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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60,896 | Balance beam assay to detect motor phenotypes in mice | 4 | dx.doi.org/10.17504/protocols.io.bp2l618edvqe/v1 | https://www.protocols.io/view/balance-beam-assay-to-detect-motor-phenotypes-in-m-b7p8rmrw | William Hancock-Cerutti, Marianna Leonzino, Pietro De Camilli | TITLE: Balance beam assay to detect motor phenotypes in mice
AUTHORS: William Hancock-Cerutti, Marianna Leonzino, Pietro De Camilli
[DESCRIPTION]
This protocol describes an assay to detect motor deficits in mice by testing their ability to traverse a thin dowel between towers.
[STEPS] | [] |
64,425 | Pellamore - 2022 Price, Side Effects And More Details | 3 | dx.doi.org/10.17504/protocols.io.j8nlkkrqdl5r/v1 | https://www.protocols.io/view/pellamore-2022-price-side-effects-and-more-details-ca6hshb6 | fluxactive | TITLE: Pellamore - 2022 Price, Side Effects And More Details
AUTHORS: fluxactive
[DESCRIPTION]
MUST SEE: (SPECIAL SAVINGS) Click Here to Get Pellamore Cream Canada For an Exclusive Discounted Price!
[STEPS] | [] |
71,787 | Immunostaining on Paraffin Sections of Fly Heads | 4 | dx.doi.org/10.17504/protocols.io.81wgby61nvpk/v2 | https://www.protocols.io/view/immunostaining-on-paraffin-sections-of-fly-heads-cicjuaun | Mel Feany | TITLE: Immunostaining on Paraffin Sections of Fly Heads
AUTHORS: Mel Feany
[DESCRIPTION]
This protocol describes how to perform immunostaining on paraffin sections of fly heads.
[STEPS]
1. Fix fly heads overnight in 4% formalin.
5. Microwave slides in 10 millimolar (mM) sodium citrate for 15 min.
Cool 20 min .
Stoc... | ["Fix fly heads overnight in 4% formalin.", "Microwave slides in 10 millimolar (mM) sodium citrate for 15 min. \nCool 20 min .\n\nStock: 100 millimolar (mM) sodium citrate, pH 6.0\nUse at least 1 L of citrate solution in large glass box to avoid drying.", "Block in PBST (PBS with 0.3% Triton) with 2% dry milk for 30 ... |
64,461 | Eagle Hemp CBD Gummies - It Really Works And Exists? | 3 | dx.doi.org/10.17504/protocols.io.dm6gpbqpplzp/v1 | https://www.protocols.io/view/eagle-hemp-cbd-gummies-it-really-works-and-exists-ca7mshk6 | Eagle Hemp CBD Gummies | TITLE: Eagle Hemp CBD Gummies - It Really Works And Exists?
AUTHORS: Eagle Hemp CBD Gummies
[DESCRIPTION]
https://www.mercurynews.com/2022/03/29/eagle-hemp-cbd-gummies-reviews-website-scam-2022-eagle-hemp-cbd-gummies-shark-tank-fact-check/
[STEPS] | [] |
17,229 | Callichthyidae (Ostariophysi: Siluriformes) dissection protocol | null | dx.doi.org/10.17504/protocols.io.u3meyk6 | null | Karina Carvalho F. Ferreira, Marcelo Ribeiro de Britto | TITLE: Callichthyidae (Ostariophysi: Siluriformes) dissection protocol
AUTHORS: Karina Carvalho F. Ferreira, Marcelo Ribeiro de Britto
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol shows how to dissect callichthyid fishes without losing importante anatomical information about the rel... | ["Continue the incision in caudal direction to the limit of the celomathic cavity, by passing the pelvic girdle and ending in the point immediately posterior to the pelvic girdle.", "Remove adipose tissue with the aidof the thin point fórceps in order to better visualize internal organs.", "Release the organs from the ... |
71,705 | Protocol of An Indirect Comparison of Efficacy including Histologic Assessment and Safety in Biologic Agents in Ulcerative Colitis: Systematic Review and Network Meta-analysis | 1 | dx.doi.org/10.17504/protocols.io.q26g7y8dkgwz/v2 | https://www.protocols.io/view/protocol-of-an-indirect-comparison-of-efficacy-inc-ch9zt976 | ksun.chae, Yeon Sook Seo, Yun Mi Yu, Min Jung Chang, Junjeong Choi | TITLE: Protocol of An Indirect Comparison of Efficacy including Histologic Assessment and Safety in Biologic Agents in Ulcerative Colitis: Systematic Review and Network Meta-analysis
AUTHORS: ksun.chae, Yeon Sook Seo, Yun Mi Yu, Min Jung Chang, Junjeong Choi
[DESCRIPTION]
Currently, treatment targets of ulcerative col... | ["[Backgroud] Currently, treatment targets of ulcerative colitis (UC) are defined as clinical remission and endoscopic improvement. However, there is debate over whether histologic target should also be considered as an additional treatment target. Multiple studies indicate histologic target as an important prognostic ... |
82,012 | Semi-automated extraction of information on open datasets mentioned in articles | 5 | dx.doi.org/10.17504/protocols.io.q26g74p39gwz/v2 | https://www.protocols.io/view/semi-automated-extraction-of-information-on-open-d-cub4wsqw | Anastasiia Iarkaeva, Evgeny Bobrov, Jan Taubitz, Benjamin Gregory Carlisle, Nico Riedel | TITLE: Semi-automated extraction of information on open datasets mentioned in articles
AUTHORS: Anastasiia Iarkaeva, Evgeny Bobrov, Jan Taubitz, Benjamin Gregory Carlisle, Nico Riedel
[DESCRIPTION]
This protocol describes how to determine for a body of research articles, whether underlying datasets have been openly s... | ["[Automated validation of publications for statements indicating Open Data using ODDPub] Collate a list of article identifiers\nBegin with a list of articles identifiers (usually DOIs), for which you want to assess the openness of the datasets underlying these articles. These idetifiers can typically be obtained by se... |
81,034 | Human FFPE Liver Pathology Assessment -- University of Minnesota Human TMC | 1 | dx.doi.org/10.17504/protocols.io.6qpvr45wpgmk/v1 | https://www.protocols.io/view/human-ffpe-liver-pathology-assessment-university-o-ctdiwi4e | Oyedele Adeyi, Andrew Nelson, Beth Thompson, Laura Niedernhofer | TITLE: Human FFPE Liver Pathology Assessment -- University of Minnesota Human TMC
AUTHORS: Oyedele Adeyi, Andrew Nelson, Beth Thompson, Laura Niedernhofer
[DESCRIPTION]
Purpose: Describe the parameters evaluated per FFPE human liver sample received/obtained for the University of Minnesota SenNet TMC. These parameters ... | ["Prepare two slides with serial sections of the FFPE liver sample -- 1 section per slide.", "Section A -- Stain with H&E.\nSection B -- Stain with trichrome.", "Schedule evaluation with pathologist (ideally with a strong liver background).", "Request assessment and record of the following scores: \n1. Steatosis, macro... |
null | null | null | dx.doi.org/10.17504/protocols.io.pg7djzn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><u>Goal </u></p>
<p><u> </u></p>
<p>This document has the objective of establishing a proceeding for RNA extraction from eukaryotic cells through phenol-chloroform method using TRIzol (Ambion) reagent.</p>
<p><u> </u></p>
<p><u>General considerations:</u></p>
<p><u> </u></p>
... | [] |
26,158 | Prepare NGM no peptone plates | null | dx.doi.org/10.17504/protocols.io.5sng6de | null | Cancer Research UK / Wellcome Gurdon Institute media kitchen | TITLE: Prepare NGM no peptone plates
AUTHORS: Cancer Research UK / Wellcome Gurdon Institute media kitchen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Prepare NGM plates without peptone. </div><div class = "text-block">Peptone is necessary for bacterial growth and thus by not adding peptone, one... | ["ABC1IngredientsQuantity2NaCl 15g3Double\n distilled H2O4.8L4Agar per 1L bottle17g5Agarper 500ml bottle8.5g\nABC1IngredientsQuantity2NaCl 15g3Double\n distilled H2O4.8L4Agar per 1L bottle17g5Agarper 500ml bottle8.5g", "A1Measure approx 4.8L double distilled H2O in 5L bell jar with a magne... |
null | null | null | dx.doi.org/10.17504/protocols.io.r73d9qn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Follow the directions to make the best picture ever!</p>
[STEPS]
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56,637 | Sequential Transfection and Transduction Protocol For HUVECs (Lipo2000 version) + HALO tag live microscopy | 4 | null | https://www.protocols.io/view/sequential-transfection-and-transduction-protocol-b3i5qkg6 | Emir Bora Akmeriç | TITLE: Sequential Transfection and Transduction Protocol For HUVECs (Lipo2000 version) + HALO tag live microscopy
AUTHORS: Emir Bora Akmeriç
[DESCRIPTION]
4 Day Protocol for transfecting lipofected plasmids, followed by viral transduction and pre live microscopy treatment. Optimized for blood flow simulation experime... | ["[Pre Transfection] Seed 500k cells to a t25 flask a day(to 1.5 days max) prior, the plate on day of transfection should be 50-70% confluent", "[Transfection] Prepare the following mixes:\n\nMix1: 325 uL opti-mem+ 5 uL Lipo2000\nMix2: 325 uL opti-mem + 8 ug Kank1:GFP Plasmid", "[Pre Transfection] 2 hours prior to tran... |
null | null | null | dx.doi.org/10.17504/protocols.io.izicf4e | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
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36,113 | NEBuilder HiFi DNA Assembly Reaction (E2621) | 1 | dx.doi.org/10.17504/protocols.io.bfhrjj56 | https://www.protocols.io/view/nebuilder-hifi-dna-assembly-reaction-e2621-bfhrjj56 | New England Biolabs | TITLE: NEBuilder HiFi DNA Assembly Reaction (E2621)
AUTHORS: New England Biolabs
[DESCRIPTION]
NEBuilder HiFi DNA Assembly Master Mix was developed to improve the efficiency and accuracy of DNA assembly. This method allows for seamless assembly of multiple DNA fragments, regardless of fragment length or end compati... | ["Set up the following reaction on ice (to 20 µL total volume):", "Determine whether your reactions will involve assembly of 2-3 fragments or 4-6 fragments and move forward with the following steps:", "Following incubation, store samples on ice or at -20 °C for subsequent transformation.", "Transform NEB 5-alpha Compet... |
88,402 | A systematic review protocol for Biometrics in healthcare: strategies for improving safety and privacy of patients’ records in sub-Saharan Countriestitled protocol | 1 | dx.doi.org/10.17504/protocols.io.rm7vzx675gx1/v1 | https://www.protocols.io/view/a-systematic-review-protocol-for-biometrics-in-hea-c2jsycne | Arnold M Hamapa, Joseph Mumba Zulu, oswellkhondowe, Choolwe Jacobs, Mercy Wamunyima Monde, Adam Silumbwe, lydiahangulu, oswellkhondowe | TITLE: A systematic review protocol for Biometrics in healthcare: strategies for improving safety and privacy of patients’ records in sub-Saharan Countriestitled protocol
AUTHORS: Arnold M Hamapa, Joseph Mumba Zulu, oswellkhondowe, Choolwe Jacobs, Mercy Wamunyima Monde, Adam Silumbwe, lydiahangulu, oswellkhondowe
[DES... | [] |
57,339 | Library preparation (dsDNA double indexing, non-UDG, 2x split) | 1 | dx.doi.org/10.17504/protocols.io.n2bvj6xqxlk5/v1 | https://www.protocols.io/view/library-preparation-dsdna-double-indexing-non-udg-b383qryn | Marcel Keller, Christiana L Scheib, Biancamaria Bonucci | TITLE: Library preparation (dsDNA double indexing, non-UDG, 2x split)
AUTHORS: Marcel Keller, Christiana L Scheib, Biancamaria Bonucci
[DESCRIPTION]
Protocol for the preparation of double indexed double-stranded DNA libraries for Illumina sequencing, optimized for ultra-short ancient DNA molecules, modified from Meyer... | ["[Blunt End Repair] Use 1.5 ml ER tube to set up the Blunt End Repair Master Mix on ice .", "[Blunt End Repair] Add 20 µl Master Mix to each tube of the ER strip.", "[Blunt End Repair] Vortex and spin down DNA extracts, add 30 µl of template DNA or water to each tube.", "[Blunt End Repair] Mix carefully by resuspendin... |
43,056 | CNV Pilot - Subject Candidate Contact Protocol | 1 | null | https://www.protocols.io/view/cnv-pilot-subject-candidate-contact-protocol-bnaqmadw | Brian Britt, Rose Mary Xavier | TITLE: CNV Pilot - Subject Candidate Contact Protocol
AUTHORS: Brian Britt, Rose Mary Xavier
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details the manner in which candidate subjects for the CNV pilot study will be contacted for recruitment.</div></div>
[STEPS]
?. [Contact protoc... | ["[Contact protocol]\nMake a first phone call to the candidate using the IRB-approved phone script", "[Contact protocol]\nSend an e-mail and physical mailer to the candidate using the IRB-approved e-mail template and the IRB-approved mail template"] |
66,332 | Condor CBD Gummies Reviews - Is It Scam? Shark Tank Alert | 1 | dx.doi.org/10.17504/protocols.io.kxygxzbpdv8j/v1 | https://www.protocols.io/view/condor-cbd-gummies-reviews-is-it-scam-shark-tank-a-ccz4sx8w | Condor Cbdgummies | TITLE: Condor CBD Gummies Reviews - Is It Scam? Shark Tank Alert
AUTHORS: Condor Cbdgummies
[DESCRIPTION]
Health
[STEPS]
1. Condor CBD Gummies contain an unadulterated, natural combination that can work on your overall wellbeing and not make any side impacts. Orally ingested chewy candies have numerous medical advan... | ["Condor CBD Gummies contain an unadulterated, natural combination that can work on your overall wellbeing and not make any side impacts. Orally ingested chewy candies have numerous medical advantages. They can be utilized day to day to keep a solid body.\n\n>> (Restricted Time Discount Offer) Click Here to Order Condo... |
90,580 | Protocol to isolate and fix nuclei from flash frozen mouse liver for IGVF | 4 | null | https://www.protocols.io/view/protocol-to-isolate-and-fix-nuclei-from-flash-froz-c4puyvnw | Elisabeth Rebboah | TITLE: Protocol to isolate and fix nuclei from flash frozen mouse liver for IGVF
AUTHORS: Elisabeth Rebboah
[DESCRIPTION]
This protocol describes isolation of nuclei from 10 week old mouse liver (tissue ID: 05) from 8 founder strains (B6J, AJ, 129S1J, NZOJ, WSBJ, NODJ, PWKJ, and CASTJ), preparation of a single nucleus... | ["[Setup] Coat SHARE-seq nuclei prep tubes with BSA. Fill 8 1.5 ml tubes with 1.5 ml 1% BSA in H2O and incubate for 30 minutes. After incubation, aspirate BSA solution and dry for 30 minutes. Store at 4C.", "[Setup] Label tubes.", "[Setup] Pre-chill centrifuge to 4C.", "[Setup] Prepare ice buckets.", "[Setup] Prepare 5... |
66,366 | Diaetoxil Avis : Où acheter en ligne {Conseils d'achat 2022} | 1 | dx.doi.org/10.17504/protocols.io.36wgq7zj3vk5/v1 | https://www.protocols.io/view/diaetoxil-avis-o-acheter-en-ligne-conseils-d-39-ac-cc26syhe | roxypins | TITLE: Diaetoxil Avis : Où acheter en ligne {Conseils d'achat 2022}
AUTHORS: roxypins
[DESCRIPTION]
Must Visit : https://www.facebook.com/DiaetoxilAvis/
https://ipsnews.net/business/2022/07/01/diaetoxil-avis-france-gelules-diaetoxil-erfahrungen-bezugsquellen-entgiftung-avis/
https://ipsnews.net/business/2022... | ["[Diaetoxil Avis] Diaetoxil Avis France : Le complément alimentaire révolutionnaire Diaetoxil Gélules, dont l’efficacité a été scientifiquement prouvée, est désormais disponible pour les personnes au régime qui souhaitent perdre du poids de la manière la plus naturelle possible tout en préservant leur santé et leur bi... |
39,818 | Restriction Endonuclease Protection Assays using Infrared-Fluorescent Probes | 1 | dx.doi.org/10.17504/protocols.io.bi5ikg4e | https://www.protocols.io/view/restriction-endonuclease-protection-assays-using-i-bi5ikg4e | Michael Van Dyke, Isabelle Gracien | TITLE: Restriction Endonuclease Protection Assays using Infrared-Fluorescent Probes
AUTHORS: Michael Van Dyke, Isabelle Gracien
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Many proteins sequence-specifically bind duplex DNA, e.g., transcriptional regulatory proteins. Analysis of their interactio... | ["[REPA set up]\nPlan REPA reactions. For the example shown here, we investigated the concentration dependence of the Thermus thermophilus HB8 transcriptional regulator SbtR to inhibit IISRE FokI cleavage of an IRD7-labeled (red) test DNA containing the SbtR consensus binding sequence as compared to an IRD8-labeled (gr... |
null | null | null | dx.doi.org/10.17504/protocols.io.sfzebp6 | null | null | TITLE: No Title
AUTHORS:
[BEFORE_START]
<p>1. Extract and purify genomic DNA.</p>
<p> </p>
<p>2. Quantitate the gDNA in samples by spectophotometry.</p>
[GUIDELINES]
<p>1 Keep all reagents protected from light until you are ready to use them. Excessive exposure to light may affect the fluorescent probes.</p>
<p> </p... | [] |
60,438 | Intracellular Cytokine (ICS) Staining Protocol | 4 | dx.doi.org/10.17504/protocols.io.e6nvwkbwdvmk/v1 | https://www.protocols.io/view/intracellular-cytokine-ics-staining-protocol-b69wrh7e | Gregory P. Williams, cecilia | TITLE: Intracellular Cytokine (ICS) Staining Protocol
AUTHORS: Gregory P. Williams, cecilia
[DESCRIPTION]
This protocol details about intracellular cytokine (ICS) staining.
[STEPS]
SECTION: Stimulus Solution
1. Label U-bottom plate with donor, stimulation solution, name and date.
SECTION: Stimulus Solution
2. Prepare... | ["[Stimulus Solution] Label U-bottom plate with donor, stimulation solution, name and date.", "[Stimulus Solution] Prepare PMA+Ionomycin and DMSO mix separately.", "[Stimulus Solution] Prepare and arrange the remaining stimulation solution. Mix thoroughly by pipetting up and down before adding to the experimental plate... |
95,585 | Live cell Imaging of yeast cells expressing human PINK1-GFP and the TOM complex subunits | 1 | dx.doi.org/10.17504/protocols.io.dm6gp3p71vzp/v1 | https://www.protocols.io/view/live-cell-imaging-of-yeast-cells-expressing-human-c9j9z4r6 | Kenneth Ehses, Olawale Raimi, Ruben Fernandez-Busnadiego | TITLE: Live cell Imaging of yeast cells expressing human PINK1-GFP and the TOM complex subunits
AUTHORS: Kenneth Ehses, Olawale Raimi, Ruben Fernandez-Busnadiego
[DESCRIPTION]
The PINK1-Parkin axis plays a major role in mitochondrial quality control and mutations have been closely associated with familial cases of Par... | ["[Yeast Cell culture] Grow yeast cells in liquid medium.", "[Yeast Cell culture] On the next day, check OD600 and dilute to OD600=0.1.", "[Yeast Cell culture] Allow the yeast cells to regrow into early exponential phase until they reach approx. OD600=0.3-0.6. At this state, we induce protein expression by addition o... |
96,114 | Creating Bacterial Glycerol Stocks for Long-term Storage | 1 | dx.doi.org/10.17504/protocols.io.e6nvwdwr7lmk/v1 | https://www.protocols.io/view/creating-bacterial-glycerol-stocks-for-long-term-s-c94sz8we | Bonnie Evans | TITLE: Creating Bacterial Glycerol Stocks for Long-term Storage
AUTHORS: Bonnie Evans
[DESCRIPTION]
Bacterial glycerol stocks are important for long-term storage. Bacteria on LB agar plate can be stored at 4°C for a few weeks. However, if you want to store bacteria for a longer time, you will need to establish glycero... | ["[Steps] Grow an overnight culture of the selected strain", "[Steps] Add 500 μL of the overnight culture to 500 μL of 50% glycerol in a 2 mL screw top tube or cryotube and gently mix", "[Steps] Freeze the glycerol stock tube at -80°C.", "[Steps] To recover bacteria from your glycerol stock, open the tube and use a ste... |
93,488 | Pole Test Assessment | 4 | dx.doi.org/10.17504/protocols.io.5qpvo34k9v4o/v1 | https://www.protocols.io/view/pole-test-assessment-c7iqzkdw | Ian N Krout, Alexandria White, Tim Sampson | TITLE: Pole Test Assessment
AUTHORS: Ian N Krout, Alexandria White, Tim Sampson
[DESCRIPTION]
Pole test is a simple behavior test used to assess fine motor coordination. Mice are placed at the top of a 50-60 cm vertical pole with a diameter of 1 cm. The pole is attached to a base that is placed in the home cage so tha... | ["[Pole set-up] Find a metal pole 1cm in diameter with a height of ~50-60cm. This should have a base that is able to fit inside of a standard mouse cage.", "[Training Day 1] Determine the order of assessment that you will use for the length of the training and assessment, record this in lab notebook.", "[Assessment] N... |
96,571 | Solvent Extraction of Polydimethylsiloxane (PDMS) Tubing to capture Volatile Organic Compounds from the Headspace and the Rhizosphere | 0 | dx.doi.org/10.17504/protocols.io.eq2lyjmqrlx9/v1 | https://www.protocols.io/view/solvent-extraction-of-polydimethylsiloxane-pdms-tu-dai32cgn | Gareth Thomas, Anusha Mohan-Kumar, Alexander N. Borg, John Caulfield, Michael A. Birkett, József Vuts | TITLE: Solvent Extraction of Polydimethylsiloxane (PDMS) Tubing to capture Volatile Organic Compounds from the Headspace and the Rhizosphere
AUTHORS: Gareth Thomas, Anusha Mohan-Kumar, Alexander N. Borg, John Caulfield, Michael A. Birkett, József Vuts
[DESCRIPTION]
This protocol describes a step-by-step guide for samp... | ["[Conditioning PDMS tubes prior to headspace collection] Cut PDMS tubing (1 mm i.d. × 0.4 mm wall thickness) to desired length. The length of tubing can be variable depending on the headspace or rhizosphere set-up. In our previous work, the following lengths of PDMS tubing were used:\n\nFor headspace Volatile Organic ... |
58,457 | Thawing frozen hematopoietic stem cells (HPCs) | 4 | null | https://www.protocols.io/view/thawing-frozen-hematopoietic-stem-cells-hpcs-b5bzq2p6 | Jessie Buth | TITLE: Thawing frozen hematopoietic stem cells (HPCs)
AUTHORS: Jessie Buth
[DESCRIPTION]
Protocol to thaw frozen hematopoietic stem cells made with the StemDiff Hematopoietic Kit for subsequent differentiation into microglia.
[BEFORE_START]
Make sure you have:
Enough GFR matrigel + DMEM/F12 to coat the plates
Micro... | ["[Prep Matrigel Plates] Coat tissue culture treated plates with 1 mg/mL GFR Matrigel (Growth GFR Matrigel (Growth factor reduced).", "[Prep Matrigel Plates] Get a frozen aliquot of GFR Matrigel from the hallway -30. The aliquots are typically labeled \"6.5\" or \"12.5\", this is the number of mL DMEM/F12 you will add.... |
100,557 | Protocol PROCI | 0 | dx.doi.org/10.17504/protocols.io.261ge56qwg47/v3 | https://www.protocols.io/view/protocol-proci-defm3bk6 | Chiara Parravicini, Daniele Spedicati, Matteo Guenci, Nicole Liggeri | TITLE: Protocol PROCI
AUTHORS: Chiara Parravicini, Daniele Spedicati, Matteo Guenci, Nicole Liggeri
[DESCRIPTION]
We present a step-by-step methodology for the systematic extraction, alignment, and analysis of peer review data from Crossref to enhance the OpenCitations Index.
The protocol delineates four key phases: ... | ["[Gathering Data] In order to answer to our research questions, we gathered data from Crossref (dump released on April 2023, zip file of 185.88GB) and OpenCitations Meta (dump released on April 2024, zip file of 11GB).", "[Post-processing] The main purpose of this phase of the worklflow is using the processed data abo... |
30,769 | Precision Count Beads™ Protocol and Applications | null | dx.doi.org/10.17504/protocols.io.baariad6 | null | Sam Li | TITLE: Precision Count Beads™ Protocol and Applications
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Precision Count Beads™ are designed for counting the absolute number of cells in a complex mix population and other particles by flow cytometry. Precision Count Beads™ are excited ... | ["[Sample Preparation]\nPerform sample preparation and staining as usual. Some examples of sample that may be used are:Cell linesWhole bloodPBMCCells from migration assaysTip: Sample handling such as centrifugation, decanting, or transferring between different tubes can significantly affect cell counts and should be ke... |
36,124 | Protein expression on the surface of Escherichia coli | 1 | dx.doi.org/10.17504/protocols.io.bfh4jj8w | https://www.protocols.io/view/protein-expression-on-the-surface-of-escherichia-c-bfh4jj8w | Maja Rennig, Kristoffer Bach Falkenberg, Cristina Hernandez Rollan, Andreas Birk Bertelsen, Morten Norholm | TITLE: Protein expression on the surface of Escherichia coli
AUTHORS: Maja Rennig, Kristoffer Bach Falkenberg, Cristina Hernandez Rollan, Andreas Birk Bertelsen, Morten Norholm
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Display of proteins on the bacterial cell surface has always been an attrac... | ["[Pre culture - Day 1]\nPick a fresh colony of your BL21 (DE3) strain with your expression vector, and inoculate it in LB supplemented with relevant antibiotics. Grow the culture at at 250 RPM shaking . The volume of the overnight culture depends on the volume of the expression culture and should be at least 1/100 of... |
60,181 | How to select the best gRNA(s) for frameshift knockouts in zebrafish | 5 | dx.doi.org/10.17504/protocols.io.81wgb6r5qlpk/v1 | https://www.protocols.io/view/how-to-select-the-best-grna-s-for-frameshift-knock-b6zvrf66 | Francois Kroll | TITLE: How to select the best gRNA(s) for frameshift knockouts in zebrafish
AUTHORS: Francois Kroll
[DESCRIPTION]
Remember to cite the protocol if it is helpful to you!
This protocol describes my approach (as of April 2022) to select gRNAs to generate frameshift knockouts in zebrafish using CRISPR-Cas9. It assumes y... | ["Choose the exon(s) you want to target\n_________________________________________________________________\n\n\nWe will use the gene appa as an example.\n\nOpen the Ensembl page for your gene of interest, e.g. https://www.ensembl.org/Danio_rerio/Gene/Summary?db=core;g=ENSDARG00000104279;r=1:617620-656693\n\nLook at the... |
24,357 | Prep for FACS on blood samples | null | dx.doi.org/10.17504/protocols.io.32dgqa6 | null | Grace Burgin, Inbal Benhar | TITLE: Prep for FACS on blood samples
AUTHORS: Grace Burgin, Inbal Benhar
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">To prepare blood samples for flow </div></div>
[STEPS]
?. Collect blood into EDTA coated tubes
?. Transfer 50ul into clean tube - include 1 unstained***mix from several mice to ... | ["Collect blood into EDTA coated tubes", "Transfer 50ul into clean tube - include 1 unstained***mix from several mice to have 50ul for unstained ctrl tube", "Add 1ml ACK, incubate at RT for 7 min, centrifuge 5’ 350g", "Resuspend pellet in FACS buffer + antibody mix", "Incubate in dark for 15’ on ice", "Wash (centrifuge... |
83,663 | P5ARP/P10ARP Media Preparation | 1 | null | https://www.protocols.click/view/p5arp-p10arp-media-preparation-cvxpw7mn | rebecca.bennett | TITLE: P5ARP/P10ARP Media Preparation
AUTHORS: rebecca.bennett
[DESCRIPTION]
How to make P5ARP and P10ARP media plates, simplified from https://wiki.bugwood.org/PARP_or_PARP
Contains: pimarcin, ampicillin, rifampicin, pentachloronitrobenzens.
Pimaricin is a broad-spectrum antifungal antibiotic that inhibits the true... | ["[Preparation] Sign up for Autoclave and turn on.", "[Preparation] Add 17 g of Difco cornmeal agar to each 2 L Erlenmeyer flask", "[Preparation] Add RO water to 1000 mL line (pre-measure line and mark with sharpie or use a graduated cylinder).\nCover top with foil so that at least 2\" of foil is below flask lip.", "[P... |
42,213 | Chapter 1: Handling and Housing | 4 | null | https://www.protocols.io/view/chapter-1-handling-and-housing-bmgdk3s6 | Kerri Wolter | TITLE: Chapter 1: Handling and Housing
AUTHORS: Kerri Wolter
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Rehabilitation of any injured wild animal is an honourable and laudable activity. However, in taking any animal into care, the rescuer accepts the responsibilities of ‘ownership’ for the anim... | ["[Catching vultures]\nApproach the bird in such a manner as to avoid scaring it away or causing unnecessary stress.\nVultures need to be approached quietly, confidently, and sympathetically; there is no need to ‘rugby-tackle’ them at all. It is recommended that no more than three persons should be involved in this cap... |
null | null | null | dx.doi.org/10.17504/protocols.io.tjwekpe | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<strong>Reagent List:</strong><br />
<ul>
<li>Cell Staining Buffer (BioLegend Cat. No. 420201)</li>
<li>Red Cell Lysis Buffer (BioLegend Cat. No. 420301)</li>
<li>7-AAD Viability Staining Solution (BioLegend Cat. No. 420403)</li>
<li>TruStain FcX™ (anti-CD16/32, BioLegend Cat. No... | ["Add predetermined optimum concentrations of desired fluorochrome conjugated, biotinylated, or purified primary antibodies to 100 μl of anti-coagulated whole blood.", "{\"blocks\":[{\"key\":\"el3ho\",\"text\":\"Incubate at room temperature for 15-20 minutes in the dark. \",\"type\":\"unstyled\",\"depth\":0,\"inlineSty... |
91,182 | A Protocol for Semi-Structured Interviews in Autobiographical Research: Exploring Narratives from the Spanish Civil War | 1 | dx.doi.org/10.17504/protocols.io.6qpvr3283vmk/v1 | https://www.protocols.io/view/a-protocol-for-semi-structured-interviews-in-autob-c5any2de | Francisco J Leira-Castiñeira, Andrés Domínguez-Almansa, Raquel Martín-Ríos | TITLE: A Protocol for Semi-Structured Interviews in Autobiographical Research: Exploring Narratives from the Spanish Civil War
AUTHORS: Francisco J Leira-Castiñeira, Andrés Domínguez-Almansa, Raquel Martín-Ríos
[DESCRIPTION]
The protocol outlines a method for conducting semi-structured interviews, specifically focusin... | ["[Theoretical Framework] \"Life Stories\" - Semi-Structured Interviews: These interviews revolved around the life experiences of the participants and were semi-structured in nature. The interviewer directed the conversation towards aspects pertinent to the research, in this case, focusing on the participant’s experien... |
79,528 | Neuromelanin staining (Fontana-Masson staining)+ TH-DAB staining on midbrain organoids | 1 | dx.doi.org/10.17504/protocols.io.5jyl8jon8g2w/v1 | https://www.protocols.io/view/neuromelanin-staining-fontana-masson-staining-th-d-crwgv7bw | michela.deleidi, Federico Bertoli, Hariam Raji | TITLE: Neuromelanin staining (Fontana-Masson staining)+ TH-DAB staining on midbrain organoids
AUTHORS: michela.deleidi, Federico Bertoli, Hariam Raji
[DESCRIPTION]
Fontana-Masson staining is a silver staining technique that is commonly used to identify melanin-containing cells. We combined it with DAB-TH staining th... | ["[Neuromelanin staining] Incubate human midbrain organoid sections in a fresh solution of 3:1 methanol (MeOH)/3% hydrogen peroxide at Room temperature for 20 min.", "[Neuromelanin staining] Wash the slides and block it.", "[Neuromelanin staining] Apply primary antibodies in NGS 5% in PBS+ Triton-X 0.2% solution 60 min... |
47,900 | Protein extraction and BCA assay from MCAS sorted cells | 4 | null | https://www.protocols.io/view/protein-extraction-and-bca-assay-from-mcas-sorted-bsz4nf8w | Daniel Manrique-Castano | TITLE: Protein extraction and BCA assay from MCAS sorted cells
AUTHORS: Daniel Manrique-Castano
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol allows proteins extraction from cells sorted employing the MACS Adult Dissociation Brain kit (Miltenyi Biotec).</div></div>
[STEPS]
?. [Prote... | ["[Protein Extraction]\nFollowing final centrifugation after MACS cells sorting, discard the supernatant and place the cells to prevent protein degradation.\non ice", "[Protein Extraction]\nPrepare NP-40 lysis buffer and add it to the cells according to the number of expected proteins.\nUsually - when protein conc... |
45,260 | SPOT1 revised protocol | 4 | dx.doi.org/10.17504/protocols.io.bqfkmtkw | https://www.protocols.io/view/spot1-revised-protocol-bqfkmtkw | Guanhua Xun, Huimin Zhao, stlane2 | TITLE: SPOT1 revised protocol
AUTHORS: Guanhua Xun, Huimin Zhao, stlane2
[STEPS]
?. Using the first provided microcap, collect a saliva sample into capillary A, containing QuickExtract DNA Extraction Solution (Lucigen). Insert the capillary into the SPOT1 device and press the "Start" button to run the 5-minute pretr... | ["Using the first provided microcap, collect a saliva sample into capillary A, containing QuickExtract DNA Extraction Solution (Lucigen). Insert the capillary into the SPOT1 device and press the \"Start\" button to run the 5-minute pretreatment.\n95 °C", "After pretreatment, remove capillary A from the SPOT1 device an... |
79,601 | Molding microchambers in agar with PDMS stamps for live imaging | 1 | dx.doi.org/10.17504/protocols.io.j8nlkwpk1l5r/v1 | https://www.protocols.io/view/molding-microchambers-in-agar-with-pdms-stamps-for-cryrv7v6 | Tara Essock-Burns, Galo Garcia, David Matus | TITLE: Molding microchambers in agar with PDMS stamps for live imaging
AUTHORS: Tara Essock-Burns, Galo Garcia, David Matus
[DESCRIPTION]
This is a step-by-step guide for preparing agar microchambers using a patterned stamp. The protocol includes detailed instructions on selecting the appropriate stamp, preparing the ... | ["[Gather materials and prepare setup] Familiarize yourself with the protocol and make sure to click the appropriate tab based on whether this is your first time doing this, a subsequent time, or your first time using a new stamp.", "[Gather materials and prepare setup] Stack four glass slides and bind each end of the ... |
47,723 | Glutathione peroxidase (GPx) activity assessment for zebrafish brain tissue | 6 | dx.doi.org/10.17504/protocols.io.bsujneun | https://www.protocols.io/view/glutathione-peroxidase-gpx-activity-assessment-for-bsujneun | Adrieli Sachett, Matheus Gallas-Lopes, Greicy M M Conterato, Ana Herrmann, Angelo Piato | TITLE: Glutathione peroxidase (GPx) activity assessment for zebrafish brain tissue
AUTHORS: Adrieli Sachett, Matheus Gallas-Lopes, Greicy M M Conterato, Ana Herrmann, Angelo Piato
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Zebrafish are being increasingly used as a model animal in neuroscience ... | ["[Preparing the reagents]\nThe first step is to prepare the reagents to be used in the assessment of glutathione peroxidase activity;", "[Preparing the reagents]\nPotassium phosphate buffer : 1.1.1 Weigh of monobasic potassium phosphate (KH2PO4) in a beaker of appropriate size; 1.1.2 Dissolve the salt with of ... |
78,540 | 5. Metagenomics of Parkinson’s disease implicates the gut microbiome in multiple disease mechanisms | 1 | dx.doi.org/10.17504/protocols.io.5qpvord97v4o/v1 | https://www.protocols.io/view/5-metagenomics-of-parkinson-s-disease-implicates-t-cqxkvxkw | Haydeh Payami | TITLE: 5. Metagenomics of Parkinson’s disease implicates the gut microbiome in multiple disease mechanisms
AUTHORS: Haydeh Payami
[DESCRIPTION]
The protocol details the final product , the published manuscript with step-by-step methods. It describes the whole process from start to end using the article "Metagenomics o... | [] |
99,147 | COI Metabarcoding Library Prep: Dual-PCR Method | 1 | null | https://www.protocols.io/view/coi-metabarcoding-library-prep-dual-pcr-method-dc3j2ykn | Colleen Kellogg, Andreas Novotny | TITLE: COI Metabarcoding Library Prep: Dual-PCR Method
AUTHORS: Colleen Kellogg, Andreas Novotny
[DESCRIPTION]
Draft!
[BEFORE_START]
Read background information, MIOP and BePOP-OBON information under the "Guidelines" tab.
[GUIDELINES]
MIOP: Minimum Information about an Omics Protocol
AUTHORS
RELATED PROTO... | ["[PREPARATIONS] Ensure that the laboratory is appropriately configured and that staff has appropriate training. See \"Guidelines\" for more information. Pay attention to the separation of pre and post-PCR spaces and equipment.", "[Triplicate PCR Amplification (1st PCR)] Preparations\n\n \n\n Reagents:\n (Or equal)\n ... |
null | null | null | dx.doi.org/10.17504/protocols.io.de63hd | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Humus is a complex mixture of heterogeneous organic compounds derived from plant and animal residues and is formed by the reaction of decomposition, synthesis, and polymerization. It is an integral part of soil organic matter and can be extracted by neutral salts or alkali ... | [] |
24,559 | SOAP-denovo-trans assembly | null | dx.doi.org/10.17504/protocols.io.38pgrvn | null | Eric J. Carpenter, Naim Matasci, Shuangxiu Wu, Jing Sun, Jun Yu, Fabio Rocha Jimenez Vieira, Chris Bowler, Richard G. Dorrell, Matt Gitzendanner, Ling Li, Wensi Du, Kristian Ullrich, Michael S. Barker, James H. Leebens-Mack, Gane Ka-Shu Wong | TITLE: SOAP-denovo-trans assembly
AUTHORS: Eric J. Carpenter, Naim Matasci, Shuangxiu Wu, Jing Sun, Jun Yu, Fabio Rocha Jimenez Vieira, Chris Bowler, Richard G. Dorrell, Matt Gitzendanner, Ling Li, Wensi Du, Kristian Ullrich, Michael S. Barker, James H. Leebens-Mack, Gane Ka-Shu Wong
[DESCRIPTION]
<div class = "text-b... | ["SOAPdenovo2 based DBG construction and Trinity based low frequency k-mer removal.", "Map reads to the contigs and build linkages.a) Utilizing single-end read informationb) Utilizing paired-end read informationc) Merge the linkages", "Remove erroneous and redundant linkagesa) Manage ambiguous contigsb) Linearize conti... |
72,104 | Tokuyasu processing and immuno-electron microscopy of tissue | 4 | dx.doi.org/10.17504/protocols.io.5jyl8jj9dg2w/v1 | https://www.protocols.click/view/tokuyasu-processing-and-immuno-electron-microscopy-cingudbw | Jillian C Danne, Viola Oorschot, Georg Ramm | TITLE: Tokuyasu processing and immuno-electron microscopy of tissue
AUTHORS: Jillian C Danne, Viola Oorschot, Georg Ramm
[DESCRIPTION]
Ultrastructural morphological information is routinely obtained from the processing of cells and tissue into plastics for transmission electron microscopy imaging. This technique invol... | ["[Fixation] All fixation steps must be performed in a fume hood wearing the appropriate personal protective equipment (PPE). The Material Safety Data Sheet (MSDS) for each chemical must be read before commencing.\n\nDissect out the tissue of interest on a Teflon plate or dental wax sheet using fine forceps and a scalp... |
48,536 | Crop FVC retrieval | 1 | dx.doi.org/10.17504/protocols.io.btmynk7w | https://www.protocols.io/view/crop-fvc-retrieval-btmynk7w | Liang Wan, Jiangpeng Zhu, Xiaoyue Du, Jiafei Zhang, Xiongzhe Han, Weijun Zhou, Xiaopeng Li, Jianli Liu, Fei Liang, Yong He, Haiyan Cen | TITLE: Crop FVC retrieval
AUTHORS: Liang Wan, Jiangpeng Zhu, Xiaoyue Du, Jiafei Zhang, Xiongzhe Han, Weijun Zhou, Xiaopeng Li, Jianli Liu, Fei Liang, Yong He, Haiyan Cen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the method of crop fractional vegetation cover (FVC) retri... | ["Make sure you have MATLAB 2014b (or newer) installed on your computer.", "Dowload the MATLAB scripts from https://github.com/WanLiangZJU/Crop-FVC-retrieval", "Please use the code in the file of PROSAIL_5B_GP. Here, we provide five main codes for different datasets as follows: Main_oilseed_rape_2017_2018.m, Main_oils... |
88,700 | Complicated Grief Assessment for interdisciplinary research: An evidence-based protocol | 1 | dx.doi.org/10.17504/protocols.io.bp2l6x8o5lqe/v1 | https://www.protocols.io/view/complicated-grief-assessment-for-interdisciplinary-c2u4yeyw | Raquel Martín-Ríos, Francisco J Leira-Castiñeira | TITLE: Complicated Grief Assessment for interdisciplinary research: An evidence-based protocol
AUTHORS: Raquel Martín-Ríos, Francisco J Leira-Castiñeira
[DESCRIPTION]
The Spanish Civil War caused a rupture in the social and cultural norms that had developed over a long period of liberalism. The violence that occurred ... | ["[Theoretical framework] In grief research, different methods and approaches such as interviews, questionnaires and direct observation are often used to collect data on how people experience and process grief. These data are then analysed in order to identify patterns and trends that help to better understand the grie... |
78,530 | INSTRUCTIONS FOR SALIVA COLLECTION | 1 | dx.doi.org/10.17504/protocols.io.261ge3krol47/v1 | https://www.protocols.io/view/instructions-for-saliva-collection-cqxavxie | null | TITLE: INSTRUCTIONS FOR SALIVA COLLECTION
AUTHORS:
[DESCRIPTION]
The protocol details the instructions for saliva collection self administered by subjects.
[STEPS] | [] |
86,376 | Pregnancy pillow interventions to support the pelvis, lower back, gravid uterus and a left lateral recumbent maternal sleeping position: A rapid systematic review protocol | 1 | dx.doi.org/10.17504/protocols.io.5jyl8pj3rg2w/v1 | https://www.protocols.io/view/pregnancy-pillow-interventions-to-support-the-pelv-cykgxutw | Delyth Wyndham, Gwenllian Wynne-Jones | TITLE: Pregnancy pillow interventions to support the pelvis, lower back, gravid uterus and a left lateral recumbent maternal sleeping position: A rapid systematic review protocol
AUTHORS: Delyth Wyndham, Gwenllian Wynne-Jones
[DESCRIPTION]
Objective:
The objective of this rapid review is to provide a systematic overv... | [] |
96,023 | SOP and tick-sheet for using TDP-43 RNA aptamer (TDP-43APT) to detect pathological TDP-43 in FFPE-preserved human tissue, as described in Spence and Waldron et al., 2024 (Acta Neuropathologica) | 0 | dx.doi.org/10.17504/protocols.io.eq2lyjo4mlx9/v1 | https://www.protocols.io/view/sop-and-tick-sheet-for-using-tdp-43-rna-aptamer-td-c9zxz77n | Holly Spence, Fergal M Waldron, Jenna Gregory | TITLE: SOP and tick-sheet for using TDP-43 RNA aptamer (TDP-43APT) to detect pathological TDP-43 in FFPE-preserved human tissue, as described in Spence and Waldron et al., 2024 (Acta Neuropathologica)
AUTHORS: Holly Spence, Fergal M Waldron, Jenna Gregory
[DESCRIPTION]
Here we provide a SOP to outline the correct proc... | [] |
69,492 | QuantiGene multiplex assay | 1 | dx.doi.org/10.17504/protocols.io.kqdg39ew7g25/v1 | https://www.protocols.io/view/quantigene-multiplex-assay-cf4utqww | Amy R Hicks | TITLE: QuantiGene multiplex assay
AUTHORS: Amy R Hicks
[DESCRIPTION]
This protocol outlines a method of simultaneously measuring the expression of up to 80 genes in any one sample using the QuantiGene multiplex assay from ThermoFisher. This protocol was adapted from the lab of Professor Gill Bates. Cells are grown in ... | ["[Sample preparation] Pre-warm lysis mixture at 37oC for 30 mins, followed by gentle swirling.30 min", "[Sample preparation] Prepare working lysis mixture by adding 10 µL of proteinase K to each 1 mL of lysis mixture required.", "[Sample preparation] Add 1/2 volume of working lysis mixture to cells in culture media ... |
56,388 | nanopore nCoV-2019 sequencing protocol (RAPID barcoding, 1200bp amplicon, combined RT-PCR) | 1 | dx.doi.org/10.17504/protocols.io.b3bcqiiw | https://www.protocols.io/view/nanopore-ncov-2019-sequencing-protocol-rapid-barco-b3bcqiiw | Anton Pembaur, Erwan Sallard, Patrick Weil, Jennifer Ortelt, Parviz Ahmad-Nejad, Jan Postberg | TITLE: nanopore nCoV-2019 sequencing protocol (RAPID barcoding, 1200bp amplicon, combined RT-PCR)
AUTHORS: Anton Pembaur, Erwan Sallard, Patrick Weil, Jennifer Ortelt, Parviz Ahmad-Nejad, Jan Postberg
[DESCRIPTION]
We established a protocol for fast, cost efficient Sars-CoV-2 sequencing with little as possible ha... | ["[Sample selection, RNA isolation] For whole genome sequencing using combined RT-PCR, samples with a Ct <20 are suitable. Higher Ct values ≤26 can be suitable as well, but we strongly recommend verification of the amplicon quality utilizing gelelectrophresis and/or microcapillary electrophoresis (Agilent) after combin... |
null | null | null | dx.doi.org/10.17504/protocols.io.gg6btze | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.mxpc7mn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Detailed protocol for chemical +/- heat antigen retrieval on sectioned tissue to increase reactivity and specificity of antibody recognition</p>
[GUIDELINES]
<p>Digital pressure cookers give the most consistent results for antigen retrieval on histological slides thanks to p... | [] |
101,181 | A new DNA / RNA isolation protocol from a single tick for molecular analysis of various pathogens such as Borrelia, Babesia, Anaplasma, TBE, Alongshan virus etc. | 0 | dx.doi.org/10.17504/protocols.io.81wgbzzk3gpk/v1 | https://www.protocols.io/view/a-new-dna-rna-isolation-protocol-from-a-single-tic-de253gg6 | Sudhir Bhatia, Gudrun Baersch | TITLE: A new DNA / RNA isolation protocol from a single tick for molecular analysis of various pathogens such as Borrelia, Babesia, Anaplasma, TBE, Alongshan virus etc.
AUTHORS: Sudhir Bhatia, Gudrun Baersch
[DESCRIPTION]
We describe here a rare protocol for the isolation of nucleic acid from a single tick sample:
Ti... | ["The tick can be sent in a letter, as shown in the picture, or in a small plastic tube (tightly closed). If the tick is still alive, care must be taken to ensure that it does not escape. It is therefore important to look at the tick with a magnifying lens, as some ticks are very small and transparent.", "Put 100µl of ... |
50,608 | protocol to use the anaerobic workstation | 4 | dx.doi.org/10.17504/protocols.io.bvnqn5dw | https://www.protocols.io/view/protocol-to-use-the-anaerobic-workstation-bvnqn5dw | dollwin.matharu | TITLE: protocol to use the anaerobic workstation
AUTHORS: dollwin.matharu
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">this is a self written protocol to use the anaerobic hood</div></div>
[STEPS]
?. [entering the chamber]
Optional- Open the side chamber from its front door and put in the tra... | ["[entering the chamber]\nOptional- Open the side chamber from its front door and put in the tray with the materials one wants to take inside, close the front door. Also, make sure that the other materials one needs are already inside", "[entering the chamber]\nSwitch on the light, and the foot control device. Also, se... |
27,581 | Multiplex Immunofluorescence on Fresh Frozen Tissue | null | dx.doi.org/10.17504/protocols.io.665hhg6 | null | Maya Brewer, Yuantee Zhu, Elizabeth Neumann, Danielle Gutierrez, Jeff Spraggins, Mark de Caestecker | TITLE: Multiplex Immunofluorescence on Fresh Frozen Tissue
AUTHORS: Maya Brewer, Yuantee Zhu, Elizabeth Neumann, Danielle Gutierrez, Jeff Spraggins, Mark de Caestecker
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Scope:</div><div class = "text-block">To describe the procedure for multiple cycles ... | ["[Immunofluorescence]\nIf sections are frozen, allow them to equilibrate to room temperature (~15 minutes). Place slides in a humidified chamber. They will remain in the chamber throughout this protocol.", "[Immunofluorescence]\nWhile slide is dry, using a hydrophobic pen, draw a large barrier around the section. Do n... |
57,722 | Cyanobacterial Growth, Harvest, and Genomic DNA Prep | 4 | dx.doi.org/10.17504/protocols.io.b4k2quye | https://www.protocols.io/view/cyanobacterial-growth-harvest-and-genomic-dna-prep-b4k2quye | Ryan D Ward, Truc Mai, Nicole Pietrasiak | TITLE: Cyanobacterial Growth, Harvest, and Genomic DNA Prep
AUTHORS: Ryan D Ward, Truc Mai, Nicole Pietrasiak
[DESCRIPTION]
This protocol is a method for the growth of terrestrial and freshwater cyanobacteria in liquid Z8 medium and the subsequent harvesting and genomic DNA extraction. Life history traits of these m... | ["[Biomass growing conditions] Transfer100 mLsterile liquid Z8 media into a .\n \nLabel the flask with the strain ID. \nInoculate with cyanobacterial specimen. \nSet vented cap with a 0.22µm pore-size PTFE membrane to the \"open\" position to allow for gas exchange.\nSecure flask into an orbital shaker at beneath a flu... |
65,160 | Palaeoproteomics protocol - arid environment samples | 4 | dx.doi.org/10.17504/protocols.io.yxmvmn1kog3p/v1 | https://www.protocols.io/view/palaeoproteomics-protocol-arid-environment-samples-cbvgsn3w | Louise Le Meillour | TITLE: Palaeoproteomics protocol - arid environment samples
AUTHORS: Louise Le Meillour
[DESCRIPTION]
The analysis of the skeletal remains of vertebrates in archaeological contexts provides information about human-animal relationship and their environment. Their taxonomic identification based on macroscopic observatio... | ["[Solutions to prepare before starting] EDTA 500 mL 0.5 Molarity (M) pH 7.4", "[Solutions to prepare before starting] NH4HCO3 200 mL 50 millimolar (mM) \nWeigh 0.7906 g of ammonium bicarbonate (Sigma Aldrich). Add the weighed powder to 100 mL of milliQ water. Shake manually until the crystals are dissolved. Make up to... |
71,079 | PCR normalization and size selection with magnetic beads | 4 | dx.doi.org/10.17504/protocols.io.q26g7y859gwz/v1 | https://www.protocols.io/view/pcr-normalization-and-size-selection-with-magnetic-chnft5bn | Dominik Buchner | TITLE: PCR normalization and size selection with magnetic beads
AUTHORS: Dominik Buchner
[DESCRIPTION]
This protocol describes how to clean up and normalize PCR products or DNA extracts and perform a size selection with carboxylated-magnetic beads and a PEG-NaCl buffer. It works by diluting the beads so that the bindi... | ["Shake the normalization solution until the beads are homogeneously resuspended", "Add 31 µL and 28 µL to a 250 µL U-bottom assay plate", "Add 9 µL", "To bind the DNA to the beads shake at", "Place the plate on a magnet to pellet the beads for 2 min", "Discard the supernatant by pipetting", "With the plate still on ... |
67,631 | RNA Extraction and RT-qPCR of Human Lung Organoids | 1 | dx.doi.org/10.17504/protocols.io.14egn7z8zv5d/v3 | https://www.protocols.io/view/rna-extraction-and-rt-qpcr-of-human-lung-organoids-ceaptadn | Morris Baumgardt, Maren Hülsemann, Maren Mieth, Doris Frey, Stefan Hippenstiel, Andreas C. Hocke, Katja Hönzke | TITLE: RNA Extraction and RT-qPCR of Human Lung Organoids
AUTHORS: Morris Baumgardt, Maren Hülsemann, Maren Mieth, Doris Frey, Stefan Hippenstiel, Andreas C. Hocke, Katja Hönzke
[DESCRIPTION]
This protocol describes the RNA extraction from human alveolar-like organoids followed by the perfomance of a RT-qPCR to quant... | ["[Organoid lysis for RNA isolation] Grow your 3D model as described.", "[Organoid lysis for RNA isolation] Remove the entire organoid medium from the wells.", "[Organoid lysis for RNA isolation] Add 1 mL ice-cold base medium and collect Cultrex with organoids in a 2 mL tube and flush well with additional 1 mL base me... |
53,735 | Quantitation of lower urinary tract afferents in 3D reconstruction of lumbosacral spinal cord sections | 1 | dx.doi.org/10.17504/protocols.io.byqfpvtn | https://www.protocols.io/view/quantitation-of-lower-urinary-tract-afferents-in-3-byqfpvtn | John-Paul Fuller-Jackson, Peregrine B Osborne, Janet R Keast | TITLE: Quantitation of lower urinary tract afferents in 3D reconstruction of lumbosacral spinal cord sections
AUTHORS: John-Paul Fuller-Jackson, Peregrine B Osborne, Janet R Keast
[DESCRIPTION]
This protocol details the 3D reconstruction of the lumbosacral spinal cord using alternating cryosections, and then goes thr... | ["[File preparation] Prior to image importation, the series of images to be aligned need to be numbered in their anatomical order (typically rostrocaudal). TissueMaker acknowledges only the last digits in the file name. For example: Section001, Section002 etc.", "[File preparation] Each file should be a single image. A... |
80,149 | Immunofluorescent staining for neuronal marker MAP2 | 1 | dx.doi.org/10.17504/protocols.io.j8nlkwj46l5r/v1 | https://www.protocols.io/view/immunofluorescent-staining-for-neuronal-marker-map-cshvwb66 | Qing Wang | TITLE: Immunofluorescent staining for neuronal marker MAP2
AUTHORS: Qing Wang
[DESCRIPTION]
This is the protocol for immunofluorescent staining for neuronal marker MAP2.
[STEPS]
1. 1. Treat differentiated SH-SY5Y cells with 40 ug/mL eumelanin or pheomelanin or PBS for 24 hours.
2. 2. Process cells using Cytofix/Cytop... | ["1. Treat differentiated SH-SY5Y cells with 40 ug/mL eumelanin or pheomelanin or PBS for 24 hours.", "2. Process cells using Cytofix/Cytoperm™ fixation/permeabilization solution (BD554714, Thermo Fisher Scientific) and block with 5% normal goat serum.", "3. Add primary antibody against microtubule-associated protein 2... |
32,382 | Active Avoidance protocol 01282020 | 1 | dx.doi.org/10.17504/protocols.io.bbu6inze | https://www.protocols.io/view/active-avoidance-protocol-01282020-bbu6inze | Teresa Macheda, Henry Snider, James B. Watson, Kelly N. Roberts, Adam Bachstetter | TITLE: Active Avoidance protocol 01282020
AUTHORS: Teresa Macheda, Henry Snider, James B. Watson, Kelly N. Roberts, Adam Bachstetter
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify"></div><style>
.justify:after {
content: "";
... | ["Experiment Design and Recommendations:Housing: Behavior is affected by the housing mode. Singly housed mice could perform differently than group housed mice. Blinding: Experimental groups of mice should be coded while the operator is testing the mice.Test order: Mice should be randomized in test order, to avoid confo... |
99,380 | WATER PRODUCTION FOR AWARE (Total Bacteria and Antibiotic Resistance Genes): | 0 | dx.doi.org/10.17504/protocols.io.kxygxyzodl8j/v1 | https://www.protocols.io/view/water-production-for-aware-total-bacteria-and-anti-ddau22ew | Celia Manaia | TITLE: WATER PRODUCTION FOR AWARE (Total Bacteria and Antibiotic Resistance Genes):
AUTHORS: Celia Manaia
[DESCRIPTION]
The protocol summarises the procedures used for analytical control. The protocol describes the Standard Operating Procedure (SOP) for the optimization of advanced tertiary treatment of water, based o... | ["[Total Bacteria and Antibiotic Resistance Genes):] The water production for AWARE main activities includes three stages – disinfection by ultraviolet C radiation (UVC), storage for1440 min-1440 min(according to water load and season) and ozonation. The water quality is monitored at these three stages, for the paramet... |
25,946 | MAGDM method based on some qROFDPPHM operators | null | dx.doi.org/10.17504/protocols.io.5j2g4qe | null | Yanru Zhong, Hong Gao, Xiuyan Guo, Yuchu Qin, Meifa Huang, Xiaonan Luo | TITLE: MAGDM method based on some qROFDPPHM operators
AUTHORS: Yanru Zhong, Hong Gao, Xiuyan Guo, Yuchu Qin, Meifa Huang, Xiaonan Luo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><a href="" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">In this paper, a set of D... | [] |
78,356 | Study design/methodology (Part 3 of "Effects of Online Exercise Intervention on Physical and Mental Conditions in Young Adults with Chronic Neck Pain") | 1 | dx.doi.org/10.17504/protocols.io.kxygx94kdg8j/v1 | https://www.protocols.io/view/study-design-methodology-part-3-of-34-effects-of-o-cqruvv6w | Yiting Lin | TITLE: Study design/methodology (Part 3 of "Effects of Online Exercise Intervention on Physical and Mental Conditions in Young Adults with Chronic Neck Pain")
AUTHORS: Yiting Lin
[DESCRIPTION]
This is a Part 3 of "Effects of Online Exercise Intervention on Physical and Mental Conditions in Young Adults with Ch... | [] |
97,106 | USDA LTAR Common Experiment measurement: Total suspended solids (TSS) | 1 | dx.doi.org/10.17504/protocols.io.261ge5pjog47/v1 | https://www.protocols.io/view/usda-ltar-common-experiment-measurement-total-susp-da3s2gne | Brent Dalzell, Oliva Pisani | TITLE: USDA LTAR Common Experiment measurement: Total suspended solids (TSS)
AUTHORS: Brent Dalzell, Oliva Pisani
[DESCRIPTION]
Total suspended solids (TSS) refers to all the material from a well-mixed sample retained by a filter media. In the case of environmental water samples, TSS is commonly used to measure sedime... | ["[Sample collection] At a minimum, collect 1 mg of TSS residue. At a maximum, TSS should not impede the flow rate of the filter media (slow filtration is more time-consuming but does not impact results).", "[Sample collection] Return samples to the laboratory on ice and filter them on collection day if possible.", "[S... |
null | null | null | dx.doi.org/10.17504/protocols.io.hmwb47e | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?. | [] |
36,856 | PBMCs isolation from CPT™ tube | 1 | null | https://www.protocols.io/view/pbmcs-isolation-from-cpt-tube-bf8yjrxw | Woong-Yang Park, Jay Shin, Shyam Prabhakar | TITLE: PBMCs isolation from CPT™ tube
AUTHORS: Woong-Yang Park, Jay Shin, Shyam Prabhakar
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details the procedure for collection and isolation of blood samples using CPT tubes.</div></div>
[STEPS]
?. [Centrifugation and Collection of Blo... | ["[Centrifugation and Collection of Blood Sample]\nCentrifuge tube/blood sample at in a horizontal rotor (swing-out head) for a minimum of at to .\n0 Room temperature\nCentrifuge: 1500 33\nCentrifuge: 1800 33\nSpeed change of accel/decel: Soft\nRemix the blood sample immediately prior to centrifugation by gently inv... |
20,349 | Transfection of constructs in diplonemids to enhance the HR pathway, using RS-1 (3-(benzylamino) sulfonyl)-4-bromo-N-(4-bromophenyl) benzamide). | null | dx.doi.org/10.17504/protocols.io.x45fqy6 | null | Binnypreet Kaur, Drahomíra Faktorová , Julius Lukeš | TITLE: Transfection of constructs in diplonemids to enhance the HR pathway, using RS-1 (3-(benzylamino) sulfonyl)-4-bromo-N-(4-bromophenyl) benzamide).
AUTHORS: Binnypreet Kaur, Drahomíra Faktorová , Julius Lukeš
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">RS-1 (RAD51-stimulatory compound 1) is... | ["Step 1: Countthe cells and plan to 1 nucleofection with 5x 107 cells for each construct.", "Step 2: Harvestthe cells by centrifugation at 1300xg for 5 min at room temperature in Swing Bucket Rotor.", "Step 3: Resuspendthe cell pellet in 100ul of AMAXA Human T- cell solution at 4C (from refrigerator combine 81.8ul of ... |
85,733 | KAPP-Sen TMC: Tissue Section Preparation for 10x Genomics Visium CytAssist | 1 | dx.doi.org/10.17504/protocols.io.81wgbx6bylpk/v1 | https://www.protocols.io/view/kapp-sen-tmc-tissue-section-preparation-for-10x-ge-cxydxps6 | Juliana Alcoforado Diniz, Elaine Bechtel, Bill Flynn, Paul Robson | TITLE: KAPP-Sen TMC: Tissue Section Preparation for 10x Genomics Visium CytAssist
AUTHORS: Juliana Alcoforado Diniz, Elaine Bechtel, Bill Flynn, Paul Robson
[DESCRIPTION]
Sectioning was performed by the JAX Histology core in BH, ME. All experiments preceding this technique were performed at 4°C and RNase-free, as desc... | ["[Preparation of Workspace] Prepare workspace according to dx.doi.org/10.17504/protocols.io.36wgq37polk5/v1", "[Curl Collection and Storage] To verify if fixation and RNA hydrolysis during storage would lead to low yield and fragmented RNA the blocks were initially submitted to an RNA quality assay.\n\nBlocks arrive w... |
70,166 | uDumBell – Circularization of rv0678 for genotypic bedaquiline resistance testing of Mycobacterium tuberculosis | 1 | dx.doi.org/10.17504/protocols.io.36wgqj9zyvk5/v1 | https://www.protocols.io/view/udumbell-circularization-of-rv0678-for-genotypic-b-cgrwtv7e | Jason D Limberis | TITLE: uDumBell – Circularization of rv0678 for genotypic bedaquiline resistance testing of Mycobacterium tuberculosis
AUTHORS: Jason D Limberis
[DESCRIPTION]
The ligation of dumbbell (hairpin) oligos to linear dsDNA produces pseudo-circular DNA. Including deoxyUridine in the PCR primer sequences causes Q5 and other h... | ["[Amplicon PCR]", "[Adapter ligation] Prepare the dumbell (hairpin) by incubating at 80 °C followed by cooling to room temperature over 30 min(this only needs to be done once)", "[Exonuclease treatment – optional] Incubate at 37 °C for 30 min\nStop reaction by adding EDTA to at least 11 mM.\nHeat Inactivation 70 °CC f... |
null | null | null | dx.doi.org/10.17504/protocols.io.dpw5pd | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
The life cycle of phages can be characterized by one-step growth experiments, which are designed in a way that allows only a single infection cycle to take place (i.e., no re-infections occurring by phages produced during the experiment).
[BEFORE_START]
To limit the phage–host ... | [] |
73,904 | Whole blood assay-Scrub typhus for flow cytometer | 1 | dx.doi.org/10.17504/protocols.io.5jyl8jd2dg2w/v1 | https://www.protocols.io/view/whole-blood-assay-scrub-typhus-for-flow-cytometer-ckequtdw | Manutsanun Inthawong | TITLE: Whole blood assay-Scrub typhus for flow cytometer
AUTHORS: Manutsanun Inthawong
[DESCRIPTION]
This is an optimized new whole blood assay for studying scrub typhus-specific cellular responses specifically suited for work in remote areas. This assay is based on stimulation with a whole cell O. tsutsugamushi anti... | ["[Day 1. Whole blood stimulation for scrub typhus study] Prepare pre-labelled 5 ml tubes to each contain 5 µl of “COCKTAIL” (co-stimulant) and NO Brefeldin A. Add the stimulants as follows to respective tubes as below", "Each subject in the study needs 3 x 5 ml tubes labelled with their ID number and stimulant (a... |
29,362 | CasX Cleavage Assay | null | dx.doi.org/10.17504/protocols.io.8wshxee | null | Liz O'Brien, Connor Tsuchida | TITLE: CasX Cleavage Assay
AUTHORS: Liz O'Brien, Connor Tsuchida
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes a CasX Cleavage Assay.</div></div>
[STEPS]
?. [Annealing Duplex DNA]
Prepare stock of labelled target strand DNA to be of .
100 µl
?. [Annealing Duplex DNA]
Mix ... | ["[Annealing Duplex DNA]\nPrepare stock of labelled target strand DNA to be of .\n100 µl", "[Annealing Duplex DNA]\nMix of labelled target strand with of unlabelled nontarget strand to make a stock of duplex substrate.\n50 µl\n50 µl\n100 µl\nReverse concentrations for labelled nontarget, unlabelled target.", "[An... |
88,600 | High-resolution imaging of the human cadaver spinal cord | 1 | dx.doi.org/10.17504/protocols.io.bp2l6x86zlqe/v1 | https://www.protocols.io/view/high-resolution-imaging-of-the-human-cadaver-spina-c2ryyd7w | Matteo Del Brocco, Lucy Liang, Lee Fisher, T Kevin Hitchens, Elvira Pirondini | TITLE: High-resolution imaging of the human cadaver spinal cord
AUTHORS: Matteo Del Brocco, Lucy Liang, Lee Fisher, T Kevin Hitchens, Elvira Pirondini
[DESCRIPTION]
Detailed description of steps to extract and prepared tissue samples to acquire ultra-high resolution images of the human cadaver spinal cord, following a... | ["[Sample Preparation] Place the cadaveric specimen in a prone position and identify the desired spinal segments by counting the spinous processes.", "[Sample Preparation]", "[Imaging Protocol] First, perform high-resolution CT imaging (250 µm resolution) on the sample to obtain good images of the vertebral column.", "... |
18,920 | Preparation of defined medium for marine holozoans. | 1 | dx.doi.org/10.17504/protocols.io.wqgfdtw | https://www.protocols.io/view/preparation-of-defined-medium-for-marine-holozoans-wqgfdtw | Sebastian R Najle, Eduard Ocaña-Pallarès, Iñaki Ruiz-Trillo | TITLE: Preparation of defined medium for marine holozoans.
AUTHORS: Sebastian R Najle, Eduard Ocaña-Pallarès, Iñaki Ruiz-Trillo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left">In order to study specific metabolic pathways in microorganisms is crucial ... | ["[Preparation of stock solutions]\nStock solution A: Trace elements.Dissolve the following components in dH2O to bring a final volume of 1 liter:Na2EDTA • 2H2O ------------------------ 4.36 gFeCl3 • 6H2O ------------------------------ 3.15 gMnCl2 • 4H2O ----------------------------- 178.1 mgZnSO4 • 7H2O --------------... |
28,956 | Aptamer 1-step conjugation protocol | null | dx.doi.org/10.17504/protocols.io.8h4ht8w | null | Jorge Fernández | TITLE: Aptamer 1-step conjugation protocol
AUTHORS: Jorge Fernández
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Adaptated version of the crosslinking bioconjugation protocol depicted in </span><a href="https://doi.org/10.1177%2F1087057106292138" style = "text-decoration:underline;color:blu... | ["[Reactive Preparations]\nPrepare a 0.4 M aqueous solution of sulfo-NHS. Weight 44.5 mg of sulfo-NHS and dissolve it in 500 μL of distilled water. Keep stored at 4 ºC. Sulfo-NHS can be stored under refrigerator for a couple of months.", "[Reactive Preparations]\nPrepare 0.32 M EDC solution. Pipette 29.5 μL of 97% EDC ... |
85,147 | Mapping Research Data at the University of Bologna: Protocol | 1 | dx.doi.org/10.17504/protocols.io.n2bvj87jpgk5/v2 | https://www.protocols.io/view/mapping-research-data-at-the-university-of-bologna-cxd3xi8n | Sara Coppini, Bianca Gualandi, Giulia Caldoni, Mario Marino, Silvio Peroni, francesca.masini | TITLE: Mapping Research Data at the University of Bologna: Protocol
AUTHORS: Sara Coppini, Bianca Gualandi, Giulia Caldoni, Mario Marino, Silvio Peroni, francesca.masini
[DESCRIPTION]
Led by data stewards at the University of Bologna, this protocol was developed within an analysis of research data generated and manage... | ["[Data collection] Using the DMPs and GAs of European projects as input, we structured the table in which to collect data information with the following variables or fields and their meaning or accepted values:\nProject identifier (project_id): alphanumeric string to identify the project to which the described data be... |
45,478 | Bicinchoninic acid Acid Protein Concentration measurement | 1 | null | https://www.protocols.io/view/bicinchoninic-acid-acid-protein-concentration-meas-bqnemvbe | JCPrice | TITLE: Bicinchoninic acid Acid Protein Concentration measurement
AUTHORS: JCPrice
[STEPS]
?. Thaw the samples on ice.
?. Prepare standards using Pierce Protein Standard-2mg/ml, 1 mg/mL, 0.5 mg/mL, 0.25 mg/mL, 0.125 mg/mL, 0.062 mg/mL, 0.031 mg/mL, 0.016 mg/mL, 0 mg/mL
?. Organize your well plate and draw a map o... | ["Thaw the samples on ice.", "Prepare standards using Pierce Protein Standard-2mg/ml, 1 mg/mL, 0.5 mg/mL, 0.25 mg/mL, 0.125 mg/mL, 0.062 mg/mL, 0.031 mg/mL, 0.016 mg/mL, 0 mg/mL", "Organize your well plate and draw a map on the lid. Group your standards and each dilution of your experimental standards to simplify ... |
71,589 | Adult human lung cell dissociation (on ice) | 1 | dx.doi.org/10.17504/protocols.io.6qpvr13zgmkn/v2 | https://www.protocols.io/view/adult-human-lung-cell-dissociation-on-ice-ch6dt9a6 | Andrew Potter | TITLE: Adult human lung cell dissociation (on ice)
AUTHORS: Andrew Potter
[DESCRIPTION]
This protocol was used to generate a single cell suspension from transbronchial biopsies from human lung. The procedure is carried out on ice, reducing artifact gene expression changes. Cell yield / mg is >5000 cells/mg with 80-90%... | ["[Isolate and mince tissue] Transport tissue in ice-cold PBS.", "[Isolate and mince tissue] Transfer 13 mg tissue to petri dish on ice with 100 µL enzyme mix; using razor blade mince thoroughly for 2 min until large chunks are broken up finely.\n2 min", "[Layer 1] Add 13 mg minced tissue to 900 µL enzyme mix (1 mL tot... |
null | null | null | dx.doi.org/10.17504/protocols.io.hn8b5hw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?. | [] |
34,125 | DSBEST v2.0 (Caroe et al. 2018) | 1 | dx.doi.org/10.17504/protocols.io.j8nlkemwxl5r/v1 | https://www.protocols.io/view/dsbest-v2-0-caroe-et-al-2018-bdjmi4k6 | Alicia Grealy | TITLE: DSBEST v2.0 (Caroe et al. 2018)
AUTHORS: Alicia Grealy
[DESCRIPTION]
This bench protocol is based on the work of Caroe et al. (2018), for preparing shotgun libraries from double-stranded DNA, typically for ancient and degraded DNA. Please cite Caroe et al. (2018) if you use this bench protocol!
[BEFORE_START]
... | ["[Preparation] \"Suit up\" in this order: hair net, nitrile gloves, facemask, coveralls, gumboots, booties, second pair of gloves.", "[Preparation] Prepare the space by decontaminating surfaces with 10% household bleach followed by 70% ethanol. UV irradiate pipettes and racks. Racks should be bleached between subseque... |
79,909 | Processamento de actígrafos pós-coleta - ActTrust | 1 | dx.doi.org/10.17504/protocols.io.ewov14kjovr2/v4 | https://www.protocols.io/view/processamento-de-act-grafos-p-s-coleta-acttrust-csadwaa6 | Daniel Vartanian | TITLE: Processamento de actígrafos pós-coleta - ActTrust
AUTHORS: Daniel Vartanian
[DESCRIPTION]
Este protocolo faz parte do processo de coleta de dados actigráficos do Grupo Interdisciplinar de Pesquisa em Ritmos Biológicos (GIPERBIO). Ele foi desenvolvido para os actígrafos da empresa Condor Instruments. Algumas das... | ["[Conexão] Conecte o actígrafo ao computador.", "[Leitura] Leia os dados do actígrafo.", "[Configuração] Desative o actígrafo.", "[Exportação e Armazenamento] Exporte e salve os dados actigráficos.", "[Registro] Preencha e envie o formulário de processamento de actígrafos.", "[Finalização] Guarde o actígrafo dentro de... |
27,391 | Tissue Procurement: Cryopreservation with OCT Compound | 1 | dx.doi.org/10.17504/protocols.io.6y7hfzn | https://www.protocols.io/view/tissue-procurement-cryopreservation-with-oct-compo-6y7hfzn | Kerry Wiles | TITLE: Tissue Procurement: Cryopreservation with OCT Compound
AUTHORS: Kerry Wiles
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Specimens are frozen to provide a hardened matrix for sectioning and to preserve the morphological, biochemical, and immunological properties of cells and tissues. Freez... | ["[Tissue Procurement: Cryopreservation]\nProcure anatomic site and tissue type per request, but sizes should be no larger than 0.4cm x 0.4cm x 0.3cm. OCT ratio should be 30:1 to properly infiltrate the tissue.", "[Tissue Procurement: Cryopreservation]\nArrange the pre-labeled, UV sterilized clamshells on a block of d... |
null | null | null | dx.doi.org/10.17504/protocols.io.dqi5ud | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
For use in "<a href="https://www.protocols.io/view/Isolation-of-cyanophages-by-plaque-assays-dqg5tv" target="_blank">Isolation of cyanophages by plaque assays</a>"
[STEPS]
?. | [] |
61,968 | Non-cleavable Linkers | 6 | dx.doi.org/10.17504/protocols.io.kqdg3p3yel25/v1 | https://www.protocols.io/view/non-cleavable-linkers-b8rqrv5w | BOC Sciences | TITLE: Non-cleavable Linkers
AUTHORS: BOC Sciences
[DESCRIPTION]
Non-cleavable linkers require mAb degradation within lysosomes after ADC internalization to release the active drug. BOC Sciencesprovides synthetic non-cleavable linker products with a wide range of scales, purities, and delivery time options to mee... | [] |
31,713 | Pooled Library Amplification | null | dx.doi.org/10.17504/protocols.io.ba79ihr6 | null | Addgene The Nonprofit Plasmid Repository | TITLE: Pooled Library Amplification
AUTHORS: Addgene The Nonprofit Plasmid Repository
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes pooled library amplification. To see the full abstract and additional resources, visit </div><div class = "text-block"><a href="https://www.ad... | ["[Day 1]\nAdd DNA to each aliquot of thawed Endura Duos on ice. Flick gently to mix\n200 ng\n50 µl", "[Day 1]\nElectroporate cells (one at a time for a total of eight electroporations):\nElectroporator Conditions: Bio-Rad Micropulser Ec1 0.1 cm cuvette, 1.8 kV, 1 pulse.", "[Day 1]\nAliquot DNA-Endura into pre-chill... |
95,836 | Synogram: assessing phage-antibiotic synergistic and antagonistic interactions | 0 | null | https://www.protocols.io/view/synogram-assessing-phage-antibiotic-synergistic-an-c9t4z6qw | Carmen Gu Liu | TITLE: Synogram: assessing phage-antibiotic synergistic and antagonistic interactions
AUTHORS: Carmen Gu Liu
[DESCRIPTION]
Bacteriophage (phage) therapy is a promising approach to combat the rise of multidrug-resistant bacteria. Currently, the preferred clinical modality is to pair phage with an antibiotic, a practice... | ["[Method: antibiotic] Make a 1.6 mg/mL working stock for 10 mL by diluting 0.016 g or 16 mg of antibiotic in 10 mL of solvent. Filter sterilize the antibiotic", "[Method: bacteria and master plate] Make an overnight culture before the day of experiment. On the day of experiment, inoculate 100 uL of bacteria into aroun... |
84,449 | Inducing Psychosocial Stress in the Laboratory: A Study Protocol for the Trier Social Stress Test (TSST) | 1 | dx.doi.org/10.17504/protocols.io.e6nvwj85zlmk/v3 | https://www.protocols.click/view/inducing-psychosocial-stress-in-the-laboratory-a-s-cwp9xdr6 | Johannes Bodo Heekerens | TITLE: Inducing Psychosocial Stress in the Laboratory: A Study Protocol for the Trier Social Stress Test (TSST)
AUTHORS: Johannes Bodo Heekerens
[DESCRIPTION]
This protocol details about a laboratory session aiming at inducing psychosocial stress in the laboratory using the Trier Social Stress Test (TSST). During the... | ["[Before the TSST] Before the TSST, the investigator shows and explains to the subject the devices for the assessment of heart rate (Vivalink ECG Patch), electrodermal activity (Empatica Smartwatch), and blood pressure (iHealth BP Cuff). The subject is instructed to put the devices on. The investigator makes sure that... |
48,795 | Mechanosensitive enteric neurons: incidence and abundance in the porcine submucosal plexus with ultrafast neuroimaging and immunhistochemical techniques | 1 | dx.doi.org/10.17504/protocols.io.btv3nn8n | https://www.protocols.io/view/mechanosensitive-enteric-neurons-incidence-and-abu-btv3nn8n | Gemma Mazzuoli-Weber, Kristin Elfers, Anna Katharina Filzmayer | TITLE: Mechanosensitive enteric neurons: incidence and abundance in the porcine submucosal plexus with ultrafast neuroimaging and immunhistochemical techniques
AUTHORS: Gemma Mazzuoli-Weber, Kristin Elfers, Anna Katharina Filzmayer
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is to... | ["Samples of colon were taken from apparently healthy pigs, placed in ice-cold oxygenated Krebs solution for preparation and immediately transferred to the laboratory. Tissues were then dissected in the ice-cold oxygenated Krebs solution for preparation to obtain whole-mount inner submucosal plexus preparations.", "Tis... |
74,177 | Diagnostic value of PD-L1 ≥ 1% expression status and its efficacy correlation with PD-1/PD-L1 inhibitor therapy in advanced solid cancers: a meta-analysis | 4 | dx.doi.org/10.17504/protocols.io.8epv5j2p5l1b/v1 | https://www.protocols.io/view/diagnostic-value-of-pd-l1-1-expression-status-and-ckn9uvh6 | Anonymous | TITLE: Diagnostic value of PD-L1 ≥ 1% expression status and its efficacy correlation with PD-1/PD-L1 inhibitor therapy in advanced solid cancers: a meta-analysis
AUTHORS: Anonymous
[DESCRIPTION]
Despite immune checkpoint inhibitors (ICIs) seem to have found their role in several hematological and solid tumors, several... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.gvsbw6e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Peptide purification counts after the synthesis, or other forms of making of it. For drug applied peptide like <a href="http://www.creative-peptides.com/services/cell-penetrating-peptides-synthesis-services.html" target="_blank">cell-penetrating peptides</a> are supposed to b... | [] |
93,025 | Electrophoretic mobility shift assay (EMSA) | 4 | null | https://www.protocols.io/view/electrophoretic-mobility-shift-assay-emsa-c639zgr6 | Olivier Boivin | TITLE: Electrophoretic mobility shift assay (EMSA)
AUTHORS: Olivier Boivin
[DESCRIPTION]
This protocol details an experimental procedure that can be followed to assess the DNA binding activity of a purified protein sample (recombinant yeast Cbf1 used here as example) to different sequences. DNA probes containing the d... | ["[Probe annealing] Create storage stocks by resuspending ssDNA oligos to 100uM (100pmol/ul) in 1x IDTE buffer (10 mM Tris, 0.1 mM EDTA, pH 8.0).", "[Probe annealing] Create 10uM working stocks from the 100uM storage stocks. For 100uL of working stock:", "[Probe annealing] Anneal labeled 1 units ssDNA probes to 1/1.2 u... |
79,609 | Handling and Sampling Medium-Large Mammals - ISL Peru | 1 | dx.doi.org/10.17504/protocols.io.81wgby8y1vpk/v1 | https://www.protocols.io/view/handling-and-sampling-medium-large-mammals-isl-per-cryzv7x6 | Cristian Tirapelle, Jorge Luis Mendoza-Silva, Mrinalini Watsa, Gideon Erkenswick | TITLE: Handling and Sampling Medium-Large Mammals - ISL Peru
AUTHORS: Cristian Tirapelle, Jorge Luis Mendoza-Silva, Mrinalini Watsa, Gideon Erkenswick
[DESCRIPTION]
Program Timing
Trap placement and habituation occurs toward the end of the rainy season (March - May). Sample collection occurs annually during the rainfo... | ["[ACTIVE TRAP MONITORING] At all times, one team member monitors the trap sensor alert system (SAS), while all others remain ready to take action. Shifts should be organized to ensure continuous monitoring of SAS, even during the the night.", "[ACTIVE TRAP MONITORING] When SAS is triggered, the VET and HANDLER depart ... |
44,200 | McGill Nanopore Ligation LibPrep Protocol SQK-LSK109 | 1 | dx.doi.org/10.17504/protocols.io.bpegmjbw | https://www.protocols.io/view/mcgill-nanopore-ligation-libprep-protocol-sqk-lsk1-bpegmjbw | Sarah Reiling, Shu-Huang Chen, Ioannis Ragoussis | TITLE: McGill Nanopore Ligation LibPrep Protocol SQK-LSK109
AUTHORS: Sarah Reiling, Shu-Huang Chen, Ioannis Ragoussis
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used to for both amplicon and high molecular weight DNA library preparations from genomic DNA using Nanopore ligation... | ["[DNA repair and end-prep]\nPrepare 1.5 ug of genomic DNA into a 1.5 ml Eppendorf DNA LoBind tube. Adjust the volume to 48 uL with nuclease-free water. Mix by flicking the tube and spin down briefly.\n1.5 ug genomic DNA is the default amount. We are aiming to have 5-50 fmol for MinION / PromethION loading and 3-20 fmo... |
48,529 | Immuno-correlative light and electron microscopy (iCLEM) using TEM | 4 | dx.doi.org/10.17504/protocols.io.btmrnk56 | https://www.protocols.io/view/immuno-correlative-light-and-electron-microscopy-i-btmrnk56 | Viola Oorschot, Jillian C Danne, Benjamin Lindsey, Jan Kaslin, Georg Ramm | TITLE: Immuno-correlative light and electron microscopy (iCLEM) using TEM
AUTHORS: Viola Oorschot, Jillian C Danne, Benjamin Lindsey, Jan Kaslin, Georg Ramm
[DESCRIPTION]
Immuno- correlative light and electron microscopy (iCLEM) combines ultrastructural information obtained from high resolution electron microscopy ... | ["[Tissue fixation] Dissect out the tissue of interest (example, forebrain of Tg(proliferating cell nuclear antigen:GFP) transgenic adult zebrafish with olfactory bulbs attached for tissue orientation) on a teflon plate or dental wax sheet using fine forceps and a scalpel blade, at room temperature and place in fixativ... |
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