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 |
|---|---|---|---|---|---|---|---|
69,774 | Neurogenic bladder and bowel evaluation and intervention protocol in male patients with traumatic spinal cord injury | 1 | dx.doi.org/10.17504/protocols.io.rm7vzbn3xvx1/v1 | https://www.protocols.io/view/neurogenic-bladder-and-bowel-evaluation-and-interv-cgdnts5e | Girlaine Gomes de Melo, Léa Ho Dac, Hougelle Simplício Gomes Pereira, Lilian Lira Lisboa | TITLE: Neurogenic bladder and bowel evaluation and intervention protocol in male patients with traumatic spinal cord injury
AUTHORS: Girlaine Gomes de Melo, Léa Ho Dac, Hougelle Simplício Gomes Pereira, Lilian Lira Lisboa
[DESCRIPTION]
In 2013, the World Health Organization estimated that annually about 250,000 to 500... | ["[After confirming the inclusion criteria, the initial assessment includes the following steps:] Detailed clinical history related to bladder and bowel habits.", "[After confirming the inclusion criteria, the initial assessment includes the following steps:] Bladder patterns\n\nSemi-structured assessment form: toilet ... |
98,854 | Fluorescence assay for Enterovirus D68 3C protease activity measurement | 1 | dx.doi.org/10.17504/protocols.io.261ge54jyg47/v1 | https://www.protocols.io/view/fluorescence-assay-for-enterovirus-d68-3c-protease-dcse2wbe | Charline Giroud, oleg.fedorov | TITLE: Fluorescence assay for Enterovirus D68 3C protease activity measurement
AUTHORS: Charline Giroud, oleg.fedorov
[DESCRIPTION]
This protocol details the fluorescence assay for Enterovirus D68 (EV-D68) 3C protease activity measurement. This method is intended to measure the activity of viral proteases by using a s... | ["[EV-D68 3C Pro IC50 Measurement] Add 10 µLof 2x protein 0.5 micromolar (µM) solution to each well containing the compounds to be tested previously dispensed onto the plate.", "[EV-D68 3C Pro IC50 Measurement] Incubate the mix for 60 min at Room temperature and initiate the enzymatic reaction by the addition of 10 µL ... |
101,201 | Imaging- Confocal | 0 | dx.doi.org/10.17504/protocols.io.j8nlk88y1l5r/v1 | https://www.protocols.io/view/imaging-confocal-de3r3gm6 | daniel.dautan daniel, Per Svenningsson | TITLE: Imaging- Confocal
AUTHORS: daniel.dautan daniel, Per Svenningsson
[DESCRIPTION]
Protocol for imaging using confocal microscope. Sections for analysis should be mounted on slides, stained for appropriate markers, and coverslipped. This protocol is using a Carl Zeiss LSM 880 confocal microcope.
[STEPS]
1. Using ... | ["Using the confocal microscope, capture images at 10x magnification using a resolution of either 1024x1024 or 2048x2048.", "If needed for larger area of the brain, use tile-scanning with a 0.6 zoom factor and 10% overlap for automated reconstruction.", "If acquiring z-stack images use 1-4um spacing. Use stack projecti... |
72,426 | DNA Isolation from Reptile Blood using Gentra Puregene (Qiagen) DNA Isolation Kit | 4 | dx.doi.org/10.17504/protocols.io.rm7vzbbervx1/v1 | https://www.protocols.io/view/dna-isolation-from-reptile-blood-using-gentra-pure-ciyiufue | Agl0032, tss | TITLE: DNA Isolation from Reptile Blood using Gentra Puregene (Qiagen) DNA Isolation Kit
AUTHORS: Agl0032, tss
[DESCRIPTION]
This protocol is used to isolate DNA from reptile blood (either whole or red blood cell pellets). Reptile blood has nucleated red blood cells and will produce considerably more DNA from the same... | ["[Setting Up] Turn on shaking tube incubator and set to 55 °C", "[Red Blood Cell Lysis] Set out the the blood samples to be used on ice to thaw, but stay cold. \nSet out the correct number of 1.5 mL tubes into a clean tube rack.", "[Red Blood Cell Lysis] Add 300 µL of Cell Lysis Solution (from PureGene Kit) to each tu... |
84,968 | Gene Set Enrichment Analysis | 5 | null | https://www.protocols.io/view/gene-set-enrichment-analysis-cw8gxhtw | Cameron Baker | TITLE: Gene Set Enrichment Analysis
AUTHORS: Cameron Baker
[DESCRIPTION]
Instructions for running https://www.gsea-msigdb.org/gsea/index.jsp
[STEPS]
SECTION: Introduction
1. Gene Set Enrichment Analysis (GSEA) is an alternative step to more general pathway enrichment (as performed by our standard RNA-Seq workflow) to... | ["[Introduction] Gene Set Enrichment Analysis (GSEA) is an alternative step to more general pathway enrichment (as performed by our standard RNA-Seq workflow) to determine significant expression within an experiment corresponding to predefined genesets. It is a relatively common request, and the best application for ru... |
56,851 | Staphilococcus Aureus Sampling | 4 | dx.doi.org/10.17504/protocols.io.b3rtqm6n | https://www.protocols.io/view/staphilococcus-aureus-sampling-b3rtqm6n | Pol Roca Cugat | TITLE: Staphilococcus Aureus Sampling
AUTHORS: Pol Roca Cugat
[DESCRIPTION]
This protocol is intended to study the affectation of Staphilococcus Aureus, including the MRSA variant. It outlines the basic protocol for a multi-subject study.
[GUIDELINES]
This protocol is intended to study the affectation of Staphiloco... | ["[Preparation] Wash your hands with soap. Put on your lab coat, your mask and your goggles or face shield. Make sure your mask is airtight and air cannot escape through the sides.", "[Preparation] Prepare the area where you are going to work. Disinfect the surfaces with bleach solution.\nThe subjects should not be abl... |
69,943 | RNA and protein extraction from bulk dissections | 4 | dx.doi.org/10.17504/protocols.io.4r3l275nqg1y/v1 | https://www.protocols.io/view/rna-and-protein-extraction-from-bulk-dissections-cgixtufn | miquel.vila | TITLE: RNA and protein extraction from bulk dissections
AUTHORS: miquel.vila
[DESCRIPTION]
mirVana PARIS RNA and Native Protein Purification Kit (#AM1556, Thermo Fisher Scientific )
[GUIDELINES]
*We have less tissue than 0,5mg but 500 ul is a comfortable volume to work with since we have to homogenize the sample with... | ["[First Time] (1st time): Add 375ul of 2-mercaptoethanol to 2X Denaturing Solution, Add 21ml of 100% Etanol to miRNA Wash Solution 1, Add 40ml of Etanol 100% to Wash Solution 2/3.", "[Sample disruption] Preheat Nuclease-free Water (#129114, Qiagen-Werfen) at 95oC (for elution).", "[Sample disruption] Preheat 2x Denatu... |
25,805 | Handwriting Test for Preschool Children (HT-PRE): a new tool to assess the handwriting ability of preschool children aged 5–6 years old in Mainland China | null | dx.doi.org/10.17504/protocols.io.5fmg3k6 | null | Qin Hong | TITLE: Handwriting Test for Preschool Children (HT-PRE): a new tool to assess the handwriting ability of preschool children aged 5–6 years old in Mainland China
AUTHORS: Qin Hong
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The Handwriting Test for Preschool Children (HT-PRE), which is a newly de... | ["Before the test, parents completed the \"Children's Basic Situation Questionnaire\" so that necessary information about the participants could be gathered, including the child's age, gender, medical history, and trauma history.", "The HT-PRE was then conducted one-on-one.", "Write the most familiar contents, includin... |
64,586 | SHARING W/ WS | 1 | null | https://www.protocols.io/view/sharing-w-ws-cbbisike | Maria Gul | TITLE: SHARING W/ WS
AUTHORS: Maria Gul
[DESCRIPTION]
TEST
[STEPS]
1. TEST
2. TEST 2
3. TEST 3 | ["TEST", "TEST 2", "TEST 3"] |
52,015 | International experiment on sanctions and cooperation to avert collective risk | 1 | dx.doi.org/10.17504/protocols.io.bw2ppgdn | https://www.protocols.io/view/international-experiment-on-sanctions-and-cooperat-bw2ppgdn | Gianluca Grimalda, Alexis Belianin, Heike Hennig-Schmidt, Till Requate, Marina V Ryzhkova | TITLE: International experiment on sanctions and cooperation to avert collective risk
AUTHORS: Gianluca Grimalda, Alexis Belianin, Heike Hennig-Schmidt, Till Requate, Marina V Ryzhkova
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">We report the protocol relative to the experimental project "S... | ["[Methods to ensure between-country comparability of data]\nInternational experimental research is subject to three problems that may compromise data comparability (Roth et al. 1991). We follow relevant literature in responding to such issues (Roth et al. 1991; Hermann et al., 2008; Buchan et al., 2009; Georg et al., ... |
92,989 | Quality control assessment for microbial genomes: GalaxyTrakr MicroRunQC workflow | 1 | dx.doi.org/10.17504/protocols.io.5jyl8mj16g2w/v6 | https://www.protocols.io/view/quality-control-assessment-for-microbial-genomes-g-c625zgg6 | Candace Hope Bias, Ruth Timme, Yesha Shrestha, Tina Lusk Pfefer, Paul Morin, Maria Balkey, Errol Strain | TITLE: Quality control assessment for microbial genomes: GalaxyTrakr MicroRunQC workflow
AUTHORS: Candace Hope Bias, Ruth Timme, Yesha Shrestha, Tina Lusk Pfefer, Paul Morin, Maria Balkey, Errol Strain
[DESCRIPTION]
PURPOSE: Step-by-step instructions for checking WGS sequence quality for bacterial pathogens. The Micro... | ["[Account set up] Create a GalaxyTrakr account here: https://account.galaxytrakr.org/Account/Register", "[Account set up] Log into your GalaxyTrakr account: https://galaxytrakr.org", "[Create a new history] Create a new history. \n\nWe recommend creating a new history for each new MiSeq Run and including the flow-cell... |
62,627 | Weight Crasher Keto Gummies : Where To Buy It! | 1 | dx.doi.org/10.17504/protocols.io.14egn7e1mv5d/v1 | https://www.protocols.io/view/weight-crasher-keto-gummies-where-to-buy-it-b9ebr3an | jeefbezoi | TITLE: Weight Crasher Keto Gummies : Where To Buy It!
AUTHORS: jeefbezoi
[DESCRIPTION]
Weight loss is not as hard as we think. With a proper diet or supplements, we can easily attain a slim and toned body. Exercising, and dieting may not offer instant results, but supplements like Weight Crasher Keto Gummies offer r... | ["[Weight Crasher Keto Gummies]"] |
35,866 | Reagent prep - Stanford TMC | 1 | dx.doi.org/10.17504/protocols.io.be92jh8e | https://www.protocols.io/view/reagent-prep-stanford-tmc-be92jh8e | John Hickey | TITLE: Reagent prep - Stanford TMC
AUTHORS: John Hickey
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>See our detailed protocol published with the following title: </span><span style = "font-weight:bold;">CODEX multiplexed tissue imaging with DNA-conjugated antibodies.</span></div></div>
[S... | ["See our detailed protocol published with the following title: CODEX multiplexed tissue imaging with DNA-conjugated antibodies."] |
80,689 | Eligibility Criteria | 3 | dx.doi.org/10.17504/protocols.io.3byl4jn72lo5/v1 | https://www.protocols.click/view/eligibility-criteria-cs2rwgd6 | Christopher Hawthorne, Keenan Smith, Jonathan Cavanagh, Eric Jackson, Martin Shaw, Matthew Sheridan, Malcolm Watson, Shona McKay | TITLE: Eligibility Criteria
AUTHORS: Christopher Hawthorne, Keenan Smith, Jonathan Cavanagh, Eric Jackson, Martin Shaw, Matthew Sheridan, Malcolm Watson, Shona McKay
[DESCRIPTION]
Inclusion and exclusion criteria for Predicting Cognitive Decline After Spinal Surgery (PROTECT).
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.hk3b4yn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes the extraction process of RNA and/or DNA from marine environmental samples. Samples are assumed to be collected via filtering sample seawater onto filters. Filters are then flash frozen in the first lysis buffer. The protocol describes the steps used t... | [] |
21,884 | ADP assay (Colorimetric) | null | dx.doi.org/10.17504/protocols.io.zk4f4yw | null | Kiichi Hirota, Yoshiyuki Matsuo | TITLE: ADP assay (Colorimetric)
AUTHORS: Kiichi Hirota, Yoshiyuki Matsuo
[STEPS]
?. [Standard preparation]
Reconstitute the ADP standard (1 µmol) in 100 µl of water to generate a 10 mM ADP stock solution.
?. [Standard preparation]
Dilute 10 µl of the 10 mM ADP stock solution with 90 µl of ADP Assay Buffer to prepare a... | ["[Standard preparation]\nReconstitute the ADP standard (1 µmol) in 100 µl of water to generate a 10 mM ADP stock solution.", "[Standard preparation]\nDilute 10 µl of the 10 mM ADP stock solution with 90 µl of ADP Assay Buffer to prepare a 1 mM ADP standard solution.", "[Standard preparation]\nPrepare dilutions of a AD... |
46,088 | ImageJ/FIJI Particle Analyser | 4 | null | https://www.protocols.io/view/imagej-fiji-particle-analyser-bq9gmz3w | Elizabeth Fozo | TITLE: ImageJ/FIJI Particle Analyser
AUTHORS: Elizabeth Fozo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">ImageJ/FIJI Particle Analyzer</div></div>
[STEPS]
?. [steps]
Image plates with photo doc machine. Choose plates where colonies are well spread, and not clumped - especially against the sides... | ["[steps]\nImage plates with photo doc machine. Choose plates where colonies are well spread, and not clumped - especially against the sides, where the image will be cropped.\nOvercrowded plates have inherently smaller colonies. Ensure that the images are all taken at the same distance/zoom.", "[steps]\nDownload FIJI f... |
null | null | null | dx.doi.org/10.17504/protocols.io.vbce2iw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol describes how to build up a freezer stock of a given bacterial strain.
Following this protocol will result in individual, glycercol-suspended aliquots of genetically similar bacteria originating from a clone of cells forming an isolated colony, derived from a sin... | ["{\"blocks\":[{\"key\":\"cur4h\",\"text\":\"The previous day an isolated colony will have been selected from a growth media plate and inoculated into LB broth for overnight growth as described in 'Plating bacteria to isolate a single colony'. The next day using an Absorbance Microplate Reader check to optical density ... |
53,042 | A simple and economic protocol for efficient in vitro fertilization using cryopreserved mouse sperm | 4 | dx.doi.org/10.17504/protocols.io.bx2spqee | https://www.protocols.io/view/a-simple-and-economic-protocol-for-efficient-in-vi-bx2spqee | Magdalena Wigger, Simon E Tröder, Branko Zevnik | TITLE: A simple and economic protocol for efficient in vitro fertilization using cryopreserved mouse sperm
AUTHORS: Magdalena Wigger, Simon E Tröder, Branko Zevnik
[DESCRIPTION]
The advent of genome editing tools like CRISPR/Cas has substantially increased the number of genetically engineered mouse models in recent y... | ["[Sperm cryopreservation] Prepare 20 straws for 2 sacrificed males of the same line. Use of a single male is possible as well but the number of straws and volume of media used needs to be reduced by 50%", "[Sperm cryopreservation] Mark the straws at 2.3 cm and 4.0 cm at the open end and label them at the other end (co... |
53,517 | Protocol in dev - Seq Analysis pipeline | 1 | dx.doi.org/10.17504/protocols.io.byhmpt46 | https://www.protocols.io/view/protocol-in-dev-seq-analysis-pipeline-byhmpt46 | Emma Ganley | TITLE: Protocol in dev - Seq Analysis pipeline
AUTHORS: Emma Ganley
[DESCRIPTION]
test
[STEPS]
SECTION: Section 1
1.
=sum(a1,b1,c1)
SECTION: Section 1
2. Add 50 mL A
Add 100 mL B
Leave for 10 min
Add 50 µL
50 µL
SECTION: Section 2
3.
SECTION: Section 2
4.
Download latest version of
... | ["[Section 1] =sum(a1,b1,c1)", "[Section 1] Add 50 mL A\nAdd 100 mL B\n\nLeave for 10 min\n\n\n\nAdd 50 µL \n\n50 µL", "[Section 2]", "[Section 2] Download latest version of", "[Section 2]", "[Section 2] Download latest dataset from", "[Section 2]"] |
38,552 | FCMPASS - Fluorescence calibration | 5 | dx.doi.org/10.17504/protocols.io.bhvyj67w | https://www.protocols.io/view/fcmpass-fluorescence-calibration-bhvyj67w | Joshua Welsh, Jennifer Jones | TITLE: FCMPASS - Fluorescence calibration
AUTHORS: Joshua Welsh, Jennifer Jones
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines the steps required to input fluorescence calibration parameters using the FCMPASS software. This is one of a number of protocols in the pipeline for ... | ["If fluorescence calibration is being performed click the '+' button to add a calibration parameter to the table. If fluorescence calibration is not required, click 'Next'.", "If you have not yet added the MESF reference bead information that will be used for calibration into the Catalogue', click 'Catalogue' in the t... |
90,828 | Proteome analysis | 1 | dx.doi.org/10.17504/protocols.io.5jyl8pw86g2w/v1 | https://www.protocols.io/view/proteome-analysis-c4xkyxkw | Leonardo A Parra-Rivas | TITLE: Proteome analysis
AUTHORS: Leonardo A Parra-Rivas
[DESCRIPTION]
Proteome analysis
[STEPS]
1. Mass spectrometry data was
analyzed according to a published protocol
2. Spectra were searched using Proteome Discoverer (RRID:SCR_014477) (https://www.thermofisher.com/order/catalog/product/IQLAAEGABSFAKJMAU... | ["Mass spectrometry data was\nanalyzed according to a published protocol", "Spectra were searched using Proteome Discoverer (RRID:SCR_014477) (https://www.thermofisher.com/order/catalog/product/IQLAAEGABSFAKJMAUH) software version 2.1 against 2020 mouse UniProtKB/Swiss-Prot\n(RRID:SCR_021164)( https://www.expasy.org/r... |
106,291 | Environmental DNA (eDNA) COI Metabarcoding PCR Protocol | 4 | dx.doi.org/10.17504/protocols.io.4r3l2q1ejl1y/v1 | https://www.protocols.io/view/environmental-dna-edna-coi-metabarcoding-pcr-proto-dj2t4qen | Jacoby Baker, Kathleen Pitz | TITLE: Environmental DNA (eDNA) COI Metabarcoding PCR Protocol
AUTHORS: Jacoby Baker, Kathleen Pitz
[DESCRIPTION]
This protocol is aimed at amplifying the cytochrome c oxidase subunit I (COI) mitochondrial gene in eukaryotes. The primers (forward: mlCOIintF, reverse: HCO2198) utilized in this protocol are based on the... | ["[Minimum Information about an Omics Protocol (MIOP)] 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\n18S gene\n \ncreator\n\n \nmaterials ... |
84,790 | Soil Plating Protocol | 1 | null | https://www.protocols.click/view/soil-plating-protocol-cw2wxgfe | rkdunwoo, clgordy | TITLE: Soil Plating Protocol
AUTHORS: rkdunwoo, clgordy
[DESCRIPTION]
Protocol for serial dilution of soil samples and plating.
[STEPS]
SECTION: Sample Preparation
1. Collect Soil Sample
SECTION: Sample Preparation
1.1. Collect a small amount of soil into a Ziploc bag. Your soil sample will contain some bits of roo... | ["[Sample Preparation] Collect Soil Sample", "[Sample Preparation] Collect a small amount of soil into a Ziploc bag. Your soil sample will contain some bits of roots, leaves, and rocks, but try to get a sample that is mostly soil", "[Sample Preparation] Weigh 1 g of", "[Sample Preparation] Take your sample to the bal... |
64,450 | Effect of Therapeutic Exercise, Educational booklet and Vitamin D3 Supplement for the Management of Chronic Mechanical Low Back Pain | 4 | dx.doi.org/10.17504/protocols.io.rm7vzyqz5lx1/v1 | https://www.protocols.io/view/effect-of-therapeutic-exercise-educational-booklet-ca7ashie | Muhammad Shahidul Islam, Dr. Md. Ashrafuzzaman Zahid, Professor Dr. Md. Sohrab Hossain, K M Amran Hossain | TITLE: Effect of Therapeutic Exercise, Educational booklet and Vitamin D3 Supplement for the Management of Chronic Mechanical Low Back Pain
AUTHORS: Muhammad Shahidul Islam, Dr. Md. Ashrafuzzaman Zahid, Professor Dr. Md. Sohrab Hossain, K M Amran Hossain
[DESCRIPTION]
The protocol titled "Effect of Therapeutic Exe... | ["[Protocol Description] Introduction", "[Protocol Description] Background", "[Protocol Description] Justification", "[Protocol Description] Objectives", "[Protocol Description] Literature Review", "[Protocol Description] Conceptual Framework", "[Protocol Description] Methodology", "[Protocol Description] Study Design"... |
27,985 | Electrocompetent E. coli | null | dx.doi.org/10.17504/protocols.io.7jrhkm6 | null | Alba Balletbó | TITLE: Electrocompetent E. coli
AUTHORS: Alba Balletbó
[STEPS]
?. Grow 5 mL culture of LB w/o salts overnight
?. Pre-cool centrifuge to 4ºC.
?. Inoculate 400 mL LB w/o salts with 5 ml pre-culture and incubate for 3 hours to OD600 0.5-1.0.
?. Transfer culture volume to 8 Greiner tubes of 50 mL and leave on ice for 15 ... | ["Grow 5 mL culture of LB w/o salts overnight", "Pre-cool centrifuge to 4ºC.", "Inoculate 400 mL LB w/o salts with 5 ml pre-culture and incubate for 3 hours to OD600 0.5-1.0.", "Transfer culture volume to 8 Greiner tubes of 50 mL and leave on ice for 15 minutes.", "Centrifuge for 10 minutes at 2000g and 4ºC.", "Remove ... |
98,198 | National Index of Borehole Information (NIBI): Use and Submission Guide | 0 | dx.doi.org/10.17504/protocols.io.rm7vzj872lx1/v1 | https://www.protocols.io/view/national-index-of-borehole-information-nibi-use-an-db5w2q7e | darthur Arthur | TITLE: National Index of Borehole Information (NIBI): Use and Submission Guide
AUTHORS: darthur Arthur
[DESCRIPTION]
The National Index of Borehole Information (NIBI) is a collaboration between the U.S. Geological Survey (USGS) and State Geological Surveys to meet current stakeholder and future users’ needs for access... | ["[Metadata Submission: Domain Mapping] As a metadata index or catalog, NIBI is a centralized index or catalog that connects its users to resources stored in various data repositories. In order to facilitate the FAIR data principles (Findable, Accessible, Interoperable, Reusable) while maintaining a manageable structur... |
null | null | null | dx.doi.org/10.17504/protocols.io.uu8ewzw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
amino acid analysis service, It is widely known that protein/peptide quantities is highly needed for further applications, quantitative amino acid analysis, qAAA, is a suitable assay. It can precisely determine protein quantities and provide detailed information regarding the ... | [] |
11,967 | Total RNA extraction | null | dx.doi.org/10.17504/protocols.io.pw7dphn | null | Izabela Rezende, Lívia Sacchetto | TITLE: Total RNA extraction
AUTHORS: Izabela Rezende, Lívia Sacchetto
[DESCRIPTION]
<p>For purification of viral RNA from serum and cell-culture supernatants.</p>
[STEPS]
?. Centrifuge the samples at 8000 x g for 8 min to clarify.
?. Transfer 140 µl of the supernatant into a 1.5 ml microcentrifuge tube.
?. Use this a... | ["Centrifuge the samples at 8000 x g for 8 min to clarify.", "Transfer 140 µl of the supernatant into a 1.5 ml microcentrifuge tube.", "Use this amount to RNA extraction with QIAamp® Viral RNA Mini (Qiagen, USA), according to the manufacturer's instructions. Available at: https://www.qiagen. com/br/resources/re sourced... |
null | null | null | dx.doi.org/10.17504/protocols.io.kwscxee | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The origin of animals, which occurred over 600 million years ago, left no evidence in the fossil record. To trace the earliest events in animal prehistory, we compare extant animals to their closest living relatives, the choanoflagellates, in order to reconstruct the gene con... | [] |
26,253 | Mesuring JF dye kinetics in the brain of C57/Bl mice | null | dx.doi.org/10.17504/protocols.io.5vmg646 | null | Boaz Mohar | TITLE: Mesuring JF dye kinetics in the brain of C57/Bl mice
AUTHORS: Boaz Mohar
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The purpose of this protocol is to compare the intake and clerance kinatics of JF dye systemic delivery using retro orbital injections.</div><div class = "text-block">We im... | ["[Baseline]\nUse a mouse with a window (dosen't have to be in ALM)", "[Baseline]\nMove the mouse to an induction chamber with 3% ISO and flow of ~2L.min. Wait until the mouse takes ~ 1 breaths per second", "[Baseline]\nMove the mose to the microscope and clean the window with Q-tips and 70% ethnol.", "[Baseline]\nSele... |
50,486 | Integration of a landing pad brick | 4 | dx.doi.org/10.17504/protocols.io.bviwn4fe | https://www.protocols.io/view/integration-of-a-landing-pad-brick-bviwn4fe | Carolyn Bayer, Maja Rennig, Anja Ehrmann, Morten Norholm | TITLE: Integration of a landing pad brick
AUTHORS: Carolyn Bayer, Maja Rennig, Anja Ehrmann, Morten Norholm
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">SEGA, the Standardized Genome Engineering Architecture, is a comprehensive strain collection that enables genome engineering by combining only... | ["transform your desired SEGA strain with pSIM19 (Spectinomycin resistance). From now on cultures have to be kept at to retain the plasmid (temperature-sensitive ori)\n30 °C", "[Recombineering- Day 2 ]\nPrepare:", "[Recombineering- Day 2 ]\nCold sterile water", "[Recombineering- Day 2 ]\nCold Glycerol", "[Recombineeri... |
null | null | null | dx.doi.org/10.17504/protocols.io.eaubaew | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
An alternative epifluorescence microscopy (EFM) technique for virus enumeration has been developed using polycarbonate Track Etch (PCTE) filter membranes in place of aluminum oxide Anodisc membranes. The established EFM technique, first developed by Hennes and Suttle in 1995 and... | [] |
57,398 | Environmental DNA (eDNA) metabarcoding protocol for fish species | 1 | dx.doi.org/10.17504/protocols.io.b4awqsfe | https://www.protocols.io/view/environmental-dna-edna-metabarcoding-protocol-for-b4awqsfe | Omneya Ahmed, Tomas Larsson, Mats Töpel, Alexander Eiler | TITLE: Environmental DNA (eDNA) metabarcoding protocol for fish species
AUTHORS: Omneya Ahmed, Tomas Larsson, Mats Töpel, Alexander Eiler
[DESCRIPTION]
Environmental DNA metabarcoding universal primers targeting the hypervariable region of the 12S rRNA gene
[BEFORE_START]
Laboratory work space and equipment we... | ["DNA extraction can be performed using Qiagen DNeasy power water sterivex kit. The quality of the extracted DNA was estimated using Nanodrop. \n\nQiagen DNeasy power water sterivex kit: https://www.qiagen.com/se/resources/resourcedetail?id=c5fe7d5f-070a-4ebe-ac04-4bbf05a13e91&lang=en", "Perform the first PCR (triplica... |
38,547 | Flex-T™ Fixed Peptide Tetramer Preparation and Flow Cytometry Staining Protocol | 1 | null | https://www.protocols.io/view/flex-t-fixed-peptide-tetramer-preparation-and-flow-bhvtj66n | Sam Li | TITLE: Flex-T™ Fixed Peptide Tetramer Preparation and Flow Cytometry Staining Protocol
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is optimized to generate MHC tetramers using our streptavidin fluorophore conjugates and fixed peptide monomers. Unlike our UV-exchange... | ["[Generation of Tetramers:]\nDuring the incubation, prepare blocking solution by adding 1.6 µL 50 mM D-Biotin and 6 µL 10% (w/v) NaN3to 192.4 µL PBS and mix by vortexing. After the incubation, add 2.4 µL of blocking solution and pipette up and down to stop the reaction.", "[Generation of Tetramers:]\nBring all reagent... |
82,503 | Spatially selective stimulation of the pig vagus nerve to modulate target effect versus side effect | 1 | dx.doi.org/10.17504/protocols.io.yxmvm2wzbg3p/v2 | https://www.protocols.click/view/spatially-selective-stimulation-of-the-pig-vagus-n-cutfwwjn | Stephan L Blanz, Evan N Nicolai, Kip Ludwig | TITLE: Spatially selective stimulation of the pig vagus nerve to modulate target effect versus side effect
AUTHORS: Stephan L Blanz, Evan N Nicolai, Kip Ludwig
[DESCRIPTION]
This protocol was used to collect data now published in the Journal of Neural Engineering, Spatially selective stimulation of the pig vagus nerve... | ["[Animal preparation and initial administration of anaesthesia] What we did (approved by the University of Wisconsin-Madison IACUC):\n\nWeigh pig, and perform an intramuscular injection of a mixture of telazol (6 mg/kg) and xylazine (2 mg/kg). Intubate and ventilate the pig and anesthetize using isoflurane gas (0.5-3%... |
29,924 | Scanorama | null | dx.doi.org/10.17504/protocols.io.9gch3sw | null | Brian Hie, Bryan Bryson, Bonnie Berger | TITLE: Scanorama
AUTHORS: Brian Hie, Bryan Bryson, Bonnie Berger
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Scanorama enables efficient integration of heterogeneous scRNA-seq data sets.</div></div>
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.vfse3ne | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Massively parallel single-cell RNA sequencing can precisely resolve cellular diversity in a high-throughput manner at low cost, but unbiased isolation of intact single cells from complex tissues such as adult mammalian brains is challenging. Here, we integrate sucrose-gradient-a... | ["[Nuclei Isolation] {\"blocks\":[{\"key\":\"1oes3\",\"text\":\"\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[]},{\"key\":\"eegpc\",\"text\":\"\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[]},{\"key\":\"as9dl\",\"text\":\"\",\"t... |
null | null | null | dx.doi.org/10.17504/protocols.io.d9899v | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This tutorial focuses on performing a comprehensive metagenomic analysis from whole-genome shotgun sequencing data for microbiome studies. It is divided in to different steps that use the following metagenomic, computational tools: <strong><a href="http://www.nature.com/nmeth/jo... | [] |
97,452 | DNA-extraction of Daphnia and symbionts | 0 | dx.doi.org/10.17504/protocols.io.5jyl82n96l2w/v1 | https://www.protocols.io/view/dna-extraction-of-daphnia-and-symbionts-dbek2jcw | Pascal Angst, Peter D. Fields | TITLE: DNA-extraction of Daphnia and symbionts
AUTHORS: Pascal Angst, Peter D. Fields
[DESCRIPTION]
This protocol was designed for DNA extraction of about 50 adult female Daphnia magna, it should also work for 1-150 animals but with adjusted reagent volumes. For achieving HMW DNA or maximizing yield, some modification... | ["[Tissue lysis and digest] Add and 200 µL to a 1.5 ml tube. (See abstract for how to prepare the animals.)", "[Tissue lysis and digest] Grind animals with a clean, DNA(ase)-free plastic pestle, matching the shape of the 1.5 ml tube to maximize tissue maceration.", "[Tissue lysis and digest] Add 300 µL and vortex... |
97,143 | Séquençage nanopore d'isolats de poliovirus | 0 | dx.doi.org/10.17504/protocols.io.4r3l2qmppl1y/v1 | https://www.protocols.io/view/s-quen-age-nanopore-d-39-isolats-de-poliovirus-da4x2gxn | Catherine Troman, Erika Bujaki, Joyce Akello, Shannon Fitz, Alex Shaw, Javier Martin, Nick Grassly | TITLE: Séquençage nanopore d'isolats de poliovirus
AUTHORS: Catherine Troman, Erika Bujaki, Joyce Akello, Shannon Fitz, Alex Shaw, Javier Martin, Nick Grassly
[DESCRIPTION]
ABSTRAIT
Ce protocole est adapté du protocole "Détection directe du poliovirus par séquençage nanopore - les échantillons de selles" pour le ... | ["[Organisation des échantillons] Les paires d'échantillons (avec le même EPID) peuvent avoir des codes-barres consécutifs, mais essayez de ne pas regrouper les échantillons de la même zone géographique. Cela permet de détecter toute contamination croisée potentielle, car il est alors peu probable que des séquences ide... |
72,875 | DNA Extraction of Placenta Tissue | 4 | null | https://www.protocols.io/view/dna-extraction-of-placenta-tissue-cjejujcn | Cayla Mason | TITLE: DNA Extraction of Placenta Tissue
AUTHORS: Cayla Mason
[DESCRIPTION]
This protocol describes extracting DNA from placenta tissue, starting with dissociation.
[STEPS]
SECTION: Tissue Dissociation and Lysis
1. Place placenta tissue samples in screw cap tubes with O-ring gaskets on ice to thaw.
SECTION: Tissue D... | ["[Tissue Dissociation and Lysis] Place placenta tissue samples in screw cap tubes with O-ring gaskets on ice to thaw.", "[Tissue Dissociation and Lysis] Label a 1.5 mL microcentrifuge tube for each placenta sample. Aliquot 1 mL silica beads per tube.", "[Tissue Dissociation and Lysis] Add 540 uL Buffer ATL and 20 uL P... |
103,431 | Coronal cryosectioning of mouse brains | 0 | dx.doi.org/10.17504/protocols.io.q26g713w9gwz/v1 | https://www.protocols.io/view/coronal-cryosectioning-of-mouse-brains-dg9f3z3n | Lauren C. Faget, Thomas Hnasko | TITLE: Coronal cryosectioning of mouse brains
AUTHORS: Lauren C. Faget, Thomas Hnasko
[DESCRIPTION]
Cryostat coronal cryosectioning of mouse brain tissue
[BEFORE_START]
PFA-perfused, 30% sucrose-cryoprotected, and flash-frozen mouse brains are stored at -80C until cryosectioning
[STEPS]
SECTION: Procedure
1. Retriev... | ["[Procedure] Retrieve frozen mouse brain stored at -80 °C.", "[Procedure] Place brain in cryostat. Set chamber temperature to -16 °C to -20 °C. Set brain holder temperature to -20 °C. Let brain equilibrate to temperature for at least 20 min before sectioning.", "[Procedure] Insert chuck and blade into cryostat.", "[Pr... |
61,852 | Membrane Tube Image Analysis | 1 | dx.doi.org/10.17504/protocols.io.5jyl891e9v2w/v1 | https://www.protocols.io/view/membrane-tube-image-analysis-b8m4ru8w | Liv Jensen | TITLE: Membrane Tube Image Analysis
AUTHORS: Liv Jensen
[DESCRIPTION]
This protocol details Membrane Tube Image Analysis.
[STEPS]
SECTION: Membrane Tube Image Analysis
1. In FIJI, create new image stacks from two rectangular selections: one containing a section of the membrane tube, and one containing the approxima... | ["[Membrane Tube Image Analysis] In FIJI, create new image stacks from two rectangular selections: one containing a section of the membrane tube, and one containing the approximately horizontal section of the guv.", "[Membrane Tube Image Analysis] Save these new stacks as .tif files and paste paths into enrichment quan... |
27,654 | MojoSort™ Nanobeads Column Protocol - 2 | null | dx.doi.org/10.17504/protocols.io.69ehh3e | null | Sam Li | TITLE: MojoSort™ Nanobeads Column Protocol - 2
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>BioLegend MojoSort™ nanobeads work in commonly used separation columns, based on our internal research as well as validation by external testing by academic labs. This simple protocol... | ["Prepare cells from your tissue of interest or blood without lysing erythrocytes.", "In the final wash of your sample preparation, resuspend the cells in MojoSort™ Buffer by adding up to 4 mL in a 5 mL (12 x 75 mm) polypropylene tube.Note: Keep MojoSort™ Buffer on ice throughout the procedure.", "Filter the cells with... |
95,781 | GENERATION OF RECOMBINANT αS AND PFF PROTOCOL | 0 | dx.doi.org/10.17504/protocols.io.81wgbxjx3lpk/v1 | https://www.protocols.io/view/generation-of-recombinant-s-and-pff-protocol-c9sdz6a6 | Scott Vermilyea | TITLE: GENERATION OF RECOMBINANT αS AND PFF PROTOCOL
AUTHORS: Scott Vermilyea
[DESCRIPTION]
This is a collection of protocols including recombinant αS purification and αS PFF assembly.
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.kevcte6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol details how to perform read recruitement to the contigs generated from the previous protocol using Bowtie2. </p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
95,206 | Protocol name | 1 | null | https://www.protocols.io/view/protocol-name-c88ezzte | Joanna Sendecka | TITLE: Protocol name
AUTHORS: Joanna Sendecka
[DESCRIPTION]
This is a test protocol created for the purpose of developing guidelines.
[STEPS]
SECTION: Section one
1. Here we start writing the protocol. It will last 10 min
SECTION: Section one
1.1. and here we continue
SECTION: Section one
2. We give examples of amo... | ["[Section one] Here we start writing the protocol. It will last 10 min", "[Section one] and here we continue", "[Section one] We give examples of amounts e.g. volume 0.5 L or weight 200 g or voltage 3 V", "[Section one]"] |
14,821 | Intracellular Cytokine Staining | 1 | dx.doi.org/10.17504/protocols.io.sqdeds6 | https://www.protocols.io/view/intracellular-cytokine-staining-sqdeds6 | Kristin Anderson | TITLE: Intracellular Cytokine Staining
AUTHORS: Kristin Anderson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines the steps used for Intracellular cytokine staining.</div><div class = "text-block"><span>In brief: Cells were treated with protein transport inhibitor containing Br... | ["Prepare a flat bottom 96 well plate. Resuspend cells at 10e6 cells/ml in T cell media. Transfer at least 350ul of cells per condition into a fresh tube (you want at least 3 replicate wells at 100ul/well for each condition).", "Dilute Golgi Plug to 1:50 (2mg/ml) in cells for the experiment. (Once the treatment conditi... |
76,293 | Pharmacological treatment with corticoid or hyaluronic acid injections into subtalar joint via lateral access | 4 | dx.doi.org/10.17504/protocols.io.ewov1o5zplr2/v1 | https://www.protocols.io/view/pharmacological-treatment-with-corticoid-or-hyalur-cnrdvd26 | Fernanda Ferreira Gomes, Isnar M. de Castro Junior, João Antônio M. Guimarães, Aline Cordeiro | TITLE: Pharmacological treatment with corticoid or hyaluronic acid injections into subtalar joint via lateral access
AUTHORS: Fernanda Ferreira Gomes, Isnar M. de Castro Junior, João Antônio M. Guimarães, Aline Cordeiro
[DESCRIPTION]
Pharmacological treatment, such as corticoid or hyaluronic acid intra-articular injec... | ["[Patient preparation and positioning] Wash the patient's foot with degerming chlorhexidine and saline solution abundantly using a basin to store the liquid;", "[Patient preparation and positioning] Dry the patient's foot with a sterile compress;", "[Patient preparation and positioning] Dispose of the washing liquid i... |
72,588 | Colorimetric LAMP/RT-LAMP Protocol | 4 | null | https://www.protocols.io/view/colorimetric-lamp-rt-lamp-protocol-ci5kug4w | Felipe Navarro Martínez, Fernan Federici | TITLE: Colorimetric LAMP/RT-LAMP Protocol
AUTHORS: Felipe Navarro Martínez, Fernan Federici
[DESCRIPTION]
This protocol describes how to perform colorimetric LAMP / RT-LAMP reactions with homemade buffers, together with home-brewed BstLF and MMLV enzymes.
It is based on previous protocols of our lab (see LAMP/RT-LAM... | ["[2X Buffer Preparation] Prepare 1000 µL of 2X Colorimetric Buffer Mix according to the following table:\n\n \nTwo main differences compared to non-colorimetric LAMP reaction are the addition of dNTPs in the buffer, as they influence the reaction pH, and the removal of Tris-HCl as this component is vital to maintain t... |
106,620 | Proximity ligation assay | 0 | dx.doi.org/10.17504/protocols.io.kqdg32n57v25/v1 | https://www.protocols.io/view/proximity-ligation-assay-dkc44syw | Isabel Lam, Alain Ndayisaba, Vikram Khurana | TITLE: Proximity ligation assay
AUTHORS: Isabel Lam, Alain Ndayisaba, Vikram Khurana
[DESCRIPTION]
Proximity ligation assay
[STEPS]
1. | [] |
45,908 | qPCR assay for detecting round goby invasive fish species Neogobius melanostomus | 4 | dx.doi.org/10.17504/protocols.io.bq3umynw | https://www.protocols.io/view/qpcr-assay-for-detecting-round-goby-invasive-fish-bq3umynw | Omneya Ahmed, Alexander Eiler | TITLE: qPCR assay for detecting round goby invasive fish species Neogobius melanostomus
AUTHORS: Omneya Ahmed, Alexander Eiler
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Members of Ponto-Caspian gobies are predatory fish which have colonized freshwaters and brackish waters in Europe and North A... | ["[DNA extraction]\nA tissue of round goby was extracted with Qiagen DNeasy blood and tissue extraction kithttps://www.qiagen.com/us/shop/pcr/dneasy-blood-and-tissue-kit/The quality of DNA and 260/280 ratio were checked by NanoDrop instrument for nucleic acid measurements.", "[DNA extraction]\nPrimersNeogobius melanost... |
null | null | null | dx.doi.org/10.17504/protocols.io.k4gcytw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Ten healthy male volunteers took 5 g dose of either TJ-100 or lactose without knowing the identity of the substance. Each volunteer underwent two MR examinations after taking the other substance (TJ-100 or lactose) on separate days; they drank 1200 mL tap water and underwent ... | [] |
35,666 | The role of multiprotein bridging factor 1 (MBF1c) in Funariaceae species under salt stress | null | dx.doi.org/10.17504/protocols.io.be3sjgne | null | Maria Victória Magalhães de Vargas, Guilherme Afonso Kessler de Andrade, Sara Navarrete Bohi Goulart, Bruna Mota Bernardes, Filipe Victoria | TITLE: The role of multiprotein bridging factor 1 (MBF1c) in Funariaceae species under salt stress
AUTHORS: Maria Victória Magalhães de Vargas, Guilherme Afonso Kessler de Andrade, Sara Navarrete Bohi Goulart, Bruna Mota Bernardes, Filipe Victoria
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><spa... | [] |
34,462 | Generation of SARS-COV-2 RNA transcript standards for qRT-PCR detection assays | null | dx.doi.org/10.17504/protocols.io.bdv6i69e | null | Chantal Vogels, Joseph Fauver, Isabel Ott, Nathan Grubaugh | TITLE: Generation of SARS-COV-2 RNA transcript standards for qRT-PCR detection assays
AUTHORS: Chantal Vogels, Joseph Fauver, Isabel Ott, Nathan Grubaugh
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The protocol describes how to generate high-quality single-stranded RNA transcript standards... | ["[Preparation of cDNA]\nIsolate viral RNA using Omega Viral DNA/RNA kit, Trizol, or equivalent.", "[Preparation of cDNA]\nMany different cDNA synthesis kits can be used, but choose something that is relatively high-fidelity. The current protocol uses SuperScript IV VILO Master Mix because the enzyme has low error rate... |
70,490 | Establishment of primary intestinal epithelial cells and leukocytes from the three-spined stickleback, Gasterosteus aculeatus | 1 | dx.doi.org/10.17504/protocols.io.36wgqj565vk5/v1 | https://www.protocols.io/view/establishment-of-primary-intestinal-epithelial-cel-cg32tyqe | abdelmounaim_nouri, Maria L. Rodgers, Daniel L. Bolnick, Natalie C. Steinel | TITLE: Establishment of primary intestinal epithelial cells and leukocytes from the three-spined stickleback, Gasterosteus aculeatus
AUTHORS: abdelmounaim_nouri, Maria L. Rodgers, Daniel L. Bolnick, Natalie C. Steinel
[DESCRIPTION]
This protocol details the Establishment of primary intestinal epithelial cells and leuk... | ["[Fish dissection] After following approved euthanasia procedures, place the fish’s body on ice.", "[Fish dissection] Make a ventral incision from the cloaca to the jaw using sharp surgical scissors.", "[Fish dissection] Make two lateral incisions just behind the opercular flaps down to the lateral line of the fish.",... |
93,209 | Bulk growth and migration functional CRISPRi screens | 4 | dx.doi.org/10.17504/protocols.io.81wgbxoeolpk/v1 | https://www.protocols.io/view/bulk-growth-and-migration-functional-crispri-scree-c69zzh76 | Brian D. Cosgrove, Lexi Bounds, Carson Key Taylor, Alan L. Su, Anthony J. Rizzo, Alejandro Barrera, Andrea R Daniel, Gregory E. Crawford, Brenton D. Hoffman, Charles A. Gersbach | TITLE: Bulk growth and migration functional CRISPRi screens
AUTHORS: Brian D. Cosgrove, Lexi Bounds, Carson Key Taylor, Alan L. Su, Anthony J. Rizzo, Alejandro Barrera, Andrea R Daniel, Gregory E. Crawford, Brenton D. Hoffman, Charles A. Gersbach
[DESCRIPTION]
This protocol describes methods for a CRISPR interference ... | ["[Library design and cloning] A library of 21,458 gRNA targeting the top 1000 non-promoter ATAC-seq peaks ranked by increased accessibility on stiff substrate (50kPa) compared to the soft 1 kPa substrate hydrogels. For each peak, any gRNA that had a GuideScan specificity score of > 0.2 is included, which has previousl... |
null | null | null | dx.doi.org/10.17504/protocols.io.fw9bph6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?. | [] |
28,616 | Microscopy | 1 | dx.doi.org/10.17504/protocols.io.77ghrjw | https://www.protocols.io/view/microscopy-77ghrjw | Ricardo Quiteres, Alvaro Crevenna, Zach Hensel, Federico Herrera | TITLE: Microscopy
AUTHORS: Ricardo Quiteres, Alvaro Crevenna, Zach Hensel, Federico Herrera
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Live-cell images of U251 cells were acquired at Instituto Gulbenkian de Ciência on a commercial widefield Nikon High Content Screening microscope, equippe... | [] |
50,362 | DNA Library Prep for BGISEQ-500/MGISEQ-2000/DNBSEQ-G400/MGISEQ-200/DNBSEQ-G50 | 4 | dx.doi.org/10.17504/protocols.io.bve2n3ge | https://www.protocols.io/view/dna-library-prep-for-bgiseq-500-mgiseq-2000-dnbseq-bve2n3ge | Hongfang Zhang | TITLE: DNA Library Prep for BGISEQ-500/MGISEQ-2000/DNBSEQ-G400/MGISEQ-200/DNBSEQ-G50
AUTHORS: Hongfang Zhang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This DNA library prep protocol is specifically designed for WGS library construction for MGI highthroughput sequencing platforms. It's ap... | ["Fragmentation", "Transfer genomic DNA to a new 0.2 mL PCR tube. The volume should be less than or equal to . If the volume is less than , add dilution buffer to bring the final volume to\n45 µl\n45 µl\n45 µl", "Mix Frag Enzyme II by inverting 10 times then centrifuge briefly and place on ice for use. DO NOT vortex Fr... |
37,135 | A Simple RNA Preparation Method for SARS-CoV-2 detection by RT-qPCR | 2 | null | https://www.protocols.io/view/a-simple-rna-preparation-method-for-sars-cov-2-det-bghpjt5n | Aniela Wozniak, Catalina Ibarra-Henriquez, Valentina Sebastian, Grace Armijo, Liliana Lamig, Carolina Miranda, Marcela Lagos, Sandra Solari, Ana María Guzmán, Teresa Quiroga, Susan Hitschfeld, Eleodoro Riveras, Marcela Ferres, Rodrigo A. Gutiérrez, Patricia García, Ariel Cerda | TITLE: A Simple RNA Preparation Method for SARS-CoV-2 detection by RT-qPCR
AUTHORS: Aniela Wozniak, Catalina Ibarra-Henriquez, Valentina Sebastian, Grace Armijo, Liliana Lamig, Carolina Miranda, Marcela Lagos, Sandra Solari, Ana María Guzmán, Teresa Quiroga, Susan Hitschfeld, Eleodoro Riveras, Marcela Ferres, Rodrigo A... | [] |
58,773 | Indoor active search for adult Aedes sp. and Culex sp. mosquitoes | 2 | null | https://www.protocols.io/view/indoor-active-search-for-adult-aedes-sp-and-culex-b5mvq466 | Catalina Marceló | TITLE: Indoor active search for adult Aedes sp. and Culex sp. mosquitoes
AUTHORS: Catalina Marceló
[DESCRIPTION]
This protocol details the indoor active search carried out in the research project: "Spatial stratification of dengue based on the identification of risk factors: a pilot trial in Cauca, Colombia"
[STEP... | [] |
87,769 | MicroCT Imaging of the Fascicular Structure in the Porcine Right and Left Cervical Vagus Nerve | 6 | dx.doi.org/10.17504/protocols.io.ewov1qd2ygr2/v1 | https://www.protocols.io/view/microct-imaging-of-the-fascicular-structure-in-the-czxzx7p6 | Bettina Kronsteiner, Max Haberbusch, Francesco Moscato | TITLE: MicroCT Imaging of the Fascicular Structure in the Porcine Right and Left Cervical Vagus Nerve
AUTHORS: Bettina Kronsteiner, Max Haberbusch, Francesco Moscato
[DESCRIPTION]
This protocol outlines the procedure to dissect, prepare, and perform micro-CT imaging of the fascicular anatomy of the right and left vagu... | ["[Surgical Dissection and Macroscopic Examination of Nerve Samples] Acquire fresh cadavers of male and/or female domestic pigs.", "[Surgical Dissection and Macroscopic Examination of Nerve Samples] Place cadavers in the dorsal recumbence position.", "[Surgical Dissection and Macroscopic Examination of Nerve Samples] M... |
null | null | null | dx.doi.org/10.17504/protocols.io.jwqcpdw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Electrophoresis and transfer steps using the Life Technologies Bolt system as done by Campbell Lab for immunoquantitation of phytoplankton proteins.</p>
[STEPS] | [] |
52,479 | Isopropanol DNA Precipitation - Best for DNA Concentration | 4 | dx.doi.org/10.17504/protocols.io.bxg7pjzn | https://www.protocols.io/view/isopropanol-dna-precipitation-best-for-dna-concent-bxg7pjzn | Lynn Doran | TITLE: Isopropanol DNA Precipitation - Best for DNA Concentration
AUTHORS: Lynn Doran
[DESCRIPTION]
Protocol to precipitate extracted DNA from an aqueous solution to increase concentration or resolubilize in a different storage buffer.
*Use isopropanol DNA precipitation if your DNA is suspended in a very large vol... | ["Transfer desired amount of aqueous DNA solution to a fresh microtube. (70 ul)", "Add 3.0 M pH 5.2 sodium acetate to the DNA solution to result in a final concentration of 0.3 M sodium acetate. (7 ul)", "Add 0.6–0.7 volume of isopropanol at room temperature and mix well. (50 ul)", "Point caps of tubes out to help iden... |
null | null | null | dx.doi.org/10.17504/protocols.io.u8cezsw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol decribes how to plate bacteria in order to isolate a single colony of bacteria. Once this protocol is completed the isolated single colony can be used directly for experimental purposes or used to build up a freezer stock of the bacterial species.
For further inf... | ["Take previously grown bacterial colony- either frozen aliquot of bacteria in glycerol suspension or lawn of bacteria on agar media plate.", "Using a sterile inoculation loop, collect a small fragment of bacteria and inoculate in 10 mL LB broth in a 50 mL falcon tube. Shake loop in media until the fragment has come lo... |
71,942 | Calcium imaging in astrocytes | 4 | null | https://www.protocols.io/view/calcium-imaging-in-astrocytes-ciheub3e | gustavo.parfitt | TITLE: Calcium imaging in astrocytes
AUTHORS: gustavo.parfitt
[DESCRIPTION]
Calcium imaging in astrocytes
[STEPS]
1. Coat a 10 cm plate with 0.1% gelatin for 20 min
11. Plate 50k astrocytes of infected astrocytes
2. From a 80% confluent 10 cm plate of astrocytes obtained from protocol https://www.protocols.io/vi... | ["Coat a 10 cm plate with 0.1% gelatin for 20 min", "Plate 50k astrocytes of infected astrocytes", "From a 80% confluent 10 cm plate of astrocytes obtained from protocol https://www.protocols.io/view/astrocyte-extraction-from-brain-organoids-261ge364wl47/v2", "Add 3 mL of for 5 min", "300 rcf, 3 min, 25 °C", "Add pT... |
47,215 | High throughput Zika virus reporter virus particle microneutralization assay: Laboratory Procedure | 3 | dx.doi.org/10.17504/protocols.io.bscpnavn | https://www.protocols.io/view/high-throughput-zika-virus-reporter-virus-particle-bscpnavn | TITLE: High throughput Zika virus reporter virus particle microneutralization assay: Laboratory Procedure
AUTHORS:
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Zika virus is a Flavivirus, transmitted via </span><span style = "font-style:italic;">Aedes </span><span>mosquitos, that causes a... | [] | |
58,792 | MLA Medium Preparation | 3 | null | https://www.protocols.io/view/mla-medium-preparation-b5ngq5bw | Katherine Hunsberger, Kristel Sanchez | TITLE: MLA Medium Preparation
AUTHORS: Katherine Hunsberger, Kristel Sanchez
[DESCRIPTION]
This recipe is used to grow algae in the genus Anabaena, Dolichospermum, and Aphanizomenon in the Duffy lab. It can be used to grow other freshwater cyanobacteria cultures.
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.cyrxv5 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?. | [] |
81,773 | Mouse Organ Collection (Brain, Bone, Colon, Liver, and Mammary) | 4 | dx.doi.org/10.17504/protocols.io.j8nlkwx7wl5r/v1 | https://www.protocols.io/view/mouse-organ-collection-brain-bone-colon-liver-and-ct4mwqu6 | Andrew Davis, Aaron Havas, Sha Li, Laurence Haddadin, Diana Jurk, Kenneth Kim, Peter Adams | TITLE: Mouse Organ Collection (Brain, Bone, Colon, Liver, and Mammary)
AUTHORS: Andrew Davis, Aaron Havas, Sha Li, Laurence Haddadin, Diana Jurk, Kenneth Kim, Peter Adams
[DESCRIPTION]
This is a mouse dissection protocol intended to collect the 5 organs outlined in the SBPMDI TMC: Brain, Bone Marrow, Colon, Liver, and... | ["[Pre-collection (at least 1 day before)] Re-melt and cool wax pad to ensure stable surface for pinning", "[Pre-collection (at least 1 day before)] Prepare labeled 50ml conical tubes with 30-50ml of 4%PFA for each mouse. Store at 4°C, can be made up to a week before dissection date.", "[Pre-collection (at least 1 day ... |
null | null | null | dx.doi.org/10.17504/protocols.io.gvvbw66 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes the library preparation for Nanopore sequencing according to the SQK-MAP006 protocol. </p>
<p>It accompanies the <em>GigaScience</em> publication:</p>
<p> </p>
<p>Benjamin Istace, et al. (2017) De novo assembly and population genomic survey of natural ... | [] |
48,833 | RNA Extraction Protocol for Shorea | 4 | null | https://www.protocols.io/view/rna-extraction-protocol-for-shorea-btw9nph6 | mpfsum | TITLE: RNA Extraction Protocol for Shorea
AUTHORS: mpfsum
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>RNA extraction protocol using CTAB method optimized for leaf and bud samples from </span><span style = "font-style:italic;">Shorea </span><span>sp.</span></div></div>
[STEPS]
?. [Lysis]
... | ["[Lysis]\nWeigh BUD or LEAF and transfer into a 1.5 mL tube.\n[(25-40 mg)]\n[(50-70 mg)]", "[Lysis]\nIncubate at for .\n60 °C", "[Resuspension]\nResuspend the pellet in RNAse-free water.Flick the tube until the pellet is no longer visible.If the pellet is difficult to dissolve, leave it for ~30 min before flicking... |
77,532 | The relationship between naturalized and native plant species: insights from oceanic islands of the south-east Pacific after 200 years of records. | 1 | dx.doi.org/10.17504/protocols.io.kxygx922og8j/v1 | https://www.protocols.io/view/the-relationship-between-naturalized-and-native-pl-cpx4vpqw | Luis Cáceres-Polgrossi, Maura Di Rico, Diego Parra, Hanno Seebens, Stephen Galvin, Hans Juergen Boehmer | TITLE: The relationship between naturalized and native plant species: insights from oceanic islands of the south-east Pacific after 200 years of records.
AUTHORS: Luis Cáceres-Polgrossi, Maura Di Rico, Diego Parra, Hanno Seebens, Stephen Galvin, Hans Juergen Boehmer
[DESCRIPTION]
We assembled the most comprehensive da... | ["[Data Assembly] Collecting previous flora works of the Desventuradas islands (Skottsberg, 1937; Sparre, 1949; Hoffmann and Marticorena, 1987; Hoffmann and Tellier, 1991; Muñoz-Schick, 1995; Mueller-Dombois and Fosberg, 1998; Cuvertino, 2001; Escobar et al., 2011), Juan Fernandez Archipelago (Danton et al., 2006; Dant... |
9,087 | Preparation and Genetic Transformation of Parastagonospora nodorum Protoplasts | 1 | dx.doi.org/10.17504/protocols.io.n2bvjbmbgk5w/v1 | https://www.protocols.io/view/preparation-and-genetic-transformation-of-parastag-k47cyzn | Mitt Coats | TITLE: Preparation and Genetic Transformation of Parastagonospora nodorum Protoplasts
AUTHORS: Mitt Coats
[DESCRIPTION]
An Abstract
[STEPS]
1. Day 1 – Overnight culture
Prepare an overnight culture of S. nodorum by inoculation of 100 mL CzV8CS liquid medium (250 mL flask) with a concentrated spore suspension (~108 ... | ["Day 1 – Overnight culture\n \nPrepare an overnight culture of S. nodorum by inoculation of 100 mL CzV8CS liquid medium (250 mL flask) with a concentrated spore suspension (~108 spores). Incubate culture at 22ºC with shaking (140 rpm). Start culture after lunch on Day 1 to ensure a good yield of mycelium.", "Prepare C... |
53,875 | Restriction endonuclease reactions | 4 | dx.doi.org/10.17504/protocols.io.byutpwwn | https://www.protocols.io/view/restriction-endonuclease-reactions-byutpwwn | Shuning Guo | TITLE: Restriction endonuclease reactions
AUTHORS: Shuning Guo
[DESCRIPTION]
This protocol is used to having restriction endonuclease reactions based on endonuclease by NEB.
[STEPS]
1. Add the following reagents to a PCR tube (e.g. 50μl) on ice.
2. Incubate at 37℃ in water bath for 1 hour.
3. Stop the reaction... | ["Add the following reagents to a PCR tube (e.g. 50μl) on ice.", "Incubate at 37℃ in water bath for 1 hour.", "Stop the reaction by heat inactivation. Temperature and time for inactivation depends on the enzyme.", "Use electrophoresis to confirm if correct construct was present."] |
40,452 | Alveo be.well COVID-19 Test: Clinical Study IFU | 4 | dx.doi.org/10.17504/protocols.io.bjrckm2w | https://www.protocols.io/view/alveo-be-well-covid-19-test-clinical-study-ifu-bjrckm2w | Brenna Lord | TITLE: Alveo be.well COVID-19 Test: Clinical Study IFU
AUTHORS: Brenna Lord
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left"><a href="#" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;"> </span></a><span style = ":;"> <... | ["[Materials]\nAdditional Required MaterialsYou will also need a reusable be.well analyzer and an internet-connected mobile device with the be.well app downloaded (listed here as equipment) and appropriate Personal Protective Equipment (PPE):be.well Analyzer (1): Available for purchase from Alveo through the be.well mo... |
85,727 | CAMbank: CPT Field Processing v1 | 4 | null | https://www.protocols.io/view/cambank-cpt-field-processing-v1-cxx7xprn | Eliah G Overbey | TITLE: CAMbank: CPT Field Processing v1
AUTHORS: Eliah G Overbey
[DESCRIPTION]
Field processing of CPT vacutainers for the Cornell Aerospace Medicine Biobank (CAMbank).
Instructions for preserving: Plasma, PBMCs, and RBC Pellets.
[STEPS]
SECTION: Perform Venipuncture
1. After venipuncture, invert the tubes 8 to 10 t... | ["[Perform Venipuncture] After venipuncture, invert the tubes 8 to 10 times to fully mix in the sodium citrate anticoagulant.\n\nStore the tube upright at room temperature until centrifugation.\n\nTo ensure proper barrier formation, blood samples should be centrifuged within 2 hours of blood collection. Centrifugation ... |
28,991 | UC Davis - Intravenous Glucose Tolerance Test | null | dx.doi.org/10.17504/protocols.io.8i7huhn | null | Kent Lloyd, Kristin Grimsrud | TITLE: UC Davis - Intravenous Glucose Tolerance Test
AUTHORS: Kent Lloyd, Kristin Grimsrud
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block"><span>The intravenous glucose tolerance test is used to assess insulin sensiti... | ["Intravenous Glucose Tolerance Test (IVGTT):1. Fast mice prior to IVGTT evaluation. The fasting duration may vary depending on the investigators preference but may not exceed 18 hours. 2. Prior to intravenous injection, obtain a baseline blood sample using one of the 3 described methods below (in-dwelling catheter, ... |
47,246 | Corallochytrium limacisporum_culture method | 1 | null | https://www.protocols.io/view/corallochytrium-limacisporum-culture-method-bsdnna5e | Meritxell Antó | TITLE: Corallochytrium limacisporum_culture method
AUTHORS: Meritxell Antó
[STEPS]
?. [Growing medium]
BD Difco Marine Broth 2216 • Marine Agar 2216 https://legacy.bd.com/europe/regulatory/Assets/IFU/Difco_BBL/212185.pdf
?. [Growth conditions]
Temperature 23ºC
?. [Cryopreservation and recovery (from liquid cultures)]... | ["[Growing medium]\nBD Difco Marine Broth 2216 • Marine Agar 2216 https://legacy.bd.com/europe/regulatory/Assets/IFU/Difco_BBL/212185.pdf", "[Growth conditions]\nTemperature 23ºC", "[Cryopreservation and recovery (from liquid cultures)]\nCryopreservation (10%DMSO in Growing medium)1. Pre-grow the culture in appropriat... |
98,022 | Behavior Protocol | 0 | dx.doi.org/10.17504/protocols.io.x54v92mypl3e/v1 | https://www.protocols.io/view/behavior-protocol-dbye2pte | Sasha Burwell | TITLE: Behavior Protocol
AUTHORS: Sasha Burwell
[DESCRIPTION]
This protocol details the associative learning assay used to test extinction and conditioning behavior in mice.
[GUIDELINES]
Mice:
Surgerized with a headbar for head-fixation
Singly or pair housed
Acclimated for 1 week to a 12-hr reverse light/dark cycl... | ["[Habituation day 1] Begin water restriction: remove ad libitum water from mice.", "[Habituation day 1] Record starting body weight for all mice.", "[Habituation day 1] Calculate allotted daily water for all mice: 50 µL water per gram of weight.", "[Habituation day 1] Calculate goal weight for all mice:", "[Habituatio... |
95,895 | Odor Retention | 0 | dx.doi.org/10.17504/protocols.io.eq2lyjoeqlx9/v1 | https://www.protocols.io/view/odor-retention-c9vxz67n | sdwalto, Jeffrey Kordower, Bryan_Killinger | TITLE: Odor Retention
AUTHORS: sdwalto, Jeffrey Kordower, Bryan_Killinger
[DESCRIPTION]
Odor retention test optimized for mice. This test assesses short term olfactory memory. Mice with olfactory impairments or deficits should score lower.
[GUIDELINES]
ODERANT PAIRS: limonene (diluted 1:10) and carvone (diluted 1:10... | ["Prepare and empty rodent cage with no bedding.", "Prepare the odorants by diluting in mineral oil. (See guidelines)", "Acclimate mouse to setup (empty cage with odor cartridges). Place mouse in the cage and expose to 2 empty odor cartridges on either side of the cage for 5 mins.", "Expose mouse to the same unfamiliar... |
80,227 | In Vivo Carbon Fiber Electrode Thread (CFET) Implantation and Testing Procedures | 1 | dx.doi.org/10.17504/protocols.io.14egn2q3qg5d/v1 | https://www.protocols.io/view/in-vivo-carbon-fiber-electrode-thread-cfet-implant-cskbwcsn | Helen N Schwerdt, Michael J Cima, Ann M Graybiel | TITLE: In Vivo Carbon Fiber Electrode Thread (CFET) Implantation and Testing Procedures
AUTHORS: Helen N Schwerdt, Michael J Cima, Ann M Graybiel
[DESCRIPTION]
Procedures for implanting and testing CFET devices in rats are described.
[STEPS]
1. All procedures involving animals were approved by the Committee on Animal... | ["All procedures involving animals were approved by the Committee on Animal Care at the Massachusetts Institute of Technology and were performed strictly following the U.S. National Research Council Guide for the Care and Use of Laboratory Animals. Long–Evans male rats were used for tissue retainment testing (n = 2) an... |
63,300 | 10x Multiome Sample Processing | 1 | dx.doi.org/10.17504/protocols.io.bp2l61mqrvqe/v1 | https://www.protocols.io/view/10x-multiome-sample-processing-b93cr8iw | Allen Institute for Brain Science | TITLE: 10x Multiome Sample Processing
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
Protocol is used to profile all the open chromatin regions at a single nuclei level through the rapid generation of NGS-ready libraries, and for rapid generation of 3' transcriptomic-NGS-ready-single-cell-libraries from the ... | [] |
82,104 | In Silico Molecular Docking with Ligand Target | 1 | dx.doi.org/10.17504/protocols.io.5jyl8j4wrg2w/v1 | https://www.protocols.io/view/in-silico-molecular-docking-with-ligand-target-cueywtfw | Angelo José Rinaldi | TITLE: In Silico Molecular Docking with Ligand Target
AUTHORS: Angelo José Rinaldi
[DESCRIPTION]
This study outlines a comprehensive molecular docking protocol aimed at exploring enzyme-ligand interactions, leveraging various bioinformatics tools and databases. The protocol commences with the acquisition of the enzyme... | ["1) In this protocol we will use as an example of molecular docking, a target protein (receptor) called cyclooxygenase, which is an important enzyme in inflammatory processes. And as a ligand, the anti-inflammatory celecoxib.", "[Target receptor search:] 2) Seeking the three-dimensional (3D) structure of the receiver ... |
52,942 | cDNA protocol - Thermo Scientific RevertAid RT | 4 | dx.doi.org/10.17504/protocols.io.36wgq4zwxvk5/v1 | https://www.protocols.io/view/cdna-protocol-thermo-scientific-revertaid-rt-bxxnppme | Lauren Ponisio, Jocelyn Zorn | TITLE: cDNA protocol - Thermo Scientific RevertAid RT
AUTHORS: Lauren Ponisio, Jocelyn Zorn
[DESCRIPTION]
cDNA protocol - Thermo Scientific RevertAid RT
[STEPS]
SECTION: Prepare workspace
1. Thaw RNA and reagents on ice. Label four foil lids: one to replace RNA lid, one for reaction and two for aliquots
SECTION: Pr... | ["[Prepare workspace] Thaw RNA and reagents on ice. Label four foil lids: one to replace RNA lid, one for reaction and two for aliquots", "[Prepare workspace] UV sterilize 3 RNase free PCR plates, 8 boxes 10uL filter tips, and DEPC treated H2O", "[Prepare workspace] Once thawed, flash spin down RNA in plate centrifuge ... |
54,255 | Titan-gc SARS-CoV-2 Strain Characterization Workflow for Bioconda | 1 | null | https://www.protocols.io/view/titan-gc-sars-cov-2-strain-characterization-workfl-by8ppzvn | Michelle Su, Robert A Petit III, Technical Outreach and Assistance for States Team | TITLE: Titan-gc SARS-CoV-2 Strain Characterization Workflow for Bioconda
AUTHORS: Michelle Su, Robert A Petit III, Technical Outreach and Assistance for States Team
[DESCRIPTION]
This protocol covers the process of using Titan on the command-line, which was developed by Robert Petit at Wyoming Public Heath Laborato... | ["[Set up conda environment] The Titan workflow and its dependencies can be installed using the Conda package manager and the Bioconda channel for bioinformatics software. To install Conda, follow the instructions in Step 1.1. To update an existing Conda installation, go to Step 1.2. To add the Bioconda channel, go to ... |
49,304 | Human Islet Cell Culture | 4 | null | https://www.protocols.io/view/human-islet-cell-culture-budyns7w | Bridget Wagner | TITLE: Human Islet Cell Culture
AUTHORS: Bridget Wagner
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Human islet cell culture</div></div>
[STEPS]
?. [Cell-culture formulations]
The HTB-9 bladder carcinoma cell line (ATCC) is cultured in medium containing RPMI-1640 supplemented with 10% fetal bov... | ["[Cell-culture formulations]\nThe HTB-9 bladder carcinoma cell line (ATCC) is cultured in medium containing RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and 1 x penicillin-streptomycin.", "[Cell-culture formulations]\nIslet culture medium: Islets are cultured in CMRL-1066 supplemented with 10% FBS, 1 x pen... |
72,810 | Text mining approaches applied to patents: A scoping review protocol | 1 | dx.doi.org/10.17504/protocols.io.6qpvr43kzgmk/v1 | https://www.protocols.io/view/text-mining-approaches-applied-to-patents-a-scopin-cjciuiue | Homa Arshadi, Maryam Okhovati, Zohre Zahedi, Maryam Asharfi | TITLE: Text mining approaches applied to patents: A scoping review protocol
AUTHORS: Homa Arshadi, Maryam Okhovati, Zohre Zahedi, Maryam Asharfi
[DESCRIPTION]
This study will map the current state of different text mining approaches in patents. This will be of value to policy makers and researchers by allowing them to... | ["[Title] Text mining approaches applied to patents: A scoping review protocol", "[Stage of review at time of this submission] Review stage Started Completed Preliminary searches Yes Yes Piloting of the study selection process Yes Yes ... |
69,483 | Cas9 RNP nucleofection (CD34+ HSPCs) | 1 | dx.doi.org/10.17504/protocols.io.e6nvwe5dvmkj/v2 | https://www.protocols.io/view/cas9-rnp-nucleofection-cd34-hspcs-cf4jtqun | gregoire.cullot, Mandy Boontanrart, Mark Dewitt | TITLE: Cas9 RNP nucleofection (CD34+ HSPCs)
AUTHORS: gregoire.cullot, Mandy Boontanrart, Mark Dewitt
[DESCRIPTION]
Protocol for nucleofection of human HSPCs with Cas9 RNP.
[STEPS]
SECTION: HSPCs thawing
4. Prepare a 37 °C water bath (in a beaker) in the bead bath.
SECTION: Preparation of RNP mix
14. For one reacti... | ["[HSPCs thawing] Prepare a 37 °C water bath (in a beaker) in the bead bath.", "[Preparation of RNP mix] For one reaction (200,000 HSPCs in small cuvettes) mix following components:\n\n** first, dilute sgRNA in Cas9 Buffer 3X and then, slowly add Cas9 protein while mixing **", "[Prepare Cells] For one reaction, transfe... |
45,556 | A methodology for gathering and annotating the raw-data/characteristics of the documents citing a retracted article | 1 | dx.doi.org/10.17504/protocols.io.bqqumvww | https://www.protocols.io/view/a-methodology-for-gathering-and-annotating-the-raw-bqqumvww | Ivan Heibi, Silvio Peroni | TITLE: A methodology for gathering and annotating the raw-data/characteristics of the documents citing a retracted article
AUTHORS: Ivan Heibi, Silvio Peroni
[DESCRIPTION]
Giving a retracted article, we present a step-by-step methodology for gathering the raw-data of the documents which have cited such article (star... | ["[Identifying and retrieving the citing entities] Starting from one retracted article identified with a DOI this step gets the metadata of all the citing entities included in the COCI dataset (the OpenCitations Index of Crossref open DOI-to-DOI references). We are only interested in a subset of attributes for the citi... |
39,065 | Cement augmentation of internal fixation for trochanteric fracture: systematic review and meta-analysis | 3 | dx.doi.org/10.17504/protocols.io.bidzka76 | https://www.protocols.io/view/cement-augmentation-of-internal-fixation-for-troch-bidzka76 | Norio Yamamoto, Takahisa Ogawa, Masahiro Banno, Jun Watanabe, Tomoyuki Noda, Haggai Schermann, Toshifumi Ozaki | TITLE: Cement augmentation of internal fixation for trochanteric fracture: systematic review and meta-analysis
AUTHORS: Norio Yamamoto, Takahisa Ogawa, Masahiro Banno, Jun Watanabe, Tomoyuki Noda, Haggai Schermann, Toshifumi Ozaki
[STEPS] | [] |
56,826 | Staphilococcus Aureus Sampling | 4 | dx.doi.org/10.17504/protocols.io.b3q2qmye | https://www.protocols.io/view/staphilococcus-aureus-sampling-b3q2qmye | Pol Roca Cugat | TITLE: Staphilococcus Aureus Sampling
AUTHORS: Pol Roca Cugat
[DESCRIPTION]
This protocol is intended to study the affectation of Staphilococcus Aureus, including the MRSA variant. It outlines the basic protocol for a multi-subject study.
[GUIDELINES]
This protocol is intended to study the affectation of Staphiloco... | ["[Preparation] Wash your hands with soap. Put on your lab coat, your mask and your goggles or face shield. Make sure your mask is airtight and air cannot escape through the sides.", "[Preparation] Prepare the area where you are going to work. Disinfect the surfaces with bleach solution.\nThe subjects should not be abl... |
38,450 | ORCHARDS Household Substudy Protocol 2017 | 1 | dx.doi.org/10.17504/protocols.io.bhssj6ee | https://www.protocols.io/view/orchards-household-substudy-protocol-2017-bhssj6ee | Mitchell Arnold | TITLE: ORCHARDS Household Substudy Protocol 2017
AUTHORS: Mitchell Arnold
[STEPS] | [] |
27,881 | pTpPuc3_TpSil3p-eGFP | null | dx.doi.org/10.17504/protocols.io.7ghhjt6 | null | Jernej Turnsek | TITLE: pTpPuc3_TpSil3p-eGFP
AUTHORS: Jernej Turnsek
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Map and nucleotide sequence of the conjugation episome used to generate a TpSIl3p-EGFP expressing T. pseudonana strain reported in Faktorová D. et al. </div></div>
[STEPS]
?. | [] |
58,933 | Fecal Pellet Composition | 4 | dx.doi.org/10.17504/protocols.io.b5svq6e6 | https://www.protocols.io/view/fecal-pellet-composition-b5svq6e6 | Haley Geertsma | TITLE: Fecal Pellet Composition
AUTHORS: Haley Geertsma
[DESCRIPTION]
This protocol is used to measure the water content of mouse fecal pellets over 1 hour.
[STEPS]
1. Place mice in a clean cage and collect their fecal pellets produced over 1 hour.
2. Return mice to their home cage and weigh the fecal pellets (wet ... | ["Place mice in a clean cage and collect their fecal pellets produced over 1 hour.", "Return mice to their home cage and weigh the fecal pellets (wet weight).", "Desiccate the fecal pellets at 65oC for 19 hours then reweigh the fecal pellets (dry weight)."] |
79,527 | Mitochondrial complex activity assays | 1 | dx.doi.org/10.17504/protocols.io.14egn2oxyg5d/v1 | https://www.protocols.io/view/mitochondrial-complex-activity-assays-crwfv7bn | michela.deleidi, María José Pérez J. | TITLE: Mitochondrial complex activity assays
AUTHORS: michela.deleidi, María José Pérez J.
[DESCRIPTION]
Mitochondria complex activity assays measure the activity levels of the different complexes of the mitochondrial electron transport chain (ETC).
[STEPS]
SECTION: Mitochondrial complex activity assays
1. Isolate mi... | ["[Mitochondrial complex activity assays] Isolate mitochondria from HEK cells, iPSC-derived neurons, or midbrain organoids using the Qproteome Mitochondrial isolation kit (QIAGEN, Cat. No. / ID: 37612) according to manufacturer's instructions.", "[Mitochondrial complex activity assays] Measure Complex I (NADH oxidase/... |
62,214 | What Do We Expect After Using Testo Ultra? Read Customer Feedback! | 3 | dx.doi.org/10.17504/protocols.io.e6nvwkopdvmk/v1 | https://www.protocols.io/view/what-do-we-expect-after-using-testo-ultra-read-cus-b8zerx3e | Testo Ultra | TITLE: What Do We Expect After Using Testo Ultra? Read Customer Feedback!
AUTHORS: Testo Ultra
[DESCRIPTION]
https://spacecoastdaily.com/2021/11/testo-ultra-review-pros-cons-shocking-price-for-sale-testoultra-benefits-shark-tank-warning/
[STEPS] | [] |
75,161 | OSU TriState SenNet lung explant from IPF patients acceptance criteria | 1 | dx.doi.org/10.17504/protocols.io.dm6gpjyo1gzp/v1 | https://www.protocols.io/view/osu-tristate-sennet-lung-explant-from-ipf-patients-cmmzu476 | Sean D. Stacey, Brenda F. Reader, Lorena Rosas, Victor Peters, Ana L. Mora, Mauricio Rojas | TITLE: OSU TriState SenNet lung explant from IPF patients acceptance criteria
AUTHORS: Sean D. Stacey, Brenda F. Reader, Lorena Rosas, Victor Peters, Ana L. Mora, Mauricio Rojas
[DESCRIPTION]
This protocol describes the criteria required for inclusion of human lung specimen explants from idiopathic pulmonary fibrosis ... | ["[Inclusion Criteria] Transplant and surgical: 18-80 years of age, patient at OSUWMC, referred to OSUWMC for transplantation or has already undergone transplantation, able to understand and sign the TTCP Informed Consent and Research Authorization form, negative for HCV, HBV, and HIV, and has a pathology-confirmed dia... |
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