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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55,346 | A protocol for a scoping review of implementation strategies to scale up self-administered depot medroxyprogesterone acetate subcutaneous injectable contraception | 1 | dx.doi.org/10.17504/protocols.io.b2asqaee | https://www.protocols.io/view/a-protocol-for-a-scoping-review-of-implementation-b2asqaee | Adeniyi Kolade Aderoba, Petrus Steyn, James Njogu Kiarie | TITLE: A protocol for a scoping review of implementation strategies to scale up self-administered depot medroxyprogesterone acetate subcutaneous injectable contraception
AUTHORS: Adeniyi Kolade Aderoba, Petrus Steyn, James Njogu Kiarie
[DESCRIPTION]
Self-administration of depot medroxyprogesterone acetate subcutaneous... | ["Background\n\nResearch has shown that self-administration of depot medroxyprogesterone acetate subcutaneous injectable contraception (DMPA-SC) is feasible, safe, and effective.1 A recent meta-analysis of three randomized controlled trials found a significantly higher rate of 1-year DMPA-SC continuation among women wh... |
null | null | null | dx.doi.org/10.17504/protocols.io.c69zh5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Case 1: Quick check of viral concentration. Use this protocol when you can count your samples in a few days.<br /><br />For when long term storage of slide is required, see <a href="https://www.protocols.io/view/SYBR-Gold-Staining-for-Viral-Enumeration-Case-2-c7fzjm" target... | [] |
55,469 | Targeted ExSeq -- Tissue Preparation | 1 | dx.doi.org/10.17504/protocols.io.b2emqbc6 | https://www.protocols.io/view/targeted-exseq-tissue-preparation-b2emqbc6 | Anubhav Sinha, Yi Cui, Shahar Alon, Asmamaw T. Wassie, Fei Chen, Ed Boyden | TITLE: Targeted ExSeq -- Tissue Preparation
AUTHORS: Anubhav Sinha, Yi Cui, Shahar Alon, Asmamaw T. Wassie, Fei Chen, Ed Boyden
[DESCRIPTION]
This protocol accompanies Expansion Sequencing (ExSeq), and describes the tissue preparation for Targeted ExSeq. The steps described here are a generalizati... | ["[Preparation of Stock Solutions] Common Laboratory Stocks\n\nAll solutions prepared using nuclease-free reagents, and stored at Room temperature.\n\n1X PBS\nPBST (1X PBS with 0.1% Triton X-100 (v/v))\n70% Ethanol (v/v) in water", "[Preparation of Stock Solutions] Preparation of Reagents for LabelX RNA Anchoring\n\nLa... |
26,020 | iGEM Calibration Protocol - Flow Cytometry Cell Size | null | dx.doi.org/10.17504/protocols.io.5ncg5aw | null | Jacob Beal, Cheryl Telmer, Richard Tennant, Paul Rutten | TITLE: iGEM Calibration Protocol - Flow Cytometry Cell Size
AUTHORS: Jacob Beal, Cheryl Telmer, Richard Tennant, Paul Rutten
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Conversion from forward scatter to Eμm is not a linear function, so data cannot be converted simply by multiplying with a scali... | ["Prepare and culture experimental samples according to your desired experimental procedure.", "Prepare experimental samples as needed for running through your flow cytometer.", "Follow SpheroTech directions for preparation for PPS-6K bead sample.", "Measure all samples in flow cytometer Using the bead sample, adjust F... |
73,481 | Western blotting to detect ATP13A2 and ATP13A3 | 1 | dx.doi.org/10.17504/protocols.io.81wgbyzqovpk/v1 | https://www.protocols.io/view/western-blotting-to-detect-atp13a2-and-atp13a3-cjzhup36 | Marine Houdou, Peter Vangheluwe | TITLE: Western blotting to detect ATP13A2 and ATP13A3
AUTHORS: Marine Houdou, Peter Vangheluwe
[DESCRIPTION]
Protocol to detect ATP13A2 and ATP13A3 via Western Blotting.
[STEPS]
SECTION: Harvesting cells
1. Depending on cell type, collect the cells by scrapping them with a scrapper in Dulbecco’s Phosphate Buffered sa... | ["[Harvesting cells] Depending on cell type, collect the cells by scrapping them with a scrapper in Dulbecco’s Phosphate Buffered saline modified without calcium chloride and magnesium chloride (DPBS) (SH-SY5Y) or, using 0.25% Trypsin-EDTA (HMEC-1) for which stop enzymatic reaction by adding culture medium.", "[Harvest... |
62,823 | Regulation of mitophagy by the NSL complex underlies genetic risk for Parkinson’s disease: Drosophila Husbandry, Assays and Immunohistochemistry | 4 | dx.doi.org/10.17504/protocols.io.eq2lyn1dqvx9/v1 | https://www.protocols.io/view/regulation-of-mitophagy-by-the-nsl-complex-underli-b9kfr4tn | Natalie J. Welsh, Alexander J. Whitworth | TITLE: Regulation of mitophagy by the NSL complex underlies genetic risk for Parkinson’s disease: Drosophila Husbandry, Assays and Immunohistochemistry
AUTHORS: Natalie J. Welsh, Alexander J. Whitworth
[DESCRIPTION]
This protocol describes Drosophila stocks and husbandry, Locomotor and lifespan assays and, Immunohisto... | ["[Drosophila stocks and husbandry] Raise flies under standard conditions in a humidified, temperature-controlled incubator with a 12h:12h light:dark cycle at 25 °C, on food consisting of agar, cornmeal, molasses, propionic acid and yeast.", "[Locomotor Assay] Perform the startle induced negative geotaxis (climbing) as... |
86,324 | Confounding by Indication in Observational Studies Investigating Glucocorticoid-Associated Adverse Events in Rheumatoid Arthritis: A Protocol for a Systematic Review | 1 | dx.doi.org/10.17504/protocols.io.bp2l6x955lqe/v1 | https://www.protocols.io/view/confounding-by-indication-in-observational-studies-cyiuxuew | Andriko Palmowski, Judith Oldenkott, Anne Pankow, Anne Beenken, Eric L Matteson, Frank Buttgereit | TITLE: Confounding by Indication in Observational Studies Investigating Glucocorticoid-Associated Adverse Events in Rheumatoid Arthritis: A Protocol for a Systematic Review
AUTHORS: Andriko Palmowski, Judith Oldenkott, Anne Pankow, Anne Beenken, Eric L Matteson, Frank Buttgereit
[DESCRIPTION]
-
[STEPS]
SECTION: Abstr... | ["[Abstract] Background Glucocorticoids (GCs) are regularly used drugs in rheumatoid arthritis (RA), but they can cause adverse events (AEs). Observational studies provide important real-world evidence but can be biased. Observational studies investigating the association between AEs and GCs in RA are\nparticularly sus... |
34,934 | VIEW document | 3 | null | https://www.protocols.io/view/view-document-becwjaxe | Mariia | TITLE: VIEW document
AUTHORS: Mariia
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">text of document</div></div>
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.rvwd67e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Detergent mediated reconstitution of membrane proteins. </p>
[STEPS]
?.
?.
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?.
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?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.crmv45 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.c2zyf5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
10g/L Fe Stock Solution for Iron Chloride Precipitation of Viruses from Seawater Protocol.
[GUIDELINES]
<strong>Notes:</strong><br /><br />Solution is acidic and should be handled with care.<br /><br /> Discard solution if a cloudy precipitate forms. Do not dilute solution... | [] |
33,853 | Total Phenolic Content (TPC) | null | dx.doi.org/10.17504/protocols.io.bda5i2g6 | null | Jing Xu | TITLE: Total Phenolic Content (TPC)
AUTHORS: Jing Xu
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The TPC from samples was determined by a colorimetric methodbased on the procedure described byZhou et al. [10]2 ml Folin-Ciocalteu (FC) reagent was added to 2 ml of diluted extracts.After 3 min, 750... | [] |
94,909 | Modified RNeasy Mini Kit protocol for filter extractions - USF edition | 4 | dx.doi.org/10.17504/protocols.io.8epv59qd6g1b/v2 | https://www.protocols.io/view/modified-rneasy-mini-kit-protocol-for-filter-extra-c8w5zxg6 | Margaret M. Brisbin | TITLE: Modified RNeasy Mini Kit protocol for filter extractions - USF edition
AUTHORS: Margaret M. Brisbin
[DESCRIPTION]
RNA extraction protocol for filters - modification of RNeasy mini kit protocol
[STEPS]
SECTION: Prep
1. Wipe all surfaces inside the RNA hood with:
1. RNAase ZAP (this is a detergent so do not use ... | ["[Prep] Wipe all surfaces inside the RNA hood with:\n1. RNAase ZAP (this is a detergent so do not use much as it can leave a soapy residue)\n2. RNAse AWAY (this is a weak base, it can be used liberally but does not evaporate quickly)\n3. 70% ethanol (etOH), this can be used liberally and evaporates quickly \n\nuse lar... |
null | null | null | dx.doi.org/10.17504/protocols.io.c7dzi5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
The usefulness of cesium chloride (CsCl) step gradients and continuous gradients for the separation of viruses is based on the differing buoyant densities of viruses, bacteria, and extracellular debris. This protocol provides a method for Cesium Chloride and DNA Extraction for V... | [] |
27,021 | Safety protocols for Aquatic Microbial Ecology Research Group, Department of Microbiology, The University of Tennessee. | null | dx.doi.org/10.17504/protocols.io.6mmhc46 | null | Steven Wilhelm, Gary LeCleir, Ashley Humphrey | TITLE: Safety protocols for Aquatic Microbial Ecology Research Group, Department of Microbiology, The University of Tennessee.
AUTHORS: Steven Wilhelm, Gary LeCleir, Ashley Humphrey
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a collection of safety protocols as used by the Aquatic Microb... | [] |
18,154 | bright field pheromone imaging | null | dx.doi.org/10.17504/protocols.io.vyie7ue | null | Serena Ding | TITLE: bright field pheromone imaging
AUTHORS: Serena Ding
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">For imaging aggregation behaviour of 40 young adult C. elegans on agar using the Phoenix multi-worm tracker system. Worms are synchronised by bleaching and refeeding for 72 hours, and then 40 y... | ["[Imaging plate preparation (Day -7)]\nA separate batch of imaging plates is poured exactly seven days before each imaging day and stored at 4°C.\nImaging plates are 35 mm Petri dishes containing 3.5 mL low peptone (0.013% Difco Bacto) NGMagar (2% Bio/Agar, BioGene) to limit bacteria growth.", "[Imaging plate preparat... |
61,309 | PCR mixture and condition (2X SUPERGREEN PCR MASTER MIX) | 4 | null | https://www.protocols.io/view/pcr-mixture-and-condition-2x-supergreen-pcr-master-b745rqy6 | Yin-Tse Huang | TITLE: PCR mixture and condition (2X SUPERGREEN PCR MASTER MIX)
AUTHORS: Yin-Tse Huang
[DESCRIPTION]
PCR mixture and condition (2X SUPERGREEN PCR MASTER MIX)
[STEPS]
1. PCR mixture for generic primers
2. PCR mixture for barcoded primers
2.1. PCR condition for barcoded primers
1.1. PCR condition for generic... | ["PCR mixture for generic primers", "PCR mixture for barcoded primers", "PCR condition for barcoded primers", "PCR condition for generic primers"] |
16,842 | Bioinformatics analysis based on the results of LC-MS/MS | null | dx.doi.org/10.17504/protocols.io.upievke | null | Lihui Li | TITLE: Bioinformatics analysis based on the results of LC-MS/MS
AUTHORS: Lihui Li
[STEPS]
?. [Hierarchical Clustering]
Cluster3.0 and the Java Treeview software were used to study protein relative expression data performing hierarchicalclustering analysis. Euclidean distance algorithm for similarity measure and averag... | ["[Hierarchical Clustering]\nCluster3.0 and the Java Treeview software were used to study protein relative expression data performing hierarchicalclustering analysis. Euclidean distance algorithm for similarity measure and average linkage clustering algorithm for clusteringwere selected when performing hierarchical clu... |
null | null | null | dx.doi.org/10.17504/protocols.io.mkmc4u6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Method of isolation and culture of osteoblast coming from human subchondral bone of the knee</p>
[STEPS]
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ebjbakn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
These are protocols from: <br /><br />Paul, J. H., and M. Weinbauer. 2010. Detection of lysogeny in marine environments, p. 30–33. In S. W. Wilhelm, M. G. Weinbauer, and C. A. Suttle [eds.], Manual of Aquatic Viral Ecology. ASLO.<br /><br />Please see the <a href="http://www.asl... | [] |
89,597 | Immunoblot | 1 | dx.doi.org/10.17504/protocols.io.j8nlkom6wv5r/v1 | https://www.protocols.io/view/immunoblot-c3q5ymy6 | Núria Peñuelas | TITLE: Immunoblot
AUTHORS: Núria Peñuelas
[DESCRIPTION]
Immunoblot of rodent brain regions
[STEPS]
1. Put the frozen bulk dissections from a specific brain region in a tube with lysis buffer (50mM Tris HCl, pH 7.0; 150 mM NaCl; 5 mM EDTA; 1% SDS; NP40-1%) supplemented with protease inhibitors (Roche).
2. Homogenize ... | ["Put the frozen bulk dissections from a specific brain region in a tube with lysis buffer (50mM Tris HCl, pH 7.0; 150 mM NaCl; 5 mM EDTA; 1% SDS; NP40-1%) supplemented with protease inhibitors (Roche).", "Homogenize the tissue with syringes, pestles or a tissue homogenizer with drill. Keep on\nice during homogenizatio... |
35,198 | 3D Printed Face Shield with Closed Top | null | dx.doi.org/10.17504/protocols.io.bek6jcze | null | Julia Roßmanith | TITLE: 3D Printed Face Shield with Closed Top
AUTHORS: Julia Roßmanith
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is for building face shields with closed tops using the print template created by Hanoch Hemmerich on Thingiverse.</div></div>
[STEPS]
?. Print the head part of the f... | ["Print the head part of the face shield with the 3D printer.", "Place the overhead transparency or laminated laminating foil on the head part.", "Put a strap through both ends of the head part of the shield to fix it on your head."] |
19,675 | Media Recipes | null | dx.doi.org/10.17504/protocols.io.xf3fjqn | null | Brian Smith, baltrus@email.arizona.edu micro.tucson | TITLE: Media Recipes
AUTHORS: Brian Smith, baltrus@email.arizona.edu micro.tucson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Here you will find common media recipes used in the Baltrus Lab at the University of Arizona for growing mostly </span><span style = "font-style:italic;">Pseudomona... | [] |
61,742 | Sexual and reproductive health during Covid: a global systematic review of health system responses and service delivery adaptations | 1 | null | https://www.protocols.io/view/sexual-and-reproductive-health-during-covid-a-glob-b8inrude | hlconyers | TITLE: Sexual and reproductive health during Covid: a global systematic review of health system responses and service delivery adaptations
AUTHORS: hlconyers
[DESCRIPTION]
The COVID-19 pandemic is on-going and continues to challenge the delivery of SRH services across the globe. The impact has created imbalances in ... | ["[Background] The COVID-19 pandemic is on-going and continues to challenge the delivery of SRH services across the globe. The impact has created imbalances in healthcare provision, disruptions of routine essential services and, in most settings, require redeployment of scarce healthcare personnel across SRH services. ... |
63,078 | Deep Brain Stimulation (DBS) Implant | 4 | dx.doi.org/10.17504/protocols.io.b9uer6te | https://www.protocols.io/view/deep-brain-stimulation-dbs-implant-b9uer6te | Alexandra Nelson | TITLE: Deep Brain Stimulation (DBS) Implant
AUTHORS: Alexandra Nelson
[DESCRIPTION]
This protocols describing the steps for making implants used for deep brain stimulation (DBS) in rodents.
[STEPS]
SECTION: Twisting Wires Together
1. Gather
Ruler
Wire [A-M Systems #791000,.003’ bare, .0055 coated, half hard, 100ft ro... | ["[Twisting Wires Together] Gather\nRuler\nWire [A-M Systems #791000,.003’ bare, .0055 coated, half hard, 100ft roll] (red top box, located on shelf above electronics bench)\nSmall scissors", "[Twisting Wires Together] For each electrode, take 3 wires of 13cm.", "[Twisting Wires Together] To cut wires into 13cm, use sc... |
103,946 | Ty + AS + Thymidine Protocol | 0 | null | https://www.protocols.io/view/ty-as-thymidine-protocol-dhri354e | Eleanor Harman | TITLE: Ty + AS + Thymidine Protocol
AUTHORS: Eleanor Harman
[DESCRIPTION]
.
[STEPS]
SECTION: Media
2. Add 80% final volume of DI water to beaker
SECTION: Media
1. Yeast Extract 1.5g/500mL
Tryptone 2.5g/500mL
Thymidine 150mg/500mL
SECTION: Media
3. Add Yeast Extract, Tryptone, and Thymidine until fully dissolved
SECTI... | ["[Media] Add 80% final volume of DI water to beaker", "[Media] Yeast Extract 1.5g/500mL\nTryptone 2.5g/500mL\nThymidine 150mg/500mL", "[Media] Add Yeast Extract, Tryptone, and Thymidine until fully dissolved", "[Media] Adjust pH to 5.5", "[Media] Autoclave on Liquid 20 minute cycle"] |
67,405 | https://www.facebook.com/DiaetoxilAvis/ | 1 | dx.doi.org/10.17504/protocols.io.8epv5947dg1b/v1 | https://www.protocols.io/view/https-www-facebook-com-diaetoxilavis-cd3ms8k6 | Alexcartersz | TITLE: https://www.facebook.com/DiaetoxilAvis/
AUTHORS: Alexcartersz
[DESCRIPTION]
Diaetoxil Avis: ne personne a besoin d'avoir un corps sain. Peu importe votre richesse financière ou toutes les ressources dont vous disposez, si votre santé est mauvaise, vous attirerez de nombreux problèmes de santé dans votre conte... | ["[https://www.facebook.com/DiaetoxilAvis/]"] |
25,050 | Denaturing agarose gels for large RNAs with glyoxal | null | dx.doi.org/10.17504/protocols.io.4p2gvqe | null | Stephen Floor | TITLE: Denaturing agarose gels for large RNAs with glyoxal
AUTHORS: Stephen Floor
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">PAGE gels work great for separating small RNAs under 500 nt or so, but cannot separate larger RNAs. This protocol uses glyoxal to denature RNAs, which can then be run on ... | ["[Glyoxylate RNA]\nMix 500ng to 1ug of RNA sample 1:1 with glyoxal loading dye in ~10 ul", "[Glyoxylate RNA]\nMix the required amount of ladder 1:1 with glyoxal loading dye", "[Glyoxylate RNA]\nIncubate at 50 degrees for 30 minutes\nNote: proceed to pouring gel while glyoxylation reaction is occuring", "[Glyoxylate RN... |
62,941 | Duffy Lab Daphnia Field Sample Processing | 3 | null | https://www.protocols.io/view/duffy-lab-daphnia-field-sample-processing-b9p5r5q6 | Kira Monell, Meghan Duffy | TITLE: Duffy Lab Daphnia Field Sample Processing
AUTHORS: Kira Monell, Meghan Duffy
[DESCRIPTION]
This protocol is used to process field samples for Daphnia in the Duffy Lab. This protocol doesn't include species or parasite identification guides.
[STEPS] | [] |
97,982 | ARTIC SARS-CoV-2 sequencing protocol v4 (LSK114) | 1 | dx.doi.org/10.17504/protocols.io.bp2l6n26rgqe/v4 | https://www.protocols.io/view/artic-sars-cov-2-sequencing-protocol-v4-lsk114-dbw62phe | Josh Quick, Lauren Lansdowne | TITLE: ARTIC SARS-CoV-2 sequencing protocol v4 (LSK114)
AUTHORS: Josh Quick, Lauren Lansdowne
[DESCRIPTION]
Amplicon sequencing protocol for SARS-CoV-2 v4 (LSK114)
We thank the ARTIC network, Oxford Nanopore Technologies, New England Biolabs, BCCDC, COG-UK, CanCOGen and protocols.io commenters for their assistance de... | ["[cDNA preparation] Mix the following components in a PCR strip-tubes/plate. Gently mix by pipetting and pulse spin the tube to collect liquid.", "[cDNA preparation] Incubate the reaction as follows:\n\n 25 °C for 2 min\n 55 °C for 10 min\n 95 °C for 1 min\nHold at 4 °C", "[Multiplex PCR] Set up the two PCR reactions ... |
null | null | null | dx.doi.org/10.17504/protocols.io.tadeia6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol was used for biomechanical testing of repaired tendon.</p>
<p> </p>
[STEPS]
?. | [] |
20,280 | U Mass - Lactate dehydrogenase | null | dx.doi.org/10.17504/protocols.io.x2yfqfw | null | Jason Kim | TITLE: U Mass - Lactate dehydrogenase
AUTHORS: Jason Kim
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span><span style = "font-weight:bold;"> </span></div><div class = "text-block">
This experiment involves a spectrophotometric measurement using Roche C... | ["Perform daily quality control assessment of instrumentation before analysis.", "Load each sample into a specialized micro-sample cup for the clinical chemistry analyzer.", "Select Lactate dehydrogenase test on display and run the analysis.", "Collect and analyze the data."] |
49,886 | RNA Extraction CTAB Protocol | 4 | null | https://www.protocols.io/view/rna-extraction-ctab-protocol-bux6nxre | Simon Joly | TITLE: RNA Extraction CTAB Protocol
AUTHORS: Simon Joly
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Protocol used and fine-tuned in the Joly laboratory</span></div><div class = "text-block"><span style = "font-weight:bold;">Reference</span></div><div class = "te... | ["[Preparation]\nWorking with RNAClean bench and pipettes with RNAzapAutoclave platicsBe ultra careful!All reagents and chemicals used for RNA extractions should never be used for other purposes.Always manipulate everything with clean nitrile gloves.", "[Preparation]\nTissue grindingUse super clean mortar and pestles. ... |
96,368 | Inventaires et suivis floristiques par maille | 0 | dx.doi.org/10.17504/protocols.io.kqdg3xr2qg25/v1 | https://www.protocols.io/view/inventaires-et-suivis-floristiques-par-maille-dacq2avw | Mario KLESCZEWSKI, Mathieu Bossaert, Camille Lecompte | TITLE: Inventaires et suivis floristiques par maille
AUTHORS: Mario KLESCZEWSKI, Mathieu Bossaert, Camille Lecompte
[DESCRIPTION]
Ce protocole correspond à un inventaire couvrant une zone de façon exhaustive, donc sans échantillonnage, censé mettre en évidence, dans un premier temps, la répartition spatiale des popula... | ["[Définition des espèces visées] La première étape consiste à définir la ou les espèces à inventorier. Habituellement, celles-ci sont définies dans le document de gestion du site. Dans le cas d’inventaires initiaux de sites non encore dotés de document de gestion, l’inventaire par mailles n’est recommandé que pour les... |
null | null | null | dx.doi.org/10.17504/protocols.io.uw8exhw | null | null | TITLE: No Title
AUTHORS:
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ez7bf9n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is from:</p>
<p> </p>
<p>Mofiz E. et al., <a href="http://dx.doi.org/10.1186/s13742-016-0129-2" target="_blank">Genomic resources and draft reference assemblies of the human and porcine scabies mites, Sarcoptes scabiei var. hominis and var. suis</a>. <em>GigaSci... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.jphcmj6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>We have three program files that produced all of the results we discuss in the paper. All are iPython Jupyter Notebook files. The names are: wasps_replicator_11-single_caste.ipynb, wasps_replicator_11.ipynb, and dothegraphics.ipynb. The main code is in wasps_replicator_11.ipy... | [] |
88,217 | Wake Forest University Health Sciences Manual of Procedures Biospecimen Collection and Processing | 1 | dx.doi.org/10.17504/protocols.io.3byl4qzk8vo5/v1 | https://www.protocols.io/view/wake-forest-university-health-sciences-manual-of-p-c2dzya76 | kkennedy | TITLE: Wake Forest University Health Sciences Manual of Procedures Biospecimen Collection and Processing
AUTHORS: kkennedy
[DESCRIPTION]
This includes the methods associated with obtaining muscle, blood, and urine along with demographic, clinical, health, and functional data from younger and older participants.
[STEP... | [] |
22,157 | Efficient NGS ready gDNA from microalga | null | dx.doi.org/10.17504/protocols.io.zvmf646 | null | Reuben B. Brown, Taylor Wass, Nishanti Sudhakar | TITLE: Efficient NGS ready gDNA from microalga
AUTHORS: Reuben B. Brown, Taylor Wass, Nishanti Sudhakar
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Preparing genomic DNA extractions from microalgae specifically for long read sequencing on platforms such as Nanopore and Pac bio requires ultra-hig... | ["[Next gen Sequence ready bacteriostatic culture]\nPick a single colony from a solid media plate or proceed with the next steps to perform density gradient centrifugation for strains that will not grow on solid media", "[Next gen Sequence ready bacteriostatic culture]\nMake 100% 35ppm percoll solution: for 100ml, add... |
66,898 | ONT Flongle Flowcell Loading with Q20+ (V12) Chemistry | 4 | dx.doi.org/10.17504/protocols.io.ewov1nm5pgr2/v2 | https://www.protocols.io/view/ont-flongle-flowcell-loading-with-q20-v12-chemistr-cdjss4ne | Stephen Douglas Russell | TITLE: ONT Flongle Flowcell Loading with Q20+ (V12) Chemistry
AUTHORS: Stephen Douglas Russell
[DESCRIPTION]
Overview: This protocol describes the steps used to load a Flongle flowcell utilizing the Q20+ (V12) Ligation Sequencing Kit from ONT.
This protocol has been tested with Flongle R9.4.1 flowcells.
Time... | ["[Starting out] Before starting, watch the first 13 minutes of this video: https://vimeo.com/651243660\n\nIt covers all of the vital aspects of this protocol.", "[Starting out] Attach the USB cable from the computer to the MinION device. Place the Flongle module with the white configuration cell into the MinION device... |
79,113 | Reticulon Mutant Drug Screen | 4 | dx.doi.org/10.17504/protocols.io.dm6gpj19dgzp/v1 | https://www.protocols.io/view/reticulon-mutant-drug-screen-crhhv336 | Thomas J O'Brien | TITLE: Reticulon Mutant Drug Screen
AUTHORS: Thomas J O'Brien
[DESCRIPTION]
Protocol for comparing the effects of various compounds on the phenotype our ret-1 (RTN2 ortholog) LoF mutant vs N2 control.
[STEPS]
SECTION: Pick L4 worms for bleaching (9 days prior to tracking)
1. Pick 10 x L4 worms onto 10 x 90mm NGM-agar... | ["[Pick L4 worms for bleaching (9 days prior to tracking)] Pick 10 x L4 worms onto 10 x 90mm NGM-agar plates pre-seeded with E. coli OP50 for each strain to be tested. In this case we are comparing the response of our ret-1 LoF mutant with N2 (parental control), therefore 20 x 90 mm plates will be picked in total.", "[... |
98,844 | Crystallization of SARS-CoV-2 Mpro | 1 | dx.doi.org/10.17504/protocols.io.kqdg326y7v25/v1 | https://www.protocols.io/view/crystallization-of-sars-cov-2-mpro-dcr42v8w | blake.h.balcomb, Peter Marples, Lizbé Koekemoer, Daren Fearon, Charlie Tomlinson | TITLE: Crystallization of SARS-CoV-2 Mpro
AUTHORS: blake.h.balcomb, Peter Marples, Lizbé Koekemoer, Daren Fearon, Charlie Tomlinson
[DESCRIPTION]
The COVID-19 pandemic has highlighted the need to identify novel therapeutic interventions and strategies for pandemic preparedness against Severe Acute Respiratory Syndrome... | ["[Crystallization experiment] Protein and buffer requirements:\n43.2 µL5 mg/mL \n1.92 mL \n14.4 µL seeds, dilution 1:250", "[Crystallization experiment] Dispense 20 µL into SwissCI 3 lens plate reservoir wells using a 100 µl multi-channel pipette.\nDispense 150 nL5 mg/mL to each lens using the SPT mosquito.\nDis... |
40,432 | API Pharma Next Gen Antibody Test | 3 | dx.doi.org/10.17504/protocols.io.bjqqkmvw | https://www.protocols.io/view/api-pharma-next-gen-antibody-test-bjqqkmvw | vincent.degennaro | TITLE: API Pharma Next Gen Antibody Test
AUTHORS: vincent.degennaro
[STEPS] | [] |
59,031 | Semi-automated extraction of information on open datasets mentioned in articles | 5 | dx.doi.org/10.17504/protocols.io.q26g74p39gwz/v1 | https://www.protocols.io/view/semi-automated-extraction-of-information-on-open-d-b5vxq67n | 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... | ["[Screen a set of publications for statements indicating Open Data] Collate a list of article identifiers\nStart from a list of articles, for which you want to determine openness of datasets underlying these articles. Those can typically be obtained by searching publication databases (e.g. Pubmed, Web of Science, Dime... |
93,239 | UV decontamination of materials | 3 | dx.doi.org/10.17504/protocols.io.n2bvj3145lk5/v1 | https://www.protocols.io/view/uv-decontamination-of-materials-c7axzifn | Elena Essel | TITLE: UV decontamination of materials
AUTHORS: Elena Essel
[DESCRIPTION]
Protocol for reducing DNA contamination on tubes, bottles, zip lock bags and other reaction vessels and containers used in the ancient DNA cleanroom by UV treatment.
Change log:
Formatting edits for consistency with other documents/protocol... | [] |
25,602 | 09 Expression | null | dx.doi.org/10.17504/protocols.io.49agz2e | null | TJUSLS China | TITLE: 09 Expression
AUTHORS: TJUSLS China
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Make the big batch of bacteria culture for protein expression.</div></div>
[STEPS]
?. Add 1L LB media and then add antibiotic to 100 μg/mL final concentration. Grow them up in 37°C shaking incubator. Grow unt... | ["Add 1L LB media and then add antibiotic to 100 μg/mL final concentration. Grow them up in 37°C shaking incubator. Grow until an OD 600 nm of 0.8 to 1.2 (roughly 3-4 hours).\n1 L\n37 °C", "Induce the culture to express protein by adding 0.3 mM IPTG (isopropylthiogalactoside, MW 238 g/mol) or ~0.1 gram per 1.5 liter fl... |
17,604 | Periplasmic Bacterial Expression and Purification of Elastin-like Polymers | null | dx.doi.org/10.17504/protocols.io.vfce3iw | null | Eva Rose Balog | TITLE: Periplasmic Bacterial Expression and Purification of Elastin-like Polymers
AUTHORS: Eva Rose Balog
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describes the expression and purification procedures used in the Balog lab at the University of New England for producing reco... | ["[Transformation]\nIn a pre-chilled Eppendorf tube, mix 10-100 ng plasmid (typically 1-2 μL of mini-prep DNA) with 50-100 μL BL21(DE3) competent cells on ice. Let sit on ice for 30 min.", "[Transformation]\nHeat shock at 42 ºC in a water bath for 1 min.", "[Transformation]\nAllow cells to recover on ice for 2-3 min.",... |
54,714 | ESTABLISHMENT OF A SPECIMEN/TISSUE BANK AND ASSOCIATED DNA REFERENCE DATA FOR eDNA ANALYSIS | 4 | dx.doi.org/10.17504/protocols.io.bzn2p5ge | https://www.protocols.io/view/establishment-of-a-specimen-tissue-bank-and-associ-bzn2p5ge | Luca Mirimin, Dulaney Miller, Sara Fernandez | TITLE: ESTABLISHMENT OF A SPECIMEN/TISSUE BANK AND ASSOCIATED DNA REFERENCE DATA FOR eDNA ANALYSIS
AUTHORS: Luca Mirimin, Dulaney Miller, Sara Fernandez
[DESCRIPTION]
This protocol is intended to provide guidelines on the curation and establishment of a specimen/tissue bank and associated DNA sequence data to be us... | ["[Collection of specimens and associated metadata] Specimens can be collected following targeted surveys or opportunistically, using rapid methods (collection by hand, dredges, corers, traps, nets, etc.) or dedicated in situ approaches (e.g. SETL settlement plates; https://www.gimaris.com/Projects/SETL-project). When ... |
66,390 | Universal DNA isolation protocol | 1 | dx.doi.org/10.17504/protocols.io.yxmvmbx6g3pe/v4 | https://www.protocols.io/view/universal-dna-isolation-protocol-cc3wsype | Ruslan Kalendar | TITLE: Universal DNA isolation protocol
AUTHORS: Ruslan Kalendar
[DESCRIPTION]
The isolation of nucleic acids from a sample is an important step for many molecular biological applications and medical diagnostic assays. This protocol describes an efficient method for purification or/and isolation of nucleic acids from... | ["Eppendorf Safe-Lock microcentrifuge tube with tissue sample and glass ball (6 mm) freezes at -80°C, grind in the MM300 Mixer Mill for 2 min at 30 Hz. Alternatively, grind the sample in the lysis solution, so that there is enough empty space in the tube.", "In a 2 ml tube with mechanically disrupted tissue/seeds/leave... |
57,218 | X-ray Micro Computed Tomography (MicroCT) | 4 | dx.doi.org/10.17504/protocols.io.b35aqq2e | https://www.protocols.io/view/x-ray-micro-computed-tomography-microct-b35aqq2e | Marta Wawrzyniak, Nathalie Weber, Simon Blanchoud | TITLE: X-ray Micro Computed Tomography (MicroCT)
AUTHORS: Marta Wawrzyniak, Nathalie Weber, Simon Blanchoud
[DESCRIPTION]
This protocol has been successfully used with colonial tunicates. It has been adapted to our needs based on the following publication: " MicroCT for comparative morphology: simple staining met... | ["[Fixation] Clean the slide with the colony of your interest. See Cleaning colonial ascidians V.2.", "[Fixation] Anesthetize the animals following this protocol. See Whole colony fixation V.1", "[Fixation] Fix the animals in 4% PFA at Room temperature . See Whole colony fixation V.1", "[Fixation] Wash twice in 3.3x ... |
64,455 | Open Eye Hemp Relief Reviews [Scam Alert] | 1 | dx.doi.org/10.17504/protocols.io.q26g74929gwz/v1 | https://www.protocols.io/view/open-eye-hemp-relief-reviews-scam-alert-ca7fshjn | oehrollerbuy | TITLE: Open Eye Hemp Relief Reviews [Scam Alert]
AUTHORS: oehrollerbuy
[DESCRIPTION]
Open Eye Hemp ReliefReviews: Today, individuals in all aspects of the world experience the ill effects of different issues like BP, Diabetes, stress, and cholesterol. A few youngsters likewise experience the ill effects of mental i... | [] |
72,261 | Code_file_Caroline_Laborde_barrier_free_neighbourhoods_functional_independence_educational _inequalities | 3 | null | https://www.protocols.io/view/code-file-caroline-laborde-barrier-free-neighbourh-citduei6 | laborde_caroline | TITLE: Code_file_Caroline_Laborde_barrier_free_neighbourhoods_functional_independence_educational _inequalities
AUTHORS: laborde_caroline
[DESCRIPTION]
Code file for
"Do barrier-free neighbourhoods foster functional independence equally among older people with lower and higher educational status?"
by: Caroline Labo... | [] |
90,734 | Immunofluorescent Imaging and Analysis | 4 | dx.doi.org/10.17504/protocols.io.6qpvr37r2vmk/v1 | https://www.protocols.io/view/immunofluorescent-imaging-and-analysis-c4unywve | Dan Tudorica | TITLE: Immunofluorescent Imaging and Analysis
AUTHORS: Dan Tudorica
[DESCRIPTION]
Following treatment with antibodies/genetic methods of introducing fluorescent tags
[STEPS]
SECTION: Preparation of chambered slides
1. Seed cells on 8-well chambered slide to be 80% confluent on day of analysis.
SECTION: Preparation o... | ["[Preparation of chambered slides] Seed cells on 8-well chambered slide to be 80% confluent on day of analysis.", "[Preparation of chambered slides] Wash cells once with PBS, then fix for 15 minutes using 4% PFA diluted in PBS. Wash cells once more with PBS.", "[Preparation of chambered slides] Permeabilize cells for ... |
70,249 | Preparation and Immunohistochemistry of Mouse Small Intestine and Colon | 4 | dx.doi.org/10.17504/protocols.io.j8nlkw575l5r/v1 | https://www.protocols.io/view/preparation-and-immunohistochemistry-of-mouse-smal-cguhtwt6 | Nathan D Rossen | TITLE: Preparation and Immunohistochemistry of Mouse Small Intestine and Colon
AUTHORS: Nathan D Rossen
[DESCRIPTION]
Mice were euthanized, the small and large intestine collected, and fixed frozen sections prepared. The microscope mounted tissue sections were stained using immunohistochemistry. Expression of specif... | ["[Tissue Collection and Preparation] Mice 6 - 8 weeks old were euthanized by isolfurane administration followed by cervical dislocation.", "[Tissue Collection and Preparation] Mice were transcardially perfused with 5ml ice cold PBS.", "[Tissue Collection and Preparation] Whole small intestine and colon were collected ... |
19,854 | U Cinn - NEFA Concentration | null | dx.doi.org/10.17504/protocols.io.xmnfk5e | null | Patrick Tso, Dana Lee | TITLE: U Cinn - NEFA Concentration
AUTHORS: Patrick Tso, Dana Lee
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Quantitative determinations of non-esterified fatty acids in plasma/serum/lymph will be made using the ... | ["Prepare working Color Reagent Solutions A and B. A. Reconstitute Color Reagent A with a portion of Solvent A and then transfer entire contents into Solvent A bottle, rinsing Color Reagent vial several times. B. Reconstitute Color Reagent B with a portion of Solvent B and then transfer entire contents into Solvent B b... |
52,105 | Further Micro-scaled MEDI (Macronutrient Extraction and Determination from Invertebrates) | 6 | dx.doi.org/10.17504/protocols.io.bw5hpg36 | https://www.protocols.io/view/further-micro-scaled-medi-macronutrient-extraction-bw5hpg36 | Jordan Cuff | TITLE: Further Micro-scaled MEDI (Macronutrient Extraction and Determination from Invertebrates)
AUTHORS: Jordan Cuff
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Macronutrients, comprising carbohydrates, proteins and lipids, underpin many ecological processes, but their quantification in ecologi... | ["[Welcome to MEDI!]\nWelcome to Macronutrient Extraction and Determination from Invertebrates (further micro-scaled edition)! The following presents a micro-scaled version of the original MEDI protocol. The further micro-scaled protocol is intended particularly for invertebrates of dry volumes of 1 mg or less which ca... |
null | null | null | dx.doi.org/10.17504/protocols.io.e68bhhw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?. | [] |
92,310 | Immunohistochemical fluorescent labelling and activity readout of striatal cholinergic interneuron activity | 1 | dx.doi.org/10.17504/protocols.io.6qpvr3w33vmk/v1 | https://www.protocols.io/view/immunohistochemical-fluorescent-labelling-and-acti-c6dwza7e | Emanuel F Lopes, Stephanie J Cragg | TITLE: Immunohistochemical fluorescent labelling and activity readout of striatal cholinergic interneuron activity
AUTHORS: Emanuel F Lopes, Stephanie J Cragg
[DESCRIPTION]
This protocol delineates a method to identify choline acetyltransferase (ChAT)-expressing neurons and co-label these with a marker for global neur... | ["[Perfusion-Fixation] Habituate animal for 3 days prior to perfusion. Handle mouse, and simulate performing an intraperitoneal injection once a day (scruff and poke belly with sheathed needle & syringe).", "[Perfusion-Fixation] On the day of the perfusion, anesthetize the mouse with an i.p. injection of pentobarbital ... |
91,460 | In vivo CAR T cell tumor control assay | 4 | null | https://www.protocols.io/view/in-vivo-car-t-cell-tumor-control-assay-c5jcy4iw | Andrea R Daniel | TITLE: In vivo CAR T cell tumor control assay
AUTHORS: Andrea R Daniel
[DESCRIPTION]
This protocol describes methods for a HCC1954 cell implanted orthotopic tumor model in mice with delivery of T cells expressing HER2 CAR. Tumor volumes are measured to evaluate tumor control by CAR T cell therapy.
[STEPS]
SECTION: H... | ["[HCC1954 orthotopic tumor model] Six- to 8-week-old female immunodeficient NOD/SCID gamma (NSG) mice were obtained from Jackson Laboratory and then housed in 12-h light/dark cycles, at an ambient temperature (21 ± 3 °C) with relative humidity (50 ± 20%) and handled in pathogen-free conditions", "[HCC1954 orthotopic t... |
16,410 | EEL FISH | 1 | dx.doi.org/10.17504/protocols.io.t92er8e | https://www.protocols.io/view/eel-fish-t92er8e | Lars E. Borm | TITLE: EEL FISH
AUTHORS: Lars E. Borm
[DESCRIPTION]
Protocol to perform RNA transfer to a surface using the EEL method and detection with an automated fluidics and imaging machine called ROBOFISH.
Paper title: Scalable in situ single-cell profiling by electrophoretic capture of mRNA
Website: mousebrain.org
Instr... | ["[ITO glass cleaning] Place ITO slides in a beaker glass and submerge them in Acetone. Cover the beaker glass with aluminium foil and\nsonicate 20 min on high power.", "[ITO glass cleaning] Discard the Acetone and submerge the slides in 2-Propanol. Replace the water in the sonicator if it has warmed up. Cover the beak... |
48,270 | SalivaDirect™: RNA extraction-free SARS-CoV-2 diagnostics | 1 | dx.doi.org/10.17504/protocols.io.btdnni5e | https://www.protocols.io/view/salivadirect-rna-extraction-free-sars-cov-2-diagno-btdnni5e | Chantal Vogels, Orchid Allicock, Doug E. Brackney, Chaney Kalinich, Isabel Ott, Nathan Grubaugh, Anne Wyllie | TITLE: SalivaDirect™: RNA extraction-free SARS-CoV-2 diagnostics
AUTHORS: Chantal Vogels, Orchid Allicock, Doug E. Brackney, Chaney Kalinich, Isabel Ott, Nathan Grubaugh, Anne Wyllie
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">SalivaDirect™ is an RNA-extraction free, dual-plexed RT-qPCR method f... | ["[Sample collection]\nSaliva should be collected with the assistance of a healthcare worker or technician.", "[Sample collection]\nBefore collection, clean hands using alcohol-based sanitizer or soap and water (no fragrances) and don appropriate PPE (at minimum, gloves and a mask).", "[Sample collection]\nEnsure all c... |
106,768 | QuPath to SCiLS instructions | 0 | dx.doi.org/10.17504/protocols.io.kqdg32nq1v25/v1 | https://www.protocols.io/view/qupath-to-scils-instructions-dkhq4t5w | Naina Beishembieva, Brittney Gorman, Christopher R Anderton | TITLE: QuPath to SCiLS instructions
AUTHORS: Naina Beishembieva, Brittney Gorman, Christopher R Anderton
[DESCRIPTION]
Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) is an analytical technique which provides the molecular composition directly from cells, tissues and organs. To provid... | ["[Part 1. QuPath to SCiLS (instructions on QuPath)] Install QuPathtoSCiLS extension", "[Part 1. QuPath to SCiLS (instructions on QuPath)] Open QuPath \nFind file \"QuPathToSCiLS-1.4.jar\".\nMy pathway is: C:\\Program Files\\SCiLS\\SCiLS Lab\\QuPathPlugin", "[Part 1. QuPath to SCiLS (instructions on QuPath)] Drag the Q... |
99,136 | Embedding Four Brains For Serial Section Imaging | 0 | null | https://www.protocols.io/view/embedding-four-brains-for-serial-section-imaging-dc282yhw | Rob Campbell | TITLE: Embedding Four Brains For Serial Section Imaging
AUTHORS: Rob Campbell
[DESCRIPTION]
Describes how to embed four perfused mouse brains for serial section microscopy using the SWC's embedding molds.
[BEFORE_START]
A major advantage of serial sectioning is that it generates a seamless 3D data set that can be r... | ["[Preparing for agar embedding] Brains are to be suspended in a metal enclosure through which thin wires are inserted. We will mount the lower brains first. Insert 5 steel wires into mold as shown (colors on the tape are not meaningful).", "[Pouring the initial agar] Briefly shake the agar suspension then pour about 2... |
97,478 | Creating Custom Brain Slicing Matrices with 3D Printers | 0 | null | https://www.protocols.io/view/creating-custom-brain-slicing-matrices-with-3d-pri-dbfe2jje | Yosuke Yamazaki, Maki Yuguchi, Keitaro Isokawa | TITLE: Creating Custom Brain Slicing Matrices with 3D Printers
AUTHORS: Yosuke Yamazaki, Maki Yuguchi, Keitaro Isokawa
[DESCRIPTION]
To create reproducible brain sections, brain slicing matrices are often utilized. These matrices are designed with anatomically proportioned cavity dimensions and precisely spaced slice ... | ["[Mesuratent of the sample] The mouse brain sample is placed on the dissection mat.", "[Mesuratent of the sample] Following the specified metrics, the approximate length is measured.", "[Installation of OpenSCAD] For Windows, download the installer from https://openscad.org/ and execute the .exe file to proceed with t... |
null | null | null | dx.doi.org/10.17504/protocols.io.fazbif6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol provides materials needed and steps for collecting brooded coral larvae in the field.</p>
[BEFORE_START]
<p><strong>Gear and materials needed:</strong></p>
<p>Mallets</p>
<p>Chisel</p>
<p>Gardening gloves</p>
<p>60 pieces of ½” rebar 1 m in length, tied in bund... | [] |
22,236 | Zymoclean™ Gel DNA Recovery | null | dx.doi.org/10.17504/protocols.io.zx4f7qw | null | Sze-Xian Lim | TITLE: Zymoclean™ Gel DNA Recovery
AUTHORS: Sze-Xian Lim
[STEPS]
?. Excise the DNA fragment from the agarose gel using a razor blade, scalpel or other device and transfer it into a 1.5 ml microcentrifuge tube.
?. Weight empty 1.5 ml microcentrifuge tube.
?. Add 3 volumes of ADB to each volume of agarose excised from t... | ["Excise the DNA fragment from the agarose gel using a razor blade, scalpel or other device and transfer it into a 1.5 ml microcentrifuge tube.", "Weight empty 1.5 ml microcentrifuge tube.", "Add 3 volumes of ADB to each volume of agarose excised from the gel (e.g. add of ADB to every of agarose gel).\n[ADB]\n[agarose ... |
28,504 | Prototype Protocol | null | dx.doi.org/10.17504/protocols.io.73yhqpw | null | George Moberly | TITLE: Prototype Protocol
AUTHORS: George Moberly
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Prototype Protocol</div></div>
[STEPS]
?. Add 200 μl SWS to the tube. Pipette to mix.
?. Place on the 50°C heat block for 30 minutes.
?. Immediately place on a magnetic stand and wait until the liquid ... | ["Add 200 μl SWS to the tube. Pipette to mix.", "Place on the 50°C heat block for 30 minutes.", "Immediately place on a magnetic stand and wait until the liquid is clear (~2 minutes).", "Remove and discard all supernatant from the tube.", "Remove from the magnetic stand. 1. Add 200 μl SWS to the tube. Pipette to mix."] |
83,426 | Cloning by Gibson Assembly | 4 | dx.doi.org/10.17504/protocols.io.rm7vzxmp8gx1/v1 | https://www.protocols.click/view/cloning-by-gibson-assembly-cvqaw5se | Eric ECS Cordeiro-Spinetti | TITLE: Cloning by Gibson Assembly
AUTHORS: Eric ECS Cordeiro-Spinetti
[DESCRIPTION]
Gibson assembly is a molecular cloning method that allows for the joining of multiple DNA fragments in a single, isothermal reaction. It is named after its creator, Daniel G. Gibson, who is the chief technology officer and co-founder ... | ["PCR (vector and insert)\nTm vector primers = oC\nTm insert primers = oC", "Clean-up PCR products with 1 µL Dpn1 for 30 min at 37 °C", "Purify PCR products and resuspend in lowest volume possible (5-10 uL)", "Set up Gibson ligation\n Vector = 50-100ng\n Molar ratio Vector/Insert = 1:1-3", "Add to Gibson Maste... |
80,071 | Aromatic Monomer Analysis by UHPLC-MS/MS | 6 | dx.doi.org/10.17504/protocols.io.eq2ly7rzwlx9/v1 | https://www.protocols.io/view/aromatic-monomer-analysis-by-uhplc-ms-ms-csffwbjn | Stefan J. Haugen, Gregg T. Beckham, Kelsey J. Ramirez | TITLE: Aromatic Monomer Analysis by UHPLC-MS/MS
AUTHORS: Stefan J. Haugen, Gregg T. Beckham, Kelsey J. Ramirez
[DESCRIPTION]
An analysis method was developed to allow for quantitation of aromatic compounds by ultra high pressure liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) detection. This was achieved ... | ["[Internal Standard Preparation] This analysis uses 4-Hydroxybenzoic-2,3,5,6-d4 acid (d4-4HBA) as an internal standard. Prepare a 500 µg/mL internal standard working solution into 50:50 Acetone / MilliQ Water. Plan to prepare enough solution volume to allow for addition of d4-4HBA to each sample or standard volume at ... |
59,630 | Tagmentation and library generation for human placental bulk ATACseq | 4 | dx.doi.org/10.17504/protocols.io.261gen52jg47/v1 | https://www.protocols.io/view/tagmentation-and-library-generation-for-human-plac-b6gnrbve | Scott Lindsay-Hewett | TITLE: Tagmentation and library generation for human placental bulk ATACseq
AUTHORS: Scott Lindsay-Hewett
[DESCRIPTION]
This protocol describes the generation and amplification/indexing of tagmented libraries from freshly isolated nuclei for bulk ATACseq. It is adapted from Buenrostro et al., 2015, PMID: 25559105.
... | ["[Preparation] Pre-heat Eppendorf ThermoMixer to 37 °C.", "[Tagmentation and purification] Add 0.5 µL to 50,000 freshly prepared nuclei (5,000 nuclei/ul in tagmentation buffer), and mix by pipetting gently.", "[Tagmentation and purification] Incubate in Eppendorf ThermoMixer .", "[Tagmentation and purification] After... |
81,808 | Nuclei Isolation for FACS | 4 | dx.doi.org/10.17504/protocols.io.kxygx9jk4g8j/v3 | https://www.protocols.io/view/nuclei-isolation-for-facs-ct5qwq5w | Lakme Caceres | TITLE: Nuclei Isolation for FACS
AUTHORS: Lakme Caceres
[DESCRIPTION]
This protocol is for purifying nuclei for downstream 10X sequencing.
[GUIDELINES]
Keep tissue/nuclei on ice as much as possible.
[STEPS]
SECTION: Prepare Fresh Solutions
4. Make 3 mL Homogenization Buffer by adding 2.9 mL Nuclear Isolation Media (... | ["[Prepare Fresh Solutions] Make 3 mL Homogenization Buffer by adding 2.9 mL Nuclear Isolation Media (filtered via syringe) to a 5 mL eppendorf. Then add 3 μL 100 mM DTT and 30 μL 10% Triton X-100.", "[Prepare Stock Solutions] Make 20 mL 10% BSA by combining 2 mL of BSA with 18 mL of MilliQ water in a 50 mL falcon tube... |
null | null | null | dx.doi.org/10.17504/protocols.io.c49yz5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is a 0.05M Tris-Cl (pH 8.0), 0.01M EDTA resuspension buffer containing RNase A
[GUIDELINES]
Storage condition - 4°C after adding RNase A.<br /><strong>Note</strong>: Buffer compositions are given per liter of solution. Buffer calculations are based on Tris Base adjusted to... | [] |
35,858 | Verhoeff’s Iron Hematoxylin Staining | null | dx.doi.org/10.17504/protocols.io.be9sjh6e | https://www.protocols.io/view/verhoeff-s-iron-hematoxylin-staining-be9sjh6e | Jeff Z. Chen, Deborah A. Howatt, Michael K. Franklin, Jessica J. Moorleghen, Hisashi Sawada, Hong S. Lu, Alan Daugherty | TITLE: Verhoeff’s Iron Hematoxylin Staining
AUTHORS: Jeff Z. Chen, Deborah A. Howatt, Michael K. Franklin, Jessica J. Moorleghen, Hisashi Sawada, Hong S. Lu, Alan Daugherty
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used to stain elastic tissue.</div><div class = "text-block">T... | ["[Elastin Staining]\nAcetone to fix\nIf slides keep falling off slide, air dry for 30 mintues before fixation", "[Elastin Staining]\nWater (wash)", "[Elastin Staining]\nVerhoeff’s iron hematoxylin", "[Elastin Staining]\nWater (3 washes)", "[Elastin Staining]\nFerric chloride (2% wt/vol)Water 3 washesCheck slide for di... |
88,920 | Yale Murine TMC - Tissue Preparation Protocol | 1 | dx.doi.org/10.17504/protocols.io.kqdg3x8keg25/v1 | https://www.protocols.io/view/yale-murine-tmc-tissue-preparation-protocol-c23yygpw | Yun-Hee Youm, Yufeng Liu, Vishwa Deep Dixit, Rong Fan, Bo Tao | TITLE: Yale Murine TMC - Tissue Preparation Protocol
AUTHORS: Yun-Hee Youm, Yufeng Liu, Vishwa Deep Dixit, Rong Fan, Bo Tao
[DESCRIPTION]
Protocol for embedding murine spleen, thymus and lymph node.
[STEPS]
SECTION: RNA Buffer (use before embedding tissue in OCT)
1. 1x PBS-MC Recipe
All prepared in DNAse RNAase EDTA... | ["[RNA Buffer (use before embedding tissue in OCT)] 1x PBS-MC Recipe\nAll prepared in DNAse RNAase EDTA free deionized water\nMgCl2 (1 mM, add 1 ml of 1 M MgCl2 stock solution into 1 L of 1x PBS)\nCaCl2 (0.1 mM, add 2 ml of 0.1 M of CaCl2 stock soution into 1 L of 1x PBS)\n4% paraformaldehyde (PFA), optional\n1 X Prote... |
81,820 | NCEM Drop - Inactivation of sample in solution (TM-014) | 4 | dx.doi.org/10.17504/protocols.io.5jyl89k57v2w/v2 | https://www.protocols.io/view/ncem-drop-inactivation-of-sample-in-solution-tm-01-ct54wq8w | sandra.crameri | TITLE: NCEM Drop - Inactivation of sample in solution (TM-014)
AUTHORS: sandra.crameri
[DESCRIPTION]
This inactivation procedure is used to inactivate a sample for Biological Transfer out of PC4, proir to Conventional NCEM.
[STEPS]
SECTION: Inactivation
1. Add 50 µL 16 % volume to a Sarstedt tube with o-ring (STK#:... | ["[Inactivation] Add 50 µL 16 % volume to a Sarstedt tube with o-ring (STK#:2056-U, Catalog #61226C2).", "[Inactivation] Add 150 µL sample to the already in the tube. Leave contact time 10 min", "[Inactivation] Adsorb 10 µL sample to grid 10 min , inspect to ensure sample doesn't dry out.", "[Inactivation] Drain ex... |
55,835 | CPMU | 1 | dx.doi.org/10.17504/protocols.io.n92ld96dng5b/v2 | https://www.protocols.io/view/cpmu-b2r3qd8n | Bjorn Bartholdy, a.g.henry | TITLE: CPMU
AUTHORS: Bjorn Bartholdy, a.g.henry
[DESCRIPTION]
Mineralising solution for the oral biofilm. From Sissons et al. 1991.
[BEFORE_START]
This solution MUST be prepared in a sterile and starch-free environment.
[STEPS]
1. Add 300 mL distilled (or deionized) dH2O to a 1000 mL beaker, with stirring and heat ... | ["Add 300 mL distilled (or deionized) dH2O to a 1000 mL beaker, with stirring and heat 60 °C", "Add:\n\n- 1.55 g \n- 1.44 g \n- 0.72 g \n- 0.08 g \n- 30 g", "Add the remaining 700 mL and keep stirring until precipitate has completely dissolved\nStore in fridge at 4 °C"] |
95,829 | OMS Atlas OCT Spatial Mapping - Limited | 1 | dx.doi.org/10.17504/protocols.io.8epv5xy24g1b/v1 | https://www.protocols.io/view/oms-atlas-oct-spatial-mapping-limited-c9tvz6n6 | Brett Johnson, Danielle Galipeau, George Thomas | TITLE: OMS Atlas OCT Spatial Mapping - Limited
AUTHORS: Brett Johnson, Danielle Galipeau, George Thomas
[DESCRIPTION]
This protocol describes the procedure by which the OMS Atlas serially sections an OCT block, prepares the resulting slides and samples, and then distributes the specimens for downstream analysis.
[BEF... | ["[Preparation] Verify the identity of the OCT block to be cut against written request for sectioning.", "[Preparation] Remove OCT block from -80 °C freezer and acclimate to cryostat (-20 °C ) for minimum of 180 min.", "[Preparation] Label all slides and cryotubes with a unique BEMS ID and Part#, corresponding to the w... |
100,330 | Metabarcoding for Fish and Crustaceans in Diet Samples Using 2-PCR protocol with Unique Dual Indexing | 4 | null | https://www.protocols.io/view/metabarcoding-for-fish-and-crustaceans-in-diet-sam-dd8i29ue | Eldridge Wisely | TITLE: Metabarcoding for Fish and Crustaceans in Diet Samples Using 2-PCR protocol with Unique Dual Indexing
AUTHORS: Eldridge Wisely
[DESCRIPTION]
This protocol describes a method to metabarcode a 170bp region of the mitochondrial16S rRNA gene of crustaceans and a 163-185bp region of the mitochondrial 12S rRNA gene ... | ["[Prepare Primers] Order metabarcoding primers with diversity spacers and Illumina overhang sequences (Illumina, 2013): (Miya et al., 2015): \nTCGTCGGCAGCGTCAGATGTGTATAAGAGACAGNNNNGTCGGTAAAACTCGTGCCAGC\n \n (Miya et al., 2015): GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGNNNNCATAGTGGGGTATCTAATCCCAGTTTG\n\n Berry et al., 201... |
98,491 | Salmonella serotype prediction using the GalaxyTrakr SeqSero2 workflow | 5 | dx.doi.org/10.17504/protocols.io.4r3l24kypg1y/v2 | https://www.protocols.io/view/salmonella-serotype-prediction-using-the-galaxytra-dce32tgn | Paul Morin, Ruth Timme, Michelle Moore, Shauna Madson, Evelyn Ladines, Julia Manetas, Karen Jinneman | TITLE: Salmonella serotype prediction using the GalaxyTrakr SeqSero2 workflow
AUTHORS: Paul Morin, Ruth Timme, Michelle Moore, Shauna Madson, Evelyn Ladines, Julia Manetas, Karen Jinneman
[DESCRIPTION]
Salmonella serotypes are defined by two surface structures, O antigen and two H antigens. Traditional serotype determ... | ["[GalaxyTrakr Account set up] Login to GalaxyTrakr: https://galaxytrakr.org/root/login\n\nOtherwise, create a GalaxyTrakr account here: https://account.galaxytrakr.org/Account/Register", "[Login and import workflow] Log into GalaxyTrakr (https://galaxytrakr.org/root/login)\n\n \n\nLink to create a new GalaxyTrakr acc... |
null | null | null | dx.doi.org/10.17504/protocols.io.h6zb9f6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?. | [] |
70,348 | Test share with Gabriel | 4 | null | https://www.protocols.io/view/test-share-with-gabriel-cgxktxkw | Lenny Teytelman | TITLE: Test share with Gabriel
AUTHORS: Lenny Teytelman
[DESCRIPTION]
test
[STEPS]
1. 3000 rpm
| ["3000 rpm"] |
101,659 | Gene Expression Dual Index Library Construction | 0 | dx.doi.org/10.17504/protocols.io.n92ld8r7xv5b/v1 | https://www.protocols.io/view/gene-expression-dual-index-library-construction-dfh33j8n | Heidi Monroe, Nayra Cardenes, Melanie Königshoff, koenigshoffm, Robert Lafyatis | TITLE: Gene Expression Dual Index Library Construction
AUTHORS: Heidi Monroe, Nayra Cardenes, Melanie Königshoff, koenigshoffm, Robert Lafyatis
[DESCRIPTION]
The Chromium Single Cell Gene Expression Solution upgrades short read sequencers to deliver a scalable microfluidic platform for 3’ digital gene expression by pr... | ["[Gene Expression Dual Index Library Construction] Fragmentation, End Repair & A-tailing", "[Gene Expression Dual Index Library Construction] Prepare a thermal cycler with the following incubation protocol:", "[Gene Expression Dual Index Library Construction] Vortex fragmentation buffer. Verify there is no precipitate... |
null | null | null | dx.doi.org/10.17504/protocols.io.hnub5ew | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?. | [] |
28,330 | MojoSort™ Mouse CD45 Nanobeads Protocol - Selection | null | dx.doi.org/10.17504/protocols.io.7wihpce | null | Sam Li | TITLE: MojoSort™ Mouse CD45 Nanobeads Protocol - Selection
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Product description and procedure summary:</span></div><div class = "text-block">The cells targeted by the Nanobeads are selected by incubating... | ["Prepare cells from your tissue of interest or blood without lysing erythrocytes.", "In the final wash of your sample preparation, resuspend the cells in MojoSort™ Buffer by adding up to 4 mL in a 5 mL (12 x 75 mm) polypropylene tube.Note: Keep MojoSort™ Buffer on ice throughout the procedure.", "Filter the cells with... |
49,908 | K-ε-GG Peptide Enrichment and Analysis by Tandem Mass Tagging-based proteomics | 1 | dx.doi.org/10.17504/protocols.io.buyunxww | https://www.protocols.io/view/k-gg-peptide-enrichment-and-analysis-by-tandem-mas-buyunxww | Harper JW, Alban Ordureau | TITLE: K-ε-GG Peptide Enrichment and Analysis by Tandem Mass Tagging-based proteomics
AUTHORS: Harper JW, Alban Ordureau
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details K-ε-GG peptide enrichment and analysis by tandem mass tagging-based proteomics.</div></div>
[STEPS]
?. [Harv... | ["[Harvest, precipitation and digestion]\nLyse cells in of lysis buffer and pass through a 21G needle 10 times.\n3 mL", "[Harvest, precipitation and digestion]\nCentrifuge suspensions at (high speed) for at and collect supernatant.\nCentrifuge: 13000 33\n4 °C", "[Harvest, precipitation and digestion]\nQuantify prot... |
null | null | null | dx.doi.org/10.17504/protocols.io.iw9cfh6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>PD-L1 LDT on Dako Autostainer Link 48 (ASL48) using the concentrate 22C3 antibody. This protocol was developed in the laboratory of Dr. Paul Hofman and Dr Marius Ilie (Pasteur Hospital, Nice, France).</p>
<p>For the purpose of protocol development 95% of clinical specimens co... | [] |
48,569 | Scaled High Throughput Vacuum PhIP Protocol | 1 | null | https://www.protocols.io/view/scaled-high-throughput-vacuum-phip-protocol-btnznmf6 | Sabrina A Mann, Sara Vazquez, Gavin Sowa, anthea.mitchell , Caleigh Mandel-Brehm, Joe DeRisi | TITLE: Scaled High Throughput Vacuum PhIP Protocol
AUTHORS: Sabrina A Mann, Sara Vazquez, Gavin Sowa, anthea.mitchell , Caleigh Mandel-Brehm, Joe DeRisi
[DESCRIPTION]
This protocol was developed as a high throughput, low cost technique to perform phage display immunopreceipitation. Here we overview all the steps, f... | ["[Day 1- Blocking Plates] Make blocking solution to prevent sample and library from binding to plates, this step also helps with movement of protein A/G beads later on. \n\n Blocking solution (make fresh for every experiment):\n 3.0% BSA Fraction V\n 1x TBS-Tween\n Mix thoroughl... |
null | null | null | dx.doi.org/10.17504/protocols.io.hqnb5ve | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?. | [] |
106,570 | Pericardial fluid biomarkers as early predictors for postoperative atrial fibrillation - a systematic review protocol | 0 | dx.doi.org/10.17504/protocols.io.x54v92be1l3e/v1 | https://www.protocols.io/view/pericardial-fluid-biomarkers-as-early-predictors-f-dkbi4ske | Florin Mitu, Cristina Adam, Dragos Marcu, Alexandru Dan Costache, Radu Sebastian Gavril, Clementina Cojocaru, Andrei Tarus, Mihail Enache, Carmen Marinela Cumpat, Maria Magdalena Leon, Grigore Tinica | TITLE: Pericardial fluid biomarkers as early predictors for postoperative atrial fibrillation - a systematic review protocol
AUTHORS: Florin Mitu, Cristina Adam, Dragos Marcu, Alexandru Dan Costache, Radu Sebastian Gavril, Clementina Cojocaru, Andrei Tarus, Mihail Enache, Carmen Marinela Cumpat, Maria Magdalena Leon, G... | ["[Introduction] Review question / Objective:\nThe aim of this research is to evaluate the systematic review (SR) of prospective studies on biological predictors for postoperative atrial fibrillation (POAF) in the pericardial fluid following cardiac surgery, so as to provide the latest and comprehensive evidence-based ... |
67,466 | Ez Burn Keto Gummies Canada Reviews! Shocking Benefits! Scam Or Legit! | 1 | dx.doi.org/10.17504/protocols.io.36wgq7w45vk5/v1 | https://www.protocols.io/view/ez-burn-keto-gummies-canada-reviews-shocking-benef-cd5is84e | Ez Burn Keto Gummies Canada | TITLE: Ez Burn Keto Gummies Canada Reviews! Shocking Benefits! Scam Or Legit!
AUTHORS: Ez Burn Keto Gummies Canada
[DESCRIPTION]
What are EZ Burn Keto Gummies?
Official Website – Click Here
Weight reduction supplement these Gummies advances solid digestion and normal weight reduction. When taken, they can empower f... | [] |
36,811 | PET2015UZ: Prognostic value of pre-treatment 18FDG-PET in operable breast cancer | 1 | dx.doi.org/10.17504/protocols.io.bf7jjrkn | https://www.protocols.io/view/pet2015uz-prognostic-value-of-pre-treatment-18fdg-bf7jjrkn | Vincent Vinh-Hung, Hendrik Everaert, Mark De Ridder | TITLE: PET2015UZ: Prognostic value of pre-treatment 18FDG-PET in operable breast cancer
AUTHORS: Vincent Vinh-Hung, Hendrik Everaert, Mark De Ridder
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This retrospective-observational study hypothesizes that preoperative 18FDG-PET for breast cancer ha... | ["[Review medical records]\nCheck inclusion criteria", "[Review medical records]\nParticipating center", "[Review medical records]\nPeriod of diagnosis: 2002-2015", "[Review medical records]\nPrimary breast cancer", "[Review medical records]\nHistologically confirmed", "[Review medical records]\nOperable - curative sur... |
28,999 | Limited storage of spittlebugs or green leafhoppers (under one week) | null | dx.doi.org/10.17504/protocols.io.8jfhujn | null | Niels Appelman | TITLE: Limited storage of spittlebugs or green leafhoppers (under one week)
AUTHORS: Niels Appelman
[STEPS]
?. Cover the bottom of a PET container (e.g. https://www.world-of-bottles.co.uk/Glass-bottles/250ml-white-PET-jar-Bella-Mia-white.html) with moisturised single use towels (wetten with tapwater and squeeze to rem... | ["Cover the bottom of a PET container (e.g. https://www.world-of-bottles.co.uk/Glass-bottles/250ml-white-PET-jar-Bella-Mia-white.html) with moisturised single use towels (wetten with tapwater and squeeze to remove excess water) and provide airholes in container with an (injection) needle.", "Fill container with suitabl... |
86,431 | CAMbank: cfDNA BCT Field Processing v1 | 4 | null | https://www.protocols.io/view/cambank-cfdna-bct-field-processing-v1-cym7xu9n | Eliah G Overbey, Krista A Ryon, jak, chm2042 | TITLE: CAMbank: cfDNA BCT Field Processing v1
AUTHORS: Eliah G Overbey, Krista A Ryon, jak, chm2042
[DESCRIPTION]
Field processing of cfDNA BCTs for the Cornell Aerospace Medicine Biobank (CAMbank).
Instructions for preserving: plasma and RBC Pellets.
[STEPS]
SECTION: Perform Venipuncture
1. After venipuncture, inve... | ["[Perform Venipuncture] After venipuncture, invert the tubes gently 8 to 10 times to fully mix tube anticoagulant with blood sample.\n\nStore the tube upright at room temperature until centrifugation.", "[Centrifuge Settings: Plasma Separation] Note: A swing bucket centrifuge is required. \n\nSet centrifuge:\naccelera... |
null | null | null | dx.doi.org/10.17504/protocols.io.h4nb8ve | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?. | [] |
76,760 | SOP62v1_TGD_CUT&RUN and Library prep | 1 | dx.doi.org/10.17504/protocols.io.yxmvm2z39g3p/v1 | https://www.protocols.io/view/sop62v1-tgd-cut-amp-run-and-library-prep-cn7yvhpw | Yunkyeong Lee | TITLE: SOP62v1_TGD_CUT&RUN and Library prep
AUTHORS: Yunkyeong Lee
[DESCRIPTION]
Cleavage Under Targets & Release Using Nuclease (CUT&RUN) is a revolutionary genomic mapping strategy developed by the group of Dr. Steven Henikoff.
In CUT&RUN, cells or nuclei are immobilized to a solid support, with pAG-MNase clea... | ["CUT&RUN\n\n1. Buffer preparation: Make CUT&RUN buffers fresh the day of use. \n\n1) Add 1.8 mL Pre-Wash Buffer per sample to a 50 mL conical tube labeled \"Wash Buffer\". \n2) Dissolve 1 protease inhibitor tablet (Roche) in 2 mL water (25X stock). Add 72 uL per sample to the Wash Buffer. Store remaining 25X stock fo... |
68,650 | Picogram input multimodal sequencing (PiMmS) | 4 | null | https://www.protocols.io/view/picogram-input-multimodal-sequencing-pimms-cfaitice | christopher.laumer | TITLE: Picogram input multimodal sequencing (PiMmS)
AUTHORS: christopher.laumer
[DESCRIPTION]
This protocol describes a method for isolating and PCR amplifying low-bias long read (8-16 kb) genomic shotgun libraries from small-bodied invertebrates e.g. for de novo genome assembly. It can deliver diverse libraries and ... | ["Isolate specimen for extraction\n\nAnimals or tissue samples should be placed individually into the bottom of a 1.5 mL high recovery microcentrifuge tube. Samples may be:\n\n-Live\n-Flash-frozen at -80 C (appropriate for small specimens), on LN2/dry-ice chilled absolute ethanol. \n-Fixed (I have had success with RNAL... |
92,206 | A versatile nuclei extraction protocol for single nucleus sequencing in non model species – optimization in various Atlantic salmon tissues. | 4 | dx.doi.org/10.17504/protocols.io.261genwm7g47/v4 | https://www.protocols.io/view/a-versatile-nuclei-extraction-protocol-for-single-c6anzade | Rose Ruiz Daniels, Richard S Taylor, Ross Dobie, Sarah Salisbury, Emily Clark, Dan Macqueen, Diego Robledo | TITLE: A versatile nuclei extraction protocol for single nucleus sequencing in non model species – optimization in various Atlantic salmon tissues.
AUTHORS: Rose Ruiz Daniels, Richard S Taylor, Ross Dobie, Sarah Salisbury, Emily Clark, Dan Macqueen, Diego Robledo
[DESCRIPTION]
Single cell RNA sequencing has rapidly be... | ["[Nucleus isolation workflow for ST-based buffers] on ice, place a piece of frozen tissue into one well of a 6-well tissue culture plate with 1 mL TST.", "[Nucleus isolation workflow for ST-based buffers] on ice, mince tissue initially using Tungsten Carbide scissors for 30 s and then with Noyes Spring Scissors for ... |
37,672 | Puromycin titration of cancer cell lines | 1 | dx.doi.org/10.17504/protocols.io.bg2gjybw | https://www.protocols.io/view/puromycin-titration-of-cancer-cell-lines-bg2gjybw | Emily Souster, Verity Goodwin, Adam Jackson, Charlotte Beaver, Rizwan Ansari, Fiona Behan, Mathew Garnett | TITLE: Puromycin titration of cancer cell lines
AUTHORS: Emily Souster, Verity Goodwin, Adam Jackson, Charlotte Beaver, Rizwan Ansari, Fiona Behan, Mathew Garnett
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used to identify the most suitable puromycin concentration for the selec... | ["[Day 1: Titration plate set up]\nDetach, collect and count cells by following Steps 1-8 of the protocol: Passaging adherent cancer cell lines.", "[Day 1: Titration plate set up]\nResuspend 1x106 cells in media, at a concentration of 2x105 cells/ml.\n5 mL", "[Day 1: Titration plate set up]\nUsing a 1mg/ml stock of pur... |
34,085 | ATR FTIR Spectoscopy of Aqueous Cell Cultures | null | dx.doi.org/10.17504/protocols.io.bdidi4a6 | null | Emrulla Spahiu, Senol Dogan, Jörg Schnauß, Mayda Gursel, Feride Severcan | TITLE: ATR FTIR Spectoscopy of Aqueous Cell Cultures
AUTHORS: Emrulla Spahiu, Senol Dogan, Jörg Schnauß, Mayda Gursel, Feride Severcan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">ATR-FTIR Spectroscopy of aqueous cell culture samples is explained step-by-step. Infrared spectra acquisition, proces... | ["[Spectra acquisition]\nArrange the temperature of the working environment to\n25 °C", "[Spectra acquisition]\nClean the ATR crystal using a cellulose wipe and water-ethanol-water sequence. Scratching the crystal surface must be avoided.", "[Spectra acquisition]\nLeave the crystal to air-dry", "[Spectra acquisition]\n... |
96,431 | Rapid transposase based total DNA library preparation and sequencing using MinION | 0 | dx.doi.org/10.17504/protocols.io.j8nlko796v5r/v2 | https://www.protocols.io/view/rapid-transposase-based-total-dna-library-preparat-daep2bdn | Lavi Singh, Ashley Jones, Benjamin Schwessinger | TITLE: Rapid transposase based total DNA library preparation and sequencing using MinION
AUTHORS: Lavi Singh, Ashley Jones, Benjamin Schwessinger
[DESCRIPTION]
This protocols is part of the ANU Biosecurity mini-research project #1 "Plant Pathogen Diagnostics: Visuals, subcultures, and genomics".
You will be provide... | ["[Preparation of input DNA] This first series of steps [1.x] will be performed by the three groups we selected in week 5. We will use their total native DNA samples for sequencing. We selected these samples bases on DNA concentrations and DNA integrity. We assessed the former using Qubit and the latter agarose gel ele... |
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