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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21,002 | UC Davis - Lipoprotein profiling and partical size | null | dx.doi.org/10.17504/protocols.io.yrifv4e | null | Peter Havel | TITLE: UC Davis - Lipoprotein profiling and partical size
AUTHORS: Peter Havel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Lipoprotein profiling and Lipoprotein size will be provided for CM, VLDL, LDL and HDL as ... | ["The sample is loaded into a gel permeation column specifically designed for separating lipoprotein components. Then, lipoprotein is eluted from the column in order of larger particles to smaller ones.", "Lipoprotein fractionated by particle size is fed into reaction coils, and the degraded products after reacting wit... |
81,743 | Do, Q. B. & Nebuloni, F. et al. (2023) A fluid walled microfluidic platform for human neuronal microcircuits and axotomy. | 2 | dx.doi.org/10.17504/protocols.io.36wgqjwwxvk5/v1 | https://www.protocols.io/view/do-q-b-amp-nebuloni-f-et-al-2023-a-fluid-walled-mi-ct3pwqmn | Quyen Do, Federico Nebuloni, Richard Wade-Martins | TITLE: Do, Q. B. & Nebuloni, F. et al. (2023) A fluid walled microfluidic platform for human neuronal microcircuits and axotomy.
AUTHORS: Quyen Do, Federico Nebuloni, Richard Wade-Martins
[DESCRIPTION]
This collection contains six protocols detailing methods used in Do, Q. B. & Nebuloni, F. et al. (2023) A fluid w... | [] |
53,868 | Preparation of electrocompetent cells | 4 | dx.doi.org/10.17504/protocols.io.byukpwuw | https://www.protocols.io/view/preparation-of-electrocompetent-cells-byukpwuw | Shuning Guo | TITLE: Preparation of electrocompetent cells
AUTHORS: Shuning Guo
[DESCRIPTION]
This protocol is used to prepare electrocompetent cells with high transformation efficiency.
[BEFORE_START]
All the medium and containers used in the protocol should be sterilized by high temperature autoclave.
All the steps that expos... | ["Line the E. coli strain on a solid LB medium without resistance and culture at 37℃ for 12h.", "Pick monoclonal cells from the medium and culture them in 5 ml LB medium at 37℃ for 12h.", "Inoculate 100 ml of LB medium with 1% volume of E. coli culture from step 2.", "Grow the cells at 37℃ shaking at 200 rpm to an OD60... |
22,833 | Measurement of duodenal motility using implanted strain gauges | null | dx.doi.org/10.17504/protocols.io.2irgcd6 | null | Terry Powley, Zhenjun Tan, Matthew Ward | TITLE: Measurement of duodenal motility using implanted strain gauges
AUTHORS: Terry Powley, Zhenjun Tan, Matthew Ward
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes a process for the measurement of electrical stimulation-induced effects on duodenal motility in young adult S... | ["[Animals]\nTwo‐to four‐month‐old male rats were housed in vented rack cages in an Association for Assessment and Accreditation of Laboratory Animal Care‐approved temperature (22–24 °C) and humidity (40–60%) controlled colony room. The room was maintained on a 12‐hour light–dark schedule. Pelleted chow and filtered ta... |
null | null | null | dx.doi.org/10.17504/protocols.io.iczcax6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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null | null | null | dx.doi.org/10.17504/protocols.io.k5ecy3e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><span style="font-weight: 400;">Paraffin embedding and sectioning is a classic technique used in a variety of biological disciplines. Though the fruit fly </span><em><span style="font-weight: 400;">Drosophila melanogaster</span></em><span style="font-weight: 400;"> are one of... | [] |
80,849 | Assesing Wing Damage Index (WDI) in bats using ImageJ software | 1 | dx.doi.org/10.17504/protocols.io.j8nlkwq91l5r/v1 | https://www.protocols.io/view/assesing-wing-damage-index-wdi-in-bats-using-image-cs7rwhm6 | Nia Toshkova, Stanimira Deleva | TITLE: Assesing Wing Damage Index (WDI) in bats using ImageJ software
AUTHORS: Nia Toshkova, Stanimira Deleva
[DESCRIPTION]
Examining the visual health of bats can offer valuable insights into their overall well-being. The condition of wing membranes is essential for bats, supporting water balance and protecting again... | ["[Taking bat wing pictures in the field] Place a laminated graph paper on a convenient, flat, and stable surface. The laminated surface will allow you to write down a number code to distinguish between individuals/species and to disinfect it after each individual. Write down a code on the laminated paper containing th... |
87,524 | A computational pipeline to quantify primary cilia in mouse embryonic fibroblasts with CellProfiler | 4 | dx.doi.org/10.17504/protocols.io.bp2l6x2j5lqe/v1 | https://www.protocols.io/view/a-computational-pipeline-to-quantify-primary-cilia-czqcx5sw | Ebsy Jaimon, Herschel Dhekne, Sreeja Nair, Chloe A Hecht, Suzanne R Pfeffer | TITLE: A computational pipeline to quantify primary cilia in mouse embryonic fibroblasts with CellProfiler
AUTHORS: Ebsy Jaimon, Herschel Dhekne, Sreeja Nair, Chloe A Hecht, Suzanne R Pfeffer
[DESCRIPTION]
We present here an automated CellProfiler (Stirling et al., 2021) software pipeline to quantify the number of pri... | ["[Import data into CellProfiler and extract metadata from file names] Select the Images module, drag and drop the maximum intensity projected .TIF files as indicated", "[Group individual channels and create image subsets] Go to Names and types module \nAssign a name to : “Images matching rules” \nProcess as 3D : No\nS... |
91,921 | Antioxidant and trace metal determinations in human lavage fluids | 6 | dx.doi.org/10.17504/protocols.io.ewov1qmxygr2/v1 | https://www.protocols.io/view/antioxidant-and-trace-metal-determinations-in-huma-c5zry756 | Andreas Frølich, i.mudway, anders.blomberg, annelie.behndig | TITLE: Antioxidant and trace metal determinations in human lavage fluids
AUTHORS: Andreas Frølich, i.mudway, anders.blomberg, annelie.behndig
[DESCRIPTION]
Low molecular weight antioxidants (including ascorbate, urate and glutathione), metal transport and chelation proteins (including transferrin and ferritin) and met... | ["[Collection and preparation of bronchoalveolar lavage fluid samples for antioxidant analysis:] Bronchoalveolar lavage (BAL) was performed by the instillation and immediate aspiration of 3 consecutive aliquots of 60 mL sodium chloride (NaCl) saline pH 7.3 at 37˚ C into the lingular or middle lobe.\n\nThese recovered a... |
29,461 | Loop assembly using Labcyte Echo 550 | null | dx.doi.org/10.17504/protocols.io.8zvhx66 | null | Susana Sauret-Gueto, Anthony West | TITLE: Loop assembly using Labcyte Echo 550
AUTHORS: Susana Sauret-Gueto, Anthony West
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Loop L1 and L2 type IIS assembly protocol, automated and minituarised for assembly of 500nl final volume reactions using the Labcyte Echo 550.</div></div>
[STEPS]
?... | ["Next create LDV source plate that contain all plasmids needed but the APs.For L1 Loops, have a LDV source plate with the libary of L0 parts.For L2 Loops, have a LDV source plate with the library of L1 plasmids.Use Echo calibration 384LDV_AQ_B2 for these plates.LDV plates working range is~ 3-12 ul (maximum volume is 1... |
99,456 | Capturing and Processing Slaking Images With a Multi-Well Plate | 6 | dx.doi.org/10.17504/protocols.io.36wgqjmk5vk5/v3 | https://www.protocols.io/view/capturing-and-processing-slaking-images-with-a-mul-ddc822zw | Claire Phillips, Robert E Meadows III, Joaquin Casanova, Bryan Emmett | TITLE: Capturing and Processing Slaking Images With a Multi-Well Plate
AUTHORS: Claire Phillips, Robert E Meadows III, Joaquin Casanova, Bryan Emmett
[DESCRIPTION]
This describes a process to measure soil wet aggregate stability through slaking, or rapid immersion it water. It uses a multi-well plate to process many a... | ["[Sample preparation] Establish how you will count the wells (across or down) and create a spreadsheet identifying the sample in each well. \nExample Document:", "[Sample preparation] The well plate we provided a 3D print file for has a notch in the upper left corner to identify the first column and row.", "[Sample pr... |
37,563 | Use SSH Public Key Authentication | null | null | https://www.protocols.io/view/use-ssh-public-key-authentication-bgw3jxgn | Natapol Pornputtapong | TITLE: Use SSH Public Key Authentication
AUTHORS: Natapol Pornputtapong
[STEPS]
?.
?. | [] |
90,809 | GGAssmbler Library Construction | 1 | dx.doi.org/10.17504/protocols.io.81wgbxqkolpk/v1 | https://www.protocols.io/view/ggassmbler-library-construction-c4wzyxf6 | Shlomo Yakir Hoch, Ravit Netzer, Karen Hakeny, Sarel J Fleishman | TITLE: GGAssmbler Library Construction
AUTHORS: Shlomo Yakir Hoch, Ravit Netzer, Karen Hakeny, Sarel J Fleishman
[DESCRIPTION]
This protocol describes methods for GGAssembler.
[BEFORE_START]
Please note that protocols with Q5® High-Fidelity DNA Polymerase may differ from protocols with other polymerases. Conditions r... | ["[Amplify constant fragments] Set up the following reaction on ice:", "[Amplify constant fragments] Gently mix the reaction.", "[Amplify constant fragments] Collect all liquid to the bottom of the tube by a quick spin if necessary and overlay the sample with mineral oil if using a PCR machine without a heated lid.", "... |
null | null | null | dx.doi.org/10.17504/protocols.io.mpkc5kw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Tongcheng pigs (TC) and Yorkshire (YK) are two pig breeds with distinguished morphologies in muscle. A comprehensive study of porcine microRNAome (miRNAome) in longissimus muscle during 5 developmental stages (40, 55, 63, 70 and 90 dpc (days post coitum)) using Solexa sequenc... | [] |
88,186 | Chemical ecology in the classroom: chemotaxis assay using C. elegans | 4 | dx.doi.org/10.17504/protocols.io.e6nvwde9zlmk/v1 | https://www.protocols.io/view/chemical-ecology-in-the-classroom-chemotaxis-assay-c2c2yaye | Nicole Bradon, Katherine Fiocca, Maria D. Sallee, Lauren Cote, Daniel A. Shaykevich, Lauren A O'Connell | TITLE: Chemical ecology in the classroom: chemotaxis assay using C. elegans
AUTHORS: Nicole Bradon, Katherine Fiocca, Maria D. Sallee, Lauren Cote, Daniel A. Shaykevich, Lauren A O'Connell
[DESCRIPTION]
There are many natural products in the environment that influence other organisms. How nervous systems sense these c... | ["[Obtaining chemical extracts for use as chemotaxis stimuli] Place the collected ants in a freezer for 15 min until immobile.", "[Obtaining chemical extracts for use as chemotaxis stimuli] Wearing gloves, sort ants by species into medium weighing boats.", "[Prepare chemotaxis plates] Label chemotaxis plates.", "[Prepa... |
97,853 | Preparation, Processing and Preservation of Deceased Donor Kidney Tissue for Multiomic Studies | 1 | dx.doi.org/10.17504/protocols.io.8epv5r64jg1b/v1 | https://www.protocols.io/view/preparation-processing-and-preservation-of-decease-dbs52ng6 | Sanjay Jain, Amanda Knoten, Kristy Conlon | TITLE: Preparation, Processing and Preservation of Deceased Donor Kidney Tissue for Multiomic Studies
AUTHORS: Sanjay Jain, Amanda Knoten, Kristy Conlon
[DESCRIPTION]
Multiomic technologies are increasingly being used on human samples and generating multidimensional data. Preanalytical and tissue procurement factors c... | ["[Procurement: Procuring Kidney from organ procurement organization (OPO)] Check patient file for the following information:\nConsent to donate organs\nDowntime, if any\nWas kidney on pump?\nBUN/Cr\nKidney biopsy report/any underlying disease\nMedical history for comorbidities\nGeneral good health before the current e... |
15,309 | Updated QIAGEN PowerSoil protocol | null | dx.doi.org/10.17504/protocols.io.s7mehk6 | null | null | TITLE: Updated QIAGEN PowerSoil protocol
AUTHORS:
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Adapted from manufacturer instructions for sand extraction for Nanopore sequencing.</div><div class = "text-block">https://www.qiagen.com/au/shop//sample-technologies/dneasy-powersoil-kit/#resources</d... | [] |
47,659 | SARS-CoV-2 Sequencing on Illumina MiSeq Using ARTIC Protocol: Part 2 - Illumina DNA Prep Protocol | 1 | null | https://www.protocols.io/view/sars-cov-2-sequencing-on-illumina-miseq-using-arti-bssjnecn | Joel Sevinsky, Arian Nassiri, Heather Blankenship, Erin Young, Kevin Libuit, Kelly Oakeson, Lauren Turner, StaPH-B Consortium | TITLE: SARS-CoV-2 Sequencing on Illumina MiSeq Using ARTIC Protocol: Part 2 - Illumina DNA Prep Protocol
AUTHORS: Joel Sevinsky, Arian Nassiri, Heather Blankenship, Erin Young, Kevin Libuit, Kelly Oakeson, Lauren Turner, StaPH-B Consortium
[DESCRIPTION]
This protocol is an adaption of several circulating protocols on... | ["[DNA Prep - Before you begin] Before You Begin\n\nThis protocol is an adaptation of the Illumina DNA Prep kit (below). It is laid out specifically for using amplicons from the ARTIC Tiling PCR Protocol.\n\nThe audience is assumed to be public health laboratorians with access to instruments and reagents used for Puls... |
86,877 | Immunofluorescence staining for tissue and organoids | 4 | null | https://www.protocols.io/view/immunofluorescence-staining-for-tissue-and-organoi-cy35xyq6 | Gabriela Vallejo Flores, Annika Fendler | TITLE: Immunofluorescence staining for tissue and organoids
AUTHORS: Gabriela Vallejo Flores, Annika Fendler
[DESCRIPTION]
Immunohistochemistry (IHC) is a powerful technique that exploits the specific binding between an antibody and antigen to detect and localize specific antigens in cells and tissue, most commonly ... | ["[Blocking] Add blocking buffer A (1% BSA + 2% of host serum (secondary antibody) in TBS 1x, add 150µl for tissue and 50µl for organoids staining, incubate the sample 60 min a room temperature in the humidifying box.", "[Primary antibody] Add the primary antibody to the sample, dilute the antibody in blocking buffer B... |
20,088 | Scarless introduction of point mutations in mammalian cells with S. pyogenes Cas9 | null | dx.doi.org/10.17504/protocols.io.xuyfnxw | null | Malvika Tejura, Stephen Floor | TITLE: Scarless introduction of point mutations in mammalian cells with S. pyogenes Cas9
AUTHORS: Malvika Tejura, Stephen Floor
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines the steps to edit single point mutations into cells in a scarless manner. Uses single-stranded DNA re... | ["[Workflow]\nThe workflow for gene editing with the CRISPR/Cas9 system follows these basic steps: Designing appropriate sgRNAs (recruits Cas9 enzyme to DNA). Cas9 bound to the sgRNA is referred to as the \"RNP\" (ribonucleoprotein)Nucleofecting RNPs to test cutting efficiency for each sgRNADesigning appropriate single... |
38,921 | 3: 30mer branch melting temperatures (SABER-FISH) | 1 | null | https://www.protocols.io/view/3-30mer-branch-melting-temperatures-saber-fish-bh9hj936 | Jocelyn Y. Kishi, Sylvain W. Lapan, Brian J Beliveau, Emma R. West, Allen Zhu, Hiroshi M. Sasaki, Sinem Saka, Yu Wang, Constance L Cepko, Peng Yin | TITLE: 3: 30mer branch melting temperatures (SABER-FISH)
AUTHORS: Jocelyn Y. Kishi, Sylvain W. Lapan, Brian J Beliveau, Emma R. West, Allen Zhu, Hiroshi M. Sasaki, Sinem Saka, Yu Wang, Constance L Cepko, Peng Yin
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the design of 3... | ["It's recommended to use a temperature at least 1 degree lower than the lowest melting temperature of all branch sequences you plan to use (see plot of melting temperatures Fig. S2).You can find these melting temperature curves reported for each sequence, as well as those computed for 20mer imagers, 42mer barcode sequ... |
98,441 | Urine Lipoarabinomannan as a Biomarker for Mycobacterium tuberculosis and non-tuberculous mycobacterial infections | 0 | dx.doi.org/10.17504/protocols.io.3byl497o8go5/v1 | https://www.protocols.io/view/urine-lipoarabinomannan-as-a-biomarker-for-mycobac-dcdh2s36 | Jordan Manzer, Ibrahim Aboellail, Jerry Nick, Delphi Chatterjee, Anita G Amin | TITLE: Urine Lipoarabinomannan as a Biomarker for Mycobacterium tuberculosis and non-tuberculous mycobacterial infections
AUTHORS: Jordan Manzer, Ibrahim Aboellail, Jerry Nick, Delphi Chatterjee, Anita G Amin
[DESCRIPTION]
Lipoarabinomannan (LAM) is a unique cell wall component containing a fatty acid region with a la... | ["[Urinary LAM Tuberculostearic acid Analysis] Hexane Extraction (Removes exogenous proteins and lipids from urine)", "[Urinary LAM Tuberculostearic acid Analysis] Using 1 mL of urine in a KIMAX 13 x 100mm glass tube with teflon screw cap, 1 mL of Hexane is added.", "[Urinary LAM Tuberculostearic acid Analysis] Vortex ... |
95,955 | Viral Enumeration of Water Samples Using Wet Mount Epifluorescence Microscopy | 0 | dx.doi.org/10.17504/protocols.io.q26g7po68gwz/v2 | https://www.protocols.io/view/viral-enumeration-of-water-samples-using-wet-mount-c9xtz7nn | Madeline Bellanger, Pieter Visscher, Richard Allen White III | TITLE: Viral Enumeration of Water Samples Using Wet Mount Epifluorescence Microscopy
AUTHORS: Madeline Bellanger, Pieter Visscher, Richard Allen White III
[DESCRIPTION]
Epifluorescence microscopy (EFM) has been the gold standard method for environmental viral enumeration for over 25 years. Currently, standard EFM meth... | ["[Filtration and Cleaning] Record the starting volume of water, this will be used for calculations later.", "[Filtration and Cleaning] Filter water through a glass fiber pre filter (Whatman Grade 1 qualitative filter paper).", "[Filtration and Cleaning] Collect filtrate and filter through a 0.65 μm PVDF filter (Durapo... |
85,959 | Mitochondria purification | 4 | dx.doi.org/10.17504/protocols.io.n92ldmppnl5b/v1 | https://www.protocols.io/view/mitochondria-purification-cx7fxrjn | wusj, schekman | TITLE: Mitochondria purification
AUTHORS: wusj, schekman
[DESCRIPTION]
This protocol describes how to purify mitochondria from cell culture
[STEPS]
SECTION: Mitochondria purification
1. HEK293T cells were trypsinized (0.05% Trypsin 5 min ) and collected by centrifugation (500g 5 min).
SECTION: Mitochondria purifica... | ["[Mitochondria purification] HEK293T cells were trypsinized (0.05% Trypsin 5 min ) and collected by centrifugation (500g 5 min).", "[Mitochondria purification] Cells were washed twice with NKM buffer (1 mM Tris HCl, pH7.3, 0.13 M NaCl, 5 mM KCl, and 7.5 mM MgCl2), and resuspended in six packed cell volumes of homogeni... |
103,664 | LTEE Media Recipes | 1 | dx.doi.org/10.17504/protocols.io.81wgbyr31vpk/v4 | https://www.protocols.io/view/ltee-media-recipes-dhgq33vw | Jesus E Chavarria-Palma, Zachary D Blount, Jeffrey E Barrick | TITLE: LTEE Media Recipes
AUTHORS: Jesus E Chavarria-Palma, Zachary D Blount, Jeffrey E Barrick
[DESCRIPTION]
This protocol describes recipes to prepare growth media and reagents used in the E. coli long-term evolution experiment (LTEE).
Section 1: DM-glucose, Davis-Mingioli liquid medium supplemented with glucose
... | ["[DM-glucose: Davis-Mingioli liquid medium supplemented with glucose] To prepare 1 L of DM, follow these steps.", "[DM-glucose: Davis-Mingioli liquid medium supplemented with glucose] Weigh dry components:\na. 5.34 g of or 7 gof \nb. 2 g of \nc. 1 g of \nd. 0.5 g of", "[DM-glucose: Davis-Mingioli liquid medi... |
28,773 | Copy of Fabrication of Microneedle Patches | null | dx.doi.org/10.17504/protocols.io.8cdhss6 | null | Stephania Konstantinidi, Hana Samet | TITLE: Copy of Fabrication of Microneedle Patches
AUTHORS: Stephania Konstantinidi, Hana Samet
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The goal is to create a microneedle. patch, which, by applying it on a leaf, will extract amplification-ready DNA.</div><div class = "text-block">All MN patc... | ["[Mold preparation]\nClean the polydimethylsiloxane molds.", "[Mold preparation]\nHeat deionised water to 100 degrees Celsius using a becher.\n100 °C", "[Mold preparation]\nPut the mold(s) into the water and stir softly.", "[Mold preparation]\nRemove the molds and let them dry in a chemical hood for 1-2 hours.", "[M... |
108,296 | Mass Spectrometry Identification of Samples Separated by Liquid Chromatography | 0 | dx.doi.org/10.17504/protocols.io.bp2l625kdgqe/v1 | https://www.protocols.io/view/mass-spectrometry-identification-of-samples-separa-dmzg473w | Caroline Green | TITLE: Mass Spectrometry Identification of Samples Separated by Liquid Chromatography
AUTHORS: Caroline Green
[DESCRIPTION]
As one of the most powerful separation and analysis technologies in the field of chemistry, liquid chromatography (LC) has developed rapidly since the 1970s. Both in terms of fundamental chromato... | ["[Guide for Mass Spectrometry Identification of Samples Separated by Liquid Chromatography] Main Instruments and Equipment", "[Guide for Mass Spectrometry Identification of Samples Separated by Liquid Chromatography] Main reagents*1", "[Guide for Mass Spectrometry Identification of Samples Separated by Liquid Chromato... |
67,433 | Keto Complete Australia {AU/UK} Pills Reviews! | 3 | dx.doi.org/10.17504/protocols.io.81wgb631olpk/v1 | https://www.protocols.io/view/keto-complete-australia-au-uk-pills-reviews-cd4hs8t6 | Keto Complete Australia | TITLE: Keto Complete Australia {AU/UK} Pills Reviews!
AUTHORS: Keto Complete Australia
[DESCRIPTION]
Keto Complete Australia
[STEPS] | [] |
66,634 | Microscopy-based bead protein-protein interaction assay | 4 | dx.doi.org/10.17504/protocols.io.6qpvr6nwpvmk/v1 | https://www.protocols.io/view/microscopy-based-bead-protein-protein-interaction-cdbis2ke | Justyna Sawa-Makarska | TITLE: Microscopy-based bead protein-protein interaction assay
AUTHORS: Justyna Sawa-Makarska
[DESCRIPTION]
This protocol describes how to perform microscopy-based bead protein-protein interaction assay with GST-labelled proteins as baits and fluorescently labelled proteins as preys. The protocol requires to have puri... | ["[Interaction assay] Pipette the preys onto 384-well glass-bottom microplate (Greiner Bio-One). The minimal volume to cover the bottom of a well is 20 μl. The final concentration of the prey may vary depending on the strength of the interaction, usually between 0.1-1 μM. The number of proteins in the well can be adjus... |
null | null | null | dx.doi.org/10.17504/protocols.io.dpt5nm | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
A generally more efficient way of isolating lytic phages from marine environments is by the use of enrichment cultures. In this approach, the prefiltered water sample that is to be screened for phages against a given target bacterium, is enriched with a bacterial growth medium a... | [] |
94,458 | Tissue sampling from museum specimens of mitten crabs | 4 | dx.doi.org/10.17504/protocols.io.6qpvr3n1zvmk/v1 | https://www.protocols.io/view/tissue-sampling-from-museum-specimens-of-mitten-cr-c8g2ztye | Christine Ewers | TITLE: Tissue sampling from museum specimens of mitten crabs
AUTHORS: Christine Ewers
[DESCRIPTION]
Simple protocol for sampling tissues from mitten crabs housed in natural history collections. Mitten crabs are somewhat unique because they have hair on their chelae from which DNA can be extracted. However, the protoco... | ["Clean all surfaces with DNAaway", "Flame forceps and scalpel", "Open collection jar", "Take out one specimen", "Place in clean tray with scale (e.g. ruler). Take first picture of the collection metadata (the jar label) and then picture of the crab. This way you can trace back which crab you photographed", "Chose the ... |
69,934 | Stereology-mediated cell count using StereoInvestigator | 4 | dx.doi.org/10.17504/protocols.io.6qpvr4ekbgmk/v1 | https://www.protocols.io/view/stereology-mediated-cell-count-using-stereoinvesti-cgintude | miquel.vila | TITLE: Stereology-mediated cell count using StereoInvestigator
AUTHORS: miquel.vila
[DESCRIPTION]
Protocol for cell counting using StereoInvestigator software
[STEPS]
1. Set slide properly on the microscope and set new reference point
2. Click on Probes → Optical Fractionator Workflow → Start a new subject →
3. Ente... | ["Set slide properly on the microscope and set new reference point", "Click on Probes → Optical Fractionator Workflow → Start a new subject →", "Enter cut thickness (5 µm (cut with microtome, 20 µm or 30 µm (cut with cryostat))", "Enter interval according to the thickness: 17 if 5 µm, 6 if 20 µm or 4 if µm)", "In Sele... |
86,180 | iNDI Papain Dissociation protocol for iNeurons Version 1 | 4 | dx.doi.org/10.17504/protocols.io.kxygx392dg8j/v1 | https://www.protocols.io/view/indi-papain-dissociation-protocol-for-ineurons-ver-cyecxtaw | 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... |
75,168 | Measles whole-genome sequencing | 4 | null | https://www.protocols.io/view/measles-whole-genome-sequencing-cmm8u49w | My VT Phan, Matthew Cotten | TITLE: Measles whole-genome sequencing
AUTHORS: My VT Phan, Matthew Cotten
[DESCRIPTION]
This is an optimised protocol for PCR amplification of the Measles virus (MV) genome using specific primers designed for B3 genotype. The method generates cDNA amplicons suitable for whole genome sequencing using the MinION platfo... | ["[PCR amplification of measles virus genome] cDNA synthesis", "[PCR amplification of measles virus genome] For each FPM reaction, add the following:\n4 µL \n1 µL \n1 µL \n1 µL \n1 µL \n\nThen incubate the reactions using the following conditions:\n42 °C for 50 min \n70 °C for 10 min", "[PCR amplification of measles v... |
25,838 | Spectrophotometric assay of the mitochondrial F1F0 ATP synthase | null | dx.doi.org/10.17504/protocols.io.5gng3ve | null | Anne LOMBES, Francis Haraux | TITLE: Spectrophotometric assay of the mitochondrial F1F0 ATP synthase
AUTHORS: Anne LOMBES, Francis Haraux
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "vertical-align:sub;">F</span><span style = "vertical-align:sub;">1</span><span style = "vertical-align:sub;vertical-align:sub;">F... | ["Reagents preparation 1- Homogenization buffer (kept at 0-4°C for few weeks or at -20°C for longer period of time)= 225 mM mannitol, 75 mM sucrose, 0.1 mM EDTA, and 10 mM Tris HCl pH 7.2Anti-protease cocktail at the working concentration given by the manufacturer should be added before use2- Assay buffer (kept at 0-4°... |
40,896 | ELISA for quantification of interferon gamma (IFN-γ) in human serum or plasma. | 6 | dx.doi.org/10.17504/protocols.io.bj68krhw | https://www.protocols.io/view/elisa-for-quantification-of-interferon-gamma-ifn-bj68krhw | Angel Justiz-Vaillant, Belkis Ferrer-Cosme | TITLE: ELISA for quantification of interferon gamma (IFN-γ) in human serum or plasma.
AUTHORS: Angel Justiz-Vaillant, Belkis Ferrer-Cosme
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">IFN-γ is a key player in driving cellular immunity. It is capable of orchestrating numerous and vital prot... | ["An anti-human IFN-γ coating antibody is adsorbed onto the microwells by incubation overnight at 4°C with carbonate-bicarbonate buffer.", "Add 50 µl of human serum or plasma. Human IFN-γ present in the serum or plasma binds to antibodies adsorbed into the microwells.", "The microplate is blocked with 3% non-fat milk-P... |
46,787 | Artificial sea water | 4 | dx.doi.org/10.17504/protocols.io.brxbm7in | https://www.protocols.io/view/artificial-sea-water-brxbm7in | Simon Blanchoud | TITLE: Artificial sea water
AUTHORS: Simon Blanchoud
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Three alternative solutions for artificial seawater (ASW) have been tested successfully on our </span><span style = "font-style:italic;">Botrylloides</span><span> colonies. For routine work, ... | ["[2X CSS]\nsea salt in H2O.\n70 g\n1 L", "[2X CSS]\nMix to dissolve.", "[2X CSS]\nFilter at 10 µm", "[10x CSHP]\nTo prepare 10X CSHP take NaCl262.9g4.5MKCl7.4g100mMCaCl29.9g90mMMgCl2 6H2O60.9g300mMMgSO4 7H2O39.4g160mMH2O1000ml\nNaCl262.9g4.5MKCl7.4g100mMCaCl29.9g90mMMgCl2 6H2O60.9g300mMMgSO4 7H2O39.4g160mMH2O1000ml",... |
42,595 | NOAA-CalCOFI Ocean Genomics (NCOG) Sample Collection | 1 | dx.doi.org/10.17504/protocols.io.bmubk6sn | https://www.protocols.io/view/noaa-calcofi-ocean-genomics-ncog-sample-collection-bmubk6sn | Ariel Rabines, Rob Lampe, Lisa Zeigler Allen, Andrew Allen | TITLE: NOAA-CalCOFI Ocean Genomics (NCOG) Sample Collection
AUTHORS: Ariel Rabines, Rob Lampe, Lisa Zeigler Allen, Andrew Allen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describes our sampling strategy and techniques for the </span><a href="https://calcofi.org/LRbLa/field-w... | ["[Station sampling and depths]\nFor station positions and cruise patterns, refer to the CalCOFI website. Stations:Prodo stations refers to stations sampled around the same time of day (late morning) when primary productivity is measured. Cardinal stations refers to stations at a certain location to be sampled no matte... |
null | null | null | dx.doi.org/10.17504/protocols.io.j9qcr5w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Diet-induced obesity through administration of a western-type diet high in fat and sugar to mice can result in a higher weight of adipose and liver tissues. The increased adipose tissue weight can be due to hypertrophy (bigger cells) or hyperplasia (more cells) of adipocytes,... | [] |
89,921 | WesternBlot Paramecium bursaria (Pb) | 1 | dx.doi.org/10.17504/protocols.io.ewov1q58kgr2/v1 | https://www.protocols.io/view/westernblot-paramecium-bursaria-pb-c329yqh6 | Estelle Kilias | TITLE: WesternBlot Paramecium bursaria (Pb)
AUTHORS: Estelle Kilias
[DESCRIPTION]
Western Blot protocol for Pb including all steps from the cell harvest to the final ECL stain. Culture density is an important factor that requires checking prior starting.
[STEPS]
SECTION: Protein extraction
1. To concentrate the cultu... | ["[Protein extraction] To concentrate the culture, strain 100 ml of a dense Paramecium culture through a 40 micrometer strainer and split the volume over two 50 ml falcon tubes", "[Protein extraction] Centrifuge the strained culture for 10 min at 800xg", "[Protein extraction] Remove the supernatant from each falcon tub... |
71,457 | Immunostaining of H&E Stained Paraffin Sections of Fly Heads | 4 | dx.doi.org/10.17504/protocols.io.81wgby61nvpk/v1 | https://www.protocols.io/view/immunostaining-of-h-amp-e-stained-paraffin-section-chz9t796 | Mel Feany | TITLE: Immunostaining of H&E Stained Paraffin Sections of Fly Heads
AUTHORS: Mel Feany
[DESCRIPTION]
This protocol describes how to perform immunostaining on H&E stained paraffin sections of fly heads.
[STEPS]
1. Embed the fly heads in paraffin and stain with H&E for neuronal counting, per the following protocol:... | ["Embed the fly heads in paraffin and stain with H&E for neuronal counting, per the following protocol:\ndx.doi.org/10.17504/protocols.io.4r3l24on4g1y/v1", "Microwave slides in 10 millimolar (mM) sodium citrate for 15 min. \nCool 20 min .\n\nStock: 100 millimolar (mM) sodium citrate, pH 6.0\nUse at least 1 L of citra... |
101,120 | Purification of Lambda Protein Phosphatase | 0 | dx.doi.org/10.17504/protocols.io.kqdg322bqv25/v1 | https://www.protocols.io/view/purification-of-lambda-protein-phosphatase-dey83fzw | Elias Adriaenssens | TITLE: Purification of Lambda Protein Phosphatase
AUTHORS: Elias Adriaenssens
[DESCRIPTION]
This protocol details the purification of Lambda protein phosphatase.
[STEPS]
SECTION: Purification procedure
1. To purify Lambda protein phosphatase (λ PPase), fuse the protein phosphatase to a N-terminal 6xHis-tag through cl... | ["[Purification procedure] To purify Lambda protein phosphatase (λ PPase), fuse the protein phosphatase to a N-terminal 6xHis-tag through cloning into a pET-DUET1 vector (available from Addgene).", "[Purification procedure] After the transformation of the pET-DUET1 vector encoding 6xHis-TEV-λ PPase in E. coli Rosetta p... |
79,337 | Adhesion assay | 1 | dx.doi.org/10.17504/protocols.io.dm6gpj111gzp/v1 | https://www.protocols.click/view/adhesion-assay-crqhv5t6 | Philippa R Kennedy, Quinlan Kile | TITLE: Adhesion assay
AUTHORS: Philippa R Kennedy, Quinlan Kile
[DESCRIPTION]
Adapted from Natural Killer Cell Protocols 2009 p89-96
Enriched effector cells and tumor targets are labelled with different fluorescence. They are allowed to interact over a time-course and samples are taken and fixed at regular intervals.... | ["[Set aside cells for flow cytometer setup] The following controls will be required to setup the gates on a flow cytometer:\n1. Unlabeled cells for an unstained control\n2. Single color control (effector) e.g. CellTrace Violet labeled NK cells.\n3. Single color control (target) e.g. K562-Nuclight Red.", "[Prepare the ... |
58,605 | Utilization Patterns and Trends in The Use of Medications for Asthma Control in a Cohort of Colombian Patients, 2017-2019 | 1 | dx.doi.org/10.17504/protocols.io.b5gmq3u6 | https://www.protocols.io/view/utilization-patterns-and-trends-in-the-use-of-medi-b5gmq3u6 | Jorge Machado Alba | TITLE: Utilization Patterns and Trends in The Use of Medications for Asthma Control in a Cohort of Colombian Patients, 2017-2019
AUTHORS: Jorge Machado Alba
[DESCRIPTION]
Background:Asthma affects approximately 358 million people worldwide.
Objective:To determine the trend in the use of medications used to trea... | [] |
45,989 | Understanding the impact of sole soled footwear on toddler spatial, temporal and kinetic gait parameters. | 1 | dx.doi.org/10.17504/protocols.io.bq6dmza6 | https://www.protocols.io/view/understanding-the-impact-of-sole-soled-footwear-on-bq6dmza6 | Cylie Williams, Jessica Kolic, Wen Wu, Kade Paterson | TITLE: Understanding the impact of sole soled footwear on toddler spatial, temporal and kinetic gait parameters.
AUTHORS: Cylie Williams, Jessica Kolic, Wen Wu, Kade Paterson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A quasi-experimental pre-post study design will be used to assess whether sp... | ["Aim: To assess whether spatiotemporal parameters of gait, and in-shoe foot and lower limb kinematics differ when walking barefoot and in soft-soled footwear in newly walking toddlers. Hypothesis: Soft soled footwear would result in similar differences in gait variables as those observed in older children (ages 2-4)."... |
62,104 | Rehabilitation interventions for impaired handwriting in people with Parkinson’s disease: a protocol for a scoping review | 1 | dx.doi.org/10.17504/protocols.io.5jyl891z8v2w/v1 | https://www.protocols.io/view/rehabilitation-interventions-for-impaired-handwrit-b8vyrw7w | Andrea Gardoni, Elisabetta Sarasso, Federica Agosta, Massimo Filippi, Davide Corbetta | TITLE: Rehabilitation interventions for impaired handwriting in people with Parkinson’s disease: a protocol for a scoping review
AUTHORS: Andrea Gardoni, Elisabetta Sarasso, Federica Agosta, Massimo Filippi, Davide Corbetta
[DESCRIPTION]
Handwriting abnormalities in people with Parkinson’s disease include several dyn... | ["[Search strategy] The search strategy was runned in April 2022", "[Study records management, selection and data collection]", "[Risk of bias assessment] Requested time will depend on how many studies will be included", "[Data synthesis] Requested time will depend on how many studies will be included"] |
50,537 | Flow Cytometry ECS Surface Antigens | 4 | dx.doi.org/10.17504/protocols.io.bvkhn4t6 | https://www.protocols.io/view/flow-cytometry-ecs-surface-antigens-bvkhn4t6 | Michael Betts, Gregory Golden | TITLE: Flow Cytometry ECS Surface Antigens
AUTHORS: Michael Betts, Gregory Golden
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">High-parameter flow cytometry enables identification and characterization of a wide range of cell populations within a biological sample. Analysis of cell-surface epitope... | ["[Procedure]\nThawing and Restinga. Pre-warm R10 media in a water bath. b. Thaw samples in-vial using a water bath.c. Add thawed cells to of R10, then spin cells at 500 xg for 5 min.d. Resuspend cell pellet in of R10 and count cells. e. Rest cells at least 3 hours (up to overnight) at 2x106 cells/mL in R10 medium ... |
105,953 | Osmia lignaria laboratory rearing protocol | 1 | dx.doi.org/10.17504/protocols.io.eq2lyj4qplx9/v2 | https://www.protocols.io/view/osmia-lignaria-laboratory-rearing-protocol-djp94mr6 | Mary-Kate F. Williams, Natalie K. Boyle, Robert N. Schaeffer, Diana L Cox-Foster | TITLE: Osmia lignaria laboratory rearing protocol
AUTHORS: Mary-Kate F. Williams, Natalie K. Boyle, Robert N. Schaeffer, Diana L Cox-Foster
[DESCRIPTION]
Our protocol was designed to rear Osmia lignaria Say (Hymenoptera: Megachilidae) from immature stages to adult emergence following their natural phenology in norther... | ["[Propagation and acquiring solitary bee nests (Fig. 1)] Deploy corrugated plastic nesting boxes (Artz et al. 2013, 2014) into the orchard before bloom. Place nest blocks with straw inserts or bundles of cardboard tubes with straw inserts into nest boxes.", "[Propagation and acquiring solitary bee nests (Fig. 1)] Once... |
49,490 | Fixation of HeLa-M cells expressing Halo and SNAP fusion proteins conjugated to ligands | 4 | dx.doi.org/10.17504/protocols.io.bujsnune | https://www.protocols.io/view/fixation-of-hela-m-cells-expressing-halo-and-snap-bujsnune | OLIVIA HARDING, Erika L. F. Holzbaur | TITLE: Fixation of HeLa-M cells expressing Halo and SNAP fusion proteins conjugated to ligands
AUTHORS: OLIVIA HARDING, Erika L. F. Holzbaur
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Mitophagy is a tightly regulated mechanism in which components are sequentially recruited to a damaged mitocho... | ["[Before start]\nThe start point for this protocol is after cells grown on a glass coverslip in a 12- well plate have been transfected with YFP-Parkin, Halo-OPTN, and SNAP-TBK1 for - .", "[Before start]\nPrepare in PBS. Keep frozen at .\n[PFA]\n-20 °C\nPrepare fresh for day-of fixation or thaw directly before use.\n... |
17,062 | ChroDrip - ProteinA | null | dx.doi.org/10.17504/protocols.io.uweexbe | null | David Frommholz, Alexandra Ehl, Nadine Stefanczyk | TITLE: ChroDrip - ProteinA
AUTHORS: David Frommholz, Alexandra Ehl, Nadine Stefanczyk
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Purification Guide for the Isolation of Antibodies with ChroDrip Columns by DALEX Biotech.</span></div><div class = "text-block">Eas... | ["[Load and Wash]\nAdd your sample to the top of the column and let it flow through by gravity.\nFor optimal binding and purity, the pH of the sample should be 7.5 - 8.5 and should contain 150 - 300 mM NaCl. An easy way to achieve this is by adding 1/11 volume 0.5 M Tris, 2 M NaCl (pH 8.0) to your sample.Removal of par... |
88,357 | Protocol for abscisic acid (ABA) extraction from plant seeds | 4 | dx.doi.org/10.17504/protocols.io.81wgbxnnqlpk/v1 | https://www.protocols.io/view/protocol-for-abscisic-acid-aba-extraction-from-pla-c2idyca6 | Jian You Wang, Lamis Berqdar, Salim Al-Babili | TITLE: Protocol for abscisic acid (ABA) extraction from plant seeds
AUTHORS: Jian You Wang, Lamis Berqdar, Salim Al-Babili
[DESCRIPTION]
The plant hormone abscisic acid (ABA) regulates seed dormancy and germination. Here, we present a protocol for ABA extraction from plant seeds. We describe necessary steps required f... | ["[Sample preparation] Grind 7-8 seeds in a Safe-Lock 2.0 mL Eppendorf tube with 3-4 beads for 1 min – frequency 25-26 Hz.", "[Sample preparation] Weight 100 mg fine powder of ground seeds.", "[Sample preparation] Add 1 mL of Standard solution in each tube.", "[Sample preparation] Sonicate the samples for 15 min.", "[S... |
40,368 | Inhibition immunoassay of the HIVgp120_anti-HIVgp120 (Ab-1) reaction by anti-anti-idiotypic-HIVgp120 antibody (Ab-3). | 4 | dx.doi.org/10.17504/protocols.io.bjnqkmdw | https://www.protocols.io/view/inhibition-immunoassay-of-the-hivgp120-anti-hivgp1-bjnqkmdw | Angel Justiz-Vaillant | TITLE: Inhibition immunoassay of the HIVgp120_anti-HIVgp120 (Ab-1) reaction by anti-anti-idiotypic-HIVgp120 antibody (Ab-3).
AUTHORS: Angel Justiz-Vaillant
[STEPS]
?. Ninety six well polystyrene microplate (U-shaped bottom, Sigma-Aldrich Co, St Louis Missouri) is coated with 50 µl/well of 1 ng/µl solution of gp-120... | ["Ninety six well polystyrene microplate (U-shaped bottom, Sigma-Aldrich Co, St Louis Missouri) is coated with 50 µl/well of 1 ng/µl solution of gp-120 peptide, fragment 254-274 (Sigma) in carbonate-bicarbonate buffer pH 9.6 (Sigma) for 4 hours at 37°C.", "The microplate is then washed 4 times with PBS Tween-20.", "The... |
28,992 | Crude extraction of Xylella fastidiosa from infected leaves | null | dx.doi.org/10.17504/protocols.io.8i8huhw | null | Niels Appelman | TITLE: Crude extraction of Xylella fastidiosa from infected leaves
AUTHORS: Niels Appelman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol can be used to (crudely) extract Xylella fastidiosa from infected leaves.</div></div>
[STEPS]
?. Pick leaves from plants infected with X. fastidio... | ["Pick leaves from plants infected with X. fastidiosa", "With a scalpel, remove the first 2 cm of the central nerve of the plant was removed.Note: X. fastidiosa is located in the xylem in this nerve. Including mesophyll will reduce the yield.", "Crush the central nerve and extract bacteria with 50 ml of 0.01 M potassiu... |
null | null | null | dx.doi.org/10.17504/protocols.io.shteb6n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The importance of fungal species differentiation is critical for plant pathology research and disease control purposes. Traditionally, fungal species have been identified by a range of cultural and morphological characteristics, such as conidial morphology, presence or absenc... | [] |
38,918 | SABER-FISH – Signal amplification for multiplexed fluorescence in situ hybridization assays | 2 | null | https://www.protocols.io/view/saber-fish-signal-amplification-for-multiplexed-fl-bh9ej93e | Jocelyn Y. Kishi, Sylvain W. Lapan, Brian J Beliveau, Emma R. West, Allen Zhu, Hiroshi M. Sasaki, Sinem Saka, Yu Wang, Constance L Cepko, Peng Yin | TITLE: SABER-FISH – Signal amplification for multiplexed fluorescence in situ hybridization assays
AUTHORS: Jocelyn Y. Kishi, Sylvain W. Lapan, Brian J Beliveau, Emma R. West, Allen Zhu, Hiroshi M. Sasaki, Sinem Saka, Yu Wang, Constance L Cepko, Peng Yin
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-bloc... | [] |
50,401 | RT–PCR protocol for the detection ORF1 11288–11296 deletion (NSP6 106-108del) in SARS-CoV-2 genome | 4 | dx.doi.org/10.17504/protocols.io.bvf9n3r6 | https://www.protocols.io/view/rt-pcr-protocol-for-the-detection-orf1-11288-11296-bvf9n3r6 | Nikita Yolshin , Artem Fadeev, Andrey Komissarov | TITLE: RT–PCR protocol for the detection ORF1 11288–11296 deletion (NSP6 106-108del) in SARS-CoV-2 genome
AUTHORS: Nikita Yolshin , Artem Fadeev, Andrey Komissarov
[DESCRIPTION]
ORF1 deletion is observed in some new SARS-CoV-2 lineages and is lineage defining for B.1.1.7 and P.1. Biological effect of this mutation ... | ["Order oligonucleotides with following sequences:\n\n \n Name Sequence (5’ – 3’) ORF1-del-F GGTTGGATATGGTTGATACTAGTTTGAAG ORF1-del-R TGTCAAGACATTCATAAGTGTCCACA ORF1-del-P Cy5.5-ACTGTGTTATGTATGCATCAGCTGTAGTGTTACTAATCC-BHQ3 \n \n 2X RT-PCR Buffer 12.5 μl ... |
35,927 | Quant-iT™ RiboGreen™ RNA Quantification | null | dx.doi.org/10.17504/protocols.io.bfbxjipn | https://www.protocols.io/view/quant-it-ribogreen-rna-quantification-bfbxjipn | Roey Angel, Eva Petrova | TITLE: Quant-iT™ RiboGreen™ RNA Quantification
AUTHORS: Roey Angel, Eva Petrova
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The following protocol is intended for the quantification of RNA using </span><a href="https://www.thermofisher.com/order/catalog/product/R11490#/R11490" style = "tex... | ["[Prepare the reaction]\nTake out all reagents from the fridge and bring them to room temperature.Take out the RNA samples from the freezer. RNA samples should be slowly thawed on ice.\nQuant-iT™ RiboGreen® RNA reagent is dissolved in dimethylsulfoxide (DMSO), which freezes below 19 °C. The reagent must be completely ... |
40,359 | Protein quantification protocol optimized for zebrafish brain tissue (Bradford method) | 6 | dx.doi.org/10.17504/protocols.io.bjnfkmbn | https://www.protocols.io/view/protein-quantification-protocol-optimized-for-zebr-bjnfkmbn | Adrieli Sachett, Matheus Gallas-Lopes, Greicy M M Conterato, Radharani , Ana Herrmann, Angelo Piato | TITLE: Protein quantification protocol optimized for zebrafish brain tissue (Bradford method)
AUTHORS: Adrieli Sachett, Matheus Gallas-Lopes, Greicy M M Conterato, Radharani , Ana Herrmann, Angelo Piato
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Zebrafish are incresingly used as a model animal... | ["[Preparing the reagents]\nThe first step is to prepare the reagents to be used in protein quantification;", "[Preparing the reagents]\nBradford reagent: Prepare and use this reagent under dim or no light, making sure all glassware used is covered in aluminum foil to avoid photodegradation of the reagent. Prepare and ... |
104,065 | Automated Bar-Seq Library Preparation and Pooling | 0 | dx.doi.org/10.17504/protocols.io.3byl49qdjgo5/v2 | https://www.protocols.io/view/automated-bar-seq-library-preparation-and-pooling-dhu936z6 | David Ross, Nina Alperovich | TITLE: Automated Bar-Seq Library Preparation and Pooling
AUTHORS: David Ross, Nina Alperovich
[DESCRIPTION]
Protocol for automated Bar-Seq Library preparation
This protocol prepares 96 DNA samples, representing 24 samples from 4 different timepoints, for multiplexed Illumina sequencing. The process starts with two r... | ["[Transfer Plasmid DNA to PCR Plate and Dilute with DI water] Pre-heat the on deck thermocycler (ODTC) for 1st PCR step", "[Transfer Plasmid DNA to PCR Plate and Dilute with DI water] Remove lids from PCR-Plate 1, Sample-Plate, and Reagent Plate", "[Transfer Plasmid DNA to PCR Plate and Dilute with DI water] Transfer ... |
55,913 | Study Protocol Document for PONE-D-21-18427R2 (Prevalence and Predictors of GMD among PLWH on cART) | 3 | dx.doi.org/10.17504/protocols.io.b2uhqet6 | https://www.protocols.io/view/study-protocol-document-for-pone-d-21-18427r2-prev-b2uhqet6 | Wondmagegn T. Tadesse, Wondwossen Amonge, Eleni Akllilu, Ephrem Engidawork | TITLE: Study Protocol Document for PONE-D-21-18427R2 (Prevalence and Predictors of GMD among PLWH on cART)
AUTHORS: Wondmagegn T. Tadesse, Wondwossen Amonge, Eleni Akllilu, Ephrem Engidawork
[DESCRIPTION]
This is a document that states about sample size calculation, study participant recruitment, interview and me... | [] |
84,890 | FACS for CD45+ immune cells | 4 | dx.doi.org/10.17504/protocols.io.36wgq3465lk5/v1 | https://www.protocols.click/view/facs-for-cd45-immune-cells-cw52xg8e | Connor Monahan | TITLE: FACS for CD45+ immune cells
AUTHORS: Connor Monahan
[DESCRIPTION]
This protocol details FACS of intestinal immune cells (CD45+).
[STEPS]
SECTION: Procedure
1. Resuspended cells isolated from the small intestine with 400 µL Fc block (BD Biosciences,
Cat# 553142; Franklin Lakes, NJ), 1:200 in FACS buffer.
SECTIO... | ["[Procedure] Resuspended cells isolated from the small intestine with 400 µL Fc block (BD Biosciences,\nCat# 553142; Franklin Lakes, NJ), 1:200 in FACS buffer.", "[Procedure] Incubate for 20 min on ice.", "[Procedure] Wash cells in 500 µL FACS buffer, pellet at 1500 rpm, 2 min, then resuspend in 600 µL of FACS buffer ... |
91,169 | ReViBE: protocol for Refit Visualisation of lithic reduction sequences using the Blender Engine | 1 | dx.doi.org/10.17504/protocols.io.ewov1qxqkgr2/v1 | https://www.protocols.io/view/revibe-protocol-for-refit-visualisation-of-lithic-c499yz96 | Javier Sánchez-Martínez, Katia Calmet, Jorge Martínez-Moreno, Xavier Roda Gilabert | TITLE: ReViBE: protocol for Refit Visualisation of lithic reduction sequences using the Blender Engine
AUTHORS: Javier Sánchez-Martínez, Katia Calmet, Jorge Martínez-Moreno, Xavier Roda Gilabert
[DESCRIPTION]
Here, we introduce ReViBE, a step-by-step protocol for visualising lithic refits through the utilisation of im... | ["[Part 1 - Initial remarks and set up preparation] Place the camera on a tripod (ideally with a zoom lens with a focal length between 35mm and 80mm). Do not use an autofocus lens.", "[Part 1 - Initial remarks and set up preparation] With 3 light sources, create diffused lighting from both sides and above. Try to avoid... |
69,485 | Integra Magbead DNA and RNA Extraction for isolated colonies | 1 | dx.doi.org/10.17504/protocols.io.dm6gpjeqjgzp/v1 | https://www.protocols.io/view/integra-magbead-dna-and-rna-extraction-for-isolate-cf4mtqu6 | Sophana Chea, Sreyngim Lay, Mengheng Oum, Gechlang Tang, Cheata Hou, Manu Vanaerschot, Christina Yek, Cristina Tato, Jessica Manning, Vida Ahyong | TITLE: Integra Magbead DNA and RNA Extraction for isolated colonies
AUTHORS: Sophana Chea, Sreyngim Lay, Mengheng Oum, Gechlang Tang, Cheata Hou, Manu Vanaerschot, Christina Yek, Cristina Tato, Jessica Manning, Vida Ahyong
[DESCRIPTION]
This protocol is the process to extract DNA and RNA from isolated colonies. The e... | ["[Buffer Preparation] 1. Add 20 mL isopropanol to the MagBead DNA/RNA Wash 1 concentrate.\n2. Add30 mL isopropanol to the MagBead DNA/RNA Wash 2 concentrate.\n3. Reconstitute lyophilized Proteinase K at 20 mg/mL with Proteinase K Storage Buffer and mix by vortexing. Use immediately or store at -20 °C .\n4. Reconstitut... |
48,817 | Woodchip Ashing | 1 | null | https://www.protocols.io/view/woodchip-ashing-btwrnpd6 | Feyereisen | TITLE: Woodchip Ashing
AUTHORS: Feyereisen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Woodchip ashing protocol</div></div>
[STEPS]
?. Place up to 5 crucibles into the muffle furnace
?. Move the muffle furnace near the hood in 197 Borlaug and turn on the hood
?. Turn on the muffle furnace, set ... | ["Place up to 5 crucibles into the muffle furnace", "Move the muffle furnace near the hood in 197 Borlaug and turn on the hood", "Turn on the muffle furnace, set temperature to 300o C, leave for 1 hour", "Turn the muffle furnace temperature to 550o C and leave for 4 hours", "After 4 hours, turn off the muffle furnace a... |
90,592 | Environmental DNA (eDNA) extraction using Qiagen DNeasy 96 Blood and Tissue Kit | 1 | null | https://www.protocols.io/view/environmental-dna-edna-extraction-using-qiagen-dne-c4p8yvrw | Kathleen Pitz, jbaker, truelove | TITLE: Environmental DNA (eDNA) extraction using Qiagen DNeasy 96 Blood and Tissue Kit
AUTHORS: Kathleen Pitz, jbaker, truelove
[DESCRIPTION]
This protocol is a modified version of the Qiagen DNeasy 96-sample protocol: Purification of Total DNA from Animal Tissues.
[STEPS]
SECTION: MIOP: Minimum Information about an ... | ["[MIOP: Minimum Information about an Omics Protocol] MIOP Term\nValue\n \nmethodology category\n\n \nproject\n\n \npurpose\n\n \nanalyses\n\n \ngeographic location\n\n \nbroad-scale environmental context\n\n \nlocal environmental context\n\n \nenvironmental medium\n\n \ntarget\n\n \ncreator\n\n \nmaterials required\... |
null | null | null | dx.doi.org/10.17504/protocols.io.u3peymn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Purpose: Dry Eye Disease (DED) is part of several conditions, including Sjögren’s syndrome (SS) and no single test to diagnosis DED. The present study intends to evaluate whether a set of signs and symptoms of DED can distinguish: a) SS from other non-overlapping systemic diseas... | [] |
39,038 | Using sequins with RNA sequencing. | 1 | null | https://www.protocols.io/view/using-sequins-with-rna-sequencing-bic6kaze | Tim Mercer | TITLE: Using sequins with RNA sequencing.
AUTHORS: Tim Mercer
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left">Sequins are synthetic RNA controls that that are ‘spiked-in’ to your RNA sample, and undergo concurrent library preparation, sequencing and ... | ["[Laboratory Steps]\nReceiving sequins.Upon receipt of RNA sequins, first check to ensure they have not thawed during shipment. Please contact us if you have any concerns. Immediately transfer the RNA sequins to frozen storage at -80°C (sequins should not be stored in a -20°C frost-free freezer). Each tube contains RN... |
106,655 | Purification of GST-TEX264 | 0 | dx.doi.org/10.17504/protocols.io.q26g7178qgwz/v1 | https://www.protocols.io/view/purification-of-gst-tex264-dkd74s9n | Elias Adriaenssens | TITLE: Purification of GST-TEX264
AUTHORS: Elias Adriaenssens
[DESCRIPTION]
This protocol details the purification and analysis of GST-TEX264.
[STEPS]
SECTION: Purification procedure
1. To purify GST-TEX264, fuse the cytosol-exposed domain of TEX264 (28-313aa) to a N-terminal synthesize gene GST-tag by Genscript and... | ["[Purification procedure] To purify GST-TEX264, fuse the cytosol-exposed domain of TEX264 (28-313aa) to a N-terminal synthesize gene GST-tag by Genscript and clone into a pGEX-4T1 vector. Plasmid also available from Addgene.", "[Purification procedure] Collect the supernatant and incubate with pre-equilibrated Glutath... |
31,274 | Tissue collection and extractions for RNA-seq | null | dx.doi.org/10.17504/protocols.io.basiiece | null | David Lowry | TITLE: Tissue collection and extractions for RNA-seq
AUTHORS: David Lowry
[STEPS]
?. Pour liquid nitrogen into a polystyrene cooler or another container that can safely hold liquid nitrogen.
?. Remove tissue from plant and place in a tube. Make sure to clean scissors or foreceps with ethanol prior to collections.
?. I... | ["Pour liquid nitrogen into a polystyrene cooler or another container that can safely hold liquid nitrogen.", "Remove tissue from plant and place in a tube. Make sure to clean scissors or foreceps with ethanol prior to collections.", "Immediately plunge tube into liquid nitrogen (transcription profiles change rapidly, ... |
101,754 | BAF_S04_LABCONCO freeze dryer | 0 | dx.doi.org/10.17504/protocols.io.261ge5r87g47/v1 | https://www.protocols.io/view/baf-s04-labconco-freeze-dryer-dfk23kye | Nicholas Sherman | TITLE: BAF_S04_LABCONCO freeze dryer
AUTHORS: Nicholas Sherman
[DESCRIPTION]
General operation of the Lyophilizer unit.
[BEFORE_START]
THIS CHECKLIST SHOULD BE FOLLOWED PRIOR TO EACH USE:
1. remove the accessory drying chamber or manifold from the collector chamber lid and using a soft, lint free paper towel, wipe t... | ["[Add samples] MAKE SURE ALL SAMPLES ARE PRE-FROZEN", "[Add samples] Connect a pre-frozen sample to a sample valve on the drying chamber or manifold using an adapter. Turn the plastic valve knob to the “VACUUM” position to open the valve, which connects the attached sample to system vacuum. The bevel on the knob shoul... |
58,091 | Catalase test for bacterial identification | 4 | dx.doi.org/10.17504/protocols.io.b4yjqxun | https://www.protocols.io/view/catalase-test-for-bacterial-identification-b4yjqxun | lydiariver | TITLE: Catalase test for bacterial identification
AUTHORS: lydiariver
[DESCRIPTION]
The catalase enzyme is found in most aerobic and facultative anaerobic bacteria that contain cytochrome, being the main exception Streptococcus. Organisms that do not have the cytochrome system also lack the enzyme catalase and there... | ["Transfer 2-4 colonies of the bacterial growth in blood agar plates to a glass\nslide using a sterile plastic loop, make circles, and let it dry.", "Place a drop of hydrogen peroxide (H 2 0 2 ) on the glass slide with an\neyedropper.", "Observe immediate results.\nPositive: The oxygen released will be observed as a fo... |
99,200 | Protocol (C): Automated segmentation of the otic vesicle and image analysis | 0 | dx.doi.org/10.17504/protocols.io.bp2l6219dgqe/v1 | https://www.protocols.io/view/protocol-c-automated-segmentation-of-the-otic-vesi-dc482yzw | Désirée A. Schmitz, Tobias Wechsler, Hongwei Bran Li, Bjoern Menze, Rolf Kümmerli | TITLE: Protocol (C): Automated segmentation of the otic vesicle and image analysis
AUTHORS: Désirée A. Schmitz, Tobias Wechsler, Hongwei Bran Li, Bjoern Menze, Rolf Kümmerli
[DESCRIPTION]
This protocol details the automated segmentation of the otic vesicle and image analysis.
[STEPS]
SECTION: Automated segmentation ... | ["[Automated segmentation of the otic vesicle and image analysis] Organize your images in a folder with two subfolders: \n\none for the brightfield images named ‘Images’, \none for all fluorescence images named ‘Fluor’. \n\nThe image file names have to contain the slice number with a Z as a prefix and the channel numbe... |
84,112 | Labeling of Zebrafish Organs and Substructures in Light Data in Amira 3D Classic Segmentation Workroom | 5 | dx.doi.org/10.17504/protocols.io.yxmvm3xobl3p/v1 | https://www.protocols.io/view/labeling-of-zebrafish-organs-and-substructures-in-cwdqxa5w | Alyson Petruncio, Aparna Dev, Virginia Ruetten, Gudrun Ihrke, Aubrey Weigel, Project Technical Resources, CellMap Project Team | TITLE: Labeling of Zebrafish Organs and Substructures in Light Data in Amira 3D Classic Segmentation Workroom
AUTHORS: Alyson Petruncio, Aparna Dev, Virginia Ruetten, Gudrun Ihrke, Aubrey Weigel, Project Technical Resources, CellMap Project Team
[DESCRIPTION]
Intended for use on light microscopy datasets of larval zeb... | ["[Amira Project and Segmentation Setup] After opening a new Amira project, select File > Open Data, or click+drag the raw data tiff to the empty space under the Project tab. Confirm coordinates and voxel size in the Image Read Parameters window. \n\nFor higher label resolution: Select the arrow of the raw data object ... |
null | null | null | dx.doi.org/10.17504/protocols.io.fkvbkw6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Experiment purpose is to monitor the time-course of a large-scale infection of host cyanobacteria by phage under variable media conditions and obtain samples for proteomic and transcriptomic analysis.</strong></p>
<p> </p>
<p><strong>9 Hourly Timepoints: 0, 1, 2, 3, 4... | [] |
23,757 | Creatinine Companion Protocol Assay (Exocell) | null | dx.doi.org/10.17504/protocols.io.3fmgjk6 | null | Kathi Burke (Frank Brosius lab), Peter Reifsnyder (Ed Leiter Lab) | TITLE: Creatinine Companion Protocol Assay (Exocell)
AUTHORS: Kathi Burke (Frank Brosius lab), Peter Reifsnyder (Ed Leiter Lab)
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">This assay is designed for companion use w... | ["[Urine Collection Protocols]\nSpot UrineBetween 8:00 and 10:00 a.m., the mouse is picked up and induced to urinate into a 1.5 ml microfuge tube. If this is not successful, or not enough is collected, attempts on successive days can be combined (urine should be stored at 4ºC between attempts). Another way to collect s... |
49,720 | Sample preparation protocol for targeted mass spectrometry analysis of pRabs, total Rabs, LRRK2-pS910, pS935 and total LRRK2 | 4 | dx.doi.org/10.17504/protocols.io.busynwfw | https://www.protocols.io/view/sample-preparation-protocol-for-targeted-mass-spec-busynwfw | Raja S. Nirujogi, Dario Alessi | TITLE: Sample preparation protocol for targeted mass spectrometry analysis of pRabs, total Rabs, LRRK2-pS910, pS935 and total LRRK2
AUTHORS: Raja S. Nirujogi, Dario Alessi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Leucine rich repeat kinase2 (LRRK2) is one of the most commonly implicated kinas... | ["[Lysate preparation from mice tissues]\nSnap freeze mouse tissue immediately after isolation in liquid nitrogen and store at .\n-80 °C", "[Lysate preparation from mice tissues]\nPulverize frozen tissue in liquid nitrogen to a fine powder and snap freeze immediately in 2ml tubes. This is done using cell crusher kit.\n... |
26,999 | PCR-based assay for genotyping of the slick mutation in cattle | null | dx.doi.org/10.17504/protocols.io.6kxhcxn | null | Elizabeth Jannaman, M. Sofia Ortega, Tad S. Sonstegard, Peter J. Hansen | TITLE: PCR-based assay for genotyping of the slick mutation in cattle
AUTHORS: Elizabeth Jannaman, M. Sofia Ortega, Tad S. Sonstegard, Peter J. Hansen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Several mutations exist in the prolactin receptor gene (PRLR) of cattle that cause a short, sleek hai... | [] |
35,371 | Artificial Cerebrospinal Fluid V (ACSF.V) | null | dx.doi.org/10.17504/protocols.io.besjjecn | null | Allen Institute for Brain Science | TITLE: Artificial Cerebrospinal Fluid V (ACSF.V)
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes how to prepare Artificial Cerebrospinal Fluid (V). Artificial Cerebrospinal Fluid (V) is used during surgical procedures to maintain tis... | [] |
42,050 | Nuclei prep for single cell RNA/ATAC seq from intestinal surgical samples | 4 | dx.doi.org/10.17504/protocols.io.bmbak2ie | https://www.protocols.io/view/nuclei-prep-for-single-cell-rna-atac-seq-from-inte-bmbak2ie | Ran Zhou, Oni Basu | TITLE: Nuclei prep for single cell RNA/ATAC seq from intestinal surgical samples
AUTHORS: Ran Zhou, Oni Basu
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Isolating high-quality nuclei from intestinal surgical tissues is critical for single cell RNA/ATAC-seq. This protocol provides details on nucl... | ["[Pre-processing of surgical samples]\nRinse surgical samples in ice-cold PBS for three times.", "[Pre-processing of surgical samples]\nPlace the surgical samples in a 100 mm petri dish with cold HBSS, and isolate mucosa layer by Iris scissors.", "[Pre-processing of surgical samples]\nWeigh mucosa layer and cut the ti... |
null | null | null | dx.doi.org/10.17504/protocols.io.cdhs35 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Protocol for Dephosphorylation of 5´-ends of DNA using CIP in Restriction Enzyme Reaction. Uses the Calf Intestinal Alkaline Phosphatase (CIP - M0290)
[STEPS]
?.
?.
?.
?.
?.
?. | [] |
36,430 | Bulk RNA - Protocol for use with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760, E7765) | 1 | dx.doi.org/10.17504/protocols.io.bftnjnme | https://www.protocols.io/view/bulk-rna-protocol-for-use-with-nebnext-poly-a-mrna-bftnjnme | Aaron Horning, New England Biolabs | TITLE: Bulk RNA - Protocol for use with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760, E7765)
AUTHORS: Aaron Horning, New England Biolabs
[DESCRIPTION]
The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina contains t... | ["[Probe Hybridization to RNA] Prepare the First Strand Synthesis Reaction Buffer and Random Primer Mix (2X) in a nuclease-free microcentrifuge tube as follows: \n\n \nYou can prepare the first strand synthesis reaction buffer later in the protocol, but it is important that it is ready before the elution in step 38. Th... |
74,383 | Collections Standard Operating Protocol, Plant group: Bryophytes | 1 | null | https://www.protocols.io/view/collections-standard-operating-protocol-plant-grou-ckvpuw5n | Laura L Forrest, Michelle Hart, David Bell | TITLE: Collections Standard Operating Protocol, Plant group: Bryophytes
AUTHORS: Laura L Forrest, Michelle Hart, David Bell
[DESCRIPTION]
This is part of the collection "DToL Taxon-specific Standard Operating Procedure (SOP) for the Plant Working Group". The SOP collection contains guidance on how to process the vario... | [] |
94,278 | SOP for DSS kinetics studies | 4 | dx.doi.org/10.17504/protocols.io.261gedbkdv47/v1 | https://www.protocols.io/view/sop-for-dss-kinetics-studies-c8bezsje | Malu G Tansey | TITLE: SOP for DSS kinetics studies
AUTHORS: Malu G Tansey
[DESCRIPTION]
SOP for DSS kinetics studies
[STEPS]
SECTION: PROTOCOL:
2. Weigh each mouse from a cage individually in small boxes. Record their weights in grams to the nearest tenth for that day.
SECTION: PROTOCOL:
3. Keep each mouse in their own box until st... | ["[PROTOCOL:] Weigh each mouse from a cage individually in small boxes. Record their weights in grams to the nearest tenth for that day.", "[PROTOCOL:] Keep each mouse in their own box until stools are passed. For a healthy mouse, this should occur quickly. A mouse can be scruffed to expedite this if needed.", "[PROTOC... |
54,557 | HCR RNA-FISH protocol for the whole-mount brains of Drosophila and other insects | 4 | dx.doi.org/10.17504/protocols.io.bzh5p386 | https://www.protocols.io/view/hcr-rna-fish-protocol-for-the-whole-mount-brains-o-bzh5p386 | Amanda A. G. Ferreira, Bogdan Sieriebriennikov, Hunter Whitbeck | TITLE: HCR RNA-FISH protocol for the whole-mount brains of Drosophila and other insects
AUTHORS: Amanda A. G. Ferreira, Bogdan Sieriebriennikov, Hunter Whitbeck
[DESCRIPTION]
This is a protocol to perform RNA fluorescent in situ hybridization (RNA-FISH) using hybridization chain reaction (HCR) on whole-mount samples ... | ["[Day 1] Prepare all solutions", "[Day 1] Pre-heat an aliquot of Probe Hybridization Buffer if proceeding with hybridization on the same day (see step case below)\n37 °C", "[Day 1] Dissect brains in cold Schneider's Medium", "[Day 1] Fix brains in 800 μL of Fixation Buffer\n20 min \nRoom temperature\n or", "[Day 1] R... |
26,326 | Creating a more isogenic strain of worms starting from parental strain | null | dx.doi.org/10.17504/protocols.io.5xwg7pe | null | Cristian Riccio | TITLE: Creating a more isogenic strain of worms starting from parental strain
AUTHORS: Cristian Riccio
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes how to create a more isogenic strain starting from a parental strain.</div></div>
[STEPS]
?. Pick a single worm into a new f... | ["Pick a single worm into a new fresh agar NGM plate. Let it move away from the point of deposition. Pick it again into a new fresh plate. This procedure of first picking into a plate and then into another makes sure that no other worms or eggs are co-picked with the single worm of interest.", "Let the single worm po... |
null | null | null | dx.doi.org/10.17504/protocols.io.fcsbiwe | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?. | [] |
20,468 | Thawing iPSC Plate | null | dx.doi.org/10.17504/protocols.io.x8ufrww | null | Celeste Karch, Rita Martinez, Jacob Marsh | TITLE: Thawing iPSC Plate
AUTHORS: Celeste Karch, Rita Martinez, Jacob Marsh
[STEPS]
?. Determine which clones to expand based on screening.
?. Coat 24 well plate with 250-300 ul Matrigel per well (1 well per well, from 96 well).
?. Incubate at for .
?. Remove Styrofoam box from and remove plate.
Check on plate afte... | ["Determine which clones to expand based on screening.", "Coat 24 well plate with 250-300 ul Matrigel per well (1 well per well, from 96 well).", "Incubate at for .", "Remove Styrofoam box from and remove plate.\nCheck on plate after to avoid over-thawing.", "To each well add mTesR1 supplemented with 10 uM Rock inh... |
25,586 | 06 Gel purification | null | dx.doi.org/10.17504/protocols.io.48sgzwe | null | TJUSLS China | TITLE: 06 Gel purification
AUTHORS: TJUSLS China
[STEPS]
?. Column balancing step: add 500ul buffer BL to the adsorption column CA2 (the adsorption column is put into the collection tube), centrifuge at 12,000 RPM (~13,400×g) for 1 min, dump the waste liquid in the collection tube, and put the adsorption column back i... | ["Column balancing step: add 500ul buffer BL to the adsorption column CA2 (the adsorption column is put into the collection tube), centrifuge at 12,000 RPM (~13,400×g) for 1 min, dump the waste liquid in the collection tube, and put the adsorption column back into the collection tube.\n500 µl", "Remove the single targe... |
98,428 | Parse Evercode WT v2 -- University of Minnesota TMCs | 0 | dx.doi.org/10.17504/protocols.io.dm6gpz8rplzp/v2 | https://www.protocols.io/view/parse-evercode-wt-v2-university-of-minnesota-tmcs-dcc42syw | Laura J Niedernhofer, David A Bernlohr | TITLE: Parse Evercode WT v2 -- University of Minnesota TMCs
AUTHORS: Laura J Niedernhofer, David A Bernlohr
[DESCRIPTION]
Combinatorial barcoding is an instrument-free method used to generate single-cell and single-nucleus RNA-sequencing libraries. Outlined here are the methods used to isolate single-nuclei from froze... | ["[Single Nuclei Dissociation]", "[Nuclei Fixation Protocol]", "[Evercode WT Protocol]", "[FASTQ Generation] BCL data from Illumina sequencer is demultiplexed and converted into FASTQ format using bcl2fastq version 2.20.0. \n\nMultiplexed FASTQ files were split by sample using a script provided by Parse Biosciences (pa... |
44,555 | Quality of Care Index (QCI) | 5 | dx.doi.org/10.17504/protocols.io.bprjmm4n | https://www.protocols.io/view/quality-of-care-index-qci-bprjmm4n | Esmaeil Mohammadi, Erfan Ghasemi, Sahar Saeedi Moghaddam, Moein Yoosefi, Shahin Roshani, Naser Ahmadi, Masoud Masinaei, Maryam Nasserinejad, Narges Ebrahimi, Sina Azadnajafabad, Mahtab Rouhifard Khalilabad, Negar Rezaei, Ali H Mokdad, Bagher Larijani, Farshad Farzadfar | TITLE: Quality of Care Index (QCI)
AUTHORS: Esmaeil Mohammadi, Erfan Ghasemi, Sahar Saeedi Moghaddam, Moein Yoosefi, Shahin Roshani, Naser Ahmadi, Masoud Masinaei, Maryam Nasserinejad, Narges Ebrahimi, Sina Azadnajafabad, Mahtab Rouhifard Khalilabad, Negar Rezaei, Ali H Mokdad, Bagher Larijani, Farshad Farzadfar
[DESC... | ["[Data acquisition]\nA. Consider retrieving data from the GBD data repository [https://vizhub.healthdata.org/gbd-compare/].B. Use the left sidebars and menus to navigate for causes.C. Primary parameters are required 1. age-standardized mortality rate 2. age-standardized prevalence rate 3. age-standardized incidence ra... |
44,724 | Cell DIVE™ Platform | Slide Clearing and Antigen Retrieval | 4 | dx.doi.org/10.17504/protocols.io.bpwumpew | https://www.protocols.io/view/cell-dive-platform-slide-clearing-and-antigen-retr-bpwumpew | Liz McDonough, Chrystal Chadwick, Fiona Ginty, Christine Surrette, Anup Sood | TITLE: Cell DIVE™ Platform | Slide Clearing and Antigen Retrieval
AUTHORS: Liz McDonough, Chrystal Chadwick, Fiona Ginty, Christine Surrette, Anup Sood
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The purpose of this protocol is to manually deparaffinize and rehydrate slides for the Cell DIVE™ Pl... | ["[Slide Baking]\nThis is the initial step of the deparaffinization process. This step serves two purposes: (1) melting of the paraffin wax and (2) ensuring tissue adherence to the slides.", "[Slide Baking]\nSet the incubator to .\n60 °C", "[Slide Baking]\nLoad tissue slides into a slide rack. All tissue slides should ... |
41,852 | Freeze-drying (Lyophilization) of CoronaDetective tubes | 4 | dx.doi.org/10.17504/protocols.io.bk44kyyw | https://www.protocols.io/view/freeze-drying-lyophilization-of-coronadetective-tu-bk44kyyw | Guy Aidelberg, Rachel Aronoff | TITLE: Freeze-drying (Lyophilization) of CoronaDetective tubes
AUTHORS: Guy Aidelberg, Rachel Aronoff
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A protocol for freeze-drying (Lyophilization) of CoronaDetective tests, </div><div class = "text-block">and more generally any QUASR RT-LAMP reaction.... | ["Thaw components (dNTPs, 10X Primer mixes (need to be made), MgSO4, Isothermal amplification buffer, and Enzymes)Vortex and quickly spin tubes down before opening for dispensing.This protocol is for one standard 96 well PCR plate and can be scaled as needed.", "10X Primer mix: assuming your primer stocks are at for... |
29,193 | WTc11 iPSC Culture and Maintenance | null | dx.doi.org/10.17504/protocols.io.8rhhv36 | null | Connor Ludwig, Ruilin Tian, Martin Kampmann | TITLE: WTc11 iPSC Culture and Maintenance
AUTHORS: Connor Ludwig, Ruilin Tian, Martin Kampmann
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol explains general culture and maintenance of the WTc11 iPSC cell line. </div></div>
[STEPS]
?. [Prepare complete StemFlex Medium]
Thaw the froz... | ["[Prepare complete StemFlex Medium]\nThaw the frozen StemFlex Supplement 10X at for ~ or overnight at to .\n0 Room temperature\n2 °C\n8 °C\nIMPORTANT! Do not thaw the frozen supplement at 37°C.", "[Prepare complete StemFlex Medium]\nMix the thawed supplement by gently inverting 3−5 times.", "[Prepare complete StemFl... |
87,394 | Staining of CD31 and CD13 in PDGFR-B/Td-tomato brain sections | 1 | dx.doi.org/10.17504/protocols.io.x54v9p2b1g3e/v1 | https://www.protocols.io/view/staining-of-cd31-and-cd13-in-pdgfr-b-td-tomato-bra-czkax4se | Daniel Manrique-Castano | TITLE: Staining of CD31 and CD13 in PDGFR-B/Td-tomato brain sections
AUTHORS: Daniel Manrique-Castano
[DESCRIPTION]
This protocol is suitable for the staining of CD31 and CD13 in PDGFR-B/Td-Tomato fixed mouse brain sections.
[GUIDELINES]
Read the entire protocol before starting the procedure.
Note that this protocol... | ["[Tissue preparation and blocking] Extract the sections from the anti-freeze media and rinse them in PBS using a 24-well plate.", "[Tissue preparation and blocking] Aspirate the PBS and incubate the sections in the Blocking solution for 60 min at Room temperature .", "[Antibody incubation] When blocking is finished, a... |
99,877 | 10% Tween 20 | 1 | dx.doi.org/10.17504/protocols.io.ewov18m7pgr2/v2 | https://www.protocols.io/view/10-tween-20-ddsd26a6 | Allen Institute for Brain Science | TITLE: 10% Tween 20
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
This protocol is used to prepare 10% Tween 20. Tween 20, when added to aqueous solutions acts as a surfactant, decreasing the surface tension of the solution. It also punches holes in membranes, allowing easier penetration of macromolecules i... | [] |
48,181 | MojoSort™ Pan DC Isolation Kit Column Protocol | 4 | null | https://www.protocols.io/view/mojosort-pan-dc-isolation-kit-column-protocol-btavnie6 | Ken Lau | TITLE: MojoSort™ Pan DC Isolation Kit Column Protocol
AUTHORS: Ken Lau
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">MojoSort™ Pan DC Isolation Kit Column Protocol</span><span></span></div></div>
[STEPS]
?. [Protocol]
Prepare cells from your tissue of interest or... | ["[Protocol]\nPrepare cells from your tissue of interest or blood without lysing erythrocytes.", "[Protocol]\nIn 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."... |
63,322 | DNA extraction (BOMB) | 4 | dx.doi.org/10.17504/protocols.io.x54v9ywq1g3e/v1 | https://www.protocols.io/view/dna-extraction-bomb-b932r8qe | Tsu-Chun Hung, Yin-Tse Huang | TITLE: DNA extraction (BOMB)
AUTHORS: Tsu-Chun Hung, Yin-Tse Huang
[DESCRIPTION]
DNA extraction (BOMB)
[STEPS]
SECTION: Sample Collection
1. Add 200 µL of 1mm beads to 1.5ml enppendorf tube
SECTION: Sample Collection
2. Add200 µL of 0.5mm beads to 1.5ml enppendorf tube
SECTION: Sample Collection
3. Add 225 µL o... | ["[Sample Collection] Add 200 µL of 1mm beads to 1.5ml enppendorf tube", "[Sample Collection] Add200 µL of 0.5mm beads to 1.5ml enppendorf tube", "[Sample Collection] Add 225 µL of TE buffer to 1.5ml enppendorf tube", "[Sample Collection] Add 375 µL of lysis buffer to 1.5ml enppendorf tube", "[Sample Collection] Collec... |
16,806 | Data File | null | dx.doi.org/10.17504/protocols.io.uneevbe | null | Yolonda Freeman-Hildreth | TITLE: Data File
AUTHORS: Yolonda Freeman-Hildreth
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Data file; </div><div class = "text-block">Total sample population</div><div class = "text-block">Facebook/Social connection group</div><div class = "text-block">Amazon Mechanical Turk group</div><div... | [] |
85,513 | GONE in 360 seconds: gentleMACS Octo Dissociator-based Nuclei Extraction | 4 | dx.doi.org/10.17504/protocols.io.dm6gp3bo8vzp/v1 | https://www.protocols.io/view/gone-in-360-seconds-gentlemacs-octo-dissociator-ba-cxrhxm36 | Deepak Balamurali, Kinga M. Wrona, Lea Eich, Anika Witten, Alba M. Albert, Marc N. Hirt, Thomas Eschenhagen, Monika Stoll | TITLE: GONE in 360 seconds: gentleMACS Octo Dissociator-based Nuclei Extraction
AUTHORS: Deepak Balamurali, Kinga M. Wrona, Lea Eich, Anika Witten, Alba M. Albert, Marc N. Hirt, Thomas Eschenhagen, Monika Stoll
[DESCRIPTION]
Single-cell and single-nuclei approaches are being extensively used to decipher the cellular h... | ["[1. Pre-processing] Pre-cool the buffers, and consumables with sample contact (e.g. gentleMACS C Tube and SmartStrainers) at 4 °C 15 min. Similarly, place the gentleMACS Octo Coolers in -20 °C .", "[2. Nuclei Extraction] Add 2 mL ice-cold lysis buffer to each pre-cooled gentleMACS C Tube.", "[4.\tQuality Check/Cont... |
109,383 | STREAM Benthic Metabarcoding Lab Protocol | 1 | dx.doi.org/10.17504/protocols.io.5jyl8ppb6g2w/v2 | https://www.protocols.io/view/stream-benthic-metabarcoding-lab-protocol-dn3f5gjn | Carley Maitland, Michael Wright, Mehrdad Hajibabaei | TITLE: STREAM Benthic Metabarcoding Lab Protocol
AUTHORS: Carley Maitland, Michael Wright, Mehrdad Hajibabaei
[DESCRIPTION]
STREAM (Sequencing the Rivers for Environmental Assessment and Monitoring; www.stream-dna.org) is a Canada-wide community-based science program established in 2018 which is led by the research la... | ["[Homogenizing] Blenders should be decontaminated ahead of homogenization. Clean by fully disassembling blender components and rinsing with water. Visually inspect to ensure all debris has been removed before scrubbing all surfaces with ELIMINase ™ and rinsing with deionized (DI) water. Treat with UV light for 30 min ... |
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