id float64 1.55k 110k ⌀ | title stringlengths 1 256 ⌀ | template_id float64 0 6 ⌀ | doi stringlengths 39 49 ⌀ | url stringlengths 40 92 ⌀ | authors stringlengths 1 933 ⌀ | protocol_text stringlengths 34 1.08M | steps_list stringlengths 2 269k |
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51,040 | Economic magnetic bead purification of PCR products | 1 | dx.doi.org/10.17504/protocols.io.bv38n8rw | https://www.protocols.io/view/economic-magnetic-bead-purification-of-pcr-product-bv38n8rw | Zaki Molvi | TITLE: Economic magnetic bead purification of PCR products
AUTHORS: Zaki Molvi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Magnetic bead-based purification is a cheap, easy, and parallelizable solution for purifying nucleic acids from PCR reactions. Compared to column-based methods, the process ... | ["[Introduction]\nMagnetic bead-based purification is a cheap, easy, and parallelizable solution for purifying nucleic acids from PCR reactions. Compared to column-based methods, the process described herein typically results in higher yields with easier handling of multiple samples, such as in a 96-well format. This p... |
89,373 | Size Exclusion Chromatography with Multiangle Light Scattering (SEC-MALS) | 1 | dx.doi.org/10.17504/protocols.io.j8nlkom4xv5r/v1 | https://www.protocols.io/view/size-exclusion-chromatography-with-multiangle-ligh-c3h5yj86 | Minghao Chen, Xuefeng Ren | TITLE: Size Exclusion Chromatography with Multiangle Light Scattering (SEC-MALS)
AUTHORS: Minghao Chen, Xuefeng Ren
[DESCRIPTION]
SEC-MALS
[STEPS]
1. Concentrate the purified protein sample to 4-5 mg/ml
2. Instruments:
Agilent 1200 HPLC system (Agilent Technologies, Santa Clara, CA)
Wyatt DAWN HELEOS-II MALS instrum... | ["Concentrate the purified protein sample to 4-5 mg/ml", "Instruments:\nAgilent 1200 HPLC system (Agilent Technologies, Santa Clara, CA)\nWyatt DAWN HELEOS-II MALS instrument\nWyatt Optilab rEX differential refractometer (Wyatt, Santa Barbara, CA)\nWTC-050S5 size-exclusion column (Wyatt) \n40 ul sample loop", "Equilibr... |
27,921 | DNA Purification from an Agarose Gel (Protocol for NucleoSpin® PCR clean-up Gel Extraction Kit) | null | dx.doi.org/10.17504/protocols.io.7hrhj56 | null | Alba Balletbó | TITLE: DNA Purification from an Agarose Gel (Protocol for NucleoSpin® PCR clean-up Gel Extraction Kit)
AUTHORS: Alba Balletbó
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Gel purification allows you to isolate and purify DNA fragments based on size. The procedure starts with standard agarose gel ... | ["[Gel Excision]\nOnce you have run your gel, move it to an open UV box (be sure to wear proper UV protection - especially for your eyes!), remove it from any gel tray as plastic will block much of the UV and with a clean, sterile razor blade, slice the desired DNA fragment from the gel.'Note':To protect the UV box, it... |
45,795 | Research Cluster: Spineless Genomics | 5 | dx.doi.org/10.17504/protocols.io.eq2lypw9plx9/v1 | https://www.protocols.io/view/research-cluster-spineless-genomics-bqybmxsn | Marina McCowin | TITLE: Research Cluster: Spineless Genomics
AUTHORS: Marina McCowin
[DESCRIPTION]
Brief explanation for how to access, log in, and navigate the research cluster server. Note that this protocol is optimized for Mac users. Windows users will likely need to adjust to running commands in Powershell. See cluster user guide... | ["[1. BEFORE USING] Log on to the UCSD VPN with your AD login credentials (Cisco AnyConnect if you're not on UCSD campus Wifi). You will need to be connected to the VPN (or be on UCSD Wifi) in order to access the cluster.", "[2. Uploading and Downloading Files (sftp)] Your login credentials will be very similar to your... |
null | null | null | dx.doi.org/10.17504/protocols.io.gyabxse | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>CasPASE™ Apoptosis Fluorometric Assay provides a simple method for assaying the activities of various caspases (proteases), a key early indicator of apoptosis in mammalian cells. </p>
[BEFORE_START]
<p><em><strong>Preparation of Kit Reagents </strong> </em></p>
<p>1. Allow ... | [] |
30,925 | Workflow for generating HMW plant DNA for third generation sequencing with high N50 and high accuracy | 1 | dx.doi.org/10.17504/protocols.io.bafmibk6 | https://www.protocols.io/view/workflow-for-generating-hmw-plant-dna-for-third-ge-bafmibk6 | Patrick Driguez, Karen Carty, Alexander Putra, Luca Ermini | TITLE: Workflow for generating HMW plant DNA for third generation sequencing with high N50 and high accuracy
AUTHORS: Patrick Driguez, Karen Carty, Alexander Putra, Luca Ermini
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">We have developed a method based on the Qiagen Genomics-Tip kit for the ext... | ["[Sample Preparation]\nIn a tray add excess liquid nitrogen to mortar and pestle. Allow most of the liquid nitrogen to evaporate and bring mortar and pestle down to cryogenic temperatures.", "[Sample Preparation]\nGrind > 1 g of frozen leaves to a very fine powder in mortar and pestle.Add small amounts of liquid nitro... |
22,743 | Almond Macaroons Recipe | null | dx.doi.org/10.17504/protocols.io.2fxgbpn | null | Lenny Teytelman | TITLE: Almond Macaroons Recipe
AUTHORS: Lenny Teytelman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is one of the EASIEST deserts to make. It takes almost no time, bakes quickly, and has no butter, wheat flour, or egg yolk. It is also infinitely flexible - add Khalua instead of vanilla, m... | ["Preheat oven to degrees.\n350 °F", "Mix almonds, almond meal, and sugar in a bowl.", "Add egg whites and vanilla, and mix thoroughly to make batter.", "Bake for , until slightly browned.", "Cool on racks."] |
39,488 | INSPECT sample tracking system | 5 | dx.doi.org/10.17504/protocols.io.bis8kehw | https://www.protocols.io/view/inspect-sample-tracking-system-bis8kehw | Shashank Sathe, Clarence Mah, Noorsher Ahmed, Michelle Franc Ragsac, John Williams | TITLE: INSPECT sample tracking system
AUTHORS: Shashank Sathe, Clarence Mah, Noorsher Ahmed, Michelle Franc Ragsac, John Williams
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>A specimen to data tracking tool for SEARCH SARS-CoV-2 tests. The application is used by SEARCH technicians to trac... | ["[Before Starting]\nBefore starting ensure that the INSPECT system is publicly accessible and that you are registered on the INSPECT user list.", "[Sample Extraction and Plating]\nFreshly received samples can be registered into INSPECT by scanning the 2D sample tube barcode into the system. This is performed in conjun... |
null | null | null | dx.doi.org/10.17504/protocols.io.szref56 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Food Microbiome dataset for comparison of 16S V3-V4 rDNA amplicon sequencing and gyrB amplicon sequencing.</p>
[STEPS]
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.qfudtnw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>This is a short tutorial on the basics of getting started with standalone BLAST+ in the Ubuntu command line.</strong></p>
<p>Code is intended for use on an Ubuntu 16.04 LTS OS.</p>
<p> </p>
<p>Note that a web server for BLASTP is also available: https://blast.ncbi.nlm... | [] |
44,700 | Freeze-drying (Lyophilization) and manufacturing of Corona Detective assay | 4 | dx.doi.org/10.17504/protocols.io.bpv4mn8w | https://www.protocols.io/view/freeze-drying-lyophilization-and-manufacturing-of-bpv4mn8w | Guy Aidelberg, Rachel Aronoff | TITLE: Freeze-drying (Lyophilization) and manufacturing of Corona Detective assay
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 QUAS... | ["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... |
81,651 | 4. Taxon Group: Cephalopoda | 4 | dx.doi.org/10.17504/protocols.io.14egn2dozg5d/v1 | https://www.protocols.io/view/4-taxon-group-cephalopoda-ctytwpwn | Kesella Scott-Somme, Inez Januszczak | TITLE: 4. Taxon Group: Cephalopoda
AUTHORS: Kesella Scott-Somme, Inez Januszczak
[DESCRIPTION]
This is part of the collection "DToL Taxon-specific Standard Operating Procedures (SOPs) for Marine Metazoa", lead by the Other Metazoa Working Group. The SOP collection contains guidance on how to process the various marine... | [] |
66,365 | https://rogerdselders.clubeo.com/news/2022/07/08/watch-this-exipure-reviews-instant-energy-like-the-latest-alive | 3 | dx.doi.org/10.17504/protocols.io.3byl4b4jjvo5/v1 | https://www.protocols.io/view/https-rogerdselders-clubeo-com-news-2022-07-08-wat-cc25syg6 | cyrusdwelch | TITLE: https://rogerdselders.clubeo.com/news/2022/07/08/watch-this-exipure-reviews-instant-energy-like-the-latest-alive
AUTHORS: cyrusdwelch
[DESCRIPTION]
Therefore, you won't need to fear approximately gaining weight and affected by the result of obesity. Before transferring in addition, knowing more about the subs... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.hpeb5je | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
81,133 | A multicenter, open label, non-comparative, 3 months study to assess the performance and safety of the new medical device Polybactum® in reducing the frequency of Recurrent Bacterial Vaginosis | 1 | dx.doi.org/10.17504/protocols.io.81wgbybbqvpk/v1 | https://www.protocols.io/view/a-multicenter-open-label-non-comparative-3-months-ctgmwju6 | Filippo Murina, Dionisio Franco Barattini, Emanuel Dogaru | TITLE: A multicenter, open label, non-comparative, 3 months study to assess the performance and safety of the new medical device Polybactum® in reducing the frequency of Recurrent Bacterial Vaginosis
AUTHORS: Filippo Murina, Dionisio Franco Barattini, Emanuel Dogaru
[DESCRIPTION]
Medical literature has evidenced in re... | ["[A multicenter, open label, non-comparative, 3 months study to assess the performance and safety of the new medical device Polybactum® in reducing the frequency of Recurrent Bacterial Vaginosis followed by PMCF protocol Observational, non-randomized, not controlled, multicentre post marketing clinical follow up (PMCF... |
73,261 | Protocol: Extrinsic Allergic Alveolitis- A Systematic Review of HLA-DR in Pigeon Breeder’s Disease | 1 | dx.doi.org/10.17504/protocols.io.dm6gpjzb5gzp/v1 | https://www.protocols.io/view/protocol-extrinsic-allergic-alveolitis-a-systemati-cjsmunc6 | Dylan Thibaut, Ryan Witcher, Anitha Kunnath, James Toldi | TITLE: Protocol: Extrinsic Allergic Alveolitis- A Systematic Review of HLA-DR in Pigeon Breeder’s Disease
AUTHORS: Dylan Thibaut, Ryan Witcher, Anitha Kunnath, James Toldi
[DESCRIPTION]
Pigeon Breeder's Pneumonitis’ complex pathogenesis affects a specific exposure group, as well as a potential genetic predisposition v... | ["[Administrative Information] Title\nProtocol: Extrinsic Allergic Alveolitis- A Systematic Review of HLA-DR in Pigeon Breeder’s Disease", "Registration \nRegistration is via protocols.io", "Authors\nDylan Thibaut: Lake Erie College of Osteopathic Medicine - Bradenton, University of Central Florida\nORCID: https://orc... |
73,825 | Deep hind paw incision model | 4 | dx.doi.org/10.17504/protocols.io.j8nlkw9k5l5r/v1 | https://www.protocols.io/view/deep-hind-paw-incision-model-ckb9usr6 | Fanglin Lu | TITLE: Deep hind paw incision model
AUTHORS: Fanglin Lu
[DESCRIPTION]
The deep hind paw incision model is established to evaluate postoperative pain.
Based on TJ Brennan's rat model of incisional pain (1996), several modifications are made.
This protocol outlines the procedures from a to data anesthesia to consciousne... | ["[Anesthesia and disinfection] The mouse placed in a prone position under sevoflurane anesthesia (4 volume% in 1 L/min oxygen) delivered via a nose cone. Sevoflurane inhalation is used, as it is safe, non-invasive, rapid, and easy to control. Adequate anesthetic depth is ascertained by loss of response to tail clamp."... |
40,988 | Determination of C3 concentration by the Mancini test. | 6 | dx.doi.org/10.17504/protocols.io.bj94kr8w | https://www.protocols.io/view/determination-of-c3-concentration-by-the-mancini-t-bj94kr8w | Angel Justiz-Vaillant | TITLE: Determination of C3 concentration by the Mancini test.
AUTHORS: Angel Justiz-Vaillant
[STEPS]
?. An appropriate anti-C3 antiserum (antibody) is poured in the center well of an agar-containing plate.
?. Carefully circular wells are cut and detached from the plates.
?. A series of standards containing known conc... | ["An appropriate anti-C3 antiserum (antibody) is poured in the center well of an agar-containing plate.", "Carefully circular wells are cut and detached from the plates.", "A series of standards containing known concentrations of C3 are placed in separate wells, while “unknown” human serum samples and control are place... |
87,908 | Whole Organoids Harvesting Procedure (Cultrex-modified) | 4 | null | https://www.protocols.io/view/whole-organoids-harvesting-procedure-cultrex-modif-cz4cx8sw | Gabriela Vallejo Flores, Annika Fendler | TITLE: Whole Organoids Harvesting Procedure (Cultrex-modified)
AUTHORS: Gabriela Vallejo Flores, Annika Fendler
[DESCRIPTION]
This protocol is use for whole organoids isolation, after isolation organoiods may be:
a. Resuspended in basement membrane matrix for further organoid culture.
b. Resuspended in freezing medium... | ["[Sample description]", "[Organoids harvesting] Aspirate cell culture media and gently wash each well with 10 volumes cold (2-8 °C) PBS (Table 2). Be careful not to disrupt the basement membrane matrix containing organoids.", "[Organoids harvesting] Add 10 volumes of cold (2-8 °C) Cultrex™ Organoid Harvesting Solution... |
57,901 | DNA Extraction from Water Samples | 4 | null | https://www.protocols.io/view/dna-extraction-from-water-samples-b4smqwc6 | Andrew Dominguez, Yanyan Zhang, Nicole Pietrasiak | TITLE: DNA Extraction from Water Samples
AUTHORS: Andrew Dominguez, Yanyan Zhang, Nicole Pietrasiak
[DESCRIPTION]
This protocol was followed to extract DNA from potable and tailored water samples used to water various turf grasses in a greenhouse study. We closely followed the extraction protocol provided in the Qi... | ["[Sample Prep] If water samples are stored at -80 °C allow time for samples to defrost depending on the volume. Large volumes can take a few hours to defrost.", "[DNA Extraction] DNA extraction was completed using with the following modifications:\nIn step 1, the specific filters used were \nIn step 21, 30 µL of S... |
100,197 | HTTM : Illumina library preparation | 4 | dx.doi.org/10.17504/protocols.io.n2bvj8oowgk5/v3 | https://www.protocols.io/view/httm-illumina-library-preparation-dd4d28s6 | Antoine Champie, Amélie De Grandmaison, Sebastien Rodrigue | TITLE: HTTM : Illumina library preparation
AUTHORS: Antoine Champie, Amélie De Grandmaison, Sebastien Rodrigue
[DESCRIPTION]
Part of the HTTM protocol dedicated to the preparation of Illumina sequencing libraries.
[BEFORE_START]
All steps and master mixes need to be kept on ice as much as possible. Thermocyclers nee... | ["[Libraries] Transfer 2.5 µL of DNA from the DNA extraction plate to a new PCR plate.", "[Libraries] Prepare a fragmentation master mix for 96 samples with :", "[Libraries] Add 1 µL of the fragmentation master mix to each well.", "[Libraries] Incubate in a thermocycler with the following protocol : \n15 minat 37 °C\n... |
94,529 | CHIP-reCHIP Protocol for Mapping Bivalent Chromatin | 4 | dx.doi.org/10.17504/protocols.io.8epv5x815g1b/v1 | https://www.protocols.io/view/chip-rechip-protocol-for-mapping-bivalent-chromati-c8i9zuh6 | Janith A Seneviratne, William W H Ho, Eleanor Glancy, Melanie A Eckersley-Maslin | TITLE: CHIP-reCHIP Protocol for Mapping Bivalent Chromatin
AUTHORS: Janith A Seneviratne, William W H Ho, Eleanor Glancy, Melanie A Eckersley-Maslin
[DESCRIPTION]
This is a detailed protocol for performing sequential ChIP-reChIP to map H3K4me3-H3K27me3 bivalent chromatin regions. It has been optimised using mouse embr... | ["[Key Resources & reagents]", "[Chromatin Fixation]", "[Chromatin Fixation] Grow cells until they are 70-80% confluent across several plates. One will be used for counting and the remaining for fixation (collection plates).", "[Chromatin Fixation] Collect and count cells on the counting plate: Remove media from th... |
null | null | null | dx.doi.org/10.17504/protocols.io.menc3de | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The first step in any MERFISH experiment is the design of the oligonucleotide probes that will be used to label individual RNA species. In our current implementation of MERFISH, each oligonucleotide encoding probe consists of three basic components as illustrated in Figure 2.... | [] |
107,673 | Polyethlyene Glycol Precipitation for wastewater samples, with extraction using MagMAX Wastewater kit | 0 | dx.doi.org/10.17504/protocols.io.j8nlk8pzdl5r/v1 | https://www.protocols.io/view/polyethlyene-glycol-precipitation-for-wastewater-s-dmdz4276 | Shannon Fitz, Alex Shaw, michael Owusu, Dilip Abraham | TITLE: Polyethlyene Glycol Precipitation for wastewater samples, with extraction using MagMAX Wastewater kit
AUTHORS: Shannon Fitz, Alex Shaw, michael Owusu, Dilip Abraham
[DESCRIPTION]
Polyethlyene glycol (PEG) precipitation serves as a method of concentrating bacterial and viral pathogens contained in wastewater. PE... | ["[Polyethlyene glycol precipitation, followed by extraction using MagMAX Wastewater kit] PEG precipitation for wastewater sample concentration", "[Polyethlyene glycol precipitation, followed by extraction using MagMAX Wastewater kit] Filter wastewater sample through a coffee filter to remove suspended solids. Transfer... |
37,862 | Paraffin wax as self-sealing insulation material for seasonal sensible heat storages - Enhancement of thermal performance - Temperature Records | 3 | dx.doi.org/10.17504/protocols.io.bg8ejzte | https://www.protocols.io/view/paraffin-wax-as-self-sealing-insulation-material-f-bg8ejzte | Christoph Bott, Ingo Dressel, Peter Bayer | TITLE: Paraffin wax as self-sealing insulation material for seasonal sensible heat storages - Enhancement of thermal performance - Temperature Records
AUTHORS: Christoph Bott, Ingo Dressel, Peter Bayer
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This supplement to the article </span><span... | [] |
28,195 | Protocol for Exonuclease VIII, truncated (NEB #M0545) | 1 | null | https://www.protocols.io/view/protocol-for-exonuclease-viii-truncated-neb-m0545-7sbhnan | New England Biolabs | TITLE: Protocol for Exonuclease VIII, truncated (NEB #M0545)
AUTHORS: New England Biolabs
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Exonuclease VIII, truncated efficiently degrades linear dsDNA from 5’ to 3’ direction, leaving supercoiled dsDNA intact.</div><div class = "text-block"><span styl... | ["Set-up the reaction as follows: AB1COMPONENTS 50 μl REACTION2DNAup to 1 µg3NEBuffer 4 (10X)5 µl (1X)4Exonuclease VIII (truncated)1 µl (10 units)5Nuclease-free H2O (NEB #B1500)up to 50 µl\nAB1COMPONENTS 50 μl REACTION2DNAup to 1 µg3NEBuffer 4 (10X)5 µl (1X)4Exonuclease VIII (truncated)1 µl (10 units)5Nuclease-free H2... |
84,852 | Dispersed Pancreas | 1 | null | https://www.protocols.click/view/dispersed-pancreas-cw4uxgww | raynock | TITLE: Dispersed Pancreas
AUTHORS: raynock
[DESCRIPTION]
Dispersed pancreas protocols
[STEPS]
SECTION: Culture Media
1. Human islets:
-Dulbecco's Modification of Eagle's Medium (DMEM, 4.5 g/L glucose, L-glutamine, sodium pyruvate)
-Fetal Bovine Serum (FBS) at 10%
-Penicillin-Streptomycin at 1%
-GlutaM... | ["[Culture Media] Human islets:\n -Dulbecco's Modification of Eagle's Medium (DMEM, 4.5 g/L glucose, L-glutamine, sodium pyruvate)\n -Fetal Bovine Serum (FBS) at 10%\n -Penicillin-Streptomycin at 1%\n -GlutaMAXTM supplement at 1%\n\nHuman exocrine tissues (ducts and acinar):\n -Dulbecco's Modification of... |
63,329 | Lean Gene: How Can I Lose Weight Safely? | 1 | dx.doi.org/10.17504/protocols.io.8epv59dy5g1b/v1 | https://www.protocols.io/view/lean-gene-how-can-i-lose-weight-safely-b939r8r6 | dfskalaio | TITLE: Lean Gene: How Can I Lose Weight Safely?
AUTHORS: dfskalaio
[DESCRIPTION]
Supplement Name - Lean Gene
Benefits - Weight Loss and Enhance Metabolism
Key Ingredients - Yerba Mate, Cinnamon Bark Extract
Product Form - Pills
Age Range - Above 18
Side Effects - No major side effects reported
Net Quantity - 1 Bottl... | [] |
74,858 | Statistical Analyis Plan for Assessing Psychological Phenotypes of Patients with Low Back Pain in the Military Health System | 1 | dx.doi.org/10.17504/protocols.io.6qpvr4k1ogmk/v1 | https://www.protocols.io/view/statistical-analyis-plan-for-assessing-psychologic-cmciu2ue | Daniel I Rhon, Trevorlentz, Steven Z George | TITLE: Statistical Analyis Plan for Assessing Psychological Phenotypes of Patients with Low Back Pain in the Military Health System
AUTHORS: Daniel I Rhon, Trevorlentz, Steven Z George
[DESCRIPTION]
This contains the details of the the statistical analysis plan for a secondary analysis using data from 2 clinical tria... | ["[Methods] Study Design and Setting\n\nWe will use data already collected from two completed randomized clinical trials for low back pain management in the Military Health System. For this study, we will use baseline data only.\n\nParticipants\nIndividuals seeking care for LBP in primary care (n=510) that participated... |
40,858 | Safety Assessment and Reporting (Part 7 of Phase 3 study of Vaccine Candidate for COVID-19) | 1 | dx.doi.org/10.17504/protocols.io.bj52kq8e | https://www.protocols.io/view/safety-assessment-and-reporting-part-7-of-phase-3-bj52kq8e | Chris Ockenhouse, Chris Gast, Renee Holt, Jorge Flores | TITLE: Safety Assessment and Reporting (Part 7 of Phase 3 study of Vaccine Candidate for COVID-19)
AUTHORS: Chris Ockenhouse, Chris Gast, Renee Holt, Jorge Flores
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This is Part 7 of "Phase 3 randomized, double-blinded, placebo-controlled trial to ... | [] |
76,433 | Protocols for the assembly and annotation of snake genomes | 2 | dx.doi.org/10.17504/protocols.io.5jyl8j6e9g2w/v2 | https://www.protocols.io/view/protocols-for-the-assembly-and-annotation-of-snake-cnvrve56 | Boyang Liu, Liangyu Cui, Zhangwen Deng, Yue Ma, Diancheng Yang, Yanan Gong, Yanchun Xu, Shuhui Yang, Song Huang | TITLE: Protocols for the assembly and annotation of snake genomes
AUTHORS: Boyang Liu, Liangyu Cui, Zhangwen Deng, Yue Ma, Diancheng Yang, Yanan Gong, Yanchun Xu, Shuhui Yang, Song Huang
[DESCRIPTION]
Background: Snakes are one of the most important wildlife resources and are widely distributed. Bungarus multicinctus... | [] |
18,364 | Cell growth assay | null | dx.doi.org/10.17504/protocols.io.v64e9gw | null | Kiichi Hirota, Yoshiyuki Matsuo | TITLE: Cell growth assay
AUTHORS: Kiichi Hirota, Yoshiyuki Matsuo
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. Cells were seeded into 96-well plates and cultivated for indicated time periods
?. 20 μl of CellTiter 96® AQueous One Solution Reagent was added to each well.
?. The plates were incubated at 37... | ["Cells were seeded into 96-well plates and cultivated for indicated time periods", "20 μl of CellTiter 96® AQueous One Solution Reagent was added to each well.", "The plates were incubated at 37 °C for 1 h prior to measuring the absorbance of each sample using an iMark™ Microplate Reader (BIO-RAD, Hercules, CA, USA) a... |
29,367 | Irritability-like behavior testing with the bottle brush | 1 | null | https://www.protocols.io/view/irritability-like-behavior-testing-with-the-bottle-8wxhxfn | Adam Kimbrough, Olivier George | TITLE: Irritability-like behavior testing with the bottle brush
AUTHORS: Adam Kimbrough, Olivier George
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><h1>Irritability Protocol</h1></div><div class = "text-block">We use the bottle-brush test to test for irritability-like behavior see previous studi... | ["Procedure:\nTesting usually begins during the dark cycle of the animals under dark conditions with a red light for researchers but may vary depending on the experiment.\n\n\nA session consists of 10 trials in a clean plastic cage (26.67 cm × 48.26 cm × 20.32 cm; Ancare, Bellmore, NY, USA) with fresh bedding. \n\n\nA ... |
70,112 | Optical Fractionator protocol | 4 | dx.doi.org/10.17504/protocols.io.yxmvm2719g3p/v1 | https://www.protocols.io/view/optical-fractionator-protocol-cgp8tvrw | Andrew Hunter | TITLE: Optical Fractionator protocol
AUTHORS: Andrew Hunter
[DESCRIPTION]
Optical Fractionator protocol
[STEPS]
SECTION: Image acquisition workflow
1.
Note, these instructions are for fluorescently labelled tissue, imaging one channel only. They will
be much the same if imaging in two or three channels, but will hav... | ["[Image acquisition workflow] Note, these instructions are for fluorescently labelled tissue, imaging one channel only. They will\nbe much the same if imaging in two or three channels, but will have to set up multi-channel\nimaging first.", "[Image acquisition workflow] To minimize bleaching turn the LED off as often ... |
25,243 | Isolation of Mononuclear Cells from Whole Blood by Density Gradient Centrifugation | null | dx.doi.org/10.17504/protocols.io.4v3gw8n | null | STEMCELL Technologies | TITLE: Isolation of Mononuclear Cells from Whole Blood by Density Gradient Centrifugation
AUTHORS: STEMCELL Technologies
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes how to isolate mononuclear cells from whole blood using density gradient centrifugation. See how to layer b... | ["Dilute the blood sample at a 1:1 volume ratio with the appropriate medium.", "Gently layer the diluted blood on top of the density gradient medium. Take care not to mix the two layers.", "Centrifuge", "Carefully harvest the cells by inserting the pipette directly through the upper plasma layer to the mononuclear cell... |
null | null | null | dx.doi.org/10.17504/protocols.io.hefb3bn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>A conventient extraction and measurement protocol for GUS activity from Phaeodactylum tricornutum.</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
98,295 | Tissue Harvesting | HuBMAP | JHU-TMC | 0 | dx.doi.org/10.17504/protocols.io.e6nvw16p7lmk/v2 | https://www.protocols.io/view/tissue-harvesting-hubmap-jhu-tmc-db8x2rxn | Kyu Sang Han, Pei-Hsun Wu, Joel Sunshine, Ashley Kiemen, Sashank Reddy, Denis Wirtz | TITLE: Tissue Harvesting | HuBMAP | JHU-TMC
AUTHORS: Kyu Sang Han, Pei-Hsun Wu, Joel Sunshine, Ashley Kiemen, Sashank Reddy, Denis Wirtz
[DESCRIPTION]
This protocol describes how to harvest human tissue biopsy and prepare it for histological processes
[STEPS]
SECTION: Prepare tissue collection container
1. For tissue... | ["[Prepare tissue collection container] For tissue collection container, we will prefill histology containers with 10% Neutral Buffered Formalin (NBF)", "[Prepare tissue collection container] Combine 100 mL of Formaldehyde (37% - 40%), 900mL of distilled water, 4g of Sodium dihydrogen phosphate monohydrate, and 6.5g of... |
4,676 | Preparation of chemically competent E. coli cells | null | dx.doi.org/10.17504/protocols.io.gtcbwiw | null | Alice Pawlowski | TITLE: Preparation of chemically competent E. coli cells
AUTHORS: Alice Pawlowski
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Standard protocol to prepare cells for highly efficient DNA uptake using CaCl</span><span style = "vertical-align:sub;">2 </span><span> (Sambrook and Russell, Molec... | ["Carefully suspend each pellet in 20 ml of icecold 100 m CaCl2 and incubate on ice for 1 h.", "Inoculate a 5 ml overnight-culture in LB-medium without antibiotics.", "Inoculate 100 ml LB-medium with 1/100 volume of the overnight culture and incubate to an OD600 = 0.5 - 0.6 at 37 °C and 230 rpm.", "Transfer cells to tw... |
36,640 | Imaging Mass Cytometry Antibody Staining | null | dx.doi.org/10.17504/protocols.io.bfz8jp9w | https://www.protocols.io/view/imaging-mass-cytometry-antibody-staining-bfz8jp9w | Michelle Daniel, Marda Jorgensen | TITLE: Imaging Mass Cytometry Antibody Staining
AUTHORS: Michelle Daniel, Marda Jorgensen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The following SOP describes procedures required for the antibody staining of formalin fixed,</div><div class = "text-block">paraffin-embedded (FFPE) samples. In ... | ["[Sample de-paraffinization and rehydration of samples]\n1. Unstained samples should have time to equilibrate to room temperature for at least 10 min beforeproceeding to the next step.2. Take the unstained samples to the dewaxing robot3. Log use of dewaxing robot in log sheet4. Make sure the levels of all reagents in ... |
80,544 | Molecular Diagnosis of Viral Hepatitis B Infection | 4 | dx.doi.org/10.17504/protocols.io.kqdg39ozeg25/v1 | https://www.protocols.io/view/molecular-diagnosis-of-viral-hepatitis-b-infection-csv8we9w | Frank Twum Aboagye, Maame Ekua Acquah | TITLE: Molecular Diagnosis of Viral Hepatitis B Infection
AUTHORS: Frank Twum Aboagye, Maame Ekua Acquah
[DESCRIPTION]
With over 400 million HBV infections, viral hepatitis B remains a global public health concern. Diagnosis is primarily based on an immunological assay approach, which utilizes the Hepatitis B surface ... | ["[HBV Nucleic Acid Isolation] Transfer 200 µL of to a sterile 1.5 mL microcentrifuge tube (pre-labeled).", "[HBV Nucleic Acid Isolation] Add 5 µL of Internal Control (provided with the amplification kit) to each specimen and vortex for 30 s", "[HBV Nucleic Acid Isolation] Add 400 µL of Genomic Lysis Buffer and 10 µL... |
58,356 | ScenGen | 3 | null | https://www.protocols.io/view/scengen-b48uqzww | Elena L. Peredo | TITLE: ScenGen
AUTHORS: Elena L. Peredo
[DESCRIPTION]
test1
[STEPS] | [] |
53,212 | Essential CBD Gummies Australia Price, Essential CBD Extract Gummies Review | 4 | dx.doi.org/10.17504/protocols.io.bx74prqw | https://www.protocols.io/view/essential-cbd-gummies-australia-price-essential-cb-bx74prqw | Essential CBD Gummies Australia Au | TITLE: Essential CBD Gummies Australia Price, Essential CBD Extract Gummies Review
AUTHORS: Essential CBD Gummies Australia Au
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify"><span>Essential CBD Gummies Australia is a moving source of CBD that atte... | [] |
98,381 | RNA-Seq protocols for non-model species | 0 | null | https://www.protocols.io/view/rna-seq-protocols-for-non-model-species-dcbm2sk6 | Chase Donnelly | TITLE: RNA-Seq protocols for non-model species
AUTHORS: Chase Donnelly
[DESCRIPTION]
This is a protocol under development for RNA seq analysis on non model plant species.
[STEPS]
SECTION: RNA Extraction
1. RNA Extraction followed a modified protocols from RNeasy plant mini kit (Qiagen), below we share only the modi... | ["[RNA Extraction] RNA Extraction followed a modified protocols from RNeasy plant mini kit (Qiagen), below we share only the modifications used to extract high qualilty RNA from difficult plant species. \nhttps://www.qiagen.com/us/products/discovery-and-translational-research/dna-rna-purification/rna-purification/total... |
21,093 | Improvements in episodic future thinking methodology: Establishing a standardized episodic thinking control | null | dx.doi.org/10.17504/protocols.io.yudfws6 | null | Kelseanna Hollis-Hansen, Sara E. O’Donnell, Jennifer S. Seidman, Spencer J. Brande, Leonard H. Epstein | TITLE: Improvements in episodic future thinking methodology: Establishing a standardized episodic thinking control
AUTHORS: Kelseanna Hollis-Hansen, Sara E. O’Donnell, Jennifer S. Seidman, Spencer J. Brande, Leonard H. Epstein
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weig... | [] |
45,883 | ‘Frankenstein’ protocol for nuclei isolation from FRESH and FROZEN tissue for snRNA-Seq (10x genomics Platform) | 1 | dx.doi.org/10.17504/protocols.io.bq23mygn | https://www.protocols.io/view/frankenstein-protocol-for-nuclei-isolation-from-f-bq23mygn | Luciano Martelotto | TITLE: ‘Frankenstein’ protocol for nuclei isolation from FRESH and FROZEN tissue for snRNA-Seq (10x genomics Platform)
AUTHORS: Luciano Martelotto
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is the result of the combination of various nuclei isolation protocols for single cell RNA... | ["[Tissue Homogenization]\nMince/chop tissue with a razor blade to small pieces. The tissue may be as small as a grain of rice.\nFor mincing the tissue, you may take the tube out of ice, however, be quick and return to ice.", "[Tissue Homogenization]\nAdd chilled Nuclei EZ Lysis Buffer to the tissue in 1.5 mL tube.\n5... |
53,977 | Multiplexed Iterative FISH Experimental Protocol SOP002.v3.5 | 4 | null | https://www.protocols.io/view/multiplexed-iterative-fish-experimental-protocol-s-byxzpxp6 | Rory Kruithoff, Lei Zhou, Douglas Shepherd | TITLE: Multiplexed Iterative FISH Experimental Protocol SOP002.v3.5
AUTHORS: Rory Kruithoff, Lei Zhou, Douglas Shepherd
[DESCRIPTION]
This document, SOP002 - Multiplexed Iterative FISH Experimental Protocol, describes the process for in-situ fluorescence labeling of RNA transcripts in cells and tissues using a layer... | ["[Part 1 - Tissue or Cell-Based Experiment Preparation] Part 1 of this protocol describes the steps to setup a multiplexed iterative FISH experiment for tissue or cell-based samples. These steps are focused on the biochemical requirements for tissue or cell preparation, probe hybridization and imaging.This protocol do... |
84,589 | HMW gDNA extraction from prokaryotic cultures and cryo preservation stocks | 4 | dx.doi.org/10.17504/protocols.io.3byl4q7nrvo5/v1 | https://www.protocols.io/view/hmw-gdna-extraction-from-prokaryotic-cultures-and-cwumxeu6 | Richard RKS Stöckl | TITLE: HMW gDNA extraction from prokaryotic cultures and cryo preservation stocks
AUTHORS: Richard RKS Stöckl
[DESCRIPTION]
This protocol can be used to extract High Molecular Weight gDNA from bacterial and archaeal cultures and cryo preservations thereof.
The resulting gDNA is usually suitable for long-read sequenci... | ["[Prepare cultures or cryopreservation capillaries] Transfer the bacteria-/archaea-suspension (~50 µL) from one cryo preservation capillary to a 1.5 mL reaction tube or pellet a well-grown culture by centrifugation 15000 rpm, 15 min , discarding the supernatant, and resuspending the cell pellet in ~50 µL media", "[Ope... |
44,312 | Cell Lysis and RNA Fragmentation | 4 | dx.doi.org/10.17504/protocols.io.bphymj7w | https://www.protocols.io/view/cell-lysis-and-rna-fragmentation-bphymj7w | Eric L. Van Nostrand, Thai B. Nguyen, Chelsea Gelboin-Burkhart, Ruth Wang, Steven M. Blue, Gabriel A. Pratt, Ashley L. Louie, Gene W. Yeo | TITLE: Cell Lysis and RNA Fragmentation
AUTHORS: Eric L. Van Nostrand, Thai B. Nguyen, Chelsea Gelboin-Burkhart, Ruth Wang, Steven M. Blue, Gabriel A. Pratt, Ashley L. Louie, Gene W. Yeo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Profiling of RNA binding protein targets in vivo provides critica... | ["[Lyse Cells]\nAdd + to each pellet.\n[cold lysis buffer]\n[200× Protease Inhibitor Cocktail III]\nRNase inhibitor addition to lysis buffer.Murine RNase inhibitor (NEB) inhibits many endogenous RNase enzymes but does not significantly inhibit RNase I. As such, it can be added either before or after RNase I treatmen... |
null | null | null | dx.doi.org/10.17504/protocols.io.jwscpee | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The Campbell Lab protocol for imaging Western Blots using ECL Select chemi-luminescent detection and the Bio-Rad VersaDoc imager for immunoquantitation of phytoplankton samples.</p>
[GUIDELINES]
<p>The ECL Select is not the most sensitive detection reagent we've tested (that... | [] |
94,964 | DNA yield estimation and custom DNA quality evaluation before shotgun metagenomic sequencing | 1 | dx.doi.org/10.17504/protocols.io.5qpvo3zzzv4o/v1 | https://www.protocols.io/view/dna-yield-estimation-and-custom-dna-quality-evalua-c8yuzxww | Benoit Quinquis , Alexandre Famechon , nathalie.galleron, Victoria Meslier, mathieu.almeida | TITLE: DNA yield estimation and custom DNA quality evaluation before shotgun metagenomic sequencing
AUTHORS: Benoit Quinquis , Alexandre Famechon , nathalie.galleron, Victoria Meslier, mathieu.almeida
[DESCRIPTION]
This protocol describes the procedures used for DNA quantification and a custom DNA quality evaluation b... | ["[DNA quantification] using the DNA-binding fluorescent Quant-it dsDNA\nBR assay", "[Custom DNA quality estimation] Genomic 50 kb kit by capillary electrophoresis using the Fragment Analyzer, followed by a custom DNA quality analysis"] |
20,385 | Seed Sterilization | null | dx.doi.org/10.17504/protocols.io.x59fq96 | null | Alex Rajewski | TITLE: Seed Sterilization
AUTHORS: Alex Rajewski
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details how to surface sterilize plant seeds for tissue culture regeneration/transformation or for other techniques requiring sterile seeds.</div></div>
[STEPS]
?. Place a 100mL beaker con... | ["Place a 100mL beaker containing approximatelyin the chaber next to the petri dish of seeds.\n[bleach]", "In a fume hood, place an empty dessication chamber with a petri dish of the seeds you wish to surface sterilize. Leave the lid of the petri dish halfway on, so that you can quickly close it later.\nA dessication c... |
19,266 | Processing Human Colon muscle layers for Single Nuclei RNA-seq using PHOX2B antibody immunoselection | 1 | dx.doi.org/10.17504/protocols.io.w3afgie | https://www.protocols.io/view/processing-human-colon-muscle-layers-for-single-nu-w3afgie | Christina M Wright, Robert O Heuckeroth | TITLE: Processing Human Colon muscle layers for Single Nuclei RNA-seq using PHOX2B antibody immunoselection
AUTHORS: Christina M Wright, Robert O Heuckeroth
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">ABSTRACT</div><div class = "text-block">INTRODUCTION: The human enteric nervous system (ENS) i... | ["[Human colon processing to collect and freeze muscle layer in O.C.T]\nHalf hour before the tissue arrives:Spray off forceps and scissors with RNase Away, and thoroughly rinse/soak in waterFetch dry ice.In the fume hood, add methylbutane to a petri dish on the dry ice. Place a few pieces of dry ice into the methylbuta... |
49,552 | Fluorescence analysis using CF imager | 1 | null | https://www.protocols.io/view/fluorescence-analysis-using-cf-imager-bumqnu5w | Steven Burgess, Lynn Doran | TITLE: Fluorescence analysis using CF imager
AUTHORS: Steven Burgess, Lynn Doran
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Measurement of photosynthesis parameters using the Chlorophyll Fluorescence Imager from Technologica</div><div class = "text-block"><a href="http://www.technologica.co.uk... | ["[Preparing plants]\nDark adapt plants for at least 20 minutes prior to taking measurements.\nThis is done to ensure the photosynthetic electron transport chain is fully oxidized and reaction centres are open. In an ideal situation plants are allowed to dark adapt overnight prior to measurement.A properly adapted, hea... |
104,140 | Library Bottlenecking Protocols | 0 | dx.doi.org/10.17504/protocols.io.x54v9227pl3e/v3 | https://www.protocols.io/view/library-bottlenecking-protocols-dhxk37kw | David Ross | TITLE: Library Bottlenecking Protocols
AUTHORS: David Ross
[DESCRIPTION]
Protocol for bottlenecking a variant library for downstream use in the Pooled, Growth-Based Assay pipeline using either a positive-displacement flow cytometer or basic microbial culture equipment.
[STEPS]
SECTION: Create the first overnight cul... | ["[Create the first overnight culture] Dilute a full 1 mL vial of the library glycerol stock into 50 mL of media in a 250 mL baffled flask.", "[Prepare all flasks and tubes] One new 250-mL baffled flask with 50 mL media. \nThis is the final flask", "[Prepare all flasks and tubes] Six 15 mL snap-cap culture tubes, each ... |
39,789 | Node Propagation of Switchgrass | 4 | dx.doi.org/10.17504/protocols.io.3byl47o2olo5/v1 | https://www.protocols.io/view/node-propagation-of-switchgrass-bi4mkgu6 | Darlene Brennan, David Lowry | TITLE: Node Propagation of Switchgrass
AUTHORS: Darlene Brennan, David Lowry
[DESCRIPTION]
This protocol can be used to clonally propagate switchgrass under sterile conditions in six weeks. It describes how to prepare and propagate the nodes on an MS-based media. These shoots are ideal for experiments that would req... | ["[Prepare Propagation Media (Plates)] MS Basal Medium: weigh amount on bottle per liter (4.4g for Sigma Aldrich product MS0404-10L), add to 800 ml ddH2O with stir bar", "[Prepare Propagation Media (Plates)] Add 30 g D+Maltose, and dissolve.", "[Prepare Propagation Media (Plates)] Adjust pH to 5.5 with 1M KOH.", "[Prep... |
27,465 | UC Davis - Protein Carbonyl | null | dx.doi.org/10.17504/protocols.io.63hhgj6 | null | Peter Havel | TITLE: UC Davis - Protein Carbonyl
AUTHORS: Peter Havel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">
Cayman Chemical's Protein Carbonyl Colorimetric Assay Kit is a convenient colorimetric assay for the measurement o... | ["Transfer 200 µl of sample to two 2 ml plastic tubes. One tube will be the sample tube (S#) and the other will be the control tube (C#).", "Add 800 µl of DNPH to the sample tube and add 800 µl of 2.5 M HCI to the control tube.", "Incubate both tubes (S# & C#) in the dark at room temperature for one hour. Vortex each t... |
null | null | null | dx.doi.org/10.17504/protocols.io.q7idzke | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The development of new insecticidal formulations is important to overcome the burgeoning hurdle of insecticide resistance in field populations of mosquitoes and other pest arthropods. In order to standardize the testing of current and future small molecule chemical agents as ... | [] |
88,105 | Spinal cord epidural stimulation to control bladder in spinal cord injury patients | 1 | dx.doi.org/10.17504/protocols.io.8epv5x2w6g1b/v1 | https://www.protocols.io/view/spinal-cord-epidural-stimulation-to-control-bladde-c2ahyab6 | Daniel Medina Aguinaga, April N. Herrity, Sevda C. Aslan, Samineh Mesbah, Ricardo Siu, Karthik Kalvakuri, Beatrice Ugiliweneza, Ahmad Mohamed, Charles H. Hubscher, Susan J. Harkema | TITLE: Spinal cord epidural stimulation to control bladder in spinal cord injury patients
AUTHORS: Daniel Medina Aguinaga, April N. Herrity, Sevda C. Aslan, Samineh Mesbah, Ricardo Siu, Karthik Kalvakuri, Beatrice Ugiliweneza, Ahmad Mohamed, Charles H. Hubscher, Susan J. Harkema
[DESCRIPTION]
Aim was to investigate ... | ["[Clinical Evaluation] The patients’ injuries were classified by two independent clinicians using the ASIA (American Spinal Injury Association) Impairment Scale (AIS)1.", "[Clinical Evaluation] The patients underwent a physical examination for medical clearance, ensuring participation safety using the following inclus... |
null | null | null | dx.doi.org/10.17504/protocols.io.gt5bwq6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol can be used to transfer total RNA from thick formaldehyde/agarose gels to Nylon membranes for downstream Northern Blot Analysis. This is useful for analyzing larger RNA molecules such as mRNA.</p>
[GUIDELINES]
<p>Always wear gloves to prevent degradation of RNA... | [] |
35,895 | Typical Protocol for NEBExpress GamS Nuclease Inhibitor when used with the NEBExpress Cell-free E. coli Protein Synthesis System (NEB #E5360) | 1 | null | https://www.protocols.io/view/typical-protocol-for-nebexpress-gams-nuclease-inhi-bfaxjifn | New England Biolabs | TITLE: Typical Protocol for NEBExpress GamS Nuclease Inhibitor when used with the NEBExpress Cell-free E. coli Protein Synthesis System (NEB #E5360)
AUTHORS: New England Biolabs
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>NEBExpress GamS Nuclease Inhibitor is a recombinant protein that inh... | ["Thaw all components .\non ice", "Gently vortex the NEBExpress S30 Synthesis Extract and Protein Synthesis Buffer to mix.", "Combine reagents in a 1.5 ml microcentrifuge tube as follows: ABCD1COMPONENTSNEGATIVE CONTROL (no DNA)POSITIVE CONTROLSAMPLE2NEBExpress S30 Synthesis Extract12 µl12 µl12 µl3Protein Synthesis B... |
52,310 | Protocol for Transfection of Bodo saltans with SaCas9 RNP complex in conjunction with eGFP-NEO plasmid by electroporation | 1 | dx.doi.org/10.17504/protocols.io.bxbwpipe | https://www.protocols.io/view/protocol-for-transfection-of-bodo-saltans-with-sac-bxbwpipe | Fatma Gomaa, Zhu-Hong Li, Roberto Docampo, Virginia Edgcomb | TITLE: Protocol for Transfection of Bodo saltans with SaCas9 RNP complex in conjunction with eGFP-NEO plasmid by electroporation
AUTHORS: Fatma Gomaa, Zhu-Hong Li, Roberto Docampo, Virginia Edgcomb
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify"><s... | ["Step 1: Plasmid construction to target the PFR-2 gene -A 2512 bp promoter-less cassette is designed to target and knock out theB. saltans 69 KDa paraflagellar rod protein 2C (PFR-2), (GenBank accession #CYKH01000743: scaffold1667, positions 3455 to 6406). -This cassette is designed to replace the PFR-2 gene with a fu... |
35,848 | Populating the NCBI pathogen metadata template | null | dx.doi.org/10.17504/protocols.io.be9gjh3w | https://www.protocols.io/view/populating-the-ncbi-pathogen-metadata-template-be9gjh3w | Ruth Timme, Maria Balkey, William Wolfgang, Errol Strain | TITLE: Populating the NCBI pathogen metadata template
AUTHORS: Ruth Timme, Maria Balkey, William Wolfgang, Errol Strain
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">PURPOSE: </span><span>Guidance on how to populate NCBI's Pathogen metadata package, maximizing int... | ["[Background]\nDownload the pathogen metadata package from NCBI:Navigate to BioSample submission: https://submit.ncbi.nlm.nih.gov/subs/biosampleClick on “Download batch submission template”, then select the “Pathogen affecting public health” and the appropriate package depending on the type of isolates. We recommend u... |
29,935 | High-Throughput Stool Metaproteome Extraction | null | dx.doi.org/10.17504/protocols.io.9gph3vn | null | Carlos Gonzalez, Josh Elias | TITLE: High-Throughput Stool Metaproteome Extraction
AUTHORS: Carlos Gonzalez, Josh Elias
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The gut microbiome is strongly associated various disease related periods. In order to better understand how the host and microbiome interact during these periods... | ["[Lysis and solubilization]\nSpin down bead beater plates for 1 minute to pull beads into well at . Aliquot approximately of stool into 96 well beads plate. This protocol will work with less stool at the risk of increasing preparative replicate bias. The samples should be arrayed in a logical way, especially if the... |
23,029 | Measles virus TaqMan RT-PCR (no longer in regular use; see Guidelines) | null | dx.doi.org/10.17504/protocols.io.2qvgdw6 | null | Mitchell Finger, Michael Lyon, Judy Northill, Ian Mackay | TITLE: Measles virus TaqMan RT-PCR (no longer in regular use; see Guidelines)
AUTHORS: Mitchell Finger, Michael Lyon, Judy Northill, Ian Mackay
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><ul style = "list-style-type:disc;"><li style = "counter-reset:ol0;list-style-type:disc;">This real-time Taq... | ["[Oligonucleotide sequences]\nAB1NameSequence 5'-3'2Primer Measles MGB FPGCTCAAATTGCTCAGATACTATACAGAAA3Primer Measles MGB RPGCAGATATGGGGTCCCGTAA\n4Probe Measles MGB ProbeFAM - CCTGTCATTATTTGGCC - MGBNFQ\nAB1NameSequence 5'-3'2Primer Measles MGB FPGCTCAAATTGCTCAGATACTATACAGAAA3Primer Measles MGB RPGCAGATATGGGGTCCCGTAA\... |
38,259 | Second opinions in elective surgery – what does the literature tell us already? A scoping review. | 1 | dx.doi.org/10.17504/protocols.io.bhktj4wn | https://www.protocols.io/view/second-opinions-in-elective-surgery-what-does-the-bhktj4wn | Barbara Prediger, Alina Nießen, Nadja Könsgen, Dawid Pieper | TITLE: Second opinions in elective surgery – what does the literature tell us already? A scoping review.
AUTHORS: Barbara Prediger, Alina Nießen, Nadja Könsgen, Dawid Pieper
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Please find detailed information on our protocol in the attached PDF file.</di... | [] |
71,350 | Modified Promega Wizard Extraction for Barcoding Macrofungi | 1 | dx.doi.org/10.17504/protocols.io.rm7vzb3p4vx1/v1 | https://www.protocols.io/view/modified-promega-wizard-extraction-for-barcoding-m-chwwt7fe | Stephen Douglas Russell | TITLE: Modified Promega Wizard Extraction for Barcoding Macrofungi
AUTHORS: Stephen Douglas Russell
[DESCRIPTION]
This protocol is best used when preparing macrofungal specimens for Sanger sequencing or as a secondary extraction protocol for ONT nanopore barcoding.
[STEPS]
1. Add 600uL of to 1.5mL eppi tubes... | ["Add 600uL of to 1.5mL eppi tubes. One tube for each specimen you are planning an extraction for.", "Place tissue from your specimens into each tube using tweezers. Utilize a piece about the size of a grain of rice. The tissue can be either fresh or dried. Label the tube with the appropriate number. Wipe the tweezer... |
45,227 | test document 12/4 | 3 | null | https://www.protocols.io/view/test-document-12-4-bqejmtcn | Maria Guliakina | TITLE: test document 12/4
AUTHORS: Maria Guliakina
[STEPS] | [] |
69,564 | DNA extraction protocol | 1 | dx.doi.org/10.17504/protocols.io.5qpvorx47v4o/v1 | https://www.protocols.io/view/dna-extraction-protocol-cf64trgw | Cecile Grondin, Jean-Luc Legras, hugo.devillers | TITLE: DNA extraction protocol
AUTHORS: Cecile Grondin, Jean-Luc Legras, hugo.devillers
[DESCRIPTION]
This DNA extraction protocol has been developed at the CIRM-Levures (INRAE, SPO, FRANCE) to extract yeast chromosomes. It is based on a phenol/chloroform DNA extraction procedure.
[STEPS]
SECTION: CELL LYSIS AND NUC... | ["[CELL LYSIS AND NUCLEIC ACID EXTRACTION] - Perform a 3 ml YPD (yeast extract 10g/l, bacto peptone 10g/l, glucose 10g/l) culture for 60h in order to harvest cells at stationary phase.", "[CELL LYSIS AND NUCLEIC ACID EXTRACTION] - Centrifuge 5 min at 5000 rpm and remove the supernatant.", "[CELL LYSIS AND NUCLEIC ACID ... |
81,630 | TS Spurr's - primary fixation Karnovsky's - tissue (TM - 013) | 4 | dx.doi.org/10.17504/protocols.io.8epv5j45jl1b/v2 | https://www.protocols.io/view/ts-spurr-39-s-primary-fixation-karnovsky-39-s-tiss-ctx6wpre | sandra.crameri | TITLE: TS Spurr's - primary fixation Karnovsky's - tissue (TM - 013)
AUTHORS: sandra.crameri
[DESCRIPTION]
This method is used for conventional processing of tissue to Spurr's resin.
[GUIDELINES]
All time are minimum times, it is acceptable to go over time specified for any given step. Good place steps to lea... | ["[HEADER] SAN:\n\n\nSPEC No:\n\n\nOPERATOR & STEPS:\n\n\nOPERATOR & STEPS:", "[CONVENTIONAL] 2.5 % volume plus 4 % volume in 0.1 Molarity (m) for at least 40 min", "[CONVENTIONAL] Wash 0.1 Molarity (M) Sorenson's Phosphate Buffer pH 07.2 (300mosmol/kg) for 15 min", "[CONVENTIONAL] 1 % volume in buffer for 60 mi... |
null | null | null | dx.doi.org/10.17504/protocols.io.rv7d69n | null | null | TITLE: No Title
AUTHORS:
[STEPS] | [] |
86,283 | S-1 SOIL FIELD SAMPLING | 4 | dx.doi.org/10.17504/protocols.io.6qpvr3d62vmk/v1 | https://www.protocols.io/view/s-1-soil-field-sampling-cyhjxt4n | REDI-NET Consortium | TITLE: S-1 SOIL FIELD SAMPLING
AUTHORS: REDI-NET Consortium
[DESCRIPTION]
This protocol describes soil field sampling.
[GUIDELINES]
OBJECTIVE
To outline steps for properly collecting sediment samples from waterholes to evaluate the risk of zoonotic disease transmission by the detection of pathogens from environmenta... | ["[SAMPLING TEAMS] Field sampling of eDNA sediment samples involves two people. One person serves as the ‘sampler’ and the other person serves as a ‘helper’. The helper can look up details in these instructions when needed, keep track of samples, handle objects that are contamination risks, serve as a second set of eye... |
44,875 | Optogenetic Control of Subcellular Protein Location and Signaling in Vertebrate Embryos | 4 | dx.doi.org/10.17504/protocols.io.bp3jmqkn | https://www.protocols.io/view/optogenetic-control-of-subcellular-protein-locatio-bp3jmqkn | Clare E. Buckley | TITLE: Optogenetic Control of Subcellular Protein Location and Signaling in Vertebrate Embryos
AUTHORS: Clare E. Buckley
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This chapter describes the use of optogenetic heterodimerization in single cells within whole-vertebrate embryos. This method allow... | ["[3.1 Plasmid Cloning (See Note 2)]\nChoose sequences encoding appropriate proteins to link to the PHYB “anchor” and PIF “bait.” For example, if you want to activate a GTPase then choose a membrane moiety such as CAAX to link to PHYB (see Fig. 1a) and the relevant guanine exchange factor (GEF) to link to PIF (see Note... |
42,585 | PCR Cloning with Blue/White Selection--CHEM 584 | 1 | dx.doi.org/10.17504/protocols.io.bmtzk6p6 | https://www.protocols.io/view/pcr-cloning-with-blue-white-selection-chem-584-bmtzk6p6 | Ken Christensen, Promega, Trevor Wagner | TITLE: PCR Cloning with Blue/White Selection--CHEM 584
AUTHORS: Ken Christensen, Promega, Trevor Wagner
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Protocol for PCR Cloning with Blue/White Selection and Easy Insert Excision using </span><a href="https://www.promega.de/products/pcr/pcr-clon... | ["[Ligation ]", "[Ligation ]\nSet up ligation reactions as follows: Use tubes known to have low DNA-binding capacity. Vortex the 2X Rapid Ligation Buffer vigorously before each use.\n2X Rapid Ligation Buffer contains ATP, which degrades during temperature fluctuations. Avoid multiple freeze-thaw cycles and exposure to ... |
47,821 | Group II Syndiniales ALV01 CARD-FISH | 4 | dx.doi.org/10.17504/protocols.io.bsxmnfk6 | https://www.protocols.io/view/group-ii-syndiniales-alv01-card-fish-bsxmnfk6 | tsehein , Rebecca Gast, Maria Pachiadaki, Laure Guillou, Virginia Edgcomb | TITLE: Group II Syndiniales ALV01 CARD-FISH
AUTHORS: tsehein , Rebecca Gast, Maria Pachiadaki, Laure Guillou, Virginia Edgcomb
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for the catalyzed reporter deposition fluorescence in-situ hybridization (CARD-FISH) technique used to enumerate Gro... | ["[Prepare sample for CARD-FISH]\nFix water samples at the point of collection with a final concentration of 4% unbuffered formalin. Store samples on ice for transport to the laboratory.", "[Prepare sample for CARD-FISH]\nPlace a Millipore Isopore filter on a vacuum manifold. - 3.0μm to collect infected hosts (Catal... |
null | null | null | dx.doi.org/10.17504/protocols.io.unveve6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?. | ["{\"blocks\":[{\"key\":\"8jd78\",\"text\":\" \",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[{\"offset\":0,\"length\":1,\"key\":0}],\"data\":[]},{\"key\":\"6sh3f\",\"text\":\"\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[]}],\"entityMap\":[{... |
34,614 | PCR Protocol for Taq DNA Polymerase with ThermoPol® Buffer (M0267) | 1 | dx.doi.org/10.17504/protocols.io.bd2wi8fe | https://www.protocols.io/view/pcr-protocol-for-taq-dna-polymerase-with-thermopol-bd2wi8fe | New England Biolabs | TITLE: PCR Protocol for Taq DNA Polymerase with ThermoPol® Buffer (M0267)
AUTHORS: New England Biolabs
[DESCRIPTION]
PCR Protocol for Taq DNA Polymerase with ThermoPol® Buffer (M0267).
[BEFORE_START]
We recommend assembling all reaction components on ice and quickly transferring the reactions to a thermocycler pre... | ["Assemble the following reaction on ice:\n Component 25 μl reaction 50 μl reaction Final Concentration 10X ThermoPol Reaction Buffer 2.5 µl 5 μl 1X 10 mM dNTPs 0.5 µl 1 μl 200 µM 10 µM Forward Primer 0.5 µl 1 μl 0.2 µM (0.05–1 µM) 10 µM Reverse Primer 0.5 µl 1 μl 0.2 µM (0.05–1 µM) Template DNA variable va... |
null | null | null | dx.doi.org/10.17504/protocols.io.c8xzxm | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
For use in <a href="https://www.protocols.io/view/Wet-mount-Method-for-Enumeration-of-Aquatic-Viruse-c8pzvm" target="_blank">Wet-mount Method for Enumeration of Aquatic Viruses</a>
[GUIDELINES]
<strong>Note:</strong> An alternative Ascorbate-EDTA Buffer can be made with MgCl2 a... | [] |
75,836 | General initiation protocol for HEK-Blue cells | 4 | null | https://www.protocols.io/view/general-initiation-protocol-for-hek-blue-cells-cna4vagw | Andreas Sagen | TITLE: General initiation protocol for HEK-Blue cells
AUTHORS: Andreas Sagen
[DESCRIPTION]
HEK-Blue is a product from Invivogen, which provide reporter cells for endotoxin-testing among others. Here is a generalized protocol for initial seeding of cells with reporter characteristics.
[BEFORE_START]
Prepare complete i... | ["[Complete initiation medium (CIM)] Initially, we want to expand the cells quickly and make them healthy. This require double the amount of FBS and no selection antibiotics in the medium for the first 2-3 passages.", "[Complete initiation medium (CIM)] In 400 mL DMEM, mix 100 mL FBS\n\n \n\nMaterials:", "[Complete ini... |
36,950 | Culture of established induced pluripotent stem cell lines | 1 | dx.doi.org/10.17504/protocols.io.bgbwjspe | https://www.protocols.io/view/culture-of-established-induced-pluripotent-stem-ce-bgbwjspe | Cellular Generation and Phenotyping | TITLE: Culture of established induced pluripotent stem cell lines
AUTHORS: Cellular Generation and Phenotyping
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines the method for thawing, passaging and cryopreserving established feeder-free induced pluripotent stem cell lines. In t... | ["[iPSC Thawing]\nPreparationCoat a 6 well plate with vitronectin and incubate according to the manufacturer's instructions. Prepare complete E8 or TeSR-E8 media according to the manufacturer's instructions.", "[iPSC Thawing]\nPrepare thawing media by supplementing culture media with rock inhibitor (Y-27632) to a final... |
100,204 | Stop codon reversal assay | 0 | dx.doi.org/10.17504/protocols.io.5jyl82j39l2w/v1 | https://www.protocols.io/view/stop-codon-reversal-assay-dd4k28uw | is Sparrow | TITLE: Stop codon reversal assay
AUTHORS: is Sparrow
[DESCRIPTION]
This protocol is used to characterize viral RNA polymerase based directed evolution tools via fluctuation analysis to calculate the mutation rate. It is specific to the stop codon reversal of the aadA gene, which we use to characterize the mutational p... | ["[DNA verification] Ensure your constructs are sequenced correctly using Plasmidsaurus, paying particular attention to your stop codon and other mutations in promoter or CDS sequences.", "[Transformation] Transform your plasmid(s) into E. coli BL21 (DE3) line, selecting for the plasmid backbone (kan) using the high ef... |
33,367 | Virus injection | null | dx.doi.org/10.17504/protocols.io.bctxiwpn | null | Liu Liu, Susu Chen, Nuo Li, Karel Svoboda | TITLE: Virus injection
AUTHORS: Liu Liu, Susu Chen, Nuo Li, Karel Svoboda
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used to inject viral vectors expressing proteins such as ion channels, transcription factors, enzymes, receptors, fluorescent proteins or other non-toxic, non-ha... | ["[Pipette preparation]\nUsing thin-walled Drummond glass, pull symmetrically on the P-2000 (Sutter) or equivalent.", "[Pipette preparation]\nUnder visual inspection (e.g. microforge or microscope) inspect the tip and carefully break the tip by hitting it against a solid surface. Aim for approximately 20μm tip diameter... |
108,231 | FUNDIS DNA Extraction | 0 | null | https://www.protocols.io/view/fundis-dna-extraction-dmxf47jn | Harte Singer | TITLE: FUNDIS DNA Extraction
AUTHORS: Harte Singer
[DESCRIPTION]
A quick and easy DNA extraction protocol for fungal tissue.
[STEPS]
SECTION: Adding Extraction Buffer and Thermal Cycling
6. Using a 5-50 µL 8-channel pipettor equipped with 100 µLpipette tips, add 15-30 µL of ES extraction buffer to each tube by carefu... | ["[Adding Extraction Buffer and Thermal Cycling] Using a 5-50 µL 8-channel pipettor equipped with 100 µLpipette tips, add 15-30 µL of ES extraction buffer to each tube by carefully holding the pipette tips above the tube openings so that the tips do not make contact with the sample. This way we can use the same row of ... |
29,800 | High Density Cultivation of Synechocystis sp. PCC 6803 using the HDC 6.10B system (CellDeg) | null | dx.doi.org/10.17504/protocols.io.9cgh2tw | null | Oliver Mantovani, Dennis Dienst, Pia Lindberg | TITLE: High Density Cultivation of Synechocystis sp. PCC 6803 using the HDC 6.10B system (CellDeg)
AUTHORS: Oliver Mantovani, Dennis Dienst, Pia Lindberg
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The </span><a href="http://celldeg.com" style = "text-decoration:underline;color:blue;cursor... | ["[Preparation of precultures]\nExample: 6 well plate preculturesprepare standard polystyrene 6 well plates → each 3 wells per strain should be sufficient to inoculate 3 replicates in the Celldeg systeminoculate 3 mL standard BG11 medium (dx.doi.org/10.17504/protocols.io.wj5fcq6) with strains of Synechocy... |
64,803 | Soil Sample (Laboratory, English) | 4 | dx.doi.org/10.17504/protocols.io.14egn7rezv5d/v1 | https://www.protocols.io/view/soil-sample-laboratory-english-cbibskan | Hsin-Mao Wu | TITLE: Soil Sample (Laboratory, English)
AUTHORS: Hsin-Mao Wu
[DESCRIPTION]
This protocol is for 1 sample site
[GUIDELINES]
This protocol is for 1 sample site
[STEPS]
SECTION: Soil sampling
1. Sample sites have 3 different types
SECTION: Soil sampling
2. In one sampling site, choose 5 places as the average
SECT... | ["[Soil sampling] Sample sites have 3 different types", "[Soil sampling] In one sampling site, choose 5 places as the average", "[Soil sampling] Remove the topsoil, take the soil at a distance of 5-7 cm from the soil surface, and put it into a plastic zipper bag", "[Soil sampling] Mix the soil evenly, and then add soil... |
87,058 | Multiplexed Immunofluorescence Staining and Imaging of Lung Sections | 4 | dx.doi.org/10.17504/protocols.io.6qpvr38dpvmk/v1 | https://www.protocols.io/view/multiplexed-immunofluorescence-staining-and-imagi-cy9sxz6e | Jeffrey Purkerson | TITLE: Multiplexed Immunofluorescence Staining and Imaging of Lung Sections
AUTHORS: Jeffrey Purkerson
[DESCRIPTION]
This protocol describes multiplexed immunofluorescent staining and imaging of FFPE lung tissue sections utilizing the Phenocycler-Fusion platform (Akoya Biosciences). The approach is based on the CODE... | ["[Lung section preparation] Bake Sections to promote tissue adherence to the slide.", "[Lung section preparation] Heat Slide in oven at 60 °C .", "[Labeling of lung tissue sections with antibody-barcode conjugates] Deparaffination and Rehydration\nIncubate slides (5 min) in Coplin Jars containing Xylene (3X) follo... |
40,664 | Direct ELISA for investigating the binding of peroxidase-labeled anti-chicken IgY conjugate with avian immunoglobulins | 6 | dx.doi.org/10.17504/protocols.io.bjxykppw | https://www.protocols.io/view/direct-elisa-for-investigating-the-binding-of-per-bjxykppw | Angel Justiz-Vaillant | TITLE: Direct ELISA for investigating the binding of peroxidase-labeled anti-chicken IgY conjugate with avian immunoglobulins
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The peroxidase-labeled anti-chicken IgY conjugate cross-reacts with many IgY present in th... | ["This ELISA is used to study the interaction of anti-chicken IgY-HRP conjugate with diverse avian immunoglobulins.", "The 96 well microtitre plate is coated overnight at 4°C with 1 µg/µl per well of purified avian immunoglobulins or 50 µl of water soluble fraction from egg yolks of avian species in carbonate-bicarbona... |
57,250 | L1 stage C. elegans dissociation for FACS isolation and RNA-seq analysis of intestine-specific cells | 4 | dx.doi.org/10.17504/protocols.io.rm7vzy365lx1/v1 | https://www.protocols.io/view/l1-stage-c-elegans-dissociation-for-facs-isolation-b36aqrae | Robert TP Williams, Erin Osborne Nishimura | TITLE: L1 stage C. elegans dissociation for FACS isolation and RNA-seq analysis of intestine-specific cells
AUTHORS: Robert TP Williams, Erin Osborne Nishimura
[DESCRIPTION]
This protocol is for generating a single cell suspension suitable for isolation of intestine-specific cells through Fluorescence Activated Cell S... | ["[Before beginning] Prepare reagents in advance\n\n\nL15-10 Buffer: Mix 500 ml Leibovitz's L-15 Medium, 50 ml Fetal Bovine Serum (heat inactivated), 50 ul of 100x Penicillin-Streptomycin solution and 7.7 g sucrose. Filter with 0.2 micron pore filter. Store at 4ºC.\n\nEgg Buffer: Mix 29.5 ml of 2M NaCl, 12 ml of 2M KCl... |
43,488 | Cell seeding | 4 | null | https://www.protocols.io/view/cell-seeding-bnp8mdrw | PMAT0001 | TITLE: Cell seeding
AUTHORS: PMAT0001
[STEPS]
?. Take cells from the freezer and thaw for in the water bath.
37 °C
?. Take a T75 plate and place all needed items in ethanol-sterilized laminar flow hood.
?. Draw the needed amount of cells into a 50mL centrifuge tube.
?. Add about of PBS into the centrifuge tube.
7... | ["Take cells from the freezer and thaw for in the water bath.\n37 °C", "Take a T75 plate and place all needed items in ethanol-sterilized laminar flow hood.", "Draw the needed amount of cells into a 50mL centrifuge tube.", "Add about of PBS into the centrifuge tube.\n7 mL", "Spin the mixture in a centrifuge for a... |
71,866 | Determining MLST allele sequences in novel STs | 3 | dx.doi.org/10.17504/protocols.io.36wgqj7kovk5/v1 | https://www.protocols.io/view/determining-mlst-allele-sequences-in-novel-sts-cie2ubge | Varun Shamanna | TITLE: Determining MLST allele sequences in novel STs
AUTHORS: Varun Shamanna
[DESCRIPTION]
Steps required to determine Novel allele sequence of MLST from the assembly files using MLSTaR R package
[STEPS] | [] |
54,546 | Veiled Chameleons (Chamaeleo calyptratus) 2021 Environmental Summary, Reptile & Aquatics, Stowers Institute for Medical Research | 3 | dx.doi.org/10.17504/protocols.io.bzhsp36e | https://www.protocols.io/view/veiled-chameleons-chamaeleo-calyptratus-2021-envir-bzhsp36e | Diana P Baumann, Richard Kupronis | TITLE: Veiled Chameleons (Chamaeleo calyptratus) 2021 Environmental Summary, Reptile & Aquatics, Stowers Institute for Medical Research
AUTHORS: Diana P Baumann, Richard Kupronis
[DESCRIPTION]
Veiled Chameleons (Chamaeleo calyptratus) are an increasingly popular model organism, and we have maintained a colony at t... | [] |
49,715 | Assay for quantifying PPM1H phosphatase activity towards LRRK2 phosphorylated Rab proteins and peptides using the Malachite Green method | 1 | dx.doi.org/10.17504/protocols.io.bustnwen | https://www.protocols.io/view/assay-for-quantifying-ppm1h-phosphatase-activity-t-bustnwen | Kerryn Berndsen, Dario Alessi | TITLE: Assay for quantifying PPM1H phosphatase activity towards LRRK2 phosphorylated Rab proteins and peptides using the Malachite Green method
AUTHORS: Kerryn Berndsen, Dario Alessi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">We describe a sensitive and non-radioactive assay that we deploy for ... | ["[Assay for quantifying PPM1H phosphatase activity towards LRRK2 phosphorylated Rab proteins and peptides using the Malachite Green method]\nSetup the assays in a 96-well flat-bottomed plate (see Figure 1, Figure 2B and Figure 3B):", "[Assay for quantifying PPM1H phosphatase activity towards LRRK2 phosphorylated Rab p... |
25,610 | 03 Ligation | null | dx.doi.org/10.17504/protocols.io.49igz4e | null | TJUSLS China | TITLE: 03 Ligation
AUTHORS: TJUSLS China
[STEPS]
?. Mix together:5×T4 DNA Ligase Buffer 2μlT4 DNA Ligase 0.5—1μlVector as requiredInsert as requiredddH2O Add to 10μl
?. Heat in water ... | ["Mix together:5×T4 DNA Ligase Buffer 2μlT4 DNA Ligase 0.5—1μlVector as requiredInsert as requiredddH2O Add to 10μl", "Heat in water bath or heat block at 22℃ for 30min.\n22 °C"] |
43,660 | Nuclei preparation from human lung using douncing for snRNA-seq | 4 | dx.doi.org/10.17504/protocols.io.bnvkme4w | https://www.protocols.io/view/nuclei-preparation-from-human-lung-using-douncing-bnvkme4w | Center for Epigenomics UCSD | TITLE: Nuclei preparation from human lung using douncing for snRNA-seq
AUTHORS: Center for Epigenomics UCSD
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol describing nuclei isolation from frozen tissue including lung using douncing for droplet-based single nucleus RNA-seq.</div></div>
[ST... | [] |
42,989 | CCMA Coculture Media (Red Cap) | 4 | dx.doi.org/10.17504/protocols.io.bm8mk9u6 | https://www.protocols.io/view/ccma-coculture-media-red-cap-bm8mk9u6 | Catherine Gohar, Ada de la Cruz | TITLE: CCMA Coculture Media (Red Cap)
AUTHORS: Catherine Gohar, Ada de la Cruz
[STEPS]
?. [Equipment for making media]
For making media you will need: 2 --> 500 mL graduated cylinders1 --> 100 mL graduated cylinder1 --> 10 mL graduated cylinder2 --> small funnels2 --> weigh boats1 --> lab spatula 1 --> pipette + tip1 ... | ["[Equipment for making media]\nFor making media you will need: 2 --> 500 mL graduated cylinders1 --> 100 mL graduated cylinder1 --> 10 mL graduated cylinder2 --> small funnels2 --> weigh boats1 --> lab spatula 1 --> pipette + tip1 --> 1000 mL or 2000 mL flask (depending on if you're making 1 L or 2 L of media)", "[Mak... |
64,368 | Super Slim Keto Gummy Bears (Scam Exposed 2022) - Is Really worth Buying? | 3 | dx.doi.org/10.17504/protocols.io.kqdg3pwdel25/v1 | https://www.protocols.io/view/super-slim-keto-gummy-bears-scam-exposed-2022-is-r-ca4qsgvw | H H | TITLE: Super Slim Keto Gummy Bears (Scam Exposed 2022) - Is Really worth Buying?
AUTHORS: H H
[DESCRIPTION]
This extraordinary keto equation centers around not one, however three types of BHB ketones, so you can get a definitive thinning mix. Inside this blend, you can track down magnesium, sodium, and calcium BHBs t... | [] |
23,735 | WILLIS -HOBBS AGAR | 1 | dx.doi.org/10.17504/protocols.io.3exgjfn | https://www.protocols.io/view/willis-hobbs-agar-3exgjfn | Roey Angel, Ana Lara-Rodriguez | TITLE: WILLIS -HOBBS AGAR
AUTHORS: Roey Angel, Ana Lara-Rodriguez
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">For the diferential isolation of Clostridium sp. </div></div>
[STEPS]
?. For the preparation of 1L of media (50 to 66 petri dishes depending of depth) weigh:Final pH ( at 25°C) 7.0±0.2
... | ["For the preparation of 1L of media (50 to 66 petri dishes depending of depth) weigh:Final pH ( at 25°C) 7.0±0.2\n[ Peptic Digest from Animal tissue]\n[ Meat Extract]\n[ NaCl]\n[ Lactose]\n[ Neutral Red]\n[Agar]\n[Egg yolk Emulsion]", "Heat to boiling to dissolve the medium completely.", "Sterilize by autoclaving at 1... |
39,773 | Bivalent binding of a fully human IgG to the SARS-CoV-2 spike proteins reveals mechanisms of potent neutralization | 2 | dx.doi.org/10.17504/protocols.io.bi35kgq6 | https://www.protocols.io/view/bivalent-binding-of-a-fully-human-igg-to-the-sars-bi35kgq6 | Bei Wang, Daniel Asarnow, Wen-Hsin Lee, Ching-Wen Huang, Bryan Faust, Patricia Miang Lon Ng, Eve Zi Xian Ngoh, Markus Bohn, David Bulkley, Andrés Pizzorno, Hwee Ching Tan, Chia-Yin Lee, Rabiatul Adawiyah Minhat, Olivier Terrier, Mun Kuen Soh, Frannie Jiuyi Teo, Yvonne Yee Chin Yeap, Yuanyu Hu, Shirley Gek Kheng Seah, S... | TITLE: Bivalent binding of a fully human IgG to the SARS-CoV-2 spike proteins reveals mechanisms of potent neutralization
AUTHORS: Bei Wang, Daniel Asarnow, Wen-Hsin Lee, Ching-Wen Huang, Bryan Faust, Patricia Miang Lon Ng, Eve Zi Xian Ngoh, Markus Bohn, David Bulkley, Andrés Pizzorno, Hwee Ching Tan, Chia-Yin Lee, Rab... | [] |
62,728 | gynecomastia surgery | 3 | dx.doi.org/10.17504/protocols.io.5jyl896y8v2w/v1 | https://www.protocols.io/view/gynecomastia-surgery-b9hgr33w | habedih | TITLE: gynecomastia surgery
AUTHORS: habedih
[DESCRIPTION]
Gynecomastia is a reviewed condition portrayed by the development of the male bosom that influences a critical extent of the male populace. Plenty of fluctuating careful methodologies at present exists in the writing; consequently, this complete audit tried ... | [] |
66,232 | CoxII degradation assay to assess mitophagy | 1 | dx.doi.org/10.17504/protocols.io.kxygxzxr4v8j/v1 | https://www.protocols.io/view/coxii-degradation-assay-to-assess-mitophagy-ccwysxfw | Thanh Ngoc Nguyen, nguyen.tha | TITLE: CoxII degradation assay to assess mitophagy
AUTHORS: Thanh Ngoc Nguyen, nguyen.tha
[DESCRIPTION]
This protocol details the procedure to assess mitophagy by analysing COXII degradation via Western blotting.
[STEPS]
SECTION: Procedures:
1. Seed the hela cells the day before the treatment day in 6 well plates.
... | ["[Procedures:] Seed the hela cells the day before the treatment day in 6 well plates.", "[Procedures:] The next day, make sure the seeded cells are spreading out (not concentrated in the middle of the well because this can affect the results).", "[Procedures:] Aspirate off the old media and treat each well with 2 mL o... |
94,617 | Preparation of viral sequencing library for Illumina using WTA2 and QIAseq FX | 1 | dx.doi.org/10.17504/protocols.io.3byl4qnqzvo5/v1 | https://www.protocols.io/view/preparation-of-viral-sequencing-library-for-illumi-c8mzzu76 | Kenichi Komabayashi | TITLE: Preparation of viral sequencing library for Illumina using WTA2 and QIAseq FX
AUTHORS: Kenichi Komabayashi
[DESCRIPTION]
This method uses a metagenomic approach to analyze the genome sequence of DNA and RNA viruses. Nucleic acids outside the viral particles are reduced using nucleases and extracted to obtain te... | ["[Reduction of nucleic acids derived from non-virus] Collect 400 µL virus culture medium in a 1.5 mL tube.", "[Reduction of nucleic acids derived from non-virus] Centrifuge 3 min at 17,000 x g and aspirate the supernatant with a 1 mL tuberculin syringe.", "[Reduction of nucleic acids derived from non-virus] Filter th... |
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