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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101,636 | Montagem de genomas de fungos (short reads) | 0 | dx.doi.org/10.17504/protocols.io.261ge5rpog47/v2 | https://www.protocols.io/view/montagem-de-genomas-de-fungos-short-reads-dfhc3j2w | Thiago Mafra Batista | TITLE: Montagem de genomas de fungos (short reads)
AUTHORS: Thiago Mafra Batista
[DESCRIPTION]
This protocol provides step-by-step instructions for students and researchers to assemble fungal nuclear genomes using Illumina short reads with SPAdes software. Before assembling the genome, we will align the short reads ag... | ["[Avaliação da qualidade do sequenciamento] Para avaliarmos os parâmetros de qualidade, sobretudo o phred score, utilizaremos dois softwares: FastQC e MultiQC.\n\n \nO fastqc gera um arquivo .html e um arquivo .zip para cada read. Os arquivos .html podem ser abertos em qualquer navegador de internet. Já o multiqc util... |
66,303 | https://www.facebook.com/ExipureErvaringen/ | 3 | dx.doi.org/10.17504/protocols.io.14egn7q8yv5d/v1 | https://www.protocols.io/view/https-www-facebook-com-exipureervaringen-ccy7sxzn | williamabarnett | TITLE: https://www.facebook.com/ExipureErvaringen/
AUTHORS: williamabarnett
[DESCRIPTION]
Exipureis a gainful weight reduction support supplement. Many specialists and medical services specialists have cooperated to carry this weight reduction supplement to the market.
[STEPS] | [] |
76,108 | Resource 4: rEV Serial Dilution | 1 | dx.doi.org/10.17504/protocols.io.kxygx9opzg8j/v1 | https://www.protocols.io/view/resource-4-rev-serial-dilution-cnjkvckw | Sean M Cook, Vera A. Tang, Joanne Lannigan, Jennifer Jones, Joshua A Welsh | TITLE: Resource 4: rEV Serial Dilution
AUTHORS: Sean M Cook, Vera A. Tang, Joanne Lannigan, Jennifer Jones, Joshua A Welsh
[DESCRIPTION]
Flow cytometry (FCM) is a common extracellular particles (EPs), including viruses and extracellular vesicles (EVs), characterization method. Frameworks such as MIFlowCyt-EV exist to ... | ["[rEV Reconstitution] Briefly centrifuge 100 x g, 5 min, 4 °C rEVs before opening.", "[rEV Reconstitution] Add 100 µL of 4 °C deionized water.", "[rEV Reconstitution] Pipet up and down to mix.", "[rEV Reconstitution] Aliquot 20 µL into low-binding Eppendorf tubes.", "[rEV Reconstitution] Store at 2-4 °C for up to one ... |
null | null | null | dx.doi.org/10.17504/protocols.io.ejebcje | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol outlines the beta-diversity analysis that we performed on the whole metagenome samples. We measured the signifiance of the dissimilarity between samples that were grouped by biological occlusion status, microenvironment (sebaceous, moist, etc), and sampling time po... | [] |
72,272 | 96-well plate CUT&RUN (BC 22.11.04) | 4 | null | https://www.protocols.io/view/96-well-plate-cut-amp-run-bc-22-11-04-citquemw | Brent Chick | TITLE: 96-well plate CUT&RUN (BC 22.11.04)
AUTHORS: Brent Chick
[DESCRIPTION]
CUT&RUN offers a convenient and practical means to perform chromatin profiling in situ for low cell number samples. This well plate format version of the assay has been adapted from the Rudensky lab (van Der Veeken et al. Immunity. 2020.... | ["[Procedure] Harvest 100,000 to 500,000 cells per replicate and transfer each sample to individual wells of a V-bottom 96 well plate (max well volume ~ 200 µL ). I use Nunc MicroWell plates (Thermo Scientific Cat #249944), however any V-bottom plate should work fine.", "[Procedure] Centrifuge plate for the equivalent ... |
28,025 | Simple Step toy Increase Gibson Assembly Efficiency | null | dx.doi.org/10.17504/protocols.io.7kzhkx6 | https://www.protocols.io/view/simple-step-toy-increase-gibson-assembly-efficienc-7kzhkx6 | Eric Danner | TITLE: Simple Step toy Increase Gibson Assembly Efficiency
AUTHORS: Eric Danner
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The Gibson assembly solutoin is extremely toxic to some bacteria cells. </div><div class = "text-block">Doing a solution change after assembly and before transforming the ... | ["[Do Normal Assembly]\nDo a normal Gibson assembly. Incubate in the PCR machine 60 min @ 50C", "[Do Normal Assembly]\nRemove the assemblies. Do a PCR quickchange/ gel extract column. This will remove the Gibson Assembly solution but keep the 100ng (or however much) of DNA.Elute in 15u -20ull TE or water", "[Do Normal ... |
30,710 | Flex-T™ HLA Class I ELISA Protocol | null | dx.doi.org/10.17504/protocols.io.98wh9xe | null | Sam Li | TITLE: Flex-T™ HLA Class I ELISA Protocol
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The HLA class I ELISA is an enzyme immunoassay based on the detection of β2-microglobulin subunit of HLA class I complexes, after capturing the complex through the conjugated biotin. To this end... | ["Dilute the 5X Coating Buffer to 1X with DI water", "Prepare Streptavidin solution to coat the plate: 24µl of Streptavidin solution 11.976 ml 1X Coating Buffer", "Calculate the amount of 1X Dilution Buffer required and prepare the solution by diluting the 10X concentrated buffer 10 times in DI water before use. The 1X... |
45,386 | HuBMAP | GE/UPitt Cell DIVE™ Modality Overview | 1 | dx.doi.org/10.17504/protocols.io.bqjimuke | https://www.protocols.io/view/hubmap-ge-upitt-cell-dive-modality-overview-bqjimuke | Liz McDonough | TITLE: HuBMAP | GE/UPitt Cell DIVE™ Modality Overview
AUTHORS: Liz McDonough
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is an overview of all protocols currently in use for the GE/UPitt Cell DIVE collaboration for the Human BioMolecular Atlas Program (HuBMAP). It includes links to each of ... | ["Confirm donor acceptance criteria for inclusion.Donor Acceptance Criteria for GE/UPitt HuBMAP Inclusion", "Prepare paraffin blocks and FFPE sections from tissue samples.HuBMAP | Formalin Fixation and Paraffin Embedding of Tissue SamplesHuBMAP | Sectioning of FFPE Specimens", "Deparaffinize and rehydrate slides.Cell D... |
64,371 | {Exposed} Keto Now Reviews Ketosis and (Scam or Legit) Shark Tank Diet Keto Now Pills – Test and Buy! | 3 | dx.doi.org/10.17504/protocols.io.eq2lynqbpvx9/v1 | https://www.protocols.io/view/exposed-keto-now-reviews-ketosis-and-scam-or-legi-ca4tsgwn | scarturnbull | TITLE: {Exposed} Keto Now Reviews Ketosis and (Scam or Legit) Shark Tank Diet Keto Now Pills – Test and Buy!
AUTHORS: scarturnbull
[DESCRIPTION]
Keto Now Reviews
[STEPS] | [] |
52,671 | Day 2: PCR | 4 | dx.doi.org/10.17504/protocols.io.bxn7pmhn | https://www.protocols.io/view/day-2-pcr-bxn7pmhn | Tom Little | TITLE: Day 2: PCR
AUTHORS: Tom Little
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">DAY 2: ADE field practical instructions for PCR </div></div>
[STEPS]
?. Retrieve your four tubes from the PCR machine.
?. Add 24ul of PCR mix to the second tube in your strip. The PCR mix includes buffer, enzyme ... | ["Retrieve your four tubes from the PCR machine.", "Add 24ul of PCR mix to the second tube in your strip. The PCR mix includes buffer, enzyme and primers to amplify the ~650 base fragment of cytochrome oxidase I (COX1) used as a \"universal\" DNA barcode for animals. Your tubes will now look like this, with the clear ... |
44,197 | Methanol-based HIV-Flow | 1 | null | https://www.protocols.io/view/methanol-based-hiv-flow-bpedmja6 | Marion Pardons, Basiel Cole | TITLE: Methanol-based HIV-Flow
AUTHORS: Marion Pardons, Basiel Cole
[STEPS]
?. [Day 1 - CD4 enrichment and stimulation]
Thaw cryopreserved PBMCs (maximum 2 vials per 50mL tube) from the HIV-infected individuals and uninfected control in FCS (1mL FCS per 50M cells). Centrifuge (1,500rpm, 5min), and discard supernatant.... | ["[Day 1 - CD4 enrichment and stimulation]\nThaw cryopreserved PBMCs (maximum 2 vials per 50mL tube) from the HIV-infected individuals and uninfected control in FCS (1mL FCS per 50M cells). Centrifuge (1,500rpm, 5min), and discard supernatant.Resuspend the cells in 25mL of cRPMI and count the cells. Centrifuge (1500rpm... |
6,569 | Pre-validation survey for the elimination of trachoma and evaluation of the effectiveness of the trachoma surveillance strategy in Ghana | 1 | dx.doi.org/10.17504/protocols.io.inhcdb6 | https://www.protocols.io/view/pre-validation-survey-for-the-elimination-of-trach-inhcdb6 | Oscar Debrah, Ernest Mensah, Laura Senyonjo, Dziedzom K. de Souza, Tei E. Hervie, David Agyemang, Didier Bakajika, Benjamin Marfo, Felix Ahorsu, Seth Wanye, Joseph Koroma, Agatha Aboe, Nana-Kwadwo Biritwum | TITLE: Pre-validation survey for the elimination of trachoma and evaluation of the effectiveness of the trachoma surveillance strategy in Ghana
AUTHORS: Oscar Debrah, Ernest Mensah, Laura Senyonjo, Dziedzom K. de Souza, Tei E. Hervie, David Agyemang, Didier Bakajika, Benjamin Marfo, Felix Ahorsu, Seth Wanye, ... | ["[Background and rationale]\nTrachoma, a result of infection with the bacterium Chlamydia trachomatis, remains the leading infectious cause of blindness worldwide [WHO, 2014a]. The intervention strategy for trachoma is the World Health Organization (WHO)-endorsed SAFE strategy (S: Surgery for in-turned eyelashes a res... |
null | null | null | dx.doi.org/10.17504/protocols.io.nv3de8n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Purpose of this protocol is to grow up single colonies of bacteria for use.</p>
[STEPS]
?.
?.
?.
?. | [] |
106,628 | Seeded amplification assay (SAA) from neuronal cell lysates | 0 | dx.doi.org/10.17504/protocols.io.5jyl82xm7l2w/v1 | https://www.protocols.io/view/seeded-amplification-assay-saa-from-neuronal-cell-dkdc4s2w | Isabel Lam, Alain Ndayisaba, Vikram Khurana | TITLE: Seeded amplification assay (SAA) from neuronal cell lysates
AUTHORS: Isabel Lam, Alain Ndayisaba, Vikram Khurana
[DESCRIPTION]
Seeded amplification assay (SAA) from neuronal cell lysates
[STEPS] | [] |
58,768 | Bristol’s Modified Medium | 3 | null | https://www.protocols.io/view/bristol-s-modified-medium-b5mqq45w | Kristel Sanchez | TITLE: Bristol’s Modified Medium
AUTHORS: Kristel Sanchez
[DESCRIPTION]
This recipe is used to culture algae of the genus Ulothrix in the lab. However, in can be used to grow other organisms such as cyanobacteria, chrysophyta, euglenophyta and other green algae.
[STEPS] | [] |
97,861 | Microbe/Phage Wastewater DNA/RNA Concentration and Extraction (Nanotrap® and NucleoMag® RNA Water) | 1 | dx.doi.org/10.17504/protocols.io.dm6gpz8p5lzp/v1 | https://www.protocols.io/view/microbe-phage-wastewater-dna-rna-concentration-and-dbtd2ni6 | Brett Rasile, Kendra Maas, Archana Anand, Michael Hajkowski | TITLE: Microbe/Phage Wastewater DNA/RNA Concentration and Extraction (Nanotrap® and NucleoMag® RNA Water)
AUTHORS: Brett Rasile, Kendra Maas, Archana Anand, Michael Hajkowski
[DESCRIPTION]
Wastewater epidemiology is a method used to study the diseases affecting a population. Conventional methods of wastewater collecti... | ["[Virus Capture & Concentration] Collect 500 mL of wastewater in a 500mL or 1L plastic sample bottle.", "[Virus Capture & Concentration] Create a 1:100 dilution of Zoetis Bovine Rhinotracheitis-Parainfluzena-Respiratory Syncytial Virus (BRSV) Vaccine in H2O.", "[Virus Capture & Concentration] Spike the500 ... |
56,586 | Pharyngeal Pumping Assay | 4 | dx.doi.org/10.17504/protocols.io.b3hiqj4e | https://www.protocols.io/view/pharyngeal-pumping-assay-b3hiqj4e | Thomas J J. O'Brien | TITLE: Pharyngeal Pumping Assay
AUTHORS: Thomas J J. O'Brien
[DESCRIPTION]
The pharynx is a is a neuromuscular pump found at the anterior end of the alimentary tract, consisting of 20 muscles and 20 neurons. A proper feeding rate in worms is coordinated by the precise timing of pharyngeal movements, with one complete ... | ["[Pick L4 worms for bleaching (Day 1)] Using an eyelash pick, pick 10 x L4s of each worm strain to be assayed onto 2 x 90 mm plates (pre-seeded with OP50) and incubate at 20 °C", "[Pour 60 mm NGM agar plates (Day 2)] Prepare and pour the following number of NGM plates per worm strain to be studied:\n5 x 60 mm (15 mL a... |
81,623 | Generating rabbit rAbs from heterohybridomas | 4 | dx.doi.org/10.17504/protocols.io.eq2ly7k4mlx9/v1 | https://www.protocols.io/view/generating-rabbit-rabs-from-heterohybridomas-ctxxwppn | Zhang, Yu Peng | TITLE: Generating rabbit rAbs from heterohybridomas
AUTHORS: Zhang, Yu Peng
[DESCRIPTION]
This protocol describes the materials and methods used to generate rabbit recombinant antibodies (rAbs) from existing heterohybridomas, from mRNA extraction to rAb production.
[STEPS]
SECTION: 1. mRNA extraction
1. Before extrac... | ["[1. mRNA extraction] Before extracting mRNA, use RNaseZap™ Wipes to wipe the outer surface of the centrifuge tube, tube rack, pipette, centrifuge, operating table, etc. to remove possible RNase to prevent mRNA degradation. Among them, using an RNase-free pipette tip with a filter within. The operator should wear a ma... |
70,457 | Assay for Dual Rab GTPase binding to the LRRK2 Armadillo Domain | 4 | dx.doi.org/10.17504/protocols.io.81wgbypzovpk/v1 | https://www.protocols.io/view/assay-for-dual-rab-gtpase-binding-to-the-lrrk2-arm-cg2ztyf6 | Claire Y Chiang, Suzanne R Pfeffer | TITLE: Assay for Dual Rab GTPase binding to the LRRK2 Armadillo Domain
AUTHORS: Claire Y Chiang, Suzanne R Pfeffer
[DESCRIPTION]
The LRRK2 Armadillo domain contains multiple Rab GTPase binding sites. To show that the sites can be occupied simultaneously, we use this assay. The idea is to immobilize Rab8A, bind Armad... | ["[Dual Rab GTPase binding to LRRK2 Armadillo Domain] Phosphorylate His-Rab10 Q68L 1-181 with His-MST3 kinase at a molar ratio of 1:3 (kinase:substrate) at 30 °C 120 min in reaction buffer. See below for details.", "[Dual Rab GTPase binding to LRRK2 Armadillo Domain] Pellet 50 µL glutathione agarose slurry at 3000 rpm... |
37,534 | 96-well CTAB-chloroform DNA extraction | 1 | dx.doi.org/10.17504/protocols.io.bgv6jw9e | https://www.protocols.io/view/96-well-ctab-chloroform-dna-extraction-bgv6jw9e | Lila Fishman | TITLE: 96-well CTAB-chloroform DNA extraction
AUTHORS: Lila Fishman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a 96-well version of the classic CTAB-chloroform plant DNA extraction (Doyle & Doyle 1987), developed by John Willis and Lila Fishman in ~2000 and since optimized by multiple l... | ["[Tissue collection]\nPre-label the FRONT of each plate with projectname_plate#, your initials, and the date. Pre-label the FRONT of each tube-strip with its number 1-12 (l-r), and mark the BACKs of the tube-strips with a line.\nUse this labeling scheme throughout. Please verify with PI or project lead that a projectn... |
38,016 | A distribution-dependent analysis of open-field test movies | 1 | dx.doi.org/10.17504/protocols.io.bhc8j2zw | https://www.protocols.io/view/a-distribution-dependent-analysis-of-open-field-te-bhc8j2zw | Tomokazu Konishi | TITLE: A distribution-dependent analysis of open-field test movies
AUTHORS: Tomokazu Konishi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Although the open-field test has been widely used, its reliability and compatibility are frequently questioned. Many indicating parameters were introduced for ... | ["Animal testPlastic container boxes are used as the open field. Those are available at DIY stores. Choice of the colors is important to obtain enough contrast to the animal. A particular part of the animals can be colored and spotted. Otherwise, the shape of the animals should be separated from the box background in b... |
57,632 | Total Lipid Extraction from Baker's yeast (Saccharomyces cerevisiae) | 4 | dx.doi.org/10.17504/protocols.io.b4h8qt9w | https://www.protocols.io/view/total-lipid-extraction-from-baker-39-s-yeast-sacch-b4h8qt9w | Israel Olayide, Monica Rieth | TITLE: Total Lipid Extraction from Baker's yeast (Saccharomyces cerevisiae)
AUTHORS: Israel Olayide, Monica Rieth
[DESCRIPTION]
This protocol outlines a method for extracting total lipids from Baker's yeast, Saccharomyces cerevisiae. It has been adapted from Roy et al., J. Lipid Res. 2018. doi: 10.1194/jlr.M0885... | ["[Day 1-3] Sterilize the inoculating loop by dipping it in the ethanol and heating it for 30 second in the flame", "[Day 1-3] Allow loop to cool the loop at least for 10 seconds", "[Day 4] Inoculate 5 mL YPD with yeast colony from plate", "[Day 4] Grow overnight at 30°C with shaking at 250 rpm", "[Day 5] Check OD600 a... |
101,202 | Imaging- Bright field | 0 | dx.doi.org/10.17504/protocols.io.rm7vzjj9rlx1/v1 | https://www.protocols.io/view/imaging-bright-field-de3s3gne | daniel.dautan daniel, Per Svenningsson | TITLE: Imaging- Bright field
AUTHORS: daniel.dautan daniel, Per Svenningsson
[DESCRIPTION]
Protocol for imaging using Hamamatsu NanoZoomer slide scanner. 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.... | ["Image slides at 40x magnification.", "Extract individual sections using the NDP.view software (https://www.hamamatsu.com/eu/en/product/life-science-and-medical-systems/digital-slide-scanner/U12388-01.html).", "Save images as tiff files.", "Open images from same structures as one single stack using the merge function... |
62,272 | Dorsal Root Ganglia stimulation-block colorectal afferents | 1 | dx.doi.org/10.17504/protocols.io.bp2l61rnzvqe/v1 | https://www.protocols.io/view/dorsal-root-ganglia-stimulation-block-colorectal-a-b828ryhw | Longtu Chen, Bin Feng | TITLE: Dorsal Root Ganglia stimulation-block colorectal afferents
AUTHORS: Longtu Chen, Bin Feng
[DESCRIPTION]
To test the feasibility of transmission block in visceral afferents by DRG stimulation, we developed an ex vivo
preparation in which mouse colorectum, pelvic nerve (PN), L6 DRG, and dorsal root (DR) were ha... | ["[Intracolonic TNBS treatment] C57BL/6 mice (8-16 weeks, 25-35 g, and either sex) were anesthetized by isoflurane inhalation.", "[Ex vivo colorectum-Pelvic Nerve-Dorsal Root Ganglia-Dorsal Root (PN-DRG-DR) preparation] Mice at 7 to 14 days after TNBS treatment were used, a time span of colorectal hypersensitivity. C57... |
22,582 | Euplotes crassus GFP artificial nanochromosome sequence | null | dx.doi.org/10.17504/protocols.io.2awgafe | null | Angela Piersanti, Rachele Cesaroni | TITLE: Euplotes crassus GFP artificial nanochromosome sequence
AUTHORS: Angela Piersanti, Rachele Cesaroni
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-style:italic;">Euplotes crassus </span><span>GFP artificial nanochromosome </span></div></div>
[STEPS]
?. CCCCAAAACCCCAAAACC... | ["CCCCAAAACCCCAAAACCCCAAAACCCCTGAAGGAAGGCCGTCAAGGCCGCATATTAACTAGGTGAAATGTTGGTTATAAATATTTAAAAATGTCTGGAGGAGAAGAACTTTTCGCTGGAATTGTTCCAGTTCTTATTGAACTTGATGGAGATGTTCATGGACATAAGTTCTCTGTTAGAGGAGAAGGAGAAGGAGATGCTGATTATGGAAAGCTTGAAATTAAGTTCATTTGTACTACTGGAAAGCTTCCAGTTCCATGGCCAACTCTTGTTACTACTCTTTGTTATGGAATTCAATGTTTCGCTAGATATCCAGAA... |
81,633 | TS Procure 812 - H&E stained section under glass coverslip on glass slide (TM - 013) | 4 | dx.doi.org/10.17504/protocols.io.81wgby3onvpk/v1 | https://www.protocols.io/view/ts-procure-812-h-amp-e-stained-section-under-glass-ctx9wpr6 | sandra.crameri | TITLE: TS Procure 812 - H&E stained section under glass coverslip on glass slide (TM - 013)
AUTHORS: sandra.crameri
[DESCRIPTION]
The method is used to process H&E stained slides through to Procure 812 resin blocks.
[GUIDELINES]
Sample is not optimal for EM, best to dissect and use only the outer 2mm of tissue m... | ["[HEADER] SAN:\n\n\n\n\nSPEC No:\n\n\n\n\nOPERATOR & STEPS:\n\n\n\n\nOPERATOR & STEPS:", "[Remove Coverslip] Remove coverslip by soaking in minimum , check to see if coverslip has slide off, if not soak another .", "[Conventional] 2.5 % volume in 0.1 Molarity (M) Sorenson's Phosphate buffer (pH 7.2, 300mosmol... |
43,781 | 3D Immunostaining for CLARITY-processed samples | 1 | dx.doi.org/10.17504/protocols.io.bnzdmf26 | https://www.protocols.io/view/3d-immunostaining-for-clarity-processed-samples-bnzdmf26 | Seth Currlin | TITLE: 3D Immunostaining for CLARITY-processed samples
AUTHORS: Seth Currlin
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This is a guide for immunostaining CLARITY-processed samples. </span><a href="https://dx.doi.org/10.17504/protocols.io.8jihuke" style = "text-decoration:underline;color:... | ["[Immunohistochemistry for large (5 mm3) tissue volumes]\nWash out residual clearing solutionThree washes in PBST, 24 hours each, 37C with gentle agitation.", "[Immunohistochemistry for large (5 mm3) tissue volumes]\nNonspecific Epitope BlockingBlocking buffer incubation: three days, 37C with gentle agitation.Note: S... |
63,565 | HyDrop Bead Generation & PCR Barcoding v1.0 | 1 | dx.doi.org/10.17504/protocols.io.n92ld9np9g5b/v10 | https://www.protocols.io/view/hydrop-bead-generation-amp-pcr-barcoding-v1-0-cabmsak6 | Florian De Rop, Suresh Poovathingal, Stein Aerts | TITLE: HyDrop Bead Generation & PCR Barcoding v1.0
AUTHORS: Florian De Rop, Suresh Poovathingal, Stein Aerts
[DESCRIPTION]
Protocol for producing dissolvable barcoded hydrogel beads used in HyDrop experiments.
[STEPS]
SECTION: Hydrogel bead generation
1.
Hydrogel bead generation
Here, we will create an emulsi... | ["[Hydrogel bead generation] Hydrogel bead generation\nHere, we will create an emulsion of acrylamide monomers in a carrier oil containing TEMED. The monomer droplets will polymerise and form hydrogel beads. Ideally, you have a bead stock of around 3 mL of beads before you barcode, but 2 mL can work as well. It is best... |
78,445 | Automated high throughput Qiagen MagAttract High Molecular Weight DNA extraction from mosquitoes | 4 | dx.doi.org/10.17504/protocols.io.ewov1o1n7lr2/v1 | https://www.protocols.io/view/automated-high-throughput-qiagen-magattract-high-m-cqumvwu6 | Fiona Teltscher, Mara Lawniczak | TITLE: Automated high throughput Qiagen MagAttract High Molecular Weight DNA extraction from mosquitoes
AUTHORS: Fiona Teltscher, Mara Lawniczak
[DESCRIPTION]
This is an automated protocol for the extraction of high molecular weight (HMW) DNA from insects. It uses the Qiagen MagAttract kit and factors in modifications... | ["[Sample preparation] Prepare an open insulated box of dry ice to store sample tubes on whilst working through steps 2-4", "[Sample preparation] Make mastermix of reagents for lysis.\n\n \nCalculate the mastermix volumes for the number of samples plus 1 for spare pipetting volume. Volumes per sample are: 200 µL ; 20... |
77,471 | MTT (Assay protocol | 4 | dx.doi.org/10.17504/protocols.io.eq2ly72emlx9/v1 | https://www.protocols.io/view/mtt-assay-protocol-cpv7vn9n | Abdulkareem Hameed Abd, Enas Jawad Kadhim, Matin Mahmood | TITLE: MTT (Assay protocol
AUTHORS: Abdulkareem Hameed Abd, Enas Jawad Kadhim, Matin Mahmood
[DESCRIPTION]
MTT ((3-(4,5-Dimethylthiazol-2-yl)-2,5-Diphenyltetrazolium Bromide)) is used to assess cell viability as a function of redox potential. Actively respiring cells convert the water-soluble MTT to an insoluble purpl... | ["[Maintenance of Cell lines] SK-GT-4 cell line, was maintained in MEM supplemented with 10% Fetal bovine, 100 units/mL penicillin, and 100 µg/mL streptomycin. Cells were passaged using Trypsin-EDTA reseeded at 50% confluence twice a week, and incubated at 37 °C", "[MTT Assay] Cell lines were seeded at 1 × 104cells/wel... |
26,539 | U Mass - Hind Limb Ischemia | null | dx.doi.org/10.17504/protocols.io.56jg9cn | null | Mark Kelly, Timothy P. Fitzgibbons | TITLE: U Mass - Hind Limb Ischemia
AUTHORS: Mark Kelly, Timothy P. Fitzgibbons
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">This is a mouse model of hind limb ischemia, a technique involving an interruption in the ar... | ["Expected procedure duration:30 minutes", "Adequacy or depth of anesthesia is monitored by:Respiratory Rate and Toe Pinch", "Frequency of anesthesia depth assessment:At the start of surgical procedure, a toe or ear pinch can be used to assess the depth of anesthesia. Visual monitoring should be performed thought-out t... |
88,518 | HPLC Analysis of Nucleotides | 4 | null | https://www.protocols.io/view/hplc-analysis-of-nucleotides-c2peydje | Xuefeng Ren, Annan SI Cook | TITLE: HPLC Analysis of Nucleotides
AUTHORS: Xuefeng Ren, Annan SI Cook
[DESCRIPTION]
Ion-pair reversed phase HPLC analysis of the nucleotide bound to PI3KC3-C1.
[STEPS]
SECTION: Denaturation of PI3KC3-C1
1. Heat the PI3KC3-C1 sample in a heat block at 90 °C for 10 min to denature the protein.
SECTION: Centrifugati... | ["[Denaturation of PI3KC3-C1] Heat the PI3KC3-C1 sample in a heat block at 90 °C for 10 min to denature the protein.", "[Centrifugation] After denaturation, centrifuge the sample at 21000 rpm, 15 min to pellet any precipitated PI3KC3-C1.", "[Supernatant Transfer] Carefully transfer the supernatant containing the releas... |
62,652 | Protein extraction protocol | 1 | dx.doi.org/10.17504/protocols.io.5jyl896o6v2w/v1 | https://www.protocols.io/view/protein-extraction-protocol-b9e4r3gw | rabdelha | TITLE: Protein extraction protocol
AUTHORS: rabdelha
[DESCRIPTION]
This protocol details protein extraction procedure.
[STEPS]
SECTION: Protein extraction protocol
1. Warm reagent to Room temperature.
SECTION: Protein extraction protocol
2. Add protease inhibitor tablet (1 tablet/10 mL) (complete EDTA free).
SECT... | ["[Protein extraction protocol] Warm reagent to Room temperature.", "[Protein extraction protocol] Add protease inhibitor tablet (1 tablet/10 mL) (complete EDTA free).", "[Protein extraction protocol] Add amount of reagent to each sample and transfer to bead beating tube.", "[Protein extraction protocol] Homogenize tis... |
79,105 | Qiagen DNeasy PowerSoil HTP 96 Kit | 1 | dx.doi.org/10.17504/protocols.io.8epv5j526l1b/v1 | https://www.protocols.io/view/qiagen-dneasy-powersoil-htp-96-kit-crg9v3z6 | QIAGEN | TITLE: Qiagen DNeasy PowerSoil HTP 96 Kit
AUTHORS: QIAGEN
[DESCRIPTION]
Introduction
The DNeasy PowerSoil HTP 96 Kit allows high-throughput isolation of DNA from up to 384 soil samples in less than one day.
Principle and procedure
This kit provides researchers with a high-throughput method for isolating genomic DN... | ["[Sample preparation & cell lysis] ADD 750 µL of PowerBead Solution to the wells of the PowerBead Plate\n\nADD 60 µL of Solution C1", "[Sample preparation & cell lysis] SECURE the Square Well Mat tightly to the plate\n\nPLACE PowerBead Plate with the mat securely fastened between 2 Adapter Plates on a 96 well ... |
95,894 | Enhancements Cascades '24: Veg and Pollinator Survey | 1 | dx.doi.org/10.17504/protocols.io.x54v9pq3zg3e/v1 | https://www.protocols.io/view/enhancements-cascades-39-24-veg-and-pollinator-sur-c9vwz67e | Lauren Ponisio, rmcdonal | TITLE: Enhancements Cascades '24: Veg and Pollinator Survey
AUTHORS: Lauren Ponisio, rmcdonal
[DESCRIPTION]
Protocol for surveying florally enhanced and control stands within the timberland forests burned by the 2020 wildfire.
[STEPS]
SECTION: Questions
1. Can native, flowering plants succeed (germinate and flow... | ["[Questions] Can native, flowering plants succeed (germinate and flower within 1-3 years after seeding) in burned slash piles with minimal site prep?\nDoes plant composition affect pollinator visitation and plant coexistence? (i.e., restoration mixes designed to promote adaptive foraging result in plant communities th... |
86,704 | Particle size analysis by laser diffraction | 6 | null | https://www.protocols.io/view/particle-size-analysis-by-laser-diffraction-cywqxxdw | Jennifer Moore | TITLE: Particle size analysis by laser diffraction
AUTHORS: Jennifer Moore
[DESCRIPTION]
This method is a relatively rapid protocol for the determination of soil particle size analysis (texture) using laser diffraction. A critical step is to wet sieve the sand fraction prior to laser analysis.
[STEPS]
SECTION: Reage... | ["[Reagents] Sodium hexametaphosphate (NaHMP) 10% solution\nChemical formula: (NaPO3)6\nMolar mass: 611.77 g/mol\nProcedure: Mix 100 g of NaHMP in 1000 mL of deionized water.", "[Sample preparation] Gather soil samples to be weighed. Samples should be dry and sieved to <2mm. Label the 125-mL wide-mouth Nalgene bottle... |
45,560 | Northern Blot Protocol | 4 | dx.doi.org/10.17504/protocols.io.bqqymvxw | https://www.protocols.io/view/northern-blot-protocol-bqqymvxw | Sibylle Mitschka, Christine Mayr | TITLE: Northern Blot Protocol
AUTHORS: Sibylle Mitschka, Christine Mayr
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Northern blot is a hybridization technique to visualize and quantify RNAs from cells or tissues using a radio-labeled probe. mRNAs only constitute a small fraction of total R... | ["[Total RNA extraction]\nThaw TRIzol samples at RT.", "[Chloroform extraction]\nadd per tube\n200 µl", "[Chloroform extraction]\nMix tubes vigorously for", "[Chloroform extraction]\nAllow samples to sit for at\n0 Room temperature", "[Chloroform extraction]\nCentrifuge samples at\nCentrifuge: 20000 34, 20 min, 4 10... |
null | null | null | dx.doi.org/10.17504/protocols.io.efpbbmn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol provides a method for predicting the locations of the open reading frames (ORFs) using the Glimmer3 toolkit. Methods based on the publication: <br /><br />Hannigan, Geoffrey D., et al. "The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity... | [] |
43,701 | Restriction Digest | 1 | dx.doi.org/10.17504/protocols.io.bnwvmfe6 | https://www.protocols.io/view/restriction-digest-bnwvmfe6 | Zhujun Wei | TITLE: Restriction Digest
AUTHORS: Zhujun Wei
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol includes three different methods of digestion.</div></div>
[STEPS]
?. Add the following reagents to a tube. ABCD1Total10ul30ul50ul2DNA0.4ug1.2ug2ug3Enzyme0.2ul0.6ul1ul4Buffer(10*)1ul3ul5ul5... | ["Add the following reagents to a tube. ABCD1Total10ul30ul50ul2DNA0.4ug1.2ug2ug3Enzyme0.2ul0.6ul1ul4Buffer(10*)1ul3ul5ul5ddwater Fill the rest with water\nABCD1Total10ul30ul50ul2DNA0.4ug1.2ug2ug3Enzyme0.2ul0.6ul1ul4Buffer(10*)1ul3ul5ul5ddwater Fill the rest with water", "Pipette up and down thoroughly.", "A... |
null | null | null | dx.doi.org/10.17504/protocols.io.rj6d4re | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The main purpose of pregnancy testing as part of a clinical research protocol is to minimize risk to an embryo or fetus from exposure to potentially harmful study interventions. The specific goal of testing may be to prevent exposure completely (by testing prior to any study... | ["{\"blocks\":[{\"key\":\"27egu\",\"text\":\"CTTI Pregnancy Testing in Clinical Trials Project Survey\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[]},{\"key\":\"87v19\",\"text\":\" \",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[]... |
null | null | null | dx.doi.org/10.17504/protocols.io.gpwbvpe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is modified from Wiegand and colleagues protocol<sup>1</sup> to fit the conditions of our experiments. </p>
<p> </p>
<p><sup>1</sup>Wiegand, Irith, Kai Hilpert and Robert E W Hancock (2008). \Agar and broth dilution methods to determine the minimal inhibitory c... | [] |
46,347 | Transformation electroporation | 4 | null | https://www.protocols.io/view/transformation-electroporation-brhjm34n | Elizabeth Fozo | TITLE: Transformation electroporation
AUTHORS: Elizabeth Fozo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Preparation of component cells and their transformation by electroporation</div></div>
[STEPS]
?. [Preparation of component cells]
Inoculate a single colony into appropriate media with anti... | ["[Preparation of component cells]\nInoculate a single colony into appropriate media with antibiotics as needed. Grow overnight at the appropriate temperature and shaking conditions.", "[Preparation of component cells]\nDilute ON culture back to an optical density of 0.01 in the morning in 25 mL of cells for every two ... |
55,814 | Rapid and direct method to extract SARS-CoV-2 RNA from municipal wastewater using the Chemagic™ 360 12-rod head platform | 4 | dx.doi.org/10.17504/protocols.io.b2reqd3e | https://www.protocols.io/view/rapid-and-direct-method-to-extract-sars-cov-2-rna-b2reqd3e | Adrian A Vasquez, Nicholas W West, Azadeh Bahmani, Jeffrey L. Ram | TITLE: Rapid and direct method to extract SARS-CoV-2 RNA from municipal wastewater using the Chemagic™ 360 12-rod head platform
AUTHORS: Adrian A Vasquez, Nicholas W West, Azadeh Bahmani, Jeffrey L. Ram
[DESCRIPTION]
Wastewater based epidemiology (WBE) has emerged as a strategy to identify, locate, predict, and man... | ["Transfer 45 ml45 mL from wastewater sample to 50 ml conical tube.", "Centrifuge the 45 ml wastewater for 15 minutes at 5000 RPM (Thermo Scientific Sorvall ST 16R centrifuge, Waltham, MA).", "Remove 10 ml10 mL from the spun down 50 ml conical tube and transfer to 50 ml conical tube containing master mix of the follo... |
80,767 | Efficacy and safety of statins and ezetimibe in primary prevention of cardiovascular disease in the elderly: A systematic review protocol. | 1 | dx.doi.org/10.17504/protocols.io.4r3l27k7qg1y/v1 | https://www.protocols.io/view/efficacy-and-safety-of-statins-and-ezetimibe-in-pr-cs47wgzn | Fernandez-Gonzalez J | TITLE: Efficacy and safety of statins and ezetimibe in primary prevention of cardiovascular disease in the elderly: A systematic review protocol.
AUTHORS: Fernandez-Gonzalez J
[DESCRIPTION]
Cardiovascular diseases (CVD) are the leading cause of death globally (1). The risk increases with age. Statins and ezetimibe are... | ["[Title] Efficacy and safety of statins and ezetimibe in primary prevention of cardiovascular disease in the elderly: A systematic review protocol.", "[Authors] Fernandez-Gonzalez J1, 2, Irigoyen-Rodriguez I1, Alzueta-Isturiz N2, 3, Echeverría-Gorriti A2, 4,\nLozano C5, Garjon-Parra J2, 4.\n1 Hospital Universitario de... |
90,274 | A. verticillata sampling in San Diego, CA | 4 | null | https://www.protocols.io/view/a-verticillata-sampling-in-san-diego-ca-c4eaytae | Ezavacki, nreyns | TITLE: A. verticillata sampling in San Diego, CA
AUTHORS: Ezavacki, nreyns
[DESCRIPTION]
This is the sampling protocol.
[STEPS]
SECTION: Amathia verticillata collection
1. Three replicate colonies (of low, medium, and high biogenic material) of A. verticillata were collected from the side of the dock by surrounding ... | ["[Amathia verticillata collection] Three replicate colonies (of low, medium, and high biogenic material) of A. verticillata were collected from the side of the dock by surrounding the colony (depending on its size) with a 100 µm, 18 x 42 cm or 10.5 x 20 cm mesh bag", "[Amathia verticillata collection] Place the sample... |
55,888 | SOP for snap-freezing tissues | 4 | dx.doi.org/10.17504/protocols.io.b2tqqemw | https://www.protocols.io/view/sop-for-snap-freezing-tissues-b2tqqemw | Jolet Y Mimpen, Claudia Paul, Lorenzo Ramos-Mucci, Tendon Seed Network, Adam Cribbs, Mathew Baldwin, Sarah Snelling | TITLE: SOP for snap-freezing tissues
AUTHORS: Jolet Y Mimpen, Claudia Paul, Lorenzo Ramos-Mucci, Tendon Seed Network, Adam Cribbs, Mathew Baldwin, Sarah Snelling
[DESCRIPTION]
The collection of (human) tissue is essential for many aspects of biomedical research. In order to maintain tissue quality and achieve re... | ["[Before collection of specimen(s)] Prepare the following items to bring to theatre for tissue collection:\n\n50 mL Falcon tube with media (supplemented with 10% FBS and 1% P/S) [or other appropriate media mixture]; keep the media at 4°C for as long as possible.\nFor each specimen to be collected, get one sterile 30mL... |
83,268 | Polyethylene terephthalic acid deconstruction product analysis by UHPLC-DAD | 1 | dx.doi.org/10.17504/protocols.io.kqdg3xeb7g25/v1 | https://www.protocols.io/view/polyethylene-terephthalic-acid-deconstruction-prod-cvjcw4iw | Hannah M. Alt, Kelsey J. Ramirez, Stefan J. Haugen, William E. Michener, Gregg T. Beckham | TITLE: Polyethylene terephthalic acid deconstruction product analysis by UHPLC-DAD
AUTHORS: Hannah M. Alt, Kelsey J. Ramirez, Stefan J. Haugen, William E. Michener, Gregg T. Beckham
[DESCRIPTION]
This analytical procedure outlines a rapid and accurate method for the quantification of three key PET deconstruction produ... | ["[Mobile Phase Preparation] Mobile Phase A:\na solution of 20 mM phosphoric acid in UPW using the ratio of 1.34 mL of 85% phosphoric acid per 1 L of UPW. Ensure sufficient volume for analysis of all samples and standards.\n\nMobile Phase B:\nMethanol", "[Sample Preparation] Samples must be filtered through a 0.2 µm or... |
14,887 | Transformation of Chemically Competent (Smart) Cells | null | dx.doi.org/10.17504/protocols.io.ssfeebn | null | Moriah Beck, Abby Jurgensmeier | TITLE: Transformation of Chemically Competent (Smart) Cells
AUTHORS: Moriah Beck, Abby Jurgensmeier
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. Remove cells from the –80 °C freezer and place directly into your ice bucket. Thaw on ice for 15 minutes.
?. Add DNA from plasmid to be transformed. For liga... | ["Remove cells from the –80 °C freezer and place directly into your ice bucket. Thaw on ice for 15 minutes.", "Add DNA from plasmid to be transformed. For ligations/PCR products use 10uL of ligation reaction per 50-100uL of cells. For purified plasmid (miniprep), use 1 uL of plasmid per aliquot of cells. Do not mix... |
67,402 | Kerassentials Reviews (Updated 2022) – Is It a Scam or Legit? | 3 | dx.doi.org/10.17504/protocols.io.rm7vzyzm5lx1/v1 | https://www.protocols.io/view/kerassentials-reviews-updated-2022-is-it-a-scam-or-cd3is8ke | Kerassentials Reviews | TITLE: Kerassentials Reviews (Updated 2022) – Is It a Scam or Legit?
AUTHORS: Kerassentials Reviews
[DESCRIPTION]
Kerassentials
[STEPS] | [] |
28,863 | Mesangial Index Quantification | null | dx.doi.org/10.17504/protocols.io.8e7hthn | null | Frank Brosius | TITLE: Mesangial Index Quantification
AUTHORS: Frank Brosius
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">This protocol describes the procedures for quantifying the percent area of the glomerulus that is PAS stained... | ["Using the camera or MetaMorph® software digitize 15 cortical glomeruli per case with a 40 X lens. Glomeruli should be chosen for a similar diameter of maximal size. Save images as uncompressed tiff files.", "Open the glomerulus tiff file in MetaMorph®. Scale the image in such a way that the entire glomerulus can be s... |
54,151 | RCA of Circular Probe | 4 | dx.doi.org/10.17504/protocols.io.by5fpy3n | https://www.protocols.io/view/rca-of-circular-probe-by5fpy3n | Chia-Hsien Shih | TITLE: RCA of Circular Probe
AUTHORS: Chia-Hsien Shih
[DESCRIPTION]
This protocol is to verify that circular probe can conduct RCA reaction.
[STEPS]
SECTION: Preparation
1. Dilute the 1µM Circular probe into 100nM
SECTION: Preparation
1.1. Add 5 µL of 1µM circular probe
SECTION: Preparation
1.2. Add 45 µL of RNase-... | ["[Preparation] Dilute the 1µM Circular probe into 100nM", "[Preparation] Add 5 µL of 1µM circular probe", "[Preparation] Add 45 µL of RNase-free water", "[Preparation] Spin down after vortex", "[Protocol] Add 17.4 µL RNase-free water into a eppendorf", "[Protocol] Add 3 µL of 10X phi29 polymerase reaction buffer", "[P... |
99,197 | Protocol (A): Zebrafish infections into the otic vesicle (2 dpf) | 0 | dx.doi.org/10.17504/protocols.io.j8nlk8kwwl5r/v1 | https://www.protocols.io/view/protocol-a-zebrafish-infections-into-the-otic-vesi-dc452yy6 | Désirée A. Schmitz, Tobias Wechsler, Hongwei Bran Li, Bjoern H. Menze, Rolf Kümmerli | TITLE: Protocol (A): Zebrafish infections into the otic vesicle (2 dpf)
AUTHORS: Désirée A. Schmitz, Tobias Wechsler, Hongwei Bran Li, Bjoern H. Menze, Rolf Kümmerli
[DESCRIPTION]
This protocol details the zebrafish infections into the otic vesicle.
[GUIDELINES]
Table SP1. Media preparation of E3 zebrafish water ... | ["[Part 0: Material preparation] Media: prepare all required media according to Table SP1 (E3 zebrafish water, PTU to avoid pigmentation, pronase for dechorionation, tricaine for anesthetizing).", "[Part 0: Material preparation] Hair loop manipulators (Fig. SP1A): tape (e.g. using 19 mm wide tape) a piece of hair as a ... |
88,429 | Mouse OpenField + ANY-Maze Protocol | 1 | null | https://www.protocols.io/view/mouse-openfield-any-maze-protocol-c2kmycu6 | Sélène Bonnet-Zahedi, Olivier George | TITLE: Mouse OpenField + ANY-Maze Protocol
AUTHORS: Sélène Bonnet-Zahedi, Olivier George
[DESCRIPTION]
OpenField setup and analysis with ANY-Maze for the mouse room. September 2023
[GUIDELINES]
Try not to move the camera too much and not tare the grey tape on the floor.
[STEPS]
SECTION: Setup and Record Experiment
... | ["[Setup and Record Experiment] - Plug the USB cord with orange tape connected to the ceiling camera to the power strip on the ground. This will turn on the camera\n- Slowly and carefully move the apparatus to align with the grey tape on the floor\n\nPLEASE BE CAREFUL NOT TO TARE THE GREY TAPE!\n\n- Set the infrared li... |
87,392 | Isolating enriched fractions of nuclear and cytoplasmic RNAs from Arabidopsis flowers | 4 | dx.doi.org/10.17504/protocols.io.kqdg3x2nqg25/v1 | https://www.protocols.io/view/isolating-enriched-fractions-of-nuclear-and-cytopl-czj8x4rw | Diep R Ganguly, Wil Prall, Susheel Sagar Bhat, Sean Hilgendorf, Brian D Gregory | TITLE: Isolating enriched fractions of nuclear and cytoplasmic RNAs from Arabidopsis flowers
AUTHORS: Diep R Ganguly, Wil Prall, Susheel Sagar Bhat, Sean Hilgendorf, Brian D Gregory
[DESCRIPTION]
This is an adapted protocol to isolate RNA fractions enriched for nuclear and cytosolic RNAs from frozen Arabidopsis flower... | ["[Lyse cells and fraction RNA] Grind frozen Arabidopsis flowers into a fine powder using a pestle. Keep samples frozen in liquid nitrogen until you are ready to add lysis buffer.", "[Lyse cells and fraction RNA] Remove samples from liquid nitrogen and immediately add Lysis Buffer J (200 μL per 20-50 mg tissue).", "[Ly... |
91,894 | Surgery free rat closed head repetitive mild injury model of traumatic brain injury | 1 | dx.doi.org/10.17504/protocols.io.x54v9pokqg3e/v1 | https://www.protocols.io/view/surgery-free-rat-closed-head-repetitive-mild-injur-c5ywy7xe | vedad.delic | TITLE: Surgery free rat closed head repetitive mild injury model of traumatic brain injury
AUTHORS: vedad.delic
[DESCRIPTION]
This is a surgery-free closed head weight drop injury protocol for repetitive mild TBI of adult rats. The model consists, of a guide tube and weight cylinders that deliver an injury to the cal... | ["[Apparatus Setup] Ensure that the TBI platform is stable with pin in the 5th hole from the bottom\n25 cm height.", "[Apparatus Setup] Load weights. If loading multiple weights into the guide tube, load smaller weights first to ensure proper balance.", "[Apparatus Setup] Turn on Isoflurane system with following settin... |
82,628 | In vitro digestion method for Atlantic salmon | 6 | dx.doi.org/10.17504/protocols.io.5jyl8j3b7g2w/v1 | https://www.protocols.io/view/in-vitro-digestion-method-for-atlantic-salmon-cuxcwxiw | Gopika Radhakrishnan, marta Silva, Ikram Belghit | TITLE: In vitro digestion method for Atlantic salmon
AUTHORS: Gopika Radhakrishnan, marta Silva, Ikram Belghit
[DESCRIPTION]
This in vitro digestion method was used to evaluate amino acid solubility of different black soldier fly larvae (BSFL) meals and experimental diets for Atlantic salmon. Three types of insect me... | ["[Extraction of crude salmon enzymes] Due to biological variability, use the viscera from at least 6 fish. The exact number of fish required will depend on the quantity of enzyme needed for the experiment.", "[Extraction of crude salmon enzymes] Feed the fish 40 g of feed 4 hours before collecting tissues (e.g. comme... |
91,486 | Determining the effects of mecamylamine in the mouse striatum using a Conditioned Preference Place (CPP) paradigm | 1 | dx.doi.org/10.17504/protocols.io.e6nvwd2ywlmk/v1 | https://www.protocols.io/view/determining-the-effects-of-mecamylamine-in-the-mou-c5j6y4re | Yan-Feng Zhang, Stephanie J Cragg | TITLE: Determining the effects of mecamylamine in the mouse striatum using a Conditioned Preference Place (CPP) paradigm
AUTHORS: Yan-Feng Zhang, Stephanie J Cragg
[DESCRIPTION]
This protocol is to determine the effects of administrating mecamylamine in the mouse brain striatum using a Conditioned Preference Place (C... | ["[Preparing the mouse for surgery] Anesthetize the mouse in an induction chamber with isoflurane (5% induction; 1.5 - 2% maintenance).", "[Conditioned Place Preference Testing] Place mice in a 40 cm × 40 cm transparent plexiglass arena that is divided into two equal chambers separated by doorway.", "[Conditioned Place... |
27,267 | Preparation of SLiCE Extract | null | dx.doi.org/10.17504/protocols.io.6vbhe2n | null | N.J. Hillson | TITLE: Preparation of SLiCE Extract
AUTHORS: N.J. Hillson
[STEPS]
?. Acquire CelLytic TM B Cell Lysis Reagent (Sigma, B7435).
?. Prepare sufficient chloramphenicol stock and streptomycin stock to produce LB agar plates (10 g/mL streptomycin and 12.5 ug/mL chloramphenicol), 1 L of 2X YT media (10 ug/mL streptomycin), ... | ["Acquire CelLytic TM B Cell Lysis Reagent (Sigma, B7435).", "Prepare sufficient chloramphenicol stock and streptomycin stock to produce LB agar plates (10 g/mL streptomycin and 12.5 ug/mL chloramphenicol), 1 L of 2X YT media (10 ug/mL streptomycin), and LB (10 ug/mL streptomycin and 12.5 ug/mL chloramphenicol).", "Pr... |
104,171 | T cell purification and activation | 0 | dx.doi.org/10.17504/protocols.io.81wgbz431gpk/v3 | https://www.protocols.io/view/t-cell-purification-and-activation-dhyj37un | Moustafa Nouh Elemeery, Salix Boulet, louis-eric.trudeau Trudeau, Nathalie Labrecque | TITLE: T cell purification and activation
AUTHORS: Moustafa Nouh Elemeery, Salix Boulet, louis-eric.trudeau Trudeau, Nathalie Labrecque
[DESCRIPTION]
This protocol details the purification and activation of Mouse Naïve CD8+ T Cell from mouse spleens using a purification kit. The cells are then activated by culturing t... | ["[Purification and activation] Dilute CD3 antibody (145-2C11) (clone KT3 can also be used) to 1 1621 in PBS.", "[Purification and activation] Coat plates with anti-CD3 antibody.", "[Purification and activation] Use 24 well (Sarstedt, cat# 83.1836.500) or 96 well (Sarstedt, cat# 82.1581.001) plates. If these plates are... |
21,762 | Extration of Scapharca broughtonii genomic DNA | null | dx.doi.org/10.17504/protocols.io.zhaf32e | null | Chang-Ming Bai | TITLE: Extration of Scapharca broughtonii genomic DNA
AUTHORS: Chang-Ming Bai
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is used to eliminate excessive polysaccharide in </span><span style = "font-style:italic;">Scapharca broughtonii</span><span> tissues during DNA extractio... | ["Collect 1 mL haemocyte into a 1.5 mL microcentrifuge tube and centrifuge at 1000 g for 10 min at 4℃, then discard the supermatant and resuspend the pellet with 200 μL PBS.", "Add 200 μL Buffer AL* and 20μL Rnase A, mix thoroughly by vortexing and put the tube at room temperature for 3-5 min.\n*: these items were prov... |
107,540 | LRRK2RCKW single molecule kinesin motility assays_2024 | 4 | dx.doi.org/10.17504/protocols.io.5qpvok4dzl4o/v1 | https://www.protocols.io/view/lrrk2rckw-single-molecule-kinesin-motility-assays-dk9u4z6w | John Salogiannis, Katherine Surridge | TITLE: LRRK2RCKW single molecule kinesin motility assays_2024
AUTHORS: John Salogiannis, Katherine Surridge
[DESCRIPTION]
This protocol is about LRRK2RCKW single molecule kinesin motility assays. Forked from dx.doi.org/10.17504/protocols.io.ewov14qykvr2/v1
[BEFORE_START]
Please take notice of the buffer preparation... | ["[Create microscope slides:] Adhere coverslips (Corning) to a microscope slide using double-sided scotch tape, creating 4 channels per slide.", "[Prepare LRRK2:] Prepare a 1 micromolar (µM) solution of LRRK2RCKW in a cold LRRK2 buffer. Centrifuge through a 0.1 μm PVDF filter to remove aggregates. Calculate the new eff... |
68,574 | Transcardial perfusion of mouse tissues | 1 | dx.doi.org/10.17504/protocols.io.rm7vzywnxlx1/v1 | https://www.protocols.io/view/transcardial-perfusion-of-mouse-tissues-ce76thre | Rain Kwan, Courtney Wright, Louise Cottle, Alejandra Rangel, Asheeta Prasad | TITLE: Transcardial perfusion of mouse tissues
AUTHORS: Rain Kwan, Courtney Wright, Louise Cottle, Alejandra Rangel, Asheeta Prasad
[DESCRIPTION]
This protocol describes how to perform transcardial perfusion and fixation of mouse brain tissues in preparation for immunohistochemical staining or histology. This process ... | ["[Experimental Outline] Attach a needle into the peristaltic pump tubing and prime the tubing by filling with Room temperature 1x PBS.", "[Experimental Outline] Lethally overdose mice with sodium pentobarbitone (100 mg/kg) via intraperitoneal injection.", "[Experimental Outline] Working in a fume hood, make a lateral ... |
68,490 | Expression and purification of recombinant UvsY protein | 1 | dx.doi.org/10.17504/protocols.io.36wgq7xwkvk5/v1 | https://www.protocols.io/view/expression-and-purification-of-recombinant-uvsy-pr-ce5itg4e | lucero.merino.c, lucero.mascaro.r | TITLE: Expression and purification of recombinant UvsY protein
AUTHORS: lucero.merino.c, lucero.mascaro.r
[DESCRIPTION]
The uvsY is a enzyme that is part for an isothermal DNA amplification based on the recombination process, the RPA reaction.
RPA uses 4 enzymes: UvsX, UvsY, Bsu and Gp32. It's an isothermal amplifica... | ["[DAY1: Transformation of competent cells] Quantify the plasmid containing the UvsY gene and determine the volume that contains 100 ng of the plasmid.", "[DAY1: Transformation of competent cells] Add the resuspension to an LB agar plate previously supplemented with 0.05 mg/mL and spread the recently transformed cells... |
33,455 | SOP Appendix for Lymph Node | null | dx.doi.org/10.17504/protocols.io.bcwpixdn | null | Marda Jorgensen | TITLE: SOP Appendix for Lymph Node
AUTHORS: Marda Jorgensen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is the appendix for lymph nodes.</div></div>
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ug9etz6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
SECTION: Recovering skeletons
?.
SECTION: Rinsing
?.
SECTION: Cleaning
?.
SECTION: Cleaning
?.
SECTION: Diluting
?.
SECTION: Rinsing
?.
SECTION: Preparing for imaging
?.
SECTION: Drying
?.
SECTION: Imaging
?. | ["[Recovering skeletons] After DNA extraction, recover skeleton from the eluted pellet under binoculars or inverted microscope. \n\nNote: During DNA extraction: dilute waste from the extraction procedure (i.e. pellet debris, containing the skeleton) in milliQ water and store skeletons at -20°C.\n\n\nProtocol adapted fr... |
61,938 | PROTAC diastereomer Design（negative control） | 6 | dx.doi.org/10.17504/protocols.io.e6nvwk8o7vmk/v1 | https://www.protocols.io/view/protac-diastereomer-design-negative-control-b8qsrvwe | boc.protac | TITLE: PROTAC diastereomer Design（negative control）
AUTHORS: boc.protac
[DESCRIPTION]
Diastereomers are stereoisomers in which molecules have two or more chiral centers and the relationship between molecules is not mirrored. In PROTAC drug development, in order to evaluate the pharmacokinetics of a single diastereom... | [] |
79,075 | Acid Wash Protocol (Alegado Lab) | 1 | dx.doi.org/10.17504/protocols.io.14egn213qg5d/v1 | https://www.protocols.io/view/acid-wash-protocol-alegado-lab-crgbv3sn | Ashleyolguin | TITLE: Acid Wash Protocol (Alegado Lab)
AUTHORS: Ashleyolguin
[DESCRIPTION]
This protocol guides lab members through the acid wash process
[STEPS]
SECTION: Pre-requisites (BEFORE proceeding to acid washing)
1. Check acid solution levels
--> Note: If it's only 1/3 full, make new solution, you will use almost all of... | ["[Pre-requisites (BEFORE proceeding to acid washing)] Check acid solution levels\n\n --> Note: If it's only 1/3 full, make new solution, you will use almost all of the current stock.", "[Pre-requisites (BEFORE proceeding to acid washing)] Gather bottles to be washed and take over to acid washing lab", "[Pre-requisites... |
null | null | null | dx.doi.org/10.17504/protocols.io.fenbjde | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>From http://depts.washington.edu/younglab/yeastprotocols%28htm%29/RNA.htm</p>
[STEPS]
?. | [] |
107,698 | Fasting Review | 0 | dx.doi.org/10.17504/protocols.io.rm7vzjrw5lx1/v1 | https://www.protocols.io/view/fasting-review-dmes43ee | Ana Priscila Eleodoro Rosa, João Paulo Souza, Vick Nogueira Pileggi, Fernando Bellissimo-Rodrigues, Leonardo Moscovici | TITLE: Fasting Review
AUTHORS: Ana Priscila Eleodoro Rosa, João Paulo Souza, Vick Nogueira Pileggi, Fernando Bellissimo-Rodrigues, Leonardo Moscovici
[DESCRIPTION]
A structured, overarching, systematic approach to the body of evidence on the
effects of fasting in human health is lacking. This systematic overview of
li... | [] |
105,002 | URMC TriState SenNet TMC Mouse Sacrifice and Organ Harvest | 0 | dx.doi.org/10.17504/protocols.io.rm7vzj2j8lx1/v1 | https://www.protocols.io/view/urmc-tristate-sennet-tmc-mouse-sacrifice-and-organ-disi4ece | Gagandeep Kaur, Irfan Rahman | TITLE: URMC TriState SenNet TMC Mouse Sacrifice and Organ Harvest
AUTHORS: Gagandeep Kaur, Irfan Rahman
[DESCRIPTION]
This protocol outlines the method used to sacrifice and harvest the mouse lung tissue to perform downstream analyses for the TriState SenNet TMC Biospecimen Core at the University of Rochester, as part... | ["Sodium Pentobarbitol ( 60-90 mg/kg of body weight) was administered intraperitoneally to anaesthetize the mice prior to organ harvest.", "After 5 min of drug administration, the animal response was assessed by pinching the mouse's foot with forceps and observing the withdrawal response/pedal reflex.", "Upon successfu... |
69,141 | High-risk postoperative opioid prescribing among chronic opioid users with Medicaid insurance | 1 | dx.doi.org/10.17504/protocols.io.3byl4jeeolo5/v1 | https://www.protocols.io/view/high-risk-postoperative-opioid-prescribing-among-c-cfrvtm66 | Limi Sharif, Vidhya Gunaseelan, Pooja Lagisetty, Mark Bicket, Jenn Waljee, Michael Englesbe, Chad Brummett | TITLE: High-risk postoperative opioid prescribing among chronic opioid users with Medicaid insurance
AUTHORS: Limi Sharif, Vidhya Gunaseelan, Pooja Lagisetty, Mark Bicket, Jenn Waljee, Michael Englesbe, Chad Brummett
[DESCRIPTION]
The objective of this study is to assess the differences in high-risk prescribing among ... | ["[Brief rationale and hypothesis] Patients with chronic opioid use experience breakdowns in transitions of care following surgery; however, it is unclear what disparities exist in this process for patients on Medicaid when compared to patients with commercial insurance.\n\nThe key research question for this study is w... |
50,419 | BioRad Trans-Blot Turbo: fast set-up with own materials | 4 | dx.doi.org/10.17504/protocols.io.bvgtn3wn | https://www.protocols.io/view/biorad-trans-blot-turbo-fast-set-up-with-own-mater-bvgtn3wn | Karla LH Feijs | TITLE: BioRad Trans-Blot Turbo: fast set-up with own materials
AUTHORS: Karla LH Feijs
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is our labs' fast protocol for BioRad Trans-Blot Turbo with our own materials. This works well for many applications, however, for high molecular weight protein... | ["Prepare all materials, such as transfer buffer, nitrocellulose membrane and WYPEALL cut to the size of the gel. Run a standard SDS-PAGE.", "Soak the gel in transfer buffer for 10 minutes. In meantime, prepare a stack of 6 WYPEALL papers on the bottom cassette and add the nitrocellulose membrane on top.", "Place the g... |
97,660 | Multiplex Labeling with Tyramide Fluorophores (Free-Floating Tissues)-Killinger Lab 2024 | 0 | dx.doi.org/10.17504/protocols.io.yxmvme7zng3p/v1 | https://www.protocols.io/view/multiplex-labeling-with-tyramide-fluorophores-free-dbk42kyw | Bryan Killinger, Solji_G_Choi, Tyler_Tittle | TITLE: Multiplex Labeling with Tyramide Fluorophores (Free-Floating Tissues)-Killinger Lab 2024
AUTHORS: Bryan Killinger, Solji_G_Choi, Tyler_Tittle
[DESCRIPTION]
This protocol details the multiplex labeling of free-floating tissues using tyramide fluorophores in the killinger lab (2024).
[STEPS]
SECTION: Day 1:
1. W... | ["[Day 1:] Wash free-floating tissue (3 x 10 minutes) in dilution media (DM).", "[Day 1:] Heat water bath 90 min before the antigen retrieval step.\n\nHuman samples: 90 °C -95 °C\nMouse samples: 80 °C -85 °C", "[Day 1:] Place the dish containing sodium citrate buffer in the water bath and heat it for 10 min.\n\na.\tSod... |
28,231 | Measurement of Left Ventricular Performance in Langendorff Perfused Mouse Hearts | null | dx.doi.org/10.17504/protocols.io.7tfhnjn | null | E. Dale Abel | TITLE: Measurement of Left Ventricular Performance in Langendorff Perfused Mouse Hearts
AUTHORS: E. Dale Abel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">This protocol describes the procedure used by the DiaComp for... | ["[Langendorff Heart Perfusion Protocol]\nHearts are isolated and the aorta is cannulated using a 20g steel cannula. Hearts are perfused at a constant pressure of 60 mmHg by an aortic cannula delivering warm (37°C) Krebs buffer containing (in mM) 118 NaCl, 4.7 KCl, 25 NaHCO³, 1.2 MgSO4, 1.2 KH2PO4, 2 CaCl² gassed with... |
87,921 | JMN-MSMP Volumetric Muscle Loss Surgery | 1 | null | https://www.protocols.io/view/jmn-msmp-volumetric-muscle-loss-surgery-cz4rx8v6 | ccherry | TITLE: JMN-MSMP Volumetric Muscle Loss Surgery
AUTHORS: ccherry
[DESCRIPTION]
VML Surgery
[STEPS]
1. Disinfect all surfaces and anesthetic equipment (induction chamber, nose cone) with Vimoba (Quip Laboratories VIMTAB).
2. Prepare sterile surgical area and a separate surgical prep area (shaving, Rimadyl injection). A... | ["Disinfect all surfaces and anesthetic equipment (induction chamber, nose cone) with Vimoba (Quip Laboratories VIMTAB).", "Prepare sterile surgical area and a separate surgical prep area (shaving, Rimadyl injection). Anesthesia should be available in both areas.", "Anesthetize the mouse. The following settings should ... |
30,840 | Propidium Iodide Cell Cycle Staining Protocol | null | dx.doi.org/10.17504/protocols.io.bacyiaxw | null | Sam Li | TITLE: Propidium Iodide Cell Cycle Staining Protocol
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. Harvest cells in the appropriate manner and wash in PBS.
?. Fix in cold 70% ethanol (do not make this with PBS as it can cause protein precipitation during fixation). Add dropwise to the cel... | ["Harvest cells in the appropriate manner and wash in PBS.", "Fix in cold 70% ethanol (do not make this with PBS as it can cause protein precipitation during fixation). Add dropwise to the cell pellet while vortexing. This should ensure fixation of all cells and minimize clumping.", "Fix for at least 30 minutes at 4°C.... |
99,381 | Protocolo de coleta de amostras para eDNA metabarcoding usando filtros Sterivex - LGC PUC Minas | 0 | dx.doi.org/10.17504/protocols.io.81wgbz623gpk/v1 | https://www.protocols.io/view/protocolo-de-coleta-de-amostras-para-edna-metabarc-ddav22e6 | Gabriel Antônio Mendes, Guilherme Costa Berger, Heron O Hilário, Daniel Cardoso de Carvalho | TITLE: Protocolo de coleta de amostras para eDNA metabarcoding usando filtros Sterivex - LGC PUC Minas
AUTHORS: Gabriel Antônio Mendes, Guilherme Costa Berger, Heron O Hilário, Daniel Cardoso de Carvalho
[DESCRIPTION]
O objetivo deste protocolo é orientar sobre a coleta de amostras de água para empregar a técnica de D... | ["[Preparação] Primeiramente, certifique-se de realizar a filtragem em um ambiente aberto\ne plano. Se possível, utilize uma superfície esterilizada para apoiar o kit de coleta e\nseus componentes durante os procedimentos. Após a filtragem e armazenamento das\namostras, lembre-se de recolher os descartáveis para efetua... |
19,505 | Dynamic distribution of gallbladder microbiota in rabbit at different ages and health states Short title: Dynamic distribution of gallbladder microbiota in rabbits | null | dx.doi.org/10.17504/protocols.io.xarfid6 | null | Yawei Xing | TITLE: Dynamic distribution of gallbladder microbiota in rabbit at different ages and health states Short title: Dynamic distribution of gallbladder microbiota in rabbits
AUTHORS: Yawei Xing
[STEPS]
?. Healthy, male New Zealand White rabbits (Medical Experimental Animal Center of Hunan Province, China) (n=12) were use... | ["Healthy, male New Zealand White rabbits (Medical Experimental Animal Center of Hunan Province, China) (n=12) were used in this study. Rabbits were weaned at 4 weeks of age. Five of them were young rabbits (3 weeks old) before weaning. The other adult rabbits (n=7, 18 weeks old) were fed regular rabbit chow. All rabbi... |
66,353 | Iron Warrior Testo Thrust Reviews | 1 | dx.doi.org/10.17504/protocols.io.8epv59q95g1b/v1 | https://www.protocols.io/view/iron-warrior-testo-thrust-reviews-cc2rsyd6 | condorcbdbit | TITLE: Iron Warrior Testo Thrust Reviews
AUTHORS: condorcbdbit
[DESCRIPTION]
Iron Warrior Testo Thrust Pills are here to assist you with getting huge in bed. What's more, they can assist you with having an enormously extraordinary exhibition, as well! In the event that you're not feeling so hot in the room, this can... | [] |
68,810 | Growth Curve Stress Test (Instructor Protocol) | 4 | null | https://www.protocols.io/view/growth-curve-stress-test-instructor-protocol-cffitjke | Brian Teague | TITLE: Growth Curve Stress Test (Instructor Protocol)
AUTHORS: Brian Teague
[DESCRIPTION]
This is the instructor protocol for
[STEPS]
SECTION: Prepare 2x synthetic media
1. Put 200 mLof deionized water in a 250 ml bottle. Then add:
0.855 g
0.335 g
2.5 g
5 mL 100X uracil solution (2 mg/mL )
5 mL 100X l... | ["[Prepare 2x synthetic media] Put 200 mLof deionized water in a 250 ml bottle. Then add:\n0.855 g \n0.335 g \n2.5 g \n5 mL 100X uracil solution (2 mg/mL )\n5 mL 100X leucine solution (12 mg/mL )", "[Prepare 2x synthetic media] Autoclave 121 °C for 30 min", "[Prepare the yeast cultures] The afternoon or evening... |
null | null | null | dx.doi.org/10.17504/protocols.io.pbhdij6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>For the past several decades, due to technical limitations, the field of transcriptomics has focused on population-level measurements that can mask significant differences between individual cells. With the advent of single-cell RNA-Seq, it is now possible to profile the resp... | [] |
94,601 | Very low-density lipoprotein receptor (VLDLR)-C-tag purification from HEK293E cells | 1 | dx.doi.org/10.17504/protocols.io.j8nlkoqw1v5r/v1 | https://www.protocols.io/view/very-low-density-lipoprotein-receptor-vldlr-c-tag-c8mhzu36 | Andreas Bracher, Patricia Yuste-Checa, F Ulrich Hartl | TITLE: Very low-density lipoprotein receptor (VLDLR)-C-tag purification from HEK293E cells
AUTHORS: Andreas Bracher, Patricia Yuste-Checa, F Ulrich Hartl
[DESCRIPTION]
This protocol details how to purify recombinant Very low-density lipoprotein receptor (VLDLR)-C-tag protein from HEK293E cells.
[STEPS]
SECTION: VLDLR... | ["[VLDLR-C-tag expression] Express VLDLR-C-tag in HEK293E cells cultured in FreeStyle 293 Expression Medium for 5760 min", "[VLDLR-C-tag expression] Centrifuge culture and keep conditioned medium.", "[VLDLR-C-tag expression] Dialyze 300 mL conditioned medium against 10 L Binding buffer.", "[CaptureSelect C-tag affini... |
null | null | null | dx.doi.org/10.17504/protocols.io.qhwdt7e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is short tutorial on one way to calculate dN/dS ratios between pairs of protein-coding nucleic acid sequences using codeml in the PAML package.</p>
<p> </p>
<p>Code is intended for use on an Ubuntu 16.04 LTS OS, but it may work on other Unix or Unix-like systems.</p>
<p>... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.e6mbhc6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is a protocol for the Isolation of Genomic DNA : PURIFICATION OF DNA FROM AMNIOTIC FLUID</p>
<p>(Cat. # <a href="http://www.gbiosciences.com/ResearchProducts/XIT_Blood.aspx" target="_blank">786‐294, 786‐295, 786‐296</a>)</p>
[BEFORE_START]
<p>Preheat a water‐bath or hea... | [] |
32,256 | Levodopa kinetic-dynamic test | null | dx.doi.org/10.17504/protocols.io.bbq8imzw | null | Manuela Contin | TITLE: Levodopa kinetic-dynamic test
AUTHORS: Manuela Contin
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;"> Levodopa oral test </span></div><div class = "text-block">Administration of a subacutest dose of levodopa (100 mg) plus benserazide (25 mg) or carbidopa (2... | ["Blood samplings are drawn by an indwelling catheter before levodopa dosing, at 15-min intervals for the first 90 min, then half-hourly, up to 3 hours after dosing.", "Blood specimens are transferred into heparinized tubes and immediately centrifuged at 1500g for 10 minutes at 4°C. Plasma samples are stored at −80°C u... |
62,250 | Pure Strength CBD Gummies 2022! Is It Really Work For Reduce Anxiety, Pain? | 3 | dx.doi.org/10.17504/protocols.io.rm7vzyonrlx1/v1 | https://www.protocols.io/view/pure-strength-cbd-gummies-2022-is-it-really-work-f-b82iryce | pure strength cbd gummies | TITLE: Pure Strength CBD Gummies 2022! Is It Really Work For Reduce Anxiety, Pain?
AUTHORS: pure strength cbd gummies
[DESCRIPTION]
pure strength cbd gummies
[STEPS] | [] |
93,857 | Concentration and nucleic acid extraction of viruses from wastewater influent | 4 | dx.doi.org/10.17504/protocols.io.j8nlko1rwv5r/v2 | https://www.protocols.io/view/concentration-and-nucleic-acid-extraction-of-virus-c7v9zn96 | Ari N Machtinger, Olivia S Hershey, William J Bradshaw, Daniel P Rice, Michael R McLaren | TITLE: Concentration and nucleic acid extraction of viruses from wastewater influent
AUTHORS: Ari N Machtinger, Olivia S Hershey, William J Bradshaw, Daniel P Rice, Michael R McLaren
[DESCRIPTION]
This protocol details our workflow for performing concentration and total nucleic acid extraction from wastewater influen... | ["[Part 1: Influent Handling, Dissociation, Centrifugation, Filtration] Add 400 µL of 10 % (v/v) Tween 20 stock solution to each centrifuge tube for a final concentration of 0.1 % (v/v) Tween 20.", "[Part 1: Influent Handling, Dissociation, Centrifugation, Filtration] Transfer influent sample (within secondary containe... |
null | null | null | dx.doi.org/10.17504/protocols.io.c45yy5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is for pSerine and pThreonine western blotting (optimized for detecting phospho FMRP protein after IP)</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?. | [] |
91,525 | Deepwell Reusual Protocol | 1 | dx.doi.org/10.17504/protocols.io.j8nlko2x6v5r/v1 | https://www.protocols.io/view/deepwell-reusual-protocol-c5mdy426 | Morris Jack | TITLE: Deepwell Reusual Protocol
AUTHORS: Morris Jack
[DESCRIPTION]
This is a protocol to reuse deepwells for sustainability practices
[STEPS]
SECTION: Growing cultures in a deep well
1. Cover a deep well with two layers of aluminium foil and tape the front and back to hold it securely. The tape also turns the alumi... | ["[Growing cultures in a deep well] Cover a deep well with two layers of aluminium foil and tape the front and back to hold it securely. The tape also turns the aluminium foil into a lid for the deep well by temporarily peeling off the front tape.", "[Growing cultures in a deep well] Autoclave at 120C for 20min. After ... |
81,497 | Commercial MIBI Walkthrough: Protocol & Instructions | 5 | null | https://www.protocols.click/view/commercial-mibi-walkthrough-protocol-amp-instructi-cttzwnp6 | Bryan Cannon, Christine Camacho | TITLE: Commercial MIBI Walkthrough: Protocol & Instructions
AUTHORS: Bryan Cannon, Christine Camacho
[DESCRIPTION]
This is the summary protocol for operating a commercial MIBI in the Bendall & Angelo Labs.
Will be updated as new internal and external features are adopted.
[STEPS]
SECTION: Pre-check
4. Unless acti... | ["[Pre-check] Unless actively navigating your tissue or slide, make sure to keep the MIBI Control in STANDBY mode (not SED or SPOT)", "[Pre-check] Ensure the machine you’re working on (P9, M13, M16) is currently UP on the machine status sheet and slack channel #mibi_instrument_status.", "[Pre-check] NOTE: If you encoun... |
49,031 | DoiClassesOfErrors | 5 | dx.doi.org/10.17504/protocols.io.bt5fnq3n | https://www.protocols.io/view/doiclassesoferrors-bt5fnq3n | Ricarda Boente, Deniz Tural, Cristian Santini, Arcangelo Massari | TITLE: DoiClassesOfErrors
AUTHORS: Ricarda Boente, Deniz Tural, Cristian Santini, Arcangelo Massari
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The purpose of this protocol is to describe an automated process to repair invalid DOIs. In particular, four classes of errors are addressed: previously... | ["[Checking the DOI names' invalidity]\nFirst, we check for each cited DOI if it is factually invalid. For this purpose, the DOI Proxy is used (https://www.doi.org/factsheets/DOIProxy.html): if the status code corresponding to that specific DOI is different from 1, it means that it is not valid; otherwise, that DOI ha... |
107,165 | ChAT and human alpha-synuclein immunofluorescence staining | 1 | dx.doi.org/10.17504/protocols.io.3byl49y2jgo5/v1 | https://www.protocols.io/view/chat-and-human-alpha-synuclein-immunofluorescence-dkv54w86 | Pietro La Vitola | TITLE: ChAT and human alpha-synuclein immunofluorescence staining
AUTHORS: Pietro La Vitola
[DESCRIPTION]
This protocol is designed for detecting choline acetyltransferase (ChAT) using the Millipore AB144P (RRID:AB_2079751) and human alpha-synuclein (Abcam, RRID:AB_2537217, MJFR1). Tissues stained with this protocol i... | ["[ChAT and human alpha-synuclein immunofluorescence staining] Wash tissue slices in tris-buffer saline (TBS: 0.05M Trizma base and 0.15M NaCl; pH: 7.6) for 10 minutes. Repeat x3.", "[ChAT and human alpha-synuclein immunofluorescence staining] Incubate in blocking buffer (5% donkey serum, 2% BSA, 0.5% triton X-100 in T... |
null | null | null | dx.doi.org/10.17504/protocols.io.jm5ck86 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Soil- and sensor specific calibration of Sentek EnviroSCAN and ML3 sensors for the Lonzée experimental site.</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
108,399 | AAV-Zombie on tissue sections | 0 | dx.doi.org/10.17504/protocols.io.14egn6k7yl5d/v1 | https://www.protocols.io/view/aav-zombie-on-tissue-sections-dm4p48vn | Gerard Michael Coughlin | TITLE: AAV-Zombie on tissue sections
AUTHORS: Gerard Michael Coughlin
[DESCRIPTION]
Detection of AAV genomes in situ can facilitate understanding of AAV transduction and processing. This protocol enables spatial detection of AAV genomes and concatemers in tissue and is based on the Zombie method published in Askary et... | ["[Reagent set up] General note on reagents and consumables", "[Sample preparation] On day of tissue harvest, prepare work area. In addition to tools and equipment for transcardial perfusion and tissue dissection, you will need:\n\nice-cold 1x PBS\nclean 10 cm petri dishes\nice\ntissue embedding molds\nO.C.T. compound\... |
null | null | null | dx.doi.org/10.17504/protocols.io.e2zbgf6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Note: If the percentage of CD45+ cells in your sample is less than 50%, please follow Protocol A. If it is higher </strong></p>
<p><strong>than 50% then please follow protocol B.</strong></p>
<p> </p>
<p>The cells targeted by the Nanobeads are either selected or deple... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.qg4dtyw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The Internal Transcribed Spacer 2 (ITS2) rRNA gene is a commonly targeted genetic marker to assess diversity of <em>Symbiodinium</em>, a dinoflagellate genus of algal endosymbionts that is pervasively associated with marine invertebrates, and notably reef-building corals. Her... | [] |
73,935 | Wisecaver Lab DNAzol-based extraction of high molecular weight DNA from photosynthetic sea slugs | 4 | dx.doi.org/10.17504/protocols.io.n92ldprrnl5b/v1 | https://www.protocols.io/view/wisecaver-lab-dnazol-based-extraction-of-high-mole-ckfputmn | Jennifer H Wisecaver, Raeya Ogas | TITLE: Wisecaver Lab DNAzol-based extraction of high molecular weight DNA from photosynthetic sea slugs
AUTHORS: Jennifer H Wisecaver, Raeya Ogas
[DESCRIPTION]
Protocol for DNAzol-based extraction of high molecular weight DNA from photosynthetic sea slugs. This streamlined protocol takes less time compared to the lab'... | ["[Homogenization and DNA extraction] Add 300 µL DNAzol. Pipet up and down to mix and transfer to a 1.5 mL centrifuge tube.", "[Homogenization and DNA extraction] Add 5 µL RNAse A. Make sure the cap is closed securely, and mix well by vigorously shaking the tube for 15 s.", "[Homogenization and DNA extraction] Incubate... |
52,640 | TGen North high throughput SARS-CoV-2 tiled amplicon sequencing | 4 | dx.doi.org/10.17504/protocols.io.bxm8pk9w | https://www.protocols.io/view/tgen-north-high-throughput-sars-cov-2-tiled-amplic-bxm8pk9w | Heather Centner, Ashlyn Pfeiffer, Tporter , Ronuck Patel, Andrew Goedderz, Timothy McDaniel, Elizabeth Driebe, Dave Engelthaler | TITLE: TGen North high throughput SARS-CoV-2 tiled amplicon sequencing
AUTHORS: Heather Centner, Ashlyn Pfeiffer, Tporter , Ronuck Patel, Andrew Goedderz, Timothy McDaniel, Elizabeth Driebe, Dave Engelthaler
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Our goal for this project was to incorporate... | ["[Sample selection]\nVerified specimen typesKnown SARS-CoV-2 positive clinical specimens, ≥50uL volume (ideally ≥500uL)NP swabs in sterile saline or viral transport mediaAnterior nasal swabs in sterile saline or vital transport mediaSalivaRemnant swabs from rapid antigen test platforms, suspended in sterile saline or ... |
21,687 | Abeoforma whisleri transient transfection protocol | null | dx.doi.org/10.17504/protocols.io.zexf3fn | null | Elena Casacuberta, Aleksandra Kozyczkowska, Sebastián Najle | TITLE: Abeoforma whisleri transient transfection protocol
AUTHORS: Elena Casacuberta, Aleksandra Kozyczkowska, Sebastián Najle
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a protocol for transient transfection of the Icthyosporean Abeoforma whisleri. This protocol has an efficiency of 1-2... | ["[Pre-Transfection]\nCount A.whisleri cells from a culture 1 to 2 weeks old grown in Marine Broth (MB) medium at 13 degrees.", "[Pre-Transfection]\nTake 2 x 105 cells/per transfection condition, and spin them down at 2000g for 5 min.", "[Pre-Transfection]\nDiscard medium and gently resuspend cells in sterile 1xPBS and... |
51,821 | Colorimetric determination of urea | 6 | dx.doi.org/10.17504/protocols.io.bwumpeu6 | https://www.protocols.io/view/colorimetric-determination-of-urea-bwumpeu6 | noah.langenfeld , Laurenpayne , Bruce Bugbee | TITLE: Colorimetric determination of urea
AUTHORS: noah.langenfeld , Laurenpayne , Bruce Bugbee
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol measures the absorbance of urea in solution in complexation with diacetyl monoxomie at 520 nm and is linearly proportional to concentration up... | ["[Mixed Acid Reagent Preparation]\nDissolve ferric chloride in deionized water in a 250 mL volumetric flask.\n2.5 mg\n45 mL", "[Mixed Acid Reagent Preparation]\nAdd phosphoric acid.\n80 µl", "[Mixed Acid Reagent Preparation]\nPrepare sulfuric acid by diluting concentrated sulfuric acid up to with deionized wat... |
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