates", "[Plate pooled library sample] Dilute 2 uL glycerol stock in 20 mL sterile PBS (1/10000 dilution).", "[Plate pooled library sample] Pipette 100 uL of diluted sample into centre of 90 mm agar plate", "[Plate pooled library sample] Put 4-5 plating bead... |
28,042 | Coverslips preparation for seqFISH | null | dx.doi.org/10.17504/protocols.io.7mihk4e | null | Nina Dar, Long Cai, Shin Lin | TITLE: Coverslips preparation for seqFISH
AUTHORS: Nina Dar, Long Cai, Shin Lin
[STEPS] | [] |
38,216 | Illumina Nextera DNA Flex library construction and sequencing for SARS-CoV-2: Adapting COVID-19 ARTIC protocol | 1 | dx.doi.org/10.17504/protocols.io.bhjgj4jw | https://www.protocols.io/view/illumina-nextera-dna-flex-library-construction-and-bhjgj4jw | Sureshnee Pillay, Jennifer Giandhari, Houriiyah Tegally, Eduan Wilkinson, Benjamin Chimukangara, Richard Lessells, Yunus Moosa, Inbal Gazy, Maryam Fish, Lavanya Singh, Khulekani Sedwell Khanyile, Vagner Fonseca, Marta Giovanetti, Luiz Carols Alcantara, Tulio de Oliveira, Jennifer Giandhari | TITLE: Illumina Nextera DNA Flex library construction and sequencing for SARS-CoV-2: Adapting COVID-19 ARTIC protocol
AUTHORS: Sureshnee Pillay, Jennifer Giandhari, Houriiyah Tegally, Eduan Wilkinson, Benjamin Chimukangara, Richard Lessells, Yunus Moosa, Inbal Gazy, Maryam Fish, Lavanya Singh, Khulekani Sedwell Khanyi... | ["[cDNA]\nPrepare the cDNA mastermix in the pre-PCR clean room. The mastermix hood must be decontaminated before and after use with 10% extran, and 70% ethanol, and sterilised with ultraviolet light (UV).", "[cDNA]\nMix the following components in a labeled 1.5ml Component: AB1ComponentVolume (ul)250μM Random Hexamers... |
21,983 | Comparative Ct method quantification (2-ΔCt method). | null | dx.doi.org/10.17504/protocols.io.zp7f5rn | null | Barbara Rizzacasa, Elena Morini, Ruggiero Mango, Chiara Vancheri, Simone Budassi, Gianluca Massaro, Sara Maletta, Massimiliano Macrini, Silvio D’Annibale, Francesco Romeo, Giuseppe Novelli, Francesca Amati | TITLE: Comparative Ct method quantification (2-ΔCt method).
AUTHORS: Barbara Rizzacasa, Elena Morini, Ruggiero Mango, Chiara Vancheri, Simone Budassi, Gianluca Massaro, Sara Maletta, Massimiliano Macrini, Silvio D’Annibale, Francesco Romeo, Giuseppe Novelli, Francesca Amati
[DESCRIPTION]
<div class = "text-blocks"><di... | ["[Evaluation of the absolute expression of miRNAs in each sample analyzed:]\nFor each sample is obtained an amplification curve in which the Ct is inversely proportional to the initial sample quantity;", "[Evaluation of the absolute expression of miRNAs in each sample analyzed:]\nNormalize the data to an internal cont... |
72,362 | Plasmid Sequence Analysis from Long Reads | 1 | dx.doi.org/10.17504/protocols.io.36wgq4n5yvk5/v8 | https://www.protocols.io/view/plasmid-sequence-analysis-from-long-reads-ciwiufce | David A Eccles | TITLE: Plasmid Sequence Analysis from Long Reads
AUTHORS: David A Eccles
[DESCRIPTION]
This protocol demonstrates how to assemble reads from plasmid DNA, and generate a circularised and non-repetitive consensus sequence
At the moment, this protocol uses Canu to de-novo assemble high-quality single-cut reads.
Input(... | ["[Read file preparation] Demultiplex reads as per protocol Demultiplexing Nanopore reads with LAST.\n\nIf this has been done, then the following command should produce output without errors:\n\n \n\nExample output:\n\n \n\nIf the barcode_counts.txt file is missing, the output will look like this:\n\n \n\nIf one or mor... |
52,175 | Hydra collecting for citizen scientists | 1 | dx.doi.org/10.17504/protocols.io.bw7pphmn | https://www.protocols.io/view/hydra-collecting-for-citizen-scientists-bw7pphmn | Callen Hyland, Kimberly Sladek | TITLE: Hydra collecting for citizen scientists
AUTHORS: Callen Hyland, Kimberly Sladek
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The freshwater cnidarian Hydra has been a model system for regeneration and developmental biology for over 250 years, but much remains unknown about their biodiversi... | ["Gather your materials:Notebook and penWhite or clear plastic container (a medium-sized food storage container is ideal)Glass Pasteur pipette + rubber bulbScrew-cap vials (either glass or plastic)Magnifying glass, high powered reading glasses, or headband magnifierOptional: plastic toothbrush holder to protect your gl... |
26,687 | SPARC - Acute surgery and experimentation of the gastrointestinal tract and vagus nerve in the ferret | null | dx.doi.org/10.17504/protocols.io.6a7hahn | null | Charles C. Horn, Derek M. Miller, Stephanie Fulton, Bill J. Yates, Lee E. Fisher, Ameya C. Nanivadekar | TITLE: SPARC - Acute surgery and experimentation of the gastrointestinal tract and vagus nerve in the ferret
AUTHORS: Charles C. Horn, Derek M. Miller, Stephanie Fulton, Bill J. Yates, Lee E. Fisher, Ameya C. Nanivadekar
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used for acute... | ["[Preparation: Before first incision]\nInduce anesthesia using isoflurane in a chamber, then move to a facemask (1 to 2%).", "[Abdominal Surgery: Placement of electrodes and gastric tube/balloon]\nMake an incision in the midline abdominal muscle to expose the organs.", "[Abdominal Surgery: Placement of electrodes and ... |
79,455 | Handling and Sampling Bats - ISL Peru | 1 | dx.doi.org/10.17504/protocols.io.q26g7y7o9gwz/v1 | https://www.protocols.io/view/handling-and-sampling-bats-isl-peru-crt7v6rn | Mrinalini Watsa, Priscila Peralta-Aguilar, Jorge Luis Mendoza-Silva, Cristian Tirapelle, Naija Cuzmar, Pamela Sánchez-Vendizú, Gideon Erkenswick | TITLE: Handling and Sampling Bats - ISL Peru
AUTHORS: Mrinalini Watsa, Priscila Peralta-Aguilar, Jorge Luis Mendoza-Silva, Cristian Tirapelle, Naija Cuzmar, Pamela Sánchez-Vendizú, Gideon Erkenswick
[DESCRIPTION]
Program Timing:
Sample collection occurs annually during the rainforest dry season (June - August). Sampl... | ["[PREPARATORY PHASE] One day prior, the team will install 4-12 nylon mist nets (6 - 12 x 2.7 m, 4 - 5 shelves, mesh size 15 - 20 mm) in the chosen areas. The number of mist nets used should reflect with the size of the bat team and frequency of bat capture at that particular site. Nets must be closed if:\n\n inadequat... |
40,605 | Vezina Lab IHC Protocol | 1 | null | https://www.protocols.io/view/vezina-lab-ihc-protocol-bjv5kn86 | Chad Vezina | TITLE: Vezina Lab IHC Protocol
AUTHORS: Chad Vezina
[STEPS]
?. [Dewaxing, antigen retrieval and blocking.]
Heat slides to 65°C for 5 min to remove wrinkles and increase tissue adhesion.
?. [Dewaxing, antigen retrieval and blocking.]
Dewax and rehydrate slides by incubating at 25°C in Xylene (3 min, repeat twice), 100%... | ["[Dewaxing, antigen retrieval and blocking.]\nHeat slides to 65°C for 5 min to remove wrinkles and increase tissue adhesion.", "[Dewaxing, antigen retrieval and blocking.]\nDewax and rehydrate slides by incubating at 25°C in Xylene (3 min, repeat twice), 100% ethanol (3 min, repeat twice), 75% ethanol (3 min, repeat t... |
null | null | null | dx.doi.org/10.17504/protocols.io.kbzcsp6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes fluorescence-activated single cell sorting using a MoFlo Astrios EQ cell sorter (Beckman Coulter) and whole genome amplification of single sorted cells in plate formats using the REPLI-g Single Cell kit (Qiagen).</p>
[GUIDELINES]
<p><strong><em>Genera... | [] |
36,064 | Time of flight mass cytometry (CyTOF) | 1 | dx.doi.org/10.17504/protocols.io.5qpvo522dl4o/v1 | https://www.protocols.io/view/time-of-flight-mass-cytometry-cytof-bff8jjrw | Peter Hinderlie, Philippa R Kennedy | TITLE: Time of flight mass cytometry (CyTOF)
AUTHORS: Peter Hinderlie, Philippa R Kennedy
[DESCRIPTION]
Staining procedure for cells analyzed by time of flight mass cytometry.
[STEPS]
3. Cells are then fixed using 2% PFA, for 20mins.
4. For intracellular staining, cells are permeabilized by incubation with Triton X ... | ["Cells are then fixed using 2% PFA, for 20mins.", "For intracellular staining, cells are permeabilized by incubation with Triton X 0.1% for 5 min at room temperature, followed by incubation with intracellular antibody cocktail for 30 min at 4 °C.", "Cells from separate donors or conditions are stained separately with ... |
null | null | null | dx.doi.org/10.17504/protocols.io.pmwdk7e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><u>Goal: </u></p>
<p>This SOP has the objective to instruct the users and establish a standard protocol for determining <em>M. leprae</em> molecular viability using qPCR method.</p>
<p><u> </u></p>
<p><u>General considerations:</u></p>
<p>This protocol is based on the method ... | [] |
38,929 | test disclaimer - to delete | 1 | null | https://www.protocols.io/view/test-disclaimer-to-delete-bh9rj956 | Maria Guliakina | TITLE: test disclaimer - to delete
AUTHORS: Maria Guliakina
[STEPS]
?. test long text Fulfilled direction use continual set him propriety continued. Saw met applauded favourite deficient engrossed concealed and her. Concluded boy perpetual old supposing. Farther related bed and passage comfort civilly. Dashwoods see f... | ["test long text Fulfilled direction use continual set him propriety continued. Saw met applauded favourite deficient engrossed concealed and her. Concluded boy perpetual old supposing. Farther related bed and passage comfort civilly. Dashwoods see frankness objection abilities the. As hastened oh produced prospect for... |
73,492 | LC3-lipidation-assay | 1 | dx.doi.org/10.17504/protocols.io.kqdg392ypg25/v1 | https://www.protocols.io/view/lc3-lipidation-assay-cjzuup6w | Liv Jensen | TITLE: LC3-lipidation-assay
AUTHORS: Liv Jensen
[DESCRIPTION]
Protocol for an in vitro LC3 lipidation assay using purified proteins and synthetic liposomes.
[STEPS]
1. Mix 2μM ATG3, 2μM ATG7, 1μM WIPI2, 200nM ATG12–ATG5-ATG16L1-GFP, 5μM LC3B
1:1 with extruded liposomes in reaction buffer.
2. Incubate at 37 ̊C
3. At 0... | ["Mix 2μM ATG3, 2μM ATG7, 1μM WIPI2, 200nM ATG12–ATG5-ATG16L1-GFP, 5μM LC3B\n1:1 with extruded liposomes in reaction buffer.", "Incubate at 37 ̊C", "At 0, 15, 30, 60, and 120 minutes, remove 12μl of reaction mixture andquench by\nadding 4ul of SDS-PAGE loading bufferandheatingat 60 ̊C for 10 minutes."] |
null | null | null | dx.doi.org/10.17504/protocols.io.cdss6d | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Nucleic acid precipitation is used to concentrate and/or purify nucleic acids. The below protocol is based on the fact that nucleic acids are less soluble in alcohol than in more polar water. Addition of salt further decreases solubility by competing for water dipoles; as does l... | [] |
31,139 | Inorganic polyphosphate in microalgae: A DAPI-based quantification in microtiter plate | 1 | null | https://www.protocols.io/view/inorganic-polyphosphate-in-microalgae-a-dapi-based-banbidan | Yingyu Hu, Zoe V Finkel | TITLE: Inorganic polyphosphate in microalgae: A DAPI-based quantification in microtiter plate
AUTHORS: Yingyu Hu, Zoe V Finkel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The DAPI-based fluorometric quantification of polyphosphate in microalgae has been widely used in field samples since the me... | ["[Preparation of reagents]\nProteinase K", "[Preparation of reagents]\nPolyP primary standard stock", "[Preparation of reagents]\nTris buffer", "[Preparation of reagents]\nIn a 1 L volumetric flask, top Tris buffer to 1 L with MilliQ\n20 mL", "[Preparation of reagents]\nFilter through Rapid-flow and store at\n0 Room ... |
106,195 | Preparation post-mortem brain for spatial transcriptomics | 0 | dx.doi.org/10.17504/protocols.io.eq2lyw46rvx9/v1 | https://www.protocols.io/view/preparation-post-mortem-brain-for-spatial-transcri-djxt4pnn | Annabel J Curle | TITLE: Preparation post-mortem brain for spatial transcriptomics
AUTHORS: Annabel J Curle
[DESCRIPTION]
This protocol describes the preparation of post-portem brain tissue for spatial transcriptomics (Xenium and GeoMx). Guidelines provided to work with flash frozen tissue (FF) and formalin-fixed paraffin embedded tiss... | ["[Flash frozen tissue (FF)] Obtain tissue: Tissue blocks from brain bank 100 mg \nStorage: -80ºC in sealed cryovials/eppendorf tubes until use.\nTransport: dry ice\nWork always in RNase-free conditions, keeping samples ice-cold at all times to maintain RNA integrity.", "[Flash frozen tissue (FF)] Collect tissue block ... |
92,671 | Primary Culture of Mouse Mesencephalic Neurons | 4 | dx.doi.org/10.17504/protocols.io.81wgb7xpyvpk/v2 | https://www.protocols.io/view/primary-culture-of-mouse-mesencephalic-neurons-c6q7zdzn | louis-eric.trudeau | TITLE: Primary Culture of Mouse Mesencephalic Neurons
AUTHORS: louis-eric.trudeau
[DESCRIPTION]
This protocol details the procedure required for the dissection and collection of primary mouse culture mesencephalic neurons.
[BEFORE_START]
Preparation of solutions for dissociation: all solution must be prepared fresh
... | ["[Dissection (preferably in pairs)] Prepare two containers of crushed ice.", "[Dissection (preferably in pairs)] Clean the dissection surface with 70% alcohol. Place the dissection tools in a beakers filled with 70% alcohol and a Kimwipe (to protect the tips of the tools).", "[Dissection (preferably in pairs)] Prepare... |
null | null | null | dx.doi.org/10.17504/protocols.io.ua4esgw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol describes how to make an acoustic droplet ejection compatible plate for liquid handling on the Echo 555 using an epMotion 5075. The protocol expects (4) 96-well gDNA plates and an empty 384-well polypropylene (PP) echo destination plate. The 4 plates will be compre... | ["[Prepare gDNA plates] Thaw and centrifuge gDNA plates.", "[Prepare gDNA plates] Appropriately label destination plate.", "[Setup epMotion automation platform] {\"blocks\":[{\"key\":\"3cngr\",\"text\":\"\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[]},{\"key\":\"3j7p1\",\"... |
72,449 | Bionic sensing system and characterization of exhaled nitric oxide detection based on canine olfaction | 1 | dx.doi.org/10.17504/protocols.io.j8nlkwwp1l5r/v1 | https://www.protocols.io/view/bionic-sensing-system-and-characterization-of-exha-ciy9ufz6 | 时野坪 | TITLE: Bionic sensing system and characterization of exhaled nitric oxide detection based on canine olfaction
AUTHORS: 时野坪
[DESCRIPTION]
section 1:Design the relative optimal bionic chamber size and the pumping flow capacity of the air pump. The chamber's length, inner diameter, and pump flow capacity are designed, ex... | ["[Bionic chamber design] The experimental factors are reasonably designed and investigated through the orthogonal test method, and the level table of orthogonal test factors is established .", "[Bionic chamber design] Bionic chambers printed in 3D according to orthogonal design results.", "[Bionic chamber design] Unde... |
52,726 | Therapeutic Hypothermia for Neonatal Encephalopathy in Low- and Middle-Income Countries: A Systematic Review and Meta-Analysis | 1 | dx.doi.org/10.17504/protocols.io.bxqwpmxe | https://www.protocols.io/view/therapeutic-hypothermia-for-neonatal-encephalopath-bxqwpmxe | Ioannis Bellos, Aakash Pandita | TITLE: Therapeutic Hypothermia for Neonatal Encephalopathy in Low- and Middle-Income Countries: A Systematic Review and Meta-Analysis
AUTHORS: Ioannis Bellos, Aakash Pandita
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Therapeutic cooling represents the main treatment strategy for neonatal hypoxi... | ["Background Hypoxic-ischemic encephalopathy (HIE) a major cause of mortality and long-term morbidity in neonates. The condition is much more common in low- and middle-income countries compared to high-income ones. Therapeutic cooling represents an important tool for HIE management. However, a recent large-scale random... |
56,092 | Isolation of nuclei from frozen human skeletal and cardiac muscle for single nucleus RNA and chromatin assays | 4 | dx.doi.org/10.17504/protocols.io.b2z4qf8w | https://www.protocols.io/view/isolation-of-nuclei-from-frozen-human-skeletal-and-b2z4qf8w | James R Hocker, Sebastian Preissl, Dinh H Diep | TITLE: Isolation of nuclei from frozen human skeletal and cardiac muscle for single nucleus RNA and chromatin assays
AUTHORS: James R Hocker, Sebastian Preissl, Dinh H Diep
[DESCRIPTION]
This protocol was adapted for the isolation of single nuclei from frozen skeletal and cardiac muscle tissues for molecular charac... | ["Section flash-frozen skeletal muscle into aliquots according to desired nuclei yield and store on dry ice or at -80 °C .", "Prepare buffers and chill components:\n\n \nPrepare buffer fresh on day of nuclei isolation\nPrecool centrifuge to 4 °C \nPrecool all buffers at 4 °C \nPlace gentleMACS dissociator in cold room ... |
18,496 | Machine learning approach yields epigenetic biomarkers of food allergy: A novel 13-gene signature to diagnose clinical reactivity | null | dx.doi.org/10.17504/protocols.io.wa8fahw | null | Ayush Alag | TITLE: Machine learning approach yields epigenetic biomarkers of food allergy: A novel 13-gene signature to diagnose clinical reactivity
AUTHORS: Ayush Alag
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Current laboratory tests have a less than 50% accuracy in distinguishing between people who hav... | ["Download the Java code from BitBucket URL https://bitbucket.org/ayushalag/allergezy_plosone_src/src/master/", "Create an Eclipse project using the src Java files downloaded. Download weka jar files from https://www.cs.waikato.ac.nz/ml/weka/downloading.html . The Eclipse project should have the src files with the Java... |
null | null | null | dx.doi.org/10.17504/protocols.io.rkud4ww | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes the basic steps neccessary to maintain and propagate Aiptasia as they are done in the Pringle lab.</p>
[GUIDELINES]
<p>If working with symbiotic anemones hosting different <em>Symbiodinium</em> strains make sure to kepp all working surfaces clean and ... | [] |
18,682 | Anaesthesia of Lumpfish (Cyclopterus lumpus) fries. | null | dx.doi.org/10.17504/protocols.io.wg2fbye | null | Julianne Valla Jacobsen, Kjell J. Nilssen | TITLE: Anaesthesia of Lumpfish (Cyclopterus lumpus) fries.
AUTHORS: Julianne Valla Jacobsen, Kjell J. Nilssen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Large numbers of lumpfish are produced for the Norwegian salmon industry and are used to combat sea lice infestations. The present work tested... | ["[Prepare anaesthetic bath for immersion anaesthesia.]\nThe following chemicals and concentrations were used in our study:Liquid Benzoak was stirred into seawater (12.5, 25, 37.5, 50, 100 mg/L), metacaine powder and the corresponding weight of sodium bicarbonate (Na2CO3) were dissolved in seawater at concentrations of... |
98,445 | CODA (part 5): nuclear coordinate generation | HuBMAP | JHU-TMC | 0 | dx.doi.org/10.17504/protocols.io.dm6gpz8z8lzp/v2 | https://www.protocols.io/view/coda-part-5-nuclear-coordinate-generation-hubmap-j-dcdm2s46 | Kyu Sang Han, Pei-Hsun Wu, Joel Sunshine, Ashley Kiemen, Sashank Reddy, Denis Wirtz | TITLE: CODA (part 5): nuclear coordinate generation | HuBMAP | JHU-TMC
AUTHORS: Kyu Sang Han, Pei-Hsun Wu, Joel Sunshine, Ashley Kiemen, Sashank Reddy, Denis Wirtz
[DESCRIPTION]
In this section, generate nuclear coordinates on the
high-resolution H&E images through color deconvolution and identification
of two-dimensi... | ["[Nuclear coordinate generation] generate a mosaic image containing tiles from nine randomly chosen high-resolution images. This will be the image used to optimize the parameters for the cell detection algorithm. Given the path to the high-resolution images, the function will randomly choose nine files (filenames can ... |
103,746 | A CellProfiler computational pipeline to quantify the density of mouse striatal dopaminergic processes | 0 | dx.doi.org/10.17504/protocols.io.x54v92km4l3e/v1 | https://www.protocols.io/view/a-cellprofiler-computational-pipeline-to-quantify-dhja34ie | Ebsy Jaimon, Sreeja V Nair, Suzanne R Pfeffer | TITLE: A CellProfiler computational pipeline to quantify the density of mouse striatal dopaminergic processes
AUTHORS: Ebsy Jaimon, Sreeja V Nair, Suzanne R Pfeffer
[DESCRIPTION]
Here, we present a CellProfiler (1) software pipeline to quantify the density and intensity of dopaminergic processes in the mouse striatum.... | ["[CellProfiler computational pipeline to quantify the density of mouse striatal dopaminergic processes] Batch process images\n \n1. Use the FIJI macro as described in dx.doi.org/10.17504/protocols.io.3byl4bpo8vo5/v1 to Z project the .czi images obtained from Zeiss LSM microscope. Open the images that need to be proces... |
null | null | null | dx.doi.org/10.17504/protocols.io.cjwupd | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?. | [] |
35,992 | Single-Cell Dissociation of Human Trabecular Meshwork | null | dx.doi.org/10.17504/protocols.io.bfdyji7w | https://www.protocols.io/view/single-cell-dissociation-of-human-trabecular-meshw-bfdyji7w | Alexi Mcadams, Tavé van Zyl | TITLE: Single-Cell Dissociation of Human Trabecular Meshwork
AUTHORS: Alexi Mcadams, Tavé van Zyl
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Fresh trabecular meshwork tissue is dissected from post-mortem human eyes and dissociated into a single cell suspension.</div></div>
[STEPS]
?. [Prepare... | ["[Prepare Working Solutions and Materials]\nPrepare Fresh Oxygenated Ames' MediumAdd 1.9 g sodium bicarbonate to a 1L container (e.g. glass bottle or flask)Empty one container of Ames' Medium powder to 1L containerFill container with 1L of ddH2O, shake to mixBubble oxygen gas (95% O2/5% CO2) through solution", "[Prepa... |
59,297 | Useful methods 3: Media for in vitro-cultivation of duckweed | 4 | null | https://www.protocols.io/view/useful-methods-3-media-for-in-vitro-cultivation-of-b559q896 | Klaus-J. Appenroth | TITLE: Useful methods 3: Media for in vitro-cultivation of duckweed
AUTHORS: Klaus-J. Appenroth
[DESCRIPTION]
This protocol details about various media for in vitro-cultivation of duckweed. It contains protocols from the The International Steering Committee on Duckweed Research and Application (ISCDRA) Newsletter. A c... | ["[Modified Steinberg-Medium] From stock solution 1 to 3, use 20 mL per litre ready-to-use media. \n Stock Compound Stock concentration Final concentration 1 KNO3 (101.1) 173mM 17.50 g/L 3.46 mM KH2PO4 (136.1) 33mM 4.50 g/L 0.66 mM K2HPO4x3H2O (228.2) 0.63 g/L 3.6mg/L 72 μM 2... |
24,793 | 96-well Growth Curve Analysis | null | dx.doi.org/10.17504/protocols.io.4fzgtp6 | null | Norman van Rhijn, Panagiotis Papastamoulis, Takanori Furukawa, Elaine Bignell, Mike Bromley, Magnus Rattray | TITLE: 96-well Growth Curve Analysis
AUTHORS: Norman van Rhijn, Panagiotis Papastamoulis, Takanori Furukawa, Elaine Bignell, Mike Bromley, Magnus Rattray
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Generally, growth assays for filamentous fungi have been performed on solid media, either as... | ["[Pre-processing]\nImport the file from the previous protocol into R studio.\n{\"blocks\":[{\"key\":\"cm990\",\"text\":\"Generally, growth assays for filamentous fungi have been performed on solid media, either as dilution series or spot tests. However, the solid media environment does not accurately mimic the environ... |
33,084 | Dissociation of fresh colorectal biopsies | 1 | dx.doi.org/10.17504/protocols.io.bci4iugw | https://www.protocols.io/view/dissociation-of-fresh-colorectal-biopsies-bci4iugw | Alan Simmons, Ken Lau | TITLE: Dissociation of fresh colorectal biopsies
AUTHORS: Alan Simmons, Ken Lau
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Current procedures for the dissociation of intestinal biopsies (<50mg)</div></div>
[STEPS]
?. [Reciept / Grossing]
Upon reciept, inspect tissue and record information such... | ["[Reciept / Grossing]\nUpon reciept, inspect tissue and record information such as: Accession # and other relevant collection metadata Size - this can be as simple as drawing a spot the size of the tissue with description (flat, round, etc.) Appearance Presence of blood Weight - in the interest of movin... |
null | null | null | dx.doi.org/10.17504/protocols.io.q58dy9w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is a protocol for running an illumina Hiseq4000 sequencer, following the process from the loaded flow cells through the sequencing run. The HiSeq 4000 uses a dual flow cell capable of processing over 400 Gb per day or 1.5 Tb per run, with up to 5 billion single reads. Se... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ki7cuhn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div title="Page 53">
<div>
<div>
<p>TG in plasma was measured with the calibrated automated thrombogram (CAT) assay as developed by Hemker and co-workers [18-20]. Briefly, 80 μl platelet poor plasma (PPP) was mixed with 20 μl of a mixture containing tissue factor (Dade-Behring)... | [] |
66,360 | F1 Keto ACV Gummies Reviews! Shocking Benefits! Scam Or Legit! | 1 | dx.doi.org/10.17504/protocols.io.yxmvmn42og3p/v1 | https://www.protocols.io/view/f1-keto-acv-gummies-reviews-shocking-benefits-scam-cc2ysyfw | Acv keto Gummies, justin furry | TITLE: F1 Keto ACV Gummies Reviews! Shocking Benefits! Scam Or Legit!
AUTHORS: Acv keto Gummies, justin furry
[DESCRIPTION]
F1 Keto ACV Gummies: Is It GoKeto Gummies? Keto F1 Scam (Exposed 2022) Shark Tank Weight Loss Gummies!
Official Website : Click Here
The load on the higher side can preclude you from doing loads... | [] |
32,293 | CODEX Antibody Staining Protocol for FFPE tissues | null | dx.doi.org/10.17504/protocols.io.bbsdina6 | null | Marda Jorgensen, Jerelyn Nick | TITLE: CODEX Antibody Staining Protocol for FFPE tissues
AUTHORS: Marda Jorgensen, Jerelyn Nick
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the method for antibody staining of FFPE tissues on coverslips using CODEX Barcoded Antibodies. Included are the stepwise protoco... | ["[Tissue Pre-treatment ent]\nTurn on the heating plate and set it at 55°C.\n55 °C", "Once the heating plate has reached 55°C, retrieve the FFPE samples on poly-l-Lysine treated coverslip(s) from 4°C storage.\n55 °C", "Using bent tip forceps, place the sample coverslip(s) on the hot plate with the tissue facin... |
84,864 | Metabolic programs drive function of therapeutic NK cells in hypoxic tumor environments | 2 | dx.doi.org/10.17504/protocols.io.5qpvo3y9xv4o/v1 | https://www.protocols.io/view/metabolic-programs-drive-function-of-therapeutic-n-cw48xgzw | Philippa R Kennedy | TITLE: Metabolic programs drive function of therapeutic NK cells in hypoxic tumor environments
AUTHORS: Philippa R Kennedy
[DESCRIPTION]
A collection of protocols associated with the publication 'Metabolic programs drive function of therapeutic NK cells in hypoxic tumor environments' by Kennedy et al.
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.nmbdc2n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Background:</strong> Acute lung injury is a life threatening condition often requiring mechanical ventilation. Lung-protective ventilation with tidal volumes of 6 mL/kg predicted body weight (PBW, based on sex and body height), is part of current recommended ventilati... | [] |
29,990 | Protocol for Pig Vagus Nerve Microdissection and Histology | 1 | dx.doi.org/10.17504/protocols.io.9ieh4be | https://www.protocols.io/view/protocol-for-pig-vagus-nerve-microdissection-and-h-9ieh4be | Megan Settell, Bruce E Knudsen, Andrea L McConico, Kip A Ludwig | TITLE: Protocol for Pig Vagus Nerve Microdissection and Histology
AUTHORS: Megan Settell, Bruce E Knudsen, Andrea L McConico, Kip A Ludwig
[STEPS]
?. Protocol for Histological AnalysisMicrodissection: 1. Following surgical experimental protocol and euthanasia, we further exposed either the right or left side vagus ... | ["Protocol for Histological AnalysisMicrodissection: 1. Following surgical experimental protocol and euthanasia, we further exposed either the right or left side vagus nerve. 2. We exposed the length of the vagus nerve from the pharyngeal branch to the recurrent laryngeal bifurcation using careful dissection, so ... |
98,795 | Longitudinal [18F]SynVesT-1 PET targeting SV2A in PPMI (PPMI SV2A PET Imaging) | 0 | dx.doi.org/10.17504/protocols.io.eq2lywp9evx9/v1 | https://www.protocols.io/view/longitudinal-18f-synvest-1-pet-targeting-sv2a-in-p-dcqj2vun | Kenneth Marek | TITLE: Longitudinal [18F]SynVesT-1 PET targeting SV2A in PPMI (PPMI SV2A PET Imaging)
AUTHORS: Kenneth Marek
[DESCRIPTION]
This protocol details the longitudinal [18F]SynVesT-1 PET targeting SV2A in PPMI (PPMI SV2A PET Imaging).
[GUIDELINES]
Appendix 1 – PPMI SV2A PET Imaging Schedule of Activities
[STE... | ["[PURPOSE OF STUDY] The overall goal of this protocol is to investigate [18F]SynVesT-1 binding in prodromal and manifest Parkinson’s Disease (PD) and to determine the change in [18F]SynVesT-1 binding in PD participants during a 24-month interval.", "[PURPOSE OF STUDY] Primary Objectives", "[PURPOSE OF STUDY] To compar... |
37,751 | Coverslipping: Use of the Leica CV5030 Coverslipper | 1 | dx.doi.org/10.17504/protocols.io.bg4xjyxn | https://www.protocols.io/view/coverslipping-use-of-the-leica-cv5030-coverslipper-bg4xjyxn | Allen Institute for Brain Science | TITLE: Coverslipping: Use of the Leica CV5030 Coverslipper
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the coverslipping of glass slides with the Leica CV5030.</div><div class = "text-block"><span style = "font-weight:bold;">Note... | [] |
91,721 | SOP52v1_TGD_IIDP-HIGISampleProcessing_Public | 4 | null | https://www.protocols.io/view/sop52v1-tgd-iidp-higisampleprocessing-public-c5thy6j6 | Varsha Rajesh | TITLE: SOP52v1_TGD_IIDP-HIGISampleProcessing_Public
AUTHORS: Varsha Rajesh
[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 Stanford University.... | ["[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 ... |
102,394 | Human Embryonic Kidney Cells (HEK-293) | 0 | dx.doi.org/10.17504/protocols.io.x54v92741l3e/v1 | https://www.protocols.io/view/human-embryonic-kidney-cells-hek-293-df823rye | Md Razaul Karim | TITLE: Human Embryonic Kidney Cells (HEK-293)
AUTHORS: Md Razaul Karim
[DESCRIPTION]
This protocol details the Human Embryonic Kidney Cells (HEK-293) culture.
[STEPS]
SECTION: Day-01 (Mon)
1. Plating with DMEM full media .
SECTION: Day-01 (Mon)
2. Warm DMEM full media, PBS, and Trypsin in the 37 °C bead bath for 30 m... | ["[Day-01 (Mon)] Plating with DMEM full media .", "[Day-01 (Mon)] Warm DMEM full media, PBS, and Trypsin in the 37 °C bead bath for 30 min. Clean the working area by using 70% ethanol.", "[Day-01 (Mon)] Sup out old media without touching cells.", "[Day-01 (Mon)] Wash by adding 5 mL PBS slowly, rinse, and rock back and ... |
20,575 | Aliquotting PCR Primer Mixture | null | dx.doi.org/10.17504/protocols.io.yb7fsrn | null | Kenneth Schackart | TITLE: Aliquotting PCR Primer Mixture
AUTHORS: Kenneth Schackart
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">How to take lyophilized PCR primers and dilute and aliquot into useful quantities and concentrations.</div></div>
[STEPS]
?. [Dilute primers to 100 μM]
Add the volume of nuclease-free wa... | ["[Dilute primers to 100 μM]\nAdd the volume of nuclease-free water to each tube according to the documentation provided by the primer.In the case of E. coli K12, the following volumes are to be used: AB1OligoVolume2F184031552 μL3R18551728 μL\nAB1OligoVolume2F184031552 μL3R18551728 μL", "[Make 100 μL stock ]\nUse the ... |
82,531 | Ancient dental calculus sampling procedure for optical microscopic analysis | 4 | dx.doi.org/10.17504/protocols.io.q26g7yqpkgwz/v1 | https://www.protocols.click/view/ancient-dental-calculus-sampling-procedure-for-opt-cuubwwsn | Dulce Neves, Emanuela Cristiani, António Faustino Carvalho, Ana Maria Silva | TITLE: Ancient dental calculus sampling procedure for optical microscopic analysis
AUTHORS: Dulce Neves, Emanuela Cristiani, António Faustino Carvalho, Ana Maria Silva
[DESCRIPTION]
This protocol describes how to sample dental calculus from individual teeth for optical microscopy analysis. The primary use-case is for ... | ["[Sampling preparation and dental calculus collection] Display aluminum foil on the working table and carefully collect the dental calculus deposit using a sterile disposable blade and under the magnifying lens", "[Sampling preparation and dental calculus collection] Clean the working table surface using alcohol and p... |
86,757 | MGH Harvard SenNet Processing murine trachea for paired single cell RNA-seq and mass spec | 4 | dx.doi.org/10.17504/protocols.io.81wgbxx93lpk/v1 | https://www.protocols.io/view/mgh-harvard-sennet-processing-murine-trachea-for-p-cyydxxs6 | gshipkovenska | TITLE: MGH Harvard SenNet Processing murine trachea for paired single cell RNA-seq and mass spec
AUTHORS: gshipkovenska
[DESCRIPTION]
Protocol for obtaining single cell suspension of murine trachea.
[STEPS]
SECTION: Dissection
2. Perfuse lungs via right ventricle.
SECTION: Dissection
3. Dissect out trachea and lungs ... | ["[Dissection] Perfuse lungs via right ventricle.", "[Dissection] Dissect out trachea and lungs and place in HBSS on ice.", "[Dissection] Euthanize mice by CO2 method.", "[Dissection] Clean up the tracheas under the dissection microscope.", "[Dissection] Bi-sect the tracheas along the ventral side.", "[Single cell susp... |
87,676 | Soil eDNA Sample Collection Protocol | 4 | null | https://www.protocols.io/view/soil-edna-sample-collection-protocol-czu4x6yw | Stephen Douglas Russell | TITLE: Soil eDNA Sample Collection Protocol
AUTHORS: Stephen Douglas Russell
[DESCRIPTION]
**This protocol represents an initial working draft for citizen-science-based collecting and processing of soil samples for eventual eDNA analysis. This notice will be removed once the protocol has been tested and revised.**
Th... | ["[Ordering the kit] This protocol requires that you have a Soil eDNA Sample Collection Kit from Mycota Lab. They can be ordered online here:\n\nhttp://www.mycota.com", "[Once you receive the kit] Join the \"Fungal eDNA Initiative\" iNaturalist Project. With Android, it is sometimes easiest to search and join the proje... |
null | null | null | dx.doi.org/10.17504/protocols.io.g2mbyc6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Detailed cell electroporation protocol from paper:</p>
<p><em>Probing cytoskeletal modulation of passive and active intracellular dynamics using nanobody-functionalized quantum dots</em><br />Eugene A Katrukha, Marina Mikhaylova, Hugo X van Brakel, Paul M van Bergen en Henego... | [] |
86,172 | Fixation of Breast Tissue from Komen Tissue Bank into FFPE or PFPE blocks and frozen tissue | 4 | dx.doi.org/10.17504/protocols.io.bp2l6x9prlqe/v1 | https://www.protocols.io/view/fixation-of-breast-tissue-from-komen-tissue-bank-i-cyd4xs8w | kschneider | TITLE: Fixation of Breast Tissue from Komen Tissue Bank into FFPE or PFPE blocks and frozen tissue
AUTHORS: kschneider
[DESCRIPTION]
FFPE blocks and frozen blocks were created as in protocol 005v8.0 and PFPE blocks were created as in protocol 005v5.0 from the Komen Tissue Bank.
[STEPS] | [] |
62,706 | Green Otter CBD Gummies Reviews - How It Works | 1 | dx.doi.org/10.17504/protocols.io.261gen2m7g47/v1 | https://www.protocols.io/view/green-otter-cbd-gummies-reviews-how-it-works-b9gsr3we | greenotterreviews | TITLE: Green Otter CBD Gummies Reviews - How It Works
AUTHORS: greenotterreviews
[DESCRIPTION]
Green Otter CBD Gummies Reviews - How It Works
[STEPS]
1. Green Otter CBD Gummies Reviews - How It Works
Green Otter CBD Gummies Review Kentucky USA It's an amazing supplement that may help you escape from all your healt... | ["Green Otter CBD Gummies Reviews - How It Works\nGreen Otter CBD Gummies Review Kentucky USA It's an amazing supplement that may help you escape from all your health issues. It's a popular product from which numerous people have served. The company which sells this product has said that this product may help you in fi... |
97,398 | Electromyogram recordings for internal capsule stimulations in non-human primates | 0 | dx.doi.org/10.17504/protocols.io.rm7vzjn8xlx1/v1 | https://www.protocols.io/view/electromyogram-recordings-for-internal-capsule-sti-dbcw2ixe | Lucy Liang, Elvira Pirondini, Jonathan C Ho | TITLE: Electromyogram recordings for internal capsule stimulations in non-human primates
AUTHORS: Lucy Liang, Elvira Pirondini, Jonathan C Ho
[DESCRIPTION]
EMG recordings is a common method to confirm implant location. In this protocol, we describe steps to perform EMG recordings during an internal capsule stimulator ... | ["[Needle electrode implants] Make a small incision on the forearm opposite to the side of the internal capsule (IC) electrode implant.", "[Needle electrode implants] Locate the flexor carpi radialis and/or any other muscle of interest, stimulate at around 1mA, 1Hz with bipolar probe electrode to confirm muscle.", "[IC... |
80,142 | Chemical degradation and determination of pheomelanin and eumelanin markers | 1 | dx.doi.org/10.17504/protocols.io.36wgqjz43vk5/v1 | https://www.protocols.io/view/chemical-degradation-and-determination-of-pheomela-cshnwb5e | Kazumasa Wakamatsu | TITLE: Chemical degradation and determination of pheomelanin and eumelanin markers
AUTHORS: Kazumasa Wakamatsu
[DESCRIPTION]
This is protocol involving chemical oxidation and reduction methods followed by high performance liquid chromatography (HPLC) detection of markers for pheomelanin and eumelanin.
[STEPS]
1. Homo... | ["Homogenize samples in water with Ten-Broeck glass homogenizer at a concentration of 10 mg/mL (if samples were < 5 mg, use 0.5 mL of water).", "100 µL aliquots are then subjected to the chemical reactions.", "Oxidation: Oxidize samples with 1.5% H2O2/K2CO3. After termination of reaction, leave mixtures for 20 hours at... |
18,514 | A systematic review of the barriers to and facilitators of the use of evidence utilised by philanthropists when determining which charities, including health charities or programmes to fund. | null | dx.doi.org/10.17504/protocols.io.wbsfane | null | Caroline Greenhalgh, Paul Montgomery | TITLE: A systematic review of the barriers to and facilitators of the use of evidence utilised by philanthropists when determining which charities, including health charities or programmes to fund.
AUTHORS: Caroline Greenhalgh, Paul Montgomery
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>To... | [] |
53,292 | SDS-PAGE Using TGX Acrylamide Kit--CHEM 584 | 4 | dx.doi.org/10.17504/protocols.io.byakpscw | https://www.protocols.io/view/sds-page-using-tgx-acrylamide-kit-chem-584-byakpscw | Ken Christensen | TITLE: SDS-PAGE Using TGX Acrylamide Kit--CHEM 584
AUTHORS: Ken Christensen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Prepare and run your SDS-PAGE gel using the Bio-Rad TGX gel system and the mini-PROTEAN gel box.</div></div>
[STEPS]
?. [Prepare the gel solutions and pour the gel]
Prepare th... | ["[Prepare the gel solutions and pour the gel]\nPrepare the resolving gel acrylamide solution by combining 2 mL of Resolver A & B solutions in a 15 mL tube.", "[Prepare the gel solutions and pour the gel]\nAdd 2 µL of TEMED and 20 µL of freshly prepared 10% w/v APS to the combined resolver solution and mix well. Use an... |
62,259 | Keto Start ACV Gummies - (2022 Update) Easy Way To Burn 1000s Calories - Get Good Shape Fast! | 3 | dx.doi.org/10.17504/protocols.io.n92ldz2y9v5b/v1 | https://www.protocols.io/view/keto-start-acv-gummies-2022-update-easy-way-to-bur-b82tryen | Keto Start ACV Gummies | TITLE: Keto Start ACV Gummies - (2022 Update) Easy Way To Burn 1000s Calories - Get Good Shape Fast!
AUTHORS: Keto Start ACV Gummies
[DESCRIPTION]
Keto Start ACV Gummies
[STEPS] | [] |
41,847 | DNA Quantification -- CHEM 584 | 1 | dx.doi.org/10.17504/protocols.io.bk4xkyxn | https://www.protocols.io/view/dna-quantification-chem-584-bk4xkyxn | Alba Balletbó, Ken Christensen | TITLE: DNA Quantification -- CHEM 584
AUTHORS: Alba Balletbó, Ken Christensen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol adapted from the NanoDrop Spectrophotometer User’s Manual. </div></div>
[STEPS]
?. Start a new experiment using the Nanodrop touchscreen.
?. Click on the correspond... | ["Start a new experiment using the Nanodrop touchscreen.", "Click on the corresponding application module (e.g., dsDNA).", "Open the sampling arm and load a blank sample (e.g., TE Buffer, MQ Water, etc.).\n2 µl", "Close the sampling arm on the machine to cover the blank sample.", "Click \"OK\" to read the blank if the ... |
85,806 | Binding Assay (His-tagged proteins) | 1 | dx.doi.org/10.17504/protocols.io.261gednqdv47/v1 | https://www.protocols.io/view/binding-assay-his-tagged-proteins-cx2nxqde | Terran D Stenger, Philippa R Kennedy | TITLE: Binding Assay (His-tagged proteins)
AUTHORS: Terran D Stenger, Philippa R Kennedy
[DESCRIPTION]
To assess the binding specificity of tri-specific killer engagers (TriKEs) to their intended target, we utilize a flow cytometry-based binding assay leveraging the 10x polyhistidine (His) tag present on the TriKE con... | ["[Live/Dead Staining and Fc Block] Prepare a solution of L/D NIR", "[Cell Preparation] Cells are resuspended in R10 at 1.5 million cells/mL, and 200 µL (300k cells) are plated in each well in a U bottom 96 well plate.", "[Cell Preparation] 300 x g, 5 min The plate is spun in a centrifuge at 300g for 5 min (this is app... |
32,033 | Detection of viable Dichelobacter nodosus by real-time PCR using PMAxx™ | null | dx.doi.org/10.17504/protocols.io.bbh9ij96 | null | Peter Kuhnert, Tobias Hidber | TITLE: Detection of viable Dichelobacter nodosus by real-time PCR using PMAxx™
AUTHORS: Peter Kuhnert, Tobias Hidber
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-style:italic;">Dichelobacter nodosus</span><span> is a gram-negative fastidious anaerobic bacterium and the causati... | ["[PMAxx treatment]\nplace or dissolve your sample containing Dichelobacter nodosus in a total voulme of 50 µl 0.85% NaCl in a transparent 1.5 ml tube", "[PMAxx treatment]\nin a darkened room add 100 µM (0.25 µl) of PMAxx™ to the tube", "[PMAxx treatment]\nvortex and incubate for 3 min at room temperature in a metal bo... |
18,153 | bright field big patch swarming imaging | null | dx.doi.org/10.17504/protocols.io.vyhe7t6 | null | Serena Ding | TITLE: bright field big patch swarming imaging
AUTHORS: Serena Ding
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">For imaging swarming behaviour of 40 young adult C. elegans on a big food patch on agar using the Phoenix multi-worm tracker system. Worms are synchronised by bleaching and refeeding f... | ["[Imaging plate preparation (Day -7)]\nA separate batch of imaging plates is poured exactly seven days before each imaging day and stored at 4°C.\nImaging plates are 35 mm Petri dishes containing 3.5 mL low peptone (0.013% Difco Bacto) NGMagar (2% Bio/Agar, BioGene) to limit bacteria growth.", "[Bleach synchronising w... |
60,042 | Characterization of osmoregulated periplasmic glucans with high resolution LCMS | 1 | dx.doi.org/10.17504/protocols.io.36wgq7djkvk5/v1 | https://www.protocols.io/view/characterization-of-osmoregulated-periplasmic-gluc-b6vire4e | lcmsmethods , Benjamin C. Orsburn, Colten Eberhard, Allison Daitsch, Namandje N. Bumpus | TITLE: Characterization of osmoregulated periplasmic glucans with high resolution LCMS
AUTHORS: lcmsmethods , Benjamin C. Orsburn, Colten Eberhard, Allison Daitsch, Namandje N. Bumpus
[DESCRIPTION]
Characterization of osmoregulated periplasmic glucans with high resolution LCMS
[STEPS]
1.
These are optimized ... | ["These are optimized methods for the characterization of osmoregulated periplasmic glucans as described in Allison Daitsch et al., 2022. \nBriefly: All analysis was performed on a Dionex UHPLC and Q Exactive quadrupole Orbitrap system (Thermo Fisher). Two micrograms of each reaction and unreacted input was injected di... |
12,410 | Phospholipid fatty acid (PLFA) analysis | 1 | dx.doi.org/10.17504/protocols.io.6qpvrj7ogmkn/v1 | https://www.protocols.io/view/phospholipid-fatty-acid-plfa-analysis-qc2dsye | Eva Petrova, Roey Angel | TITLE: Phospholipid fatty acid (PLFA) analysis
AUTHORS: Eva Petrova, Roey Angel
[DESCRIPTION]
Phospholipid fatty acid (PLFA) purification and analysis
[BEFORE_START]
Supplies and Reagents
Extraction
Supplies: Centrifuge bottles, Pipettes, test tubes, funnels, filter papers, Pasteur pipettes, beakers
... | ["[Extraction of Lipids from Soils -First Extraction] Add 5 g of soil (fresh mass) to a centrifuge bottle (250 mL).\n5 6", "[Extraction of Lipids from Soils -First Extraction] Add 5 mL of chloroform, 10 mL of methanol, and 4 mL of phosphate buffer* minus the water content of the soil. 1 mL of chloroform for each g of s... |
95,158 | ssDNA2.0: Ligation mix I | 3 | dx.doi.org/10.17504/protocols.io.6qpvr3j6bvmk/v1 | https://www.protocols.io/view/ssdna2-0-ligation-mix-i-c86wzzfe | Matthias Meyer, Sarah Nagel, Anna Schmidt | TITLE: ssDNA2.0: Ligation mix I
AUTHORS: Matthias Meyer, Sarah Nagel, Anna Schmidt
[DESCRIPTION]
Protocol for the preparation of Ligation mix I for the first adapter ligation in automated single-stranded DNA library preparation using the ssDNA2.0 method (Gansauge et al. 2020).
References
Gansauge, M.-T., Aximu-Petri... | [] |
95,605 | Protocol for "immunoperoxidase detection of alpha-synuclein in non-human primate brain samples | 0 | dx.doi.org/10.17504/protocols.io.8epv5x4wdg1b/v1 | https://www.protocols.io/view/protocol-for-34-immunoperoxidase-detection-of-alph-c9kvz4w6 | jlanciego | TITLE: Protocol for "immunoperoxidase detection of alpha-synuclein in non-human primate brain samples
AUTHORS: jlanciego
[DESCRIPTION]
Here an step-by-step protocol is provided summarizing the immunoperoxidase detection of neurons expressing alpha-synuclein in the macaque brain. Enclosed image illustrates layer V ... | ["[Immunoperoxidase protocol (all steps below are conducted in free-floating sections and at room temperature unless otherwise noted)] Frozen coronal sections (40 microns-thick) to be obtained in a sliding microtome (Leica HM400) and collected in 0.125 M phosphate buffer (PB) pH 7.4 as 10 series of adjacent sections.",... |
null | null | null | dx.doi.org/10.17504/protocols.io.t6ceraw | null | null | TITLE: No Title
AUTHORS:
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ef8bbrw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p class="p1"><span class="s1">Hurwitz, Bonnie L., and Matthew B. Sullivan. "The Pacific Ocean Virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology." <em>PLoS One</em> 8.2 (2013): e57355.</span></p>
[STEPS]
?.
?.
?.
... | [] |
73,921 | iNDI Papain Dissociation protocol for iNeurons Version 1 | 4 | dx.doi.org/10.17504/protocols.io.ewov1oddylr2/v1 | https://www.protocols.click/view/indi-papain-dissociation-protocol-for-ineurons-ver-cke9uth6 | Erika Lara Flores, Joel Reyes, Mark Cookson, Michael Ward | TITLE: iNDI Papain Dissociation protocol for iNeurons Version 1
AUTHORS: Erika Lara Flores, Joel Reyes, Mark Cookson, Michael Ward
[DESCRIPTION]
Proteolytic enzymes are widely used in cell dissociation and papain has proved less damaging with some tissues and neuronal cultures and more effective than other proteases.... | ["[Preparation of Reagents] Equilibrate EBSS/phenol red with 95%O2:5%CO2 in incubator for several hours of overnight.", "[Preparation of Reagents] Reconstitute the Ovomucoid mixture (Papain inhibitor-PI) by adding 32 mL of EBSS and allow contents to dissolve. This will yield solution at an effective concentration of 10... |
73,758 | 16S_PCR_Sequence_Analysis | 4 | dx.doi.org/10.17504/protocols.io.6qpvr49e3gmk/v1 | https://www.protocols.io/view/16s-pcr-sequence-analysis-cj96ur9e | Kenneth Acosta | TITLE: 16S_PCR_Sequence_Analysis
AUTHORS: Kenneth Acosta
[DESCRIPTION]
Protocol to generate a consensus 16S rRNA gene sequence from forward and reverse sequences.
[STEPS]
SECTION: Adding U515 sequence feature
1. Open Serial Cloner.
SECTION: Adding U515 sequence feature
2. Go to “Features” → “Manage Features”.
S... | ["[Adding U515 sequence feature] Open Serial Cloner.", "[Adding U515 sequence feature] Go to “Features” → “Manage Features”.", "[Adding U515 sequence feature] Add new collection. Name “16S rRNA Gene Conserved Regions”.", "[Adding U515 sequence feature] Add new feature. Name “U515”. Add sequence “GTGCCAGCAGCCGCGGTAA”.",... |
16,582 | AutoCUT&RUN: genome-wide profiling of chromatin proteins in a 96 well format on a Biomek | null | dx.doi.org/10.17504/protocols.io.ufeetje | null | Derek Janssens, Kami Ahmad, Steven Henikoff | TITLE: AutoCUT&RUN: genome-wide profiling of chromatin proteins in a 96 well format on a Biomek
AUTHORS: Derek Janssens, Kami Ahmad, Steven Henikoff
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>CUT&RUN is an antibody-targeted nuclease-cleavage method that profiles the genome-wide occupancy ... | ["[Binding cells to beads]\nHarvest fresh culture(s) at room temperature and count cells. The AutoCUT&RUN protocol is recommended for 50,000 to 1,000,000 mammalian cells per sample. Tissue samples can also be profiled using AutoCUT&RUN and should be processed either manually or enzymatically into a homogenous suspensio... |
72,158 | RSV whole genome sequencing using ONT | 1 | dx.doi.org/10.17504/protocols.io.6qpvr4432gmk/v1 | https://www.protocols.io/view/rsv-whole-genome-sequencing-using-ont-cip6udre | Kseniia Komissarova | TITLE: RSV whole genome sequencing using ONT
AUTHORS: Kseniia Komissarova
[DESCRIPTION]
Respiratory Syncytial Virus (RSV) is a leading cause of hospitalization due to acute lower respiratory infection in infants and young children. Monoclonal antibodies palivizumab is available option for treating RSV limited to sele... | ["Order primers according to the list from your local manufacturer", "Briefly vortex and centrifuge defrosted reagents before use.\nPrepare four RT-qPCR reactions for every RNA sample you need to amplify for sequencing. \nUse one pair of primers above (forward and reverse) per reaction\nPrepare the PCR reaction mixture... |
null | null | null | dx.doi.org/10.17504/protocols.io.h5cb82w | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?. | [] |
68,880 | In vitro kinase activity | 1 | dx.doi.org/10.17504/protocols.io.kxygxzr2kv8j/v1 | https://www.protocols.io/view/in-vitro-kinase-activity-cfhqtj5w | Xinbo Wang, Pietro De Camilli | TITLE: In vitro kinase activity
AUTHORS: Xinbo Wang, Pietro De Camilli
[DESCRIPTION]
This protocol details methods for the in vitro kinase activity testing of purified LRRK2.
[STEPS]
SECTION: In vitro kinase activity
1. Set up the reaction mixtures with 1x kinase buffer (diluted from 10x kinase buffer), 200 nanomolar... | ["[In vitro kinase activity] Set up the reaction mixtures with 1x kinase buffer (diluted from 10x kinase buffer), 200 nanomolar (nM) LRRK2 or 8 µg Rab8 protein, for the reaction group add 1 millimolar (mM) ATP, and for the control add H2O instead, the total volume we used is 40 µL.", "[In vitro kinase activity] Incubat... |
74,426 | Public Charité/BIH protocols | 2 | null | https://www.protocols.io/view/public-charit-bih-protocols-ckw2uxge | René Bernard | TITLE: Public Charité/BIH protocols
AUTHORS: René Bernard
[DESCRIPTION]
This a list of existing, published protocols from Charité and BIH community.
[STEPS] | [] |
69,222 | PSI FluorCAM protocol for Rapid Light Curve with far red pre-ilumination. | 4 | dx.doi.org/10.17504/protocols.io.x54v9deypg3e/v1 | https://www.protocols.io/view/psi-fluorcam-protocol-for-rapid-light-curve-with-f-cfuetnte | Andrei Herdean | TITLE: PSI FluorCAM protocol for Rapid Light Curve with far red pre-ilumination.
AUTHORS: Andrei Herdean
[DESCRIPTION]
PSI FluorCAM protocol for Rapid Light Curve with far red pre-ilumination.
[STEPS]
SECTION: PSI FluorCAM protocol for Rapid Light Curve with far red pre-ilumination.
1. Load the following script in ... | ["[PSI FluorCAM protocol for Rapid Light Curve with far red pre-ilumination.] Load the following script in to the FluorCam software", "[PSI FluorCAM protocol for Rapid Light Curve with far red pre-ilumination.] TS=50ms\n;Rapid light curve in Actinic light 2 for TOMI-2\n;version November 11, 2020\n;with FilterWheel\n;hi... |
27,304 | Freezing Fresh Tissue | null | dx.doi.org/10.17504/protocols.io.6wghfbw | null | Jamie Allen, Maya Brewer, Elizabeth Neumann, Danielle Gutierrez, Mark deCaestecker, Jeff Spraggins | TITLE: Freezing Fresh Tissue
AUTHORS: Jamie Allen, Maya Brewer, Elizabeth Neumann, Danielle Gutierrez, Mark deCaestecker, Jeff Spraggins
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Scope:</div><div class = "text-block">To describe the procedure for freezing fresh tissue procured from the Coopera... | ["[Freezing and Documentation]\nPlace a layer of dry ice in to box and add enough isopentane to make a slurry.", "[Freezing and Documentation]\nLabel embedding molds and add a small amount of CMC to each one (barely cover the bottom).", "[Freezing and Documentation]\nRemove sample cup from ice and document on sample sh... |
97,615 | Protocols for entomotoxicological developmental study of Phormia regina (Megnin) | 0 | dx.doi.org/10.17504/protocols.io.n2bvjnrpngk5/v1 | https://www.protocols.io/view/protocols-for-entomotoxicological-developmental-st-dbjp2kmn | Hayden S. McKee-Zech, Charity Owings | TITLE: Protocols for entomotoxicological developmental study of Phormia regina (Megnin)
AUTHORS: Hayden S. McKee-Zech, Charity Owings
[DESCRIPTION]
This protocol was developed specifically for examining the impact of drug exposure on forensically important phenotypes (i.e., developmental duration, size, survivorship) ... | ["[Egg collection] Fly colonies should be presented with a fresh protein source daily for ~1 week prior to the start of experiments. For this experiment, we exposed colonies to a kimwipe soaked in chicken blood in a 3 oz bath cup each day.", "[Egg collection] 24 - 48 hours prior to the start of experiments, provide the... |
null | null | null | dx.doi.org/10.17504/protocols.io.mdhc236 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Automated fibrosis analysis using Orbit module, is based on this modified masson trichrome staining protocol</p>
[STEPS] | [] |
102,094 | DNA Extraction from Sterivex Filters | 4 | dx.doi.org/10.17504/protocols.io.5qpvoym5xg4o/v2 | https://www.protocols.io/view/dna-extraction-from-sterivex-filters-dfxn3pme | Christopher Neil Thornton, William Brazelton | TITLE: DNA Extraction from Sterivex Filters
AUTHORS: Christopher Neil Thornton, William Brazelton
[DESCRIPTION]
Modified 2015 by the Brazelton Lab from protocols by Rika Anderson, Colleen Kellogg, Julie Huber, and Byron Crump. Incorporated some recommendations from Lever et al. (2015) Frontiers in Microbiology doi: 10... | ["[Hot Lysis] Add 1.4 mL of DEB to each Sterivex with syringe and needle. Position the needle just below the mouth of the Sterivex so that it does not come back out the top. Do not fill to the top – stop when solution covers white filter. Possible Stopping Point. Store at 20ºC", "[Hot Lysis] Possible Stopping Point. S... |
100,051 | KAT8 compound inhibition inhibits the initial steps of PINK1-dependant mitophagy | 4 | dx.doi.org/10.17504/protocols.io.eq2ly7m8qlx9/v2 | https://www.protocols.io/view/kat8-compound-inhibition-inhibits-the-initial-step-ddxt27nn | Capucine de Talhouet, Benjamin O'Callaghan, Noemi Esteras Gallego, Helene Plun-Favreau | TITLE: KAT8 compound inhibition inhibits the initial steps of PINK1-dependant mitophagy
AUTHORS: Capucine de Talhouet, Benjamin O'Callaghan, Noemi Esteras Gallego, Helene Plun-Favreau
[DESCRIPTION]
It has recently been shown that KAT8, a genome-wide association study candidate risk gene for Parkinson’s Disease, is inv... | ["[Cell Culture] Maintain cells in culture in a humified 5% CO2 incubator at 37 °C in Dulbecco's modified Eagle's medium (DMEM, Gibco, 11995-065) supplemented with 10% heat-inactivated foetal bovine serum (FBS, Gibco). Change cell medium every 3 days.", "[Cell Culture] Split cells at 75% to 90% confluency using 2 mL of... |
92,695 | Protocol for assembly of a serine integrase-based platform for functional validation of genetic switch controllers in eukaryotic cells-Plant | 1 | dx.doi.org/10.17504/protocols.io.eq2lyj4owlx9/v1 | https://www.protocols.io/view/protocol-for-assembly-of-a-serine-integrase-based-c6rxzd7n | Marco A. de Oliveira, Lilian H. Florentino, Thais T. Sales, Rayane N. Lima, Luciana R. C. Barros, Cintia G. Limia, Mariana S. M. Almeida, Maria L. Robledo, Leila M. G. Barros, Eduardo O. Melo, Daniela M. Bittencourt, Stevens K. Rehen, Martín H. Bonamino, Elibio Rech | TITLE: Protocol for assembly of a serine integrase-based platform for functional validation of genetic switch controllers in eukaryotic cells-Plant
AUTHORS: Marco A. de Oliveira, Lilian H. Florentino, Thais T. Sales, Rayane N. Lima, Luciana R. C. Barros, Cintia G. Limia, Mariana S. M. Almeida, Maria L. Robledo, Leila M... | ["[Plant growth ● Timing 4–6 weeks] Grow Arabidopsis thaliana ecotype Columbia plants in a 150 mL plastic cup with aerated, moist, fertilized and autoclaved soil in an environmentally controlled chamber with a medium photoperiod (12 h light/12 h dark at 22 °C) under low light (optimum light is approximately 150 µE.m-2.... |
99,758 | Staining Spores for Conidia Counting | 0 | dx.doi.org/10.17504/protocols.io.6qpvr8462lmk/v1 | https://www.protocols.io/view/staining-spores-for-conidia-counting-ddnn25de | IAC, Sara de Oliveira Olimpio, Rebecca Ogioni | TITLE: Staining Spores for Conidia Counting
AUTHORS: IAC, Sara de Oliveira Olimpio, Rebecca Ogioni
[DESCRIPTION]
Methylene blue has different functions depending on its concentration. Its use allows the visualization of dead tissues and bacteria, for example. As a solution, this dye allows the identification of microo... | ["[Procedure] Add sample in 1,5 mL tube;", "[Procedure] Add 100 uL of methylene blue dye;", "[Procedure] Homogenize by vortexing for 10 seconds and wait 2 minutes;", "[Procedure] Centrifuge for 1 minute at 16.000g;", "[Procedure] Pipette 50 uL into the Neubauer chamber or microscope slide and cover with a cover slip;",... |
41,212 | DetectXRv Kit | 4 | dx.doi.org/10.17504/protocols.io.bkg4ktyw | https://www.protocols.io/view/detectxrv-kit-bkg4ktyw | bkatchman | TITLE: DetectXRv Kit
AUTHORS: bkatchman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The Detect</span><span style = "vertical-align:super;">X</span><span>-Rvtest is a test based on end-point reverse transcription polymerase chain reaction (RT-PCR) coupled to DNA microarray hybridization fo... | ["[RNA Extraction]\n-\tExtract RNA with the Zymo Research Quick-DNA/RNA Viral MagBead Kit (R2140 or R2141): For a complete description view the Zymo Research Quick-DNA/RNA Viral MagBead Kit product insert. Follow the manufacturer’s guidelines for the proper use and procedure for this product.", "[RNA Extraction]\n-\tPl... |
null | null | null | dx.doi.org/10.17504/protocols.io.jhhcj36 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This collection of protocols will help you to get started with computational resources needed for the class. We will also get accounts for each of these resources.</p>
[STEPS] | [] |
57,888 | RNAi induction | 4 | dx.doi.org/10.17504/protocols.io.5qpvobb7xl4o/v1 | https://www.protocols.io/view/rnai-induction-b4r8qv9w | Ben Jenkins | TITLE: RNAi induction
AUTHORS: Ben Jenkins
[DESCRIPTION]
Back-dilution, induction, and creating frozen E. coli feeding stocks for downstream RNAi
[STEPS]
SECTION: Induction
6. Incubate with shaking at
SECTION: Induction
7. Add 60 µL (0.4 millimolar (mM)) IPTG
# This induces template expression within the L4440 p... | ["[Induction] Incubate with shaking at", "[Induction] Add 60 µL (0.4 millimolar (mM)) IPTG \n\n# This induces template expression within the L4440 plasmid construct", "[Induction] Incubate with shaking at", "[Match OD and freeze] Spin down E. coli at 3200 x g, 2 min", "[Match OD and freeze] Remove supernatant, and add ... |
83,418 | Western Blotting | 4 | dx.doi.org/10.17504/protocols.io.36wgq3rzklk5/v1 | https://www.protocols.click/view/western-blotting-cvp2w5qe | Eric ECS Cordeiro-Spinetti | TITLE: Western Blotting
AUTHORS: Eric ECS Cordeiro-Spinetti
[DESCRIPTION]
It's a classic
[STEPS]
SECTION: Before Starting
1.
Make RIPA buffer (to be used in 3 months after adding Nuclease)
RIPA buffer 100mL 50mM Tris HCl, PH 7.4 5mL (1M stock) 150mM NaCl 5mL (3M stock... | ["[Before Starting] Make RIPA buffer (to be used in 3 months after adding Nuclease)\n \n \n RIPA buffer 100mL 50mM Tris HCl, PH 7.4 5mL (1M stock) 150mM NaCl 5mL (3M stock) 1% Triton X-100 or NP-40 1 mL 0.1% SDS 1mL (10% supply center solutio... |
108,116 | Nutil Data Integration | 4 | dx.doi.org/10.17504/protocols.io.3byl4qrz8vo5/v2 | https://www.protocols.io/view/nutil-data-integration-dmtu46nw | Michael X. Henderson | TITLE: Nutil Data Integration
AUTHORS: Michael X. Henderson
[DESCRIPTION]
This protocol describes Nutil data integration from segmentation and registration of mouse brain data.
[STEPS]
SECTION: Nutil Data Quantification
1. Open Nutil and find operation tab.
SECTION: Nutil Data Quantification
2. Find the 3 folders y... | ["[Nutil Data Quantification] Open Nutil and find operation tab.", "[Nutil Data Quantification] Find the 3 folders you created at the beginning of this workflow and populated during the workflow and populate them into their corresponding list above. (segmentation is your input folder, brain atlas map folder is your atl... |
108,735 | Birchler De Allende - Using The Oxford Nanopore Ligation Sequencing Kit to Sequence Zebrafish Larvae | 0 | dx.doi.org/10.17504/protocols.io.n92ld8denv5b/v1 | https://www.protocols.io/view/birchler-de-allende-using-the-oxford-nanopore-liga-dne75bhn | Ian Birchler De Allende | TITLE: Birchler De Allende - Using The Oxford Nanopore Ligation Sequencing Kit to Sequence Zebrafish Larvae
AUTHORS: Ian Birchler De Allende
[DESCRIPTION]
Using The Oxford Nanopore Ligation Sequencing Kit to Sequence Zebrafish Larvae
[STEPS]
SECTION: Introduction
1. The protocols described outline methods for extrac... | ["[Introduction] The protocols described outline methods for extracting high-quality genomic DNA from zebrafish larvae for sequencing applications. The process typically begins with collecting a small tissue sample, such as a fin clip, from 3-day post-fertilization larvae. The QIAGEN DNeasy Blood & Tissue Kit is common... |
34,084 | 3D Printing Case for LED Controller | null | dx.doi.org/10.17504/protocols.io.bdici4aw | null | Jakub Nedbal | TITLE: 3D Printing Case for LED Controller
AUTHORS: Jakub Nedbal
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The electronics control circuit for the illuminated orbital shaker should be housed in a case to protect it from damage by short-circuit, but also to minimize injury by electrical current... | ["The electronics circuit has been designed in KiCAD. KiCAD PCB files can be opened in FreeCAD. This in turn allows exporting the 3D render of the PCB into an industry-standard STEP file format. The STEP file can then be imported into Onshape, which is a 3D CAD tool. Onshape was then used to create a 3D model of a case... |
42,264 | PLASMA- 01 - Plasma separation from human whole blood | 4 | dx.doi.org/10.17504/protocols.io.bmhyk37w | https://www.protocols.io/view/plasma-01-plasma-separation-from-human-whole-blood-bmhyk37w | Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino | TITLE: PLASMA- 01 - Plasma separation from human whole blood
AUTHORS: Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino
[STEPS]
?. Put whole blood (at least ) into a 5 mL tube.
1.5 mL
?. Centrifuge at
.justify:after {
content: ""... | ["Put whole blood (at least ) into a 5 mL tube.\n1.5 mL", "Centrifuge at \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 }\nCentrifuge: 1400 34, 5 min", "Carefully collect the supernatant (plasma). Do not touc... |
58,963 | Establishment of craniofacial exocrine gland organoid magnetic bioassembly platforms as aging multi-omic signatures | 4 | dx.doi.org/10.17504/protocols.io.b5ttq6nn | https://www.protocols.io/view/establishment-of-craniofacial-exocrine-gland-organ-b5ttq6nn | Teerapat Rodboon, Glauco Souza, Apiwat Mutirangura, Joao N. Ferreira | TITLE: Establishment of craniofacial exocrine gland organoid magnetic bioassembly platforms as aging multi-omic signatures
AUTHORS: Teerapat Rodboon, Glauco Souza, Apiwat Mutirangura, Joao N. Ferreira
[DESCRIPTION]
In the last decade, relevant biotechnology advances took place in the biofabrication of craniofacia... | ["[Mechanical and enzymatic primary cell dissociation from craniofacial exocrine glands] Gland dissection and mechanical tissue dissociation", "Clean the porcine head with sterilized water to remove any debris from the skin before disinfecting it with 0.5 % (v/v) peracetic acid solution for 15 min.", "Gently wash with ... |
44,396 | Generation and utilization of a HEK-293T murine GM-CSF expressing cell line | 3 | dx.doi.org/10.17504/protocols.io.bpkkmkuw | https://www.protocols.io/view/generation-and-utilization-of-a-hek-293t-murine-gm-bpkkmkuw | Elektra Kantzari Robinson, Sergio Covarrubias, Simon Zhou, Susan Carpenter | TITLE: Generation and utilization of a HEK-293T murine GM-CSF expressing cell line
AUTHORS: Elektra Kantzari Robinson, Sergio Covarrubias, Simon Zhou, Susan Carpenter
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.jigckbw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Maternal plasma histamine levels in normal pregnancy are generally similar to those in non-pregnant women during the first trimester, and usually decline gradually during the 2<sup>nd</sup> and 3<sup>rd</sup> trimesters (Brew and Sullivan, 2006). In some complications of preg... | [] |
106,613 | Induced Cortical Neuron Differentiation - Part 3 - Day 7 Dissociation | 0 | dx.doi.org/10.17504/protocols.io.dm6gpz1rjlzp/v1 | https://www.protocols.io/view/induced-cortical-neuron-differentiation-part-3-day-dkcv4sw6 | Isabel Lam, Alain Ndayisaba, Vikram Khurana | TITLE: Induced Cortical Neuron Differentiation - Part 3 - Day 7 Dissociation
AUTHORS: Isabel Lam, Alain Ndayisaba, Vikram Khurana
[DESCRIPTION]
Induced Cortical Neuron Differentiation - Part 3 - Day 7 Dissociation
[STEPS] | [] |
38,340 | Mouse Liver Single-Cell Dissociation with Cold Protease | 1 | dx.doi.org/10.17504/protocols.io.bhpcj5iw | https://www.protocols.io/view/mouse-liver-single-cell-dissociation-with-cold-pro-bhpcj5iw | Sanjay Subramanian, Stacey Huppert | TITLE: Mouse Liver Single-Cell Dissociation with Cold Protease
AUTHORS: Sanjay Subramanian, Stacey Huppert
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used to dissociate murine liver cells at 4 °C in an effort to preserve transcriptomic expression profiles in cells to be used fo... | ["[Tissue Isolation]\nAnesthetize mouse", "[Tissue Isolation]\nCannulate the portal vein and flush 3-5mL ice cold 1x PBS through portal vein until liver tissue is sufficiently cleared of blood\n[ice-cold 1x PBS]", "[Tissue Isolation]\nSwitch PBS syringe out for one with Bacillus licheniformis mixture while keeping the ... |
106,589 | Collection and shipment of specimen for single-nuclei RNA sequencing (snRNA-Seq) | 0 | dx.doi.org/10.17504/protocols.io.3byl4982jgo5/v1 | https://www.protocols.io/view/collection-and-shipment-of-specimen-for-single-nuc-dkb54sq6 | Laura Robinson, Susan Sheehan, Gaven Garland, Ron Korstanje | TITLE: Collection and shipment of specimen for single-nuclei RNA sequencing (snRNA-Seq)
AUTHORS: Laura Robinson, Susan Sheehan, Gaven Garland, Ron Korstanje
[DESCRIPTION]
These samples are part of the JAX-Sen project in the SenNet Consortium. Here we provide details on specimen collection and shipment to the Robson la... | ["[Reagents and Materials] 2mL Cryovials/ screw-cap tubes\nice cold 1X PBS\nKimwipes\nPetri dishes\nLiquid Nitrogen\nDry ice\nTweezers (clean, sterile)", "[Quality Key Points:] The tissue specimen should be kept at 4 degrees Celsius and RNase-free until snap-freezing and maintained at -80 degrees C or on dry ice therea... |
61,479 | 0.3M Sodium Cacodylate Buffer pH 7.4 Stock Solution Recipe | 1 | dx.doi.org/10.17504/protocols.io.q26g74x79gwz/v1 | https://www.protocols.click/view/0-3m-sodium-cacodylate-buffer-ph-7-4-stock-solutio-b8afrsbn | Mark Ellisman, Marianne Martone, Thomas Deerinck | TITLE: 0.3M Sodium Cacodylate Buffer pH 7.4 Stock Solution Recipe
AUTHORS: Mark Ellisman, Marianne Martone, Thomas Deerinck
[DESCRIPTION]
Standard preparation protocol for stock 0.3M sodium cacodylate buffer.
[GUIDELINES]
Cacodylate acid, sodium salt, trihydrate (MW = 214.03)
Vendor: Ted Pella
Product number: 18851
... | ["Add 900 ml of DDH2O to 64.209 grams of sodium cacodylate in a large 1.0L or greater container, such as a capped glass bottle. Shake and wait until powder is fully dissolved.", "Maximum HCL concentration is 12.18mole/liter (36-38%). Start with 1.3mL of 12.18 M HCL per 900 ml of sodium cacodylate dissolved solution. Ma... |
95,453 | Liquid-phase metabolomics analysis: from preparation to injection | 6 | null | https://www.protocols.io/view/liquid-phase-metabolomics-analysis-from-preparatio-c9f5z3q6 | Louise BOISSIN, axel.raux, Yann Guitton, Anne-Lise ROYER | TITLE: Liquid-phase metabolomics analysis: from preparation to injection
AUTHORS: Louise BOISSIN, axel.raux, Yann Guitton, Anne-Lise ROYER
[DESCRIPTION]
The purpose of this notice is to define two types of injection (RPLC and HILIC) on an LC-HRMS instrument for liquid-phase metabolomics analysis.
The steps cover the ... | ["[I. Sample preparation] For serum, cell culture or plasma", "[II. Quality control] Preparing the \"Mix Metabo 2\"", "[I. Sample preparation] Attention: The use of filter cones is essential for matrix sampling\n\nTriphasic preparation: Blight and Dyer\n\nThaw samples previously stored at -20 °C or -80 °C on ice\nAfter... |
88,519 | Protein Digestion and Mass Spectrometry Analysis Protocol | 4 | null | https://www.protocols.io/view/protein-digestion-and-mass-spectrometry-analysis-p-c2pfydjn | Anthony Iavarone, Annan SI Cook | TITLE: Protein Digestion and Mass Spectrometry Analysis Protocol
AUTHORS: Anthony Iavarone, Annan SI Cook
[DESCRIPTION]
This protocol details a protocol for the trypsin digestion of PI3KC3-C1 and subsequent analysis of digested peptides using LC-MS/MS.
[STEPS]
SECTION: Protein Denaturation and Reduction
1. Mix PI3KC3... | ["[Protein Denaturation and Reduction] Mix PI3KC3-C1 (mCherry-ATG14|VPS15-TSF) protein with 8 Molarity (M) urea, 50 millimolar (mM) TRIS pH 8.0, and 10 millimolar (mM) TCEP.", "[Protein Denaturation and Reduction] Add Iodoacetamide (IAA) to achieve a final concentration of 15 millimolar (mM).", "[Protein Denaturation a... |
55,670 | Performance enhancement in athletes: a survey to investigate the current clinical practice of Italian sport physiotherapists | 1 | dx.doi.org/10.17504/protocols.io.b2kwqcxe | https://www.protocols.io/view/performance-enhancement-in-athletes-a-survey-to-in-b2kwqcxe | Pasquale Alessio Sauchelli, Greta Botti, Marco Gesi, Miriam Rosa | TITLE: Performance enhancement in athletes: a survey to investigate the current clinical practice of Italian sport physiotherapists
AUTHORS: Pasquale Alessio Sauchelli, Greta Botti, Marco Gesi, Miriam Rosa
[DESCRIPTION]
Background and rationale
Professional sport physiotherapist profile is characterised by eleven spe... | [] |
103,947 | MSD + S + AS | 0 | null | https://www.protocols.io/view/msd-s-as-dhrj354n | Eleanor Harman | TITLE: MSD + S + AS
AUTHORS: Eleanor Harman
[DESCRIPTION]
.
[STEPS]
SECTION: Media
1. MS Media: 4.4g/L 2.2g/500mL
Sucrose: 30g/L 15g/500mL
Sorbitol(5%): 50g/L 25g/500mL
Thymidine: 300mg/L 150mg/500mL
2,4D: 2mg/L 1mg/500mL
Phytagel(1.4%): 14g/L 7g/500mL
SECTION: Media
2. Add 80% final volume DI water to beaker
SECTION... | ["[Media] MS Media: 4.4g/L 2.2g/500mL\nSucrose: 30g/L 15g/500mL\nSorbitol(5%): 50g/L 25g/500mL\nThymidine: 300mg/L 150mg/500mL\n2,4D: 2mg/L 1mg/500mL\nPhytagel(1.4%): 14g/L 7g/500mL", "[Media] Add 80% final volume DI water to beaker", "[Media] Add MS Media, Sucrose, Sorbitol, Thymidine, and 2,4D until fully dissolved",... |
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