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 |
|---|---|---|---|---|---|---|---|
86,417 | Behavior Tracking with Running Wheels | 4 | null | https://www.protocols.io/view/behavior-tracking-with-running-wheels-cymrxu56 | Victoria Vance, Katerina Rademacher, Ken Nakamura | TITLE: Behavior Tracking with Running Wheels
AUTHORS: Victoria Vance, Katerina Rademacher, Ken Nakamura
[DESCRIPTION]
This protocol describes tracking and analyzing behavior in mice using wireless running wheels. Because these running wheels are able to be placed inside an animal's home cage and continuously collect d... | ["[Setting Up Wheels] Single-house mice in new cages containing activity wheels at least 3 days prior to beginning drug/vehicle to collect baseline data.", "[Setting Up Wheels] Place clear wheel base holder on cage floor. If the experiment involves providing medicated water, place water bottle in the cage with sufficie... |
103,537 | Isolation of brain infiltrating lymphocytes | 0 | dx.doi.org/10.17504/protocols.io.dm6gpzo68lzp/v1 | https://www.protocols.io/view/isolation-of-brain-infiltrating-lymphocytes-dhcr32v6 | Moustafa Nouh Elemeery, Salix Boulet | TITLE: Isolation of brain infiltrating lymphocytes
AUTHORS: Moustafa Nouh Elemeery, Salix Boulet
[DESCRIPTION]
This protocol details the isolation of brain infiltrating lymphocytes. Splenic lymphocytes are screened to verify the presence/phenotype of CD8 in the periphery.
[STEPS]
SECTION: Infiltration procedure
1. I... | ["[Infiltration procedure] Inject mice intravenously with CD45-FITC 3ug/mice (6 µL from vial/mice) for 3 min-5 min, then euthanized directly by decapitating head to stop blood circulation.", "[Infiltration procedure] Collect the brain for each experimental condition vs control.", "[Infiltration procedure] Dissociate br... |
null | null | null | dx.doi.org/10.17504/protocols.io.kr2cv8e | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?. | [] |
71,134 | Ligation | 1 | dx.doi.org/10.17504/protocols.io.6qpvr4dmbgmk/v1 | https://www.protocols.io/view/ligation-chp6t5re | Georgina Elisa Diego Macías, Ana Belem García González, Irán Alessandra Chaparro Rodríguez, Jair Alexis Gardea Sáenz | TITLE: Ligation
AUTHORS: Georgina Elisa Diego Macías, Ana Belem García González, Irán Alessandra Chaparro Rodríguez, Jair Alexis Gardea Sáenz
[DESCRIPTION]
Protocol for a Ligation with Master Mix Ligase after a restriction digestion protocol had been made.
[STEPS]
1. Add5 µL of Master Mix Ligase
2. Add the a quantit... | ["Add5 µL of Master Mix Ligase", "Add the a quantity of the DNA vector digested by EcoRI and PstI in a molar ratio 1:3 with the DNA insert", "Add the a quantity of the DNA insert digested by EcoRI and PstI in a molar ratio 3:1 with the DNA vector", "Add water up to 20 µL", "Ligate for 1200 min at 22°C", "Transform with... |
38,296 | Lentiviral_vector_production_with_PEI | 4 | null | https://www.protocols.io/view/lentiviral-vector-production-with-pei-bhmyj47w | Kenneth Matreyek, Anna Bruchez | TITLE: Lentiviral_vector_production_with_PEI
AUTHORS: Kenneth Matreyek, Anna Bruchez
[STEPS]
?. [Preparation]
This protocol will require transfecting HEK 293T cells. Make sure you have some 293T cells thawed and growing for at least a couple of days before doing this protocol. Furthermore, prepare stocks of PEI and Di... | ["[Preparation]\nThis protocol will require transfecting HEK 293T cells. Make sure you have some 293T cells thawed and growing for at least a couple of days before doing this protocol. Furthermore, prepare stocks of PEI and Diluent if you have not done so already.", "[Transfection]\nPrepare the mixture in a sterile mic... |
85,701 | TCR sequencing and activation | 4 | dx.doi.org/10.17504/protocols.io.j8nlkokpxv5r/v1 | https://www.protocols.io/view/tcr-sequencing-and-activation-cxxdxpi6 | Zorea Jonathan | TITLE: TCR sequencing and activation
AUTHORS: Zorea Jonathan
[DESCRIPTION]
This protocol is a procedure we follow to isolate tumor infiltrating T cells and try to activate them with unique peptides and to characterize their TCR repertoire
[STEPS]
SECTION: Tumor implantation
1. Grow sufficient amount of cells (5*10^6... | ["[Tumor implantation] Grow sufficient amount of cells (5*10^6 per mouse). At the day cells are ready to be inject, thaw a vial of Basement Membrane Extract (Biotest, 3433-010-01) on ice. Keep 200ul tips in -20° as well.", "Once the BME is thawed, trypsinize the cells, count them using trypan blue, and resuspend them i... |
38,609 | Aspergillus nidulans protoplast isolation for transfections | 4 | dx.doi.org/10.17504/protocols.io.bhxrj7m6 | https://www.protocols.io/view/aspergillus-nidulans-protoplast-isolation-for-tran-bhxrj7m6 | Andrew Liu, Jai Denton | TITLE: Aspergillus nidulans protoplast isolation for transfections
AUTHORS: Andrew Liu, Jai Denton
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Modified </span><span style = "font-style:italic;">Aspergillus nidulans</span><span> protoplast isolation using Novozyme VinoTaste Pro as an enzyme... | ["[Grow Overnight Culutre]\nLate afternoon-evening the day before, grow scraped condispores (two arms from MM complete agar plate, ~ 1 x 108 total spores) in 30ml liquid CM, supplemented with pyridoxine and riboflavin, overnight at 25°C 18-20 hrs or 30°C 11-12 hrs on orbital shaker at 150rpm. Growth can be arrested at ... |
27,927 | Creation of low-oxygen conditions. | null | dx.doi.org/10.17504/protocols.io.7hxhj7n | null | Shengyi Yan, 宏亮 董 | TITLE: Creation of low-oxygen conditions.
AUTHORS: Shengyi Yan, 宏亮 董
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>We use Na</span><span style = "vertical-align:sub;">2</span><span>SO</span><span style = "vertical-align:sub;">3 </span><span>to create low-oxygen conditions in our experiment. ... | ["[Changes of dissolved oxygen with time in the LB medium with different concentrations of Na2SO3.]\nPrepare LB medium with different concentrations of Na2SO3.", "[Changes of dissolved oxygen with time in the LB medium with different concentrations of Na2SO3.]\nAB1Na2SO3(100g/L)LB medium20μL20mL320μL20mL440μL20mL5100μL... |
19,796 | MBARI Environmental DNA (eDNA) extraction using Qiagen DNeasy Blood and Tissue Kit | null | dx.doi.org/10.17504/protocols.io.xjufknw | null | Kristine Walz, Kevan Yamahara, Reiko P Michisaki, Francisco P. Chavez | TITLE: MBARI Environmental DNA (eDNA) extraction using Qiagen DNeasy Blood and Tissue Kit
AUTHORS: Kristine Walz, Kevan Yamahara, Reiko P Michisaki, Francisco P. Chavez
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Nucleic acids extraction from the filters using the Qiagen DNeasy Blood and Tissue... | ["[Preparation]\nNucleic acids were extracted from the filters using the Qiagen DNeasy Blood and Tissue Kit with some modifications to the manufacturer’s protocol.", "[Preparation]\nPrior to extraction, 0.5 mm and 0.1 mm glass beads (BioSpec Products) were ashed at 500 °C for 5 hours.", "[Preparation]\nBead tubes: 0.25... |
91,954 | Protocol for fixing and peeling Aedes aegypti embryos | 1 | dx.doi.org/10.17504/protocols.io.261ged88wv47/v1 | https://www.protocols.io/view/protocol-for-fixing-and-peeling-aedes-aegypti-embr-c52sy8ee | William Reid, Geyenna Sterling-Lentsch, Marc S. Halfon | TITLE: Protocol for fixing and peeling Aedes aegypti embryos
AUTHORS: William Reid, Geyenna Sterling-Lentsch, Marc S. Halfon
[DESCRIPTION]
The collection, fixing, and immunohistochemical staining of Aedes aegypti embryos is challenging in comparison to D. melanogaster since the vitelline membrane of Ae. aegypti must b... | ["[Preparation of an aspirator] Cut both ends from a 10 mL serological pipette. Save the end with the cotton plug.", "[Preparation of an aspirator] Trim the tapered tip and remove any sharp edges.", "[Preparation of an aspirator] Whittle the thinner plastic end of the serological pipette where the cotton plug is.", "[P... |
88,224 | 10x Protocols: Chromium Single Cell/Nuclei Gene Expression Flex Multiplex -- University of Minnesota TMCs (CG000527 Rev D) | 1 | dx.doi.org/10.17504/protocols.io.bp2l6x81klqe/v1 | https://www.protocols.io/view/10x-protocols-chromium-single-cell-nuclei-gene-exp-c2d8ya9w | IOx Genomics, Laura Niedernhofer | TITLE: 10x Protocols: Chromium Single Cell/Nuclei Gene Expression Flex Multiplex -- University of Minnesota TMCs (CG000527 Rev D)
AUTHORS: IOx Genomics, Laura Niedernhofer
[DESCRIPTION]
10x Genomics Chromium Single Cell Expression flex protocol for library construction.
Protocol ID# (CG) and Revision letter provide... | ["https://www.10xgenomics.com/products/single-cell-gene-expression-flex\nhttps://www.10xgenomics.com/support/single-cell-gene-expression-flex", "Complete single cell or nuclei isolation and 10x fixation prior to starting this protocol"] |
25,317 | RNA Isolation from Plant Tissue Protocol 11: Tri Reagent Method | null | dx.doi.org/10.17504/protocols.io.4ydgxs6 | null | null | TITLE: RNA Isolation from Plant Tissue Protocol 11: Tri Reagent Method
AUTHORS:
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Implemented by: Michael Melkonian and Barbara Surek</div><div class = "text-block"><span>The protocol for RNA isolation using </span><a href="https://www.protocols.io/view... | [] |
36,723 | Metabolomics and Lipidomics Sample Preparation | 1 | dx.doi.org/10.17504/protocols.io.bf4tjqwn | https://www.protocols.io/view/metabolomics-and-lipidomics-sample-preparation-bf4tjqwn | Kevin Contrepois | TITLE: Metabolomics and Lipidomics Sample Preparation
AUTHORS: Kevin Contrepois
[DESCRIPTION]
Scope:
To describe the procedure to extract metabolites and complex lipids using a biphasic separation with cold methyl tert-butyl ether (MTBE), methanol and water.
Expected outcome/data:
Metabolites and complex lipids are p... | ["Roughly 30 mg of frozen tissues were homogenized in 500 µl ice-cold methanol by bead beating (MP bioscience cat# 6913-100, Solon, OH) at 4°C (2 x 45 s).", "1 ml of MTBE was added to 300 μl of the homogenate spiked-in with 40 µL deuterated lipid internal standards (Sciex, cat#: 5040156, lot#: LPISTDKIT-101).", "The sa... |
17,415 | Impact of glucose-6-phosphate dehydrogenase deficiency on dengue infection in Myanmar childrened protocol | null | dx.doi.org/10.17504/protocols.io.u9fez3n | null | Win Lai May, Myat Phone Kyaw, Stuart D. Blacksell, Sasithon Pukrittayakamee, Kesinee Chotivanich, Borimas Hanboonkunupakarn, Khin Nyo Thein, Chae Seung Lim, Janjira Thaipadungpanit, Thomas Althaus, podjanee jittamala | TITLE: Impact of glucose-6-phosphate dehydrogenase deficiency on dengue infection in Myanmar childrened protocol
AUTHORS: Win Lai May, Myat Phone Kyaw, Stuart D. Blacksell, Sasithon Pukrittayakamee, Kesinee Chotivanich, Borimas Hanboonkunupakarn, Khin Nyo Thein, Chae Seung Lim, Janjira Thaipadungpanit, Thomas Althaus, ... | [] |
64,458 | XP Nutrition Keto Gummies: (Exposed 2022) Is XP Nutrition Keto Gummies Burn Fat? Where To Buy? Price! | 4 | dx.doi.org/10.17504/protocols.io.6qpvr6qjzvmk/v1 | https://www.protocols.io/view/xp-nutrition-keto-gummies-exposed-2022-is-xp-nutri-ca7ishke | XP Nutrition Keto Gummies | TITLE: XP Nutrition Keto Gummies: (Exposed 2022) Is XP Nutrition Keto Gummies Burn Fat? Where To Buy? Price!
AUTHORS: XP Nutrition Keto Gummies
[DESCRIPTION]
XP Nutrition Keto Gummies
[STEPS]
1.
➢Product Name —XP Nutrition Keto Gummies
➢Main benefits —Helps to reduce stress, an... | ["➢Product Name —XP Nutrition Keto Gummies\n➢Main benefits —Helps to reduce stress, anxiety, and depression\n➢Ingredients —CBD Gummies\n➢ Location —United States\n➢Dosage — As Prescribed on Bottle or Consu... |
48,144 | Identification chart for common Daphnia species in lakes in Michigan, and their most common parasites | 3 | null | https://www.protocols.io/view/identification-chart-for-common-daphnia-species-in-bs9qnh5w | Meghan Duffy, Kristel Sanchez | TITLE: Identification chart for common Daphnia species in lakes in Michigan, and their most common parasites
AUTHORS: Meghan Duffy, Kristel Sanchez
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a guide to the common Daphnia (& one Ceriodaphnia) species found in stratified lakes in Michigan... | [] |
49,052 | Pesticide Analysis Autotrace SOP | 6 | null | https://www.protocols.io/view/pesticide-analysis-autotrace-sop-bt54nq8w | Lara Frankson | TITLE: Pesticide Analysis Autotrace SOP
AUTHORS: Lara Frankson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">To test for neonics in turf runoff.</div></div>
[STEPS]
?. [Prepare Autotrace for T120 Runoff Extractions (Neonics)]
Turn on the system (doesn’t need to be turned off unless idle for >14 d... | ["[Prepare Autotrace for T120 Runoff Extractions (Neonics)]\nTurn on the system (doesn’t need to be turned off unless idle for >14 days)Open the nitrogen valve on the tank (to the right of the -40C freezer).Make sure the pressure on the regulator is no more than 100 psi.", "[Prepare Autotrace for T120 Runoff Extraction... |
61,972 | Protocol for Dead-End Ultrafiltration using REXEED 25S for Isolation of Salmonella from Surface Water | 4 | dx.doi.org/10.17504/protocols.io.bp2l613p1vqe/v1 | https://www.protocols.io/view/protocol-for-dead-end-ultrafiltration-using-rexeed-b8rurv6w | Autumn L Kraft, Manan Sharma, Jonathan G Frye, James E Wells, Abasiofiok Mark Ibekwe, NARMS EWG | TITLE: Protocol for Dead-End Ultrafiltration using REXEED 25S for Isolation of Salmonella from Surface Water
AUTHORS: Autumn L Kraft, Manan Sharma, Jonathan G Frye, James E Wells, Abasiofiok Mark Ibekwe, NARMS EWG
[DESCRIPTION]
Protocol describes dead-end ultrafiltration (DEUF) using REXEED 25S for the recovery ... | ["[Protocol] If needed, add control strain to water sample by gently tipping vial over the opening. Close sample bottle tightly and thoroughly mix sample before proceeding.", "[Protocol] Prepare for filtration by setting up Geotech pump in the biosafety cabinet (BSC). Ensure there is enough room around pump to include ... |
95,789 | Monosynaptic Rabies Tracing | 4 | dx.doi.org/10.17504/protocols.io.3byl4qp9jvo5/v1 | https://www.protocols.io/view/monosynaptic-rabies-tracing-c9smz6c6 | Alexandra Nelson, Michael Ryan | TITLE: Monosynaptic Rabies Tracing
AUTHORS: Alexandra Nelson, Michael Ryan
[DESCRIPTION]
This protocol describes the steps for performing stereotaxic surgery in mice. It is applicable to intracranial injections (e.g. virus, drug) and placement of implants (e.g. optical fibers, electrode arrays) into targeted regions o... | ["Rabies injections were performed in a BSL-2 surgical suite following the protocol described in dx.doi.org/10.17504/protocols.io.n2bvj6qynlk5/v1", "For modified, G-deleted rabies viruses, first inject a Cre-dependent helper virus (AAV-DIO-sTpEpB-GFP) to restrict expression of the EnvA receptor (TVA) and rabies glycopr... |
91,042 | Perforated patch electrophysiology recordings | 4 | dx.doi.org/10.17504/protocols.io.36wgq3y9olk5/v1 | https://www.protocols.io/view/perforated-patch-electrophysiology-recordings-c46ayzae | enrico.zampese | TITLE: Perforated patch electrophysiology recordings
AUTHORS: enrico.zampese
[DESCRIPTION]
In this protocol we detail the steps to perform ex-vivo brain slices perforated patch electrophysiology recordings.
The protocol is originally meant to record from striatal MSNs, but can be adapted to other cell types.
[BEFORE_... | ["[Prepare patch pipettes] Turn on the Sutter P-1000 puller and enter the desired pull protocol.", "[Prepare patch pipettes] Insert a thick-walled borosilicate glass capillary and press pull.", "[Prepare patch pipettes] Pipette resistance must be of 3 to 6 megaohms.", "[Setting up patch rig and environment] Turn on the... |
87,960 | External Quality Control for inter-Batch comparison | 1 | dx.doi.org/10.17504/protocols.io.yxmvm391ol3p/v1 | https://www.protocols.io/view/external-quality-control-for-inter-batch-compariso-cz5yx87w | Ricardo M. Borges | TITLE: External Quality Control for inter-Batch comparison
AUTHORS: Ricardo M. Borges
[DESCRIPTION]
Controle de Qualidade Externo (QCExt): A amostra contendo a cepa código CCMR0280 cultivada em paralelo a todos os lotes servirá como referência para estudos comparativos estudo de comparação entre as cepas do CCMR (Cul... | ["[Material] microtubos de 2 mL com tampa de rosca\ntudo de centrifugação de 50 mL tipo Falcon\nBalança analítica (AUW220 , Shimadzu)", "[Material em Estoque] Inicialmente, um lote inicial composto por 25 réplicas do cultivo da cepa código CCMR0280\nfoi (i) cultivado, (ii) coletado e combinado, (iii) submetido a liofil... |
26,237 | CULTURING i3LMNS (Basic Protocol 8) | null | dx.doi.org/10.17504/protocols.io.5u5g6y6 | null | Michael S. Fernandopulle, Ryan Prestil, Christopher Grunseich, Chao Wang, Li Gan, Michael E. Ward | TITLE: CULTURING i3LMNS (Basic Protocol 8)
AUTHORS: Michael S. Fernandopulle, Ryan Prestil, Christopher Grunseich, Chao Wang, Li Gan, Michael E. Ward
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Induction and differentiation of i</span><span style = "vertical-align:super;">3</span><span>LMN... | ["[Coating dishes]\nPrepare stock solutions of PLO, PEI, or PDL (see Table 3).", "[Coating dishes]\nAdd one-half culture volume of 1× coating solution from step 1 to the tissue culture dishes to be used for plating Day 3 partially differentiated i3LMNs.", "[Coating dishes]\nIncubate dishes for at least at .\n0 Room te... |
21,750 | Copy of Immunohistochemistry | null | dx.doi.org/10.17504/protocols.io.zgwf3xe | null | Ning Zhang, Yu Kuang | TITLE: Copy of Immunohistochemistry
AUTHORS: Ning Zhang, Yu Kuang
[STEPS]
?. Deparaffinize/hydrate sections: a.Incubate sections in three washes of xylene for 5 minutes each.b.Incubate sections in two washes of 100% ethanol for 10 minutes each.c.Incubate sections in two washes of 95% ethanol for 10 minutes each.
?. Wa... | ["Deparaffinize/hydrate sections: a.Incubate sections in three washes of xylene for 5 minutes each.b.Incubate sections in two washes of 100% ethanol for 10 minutes each.c.Incubate sections in two washes of 95% ethanol for 10 minutes each.", "Wash sections twice in dH2O for 5 minutes each.", "Incubate sections in 3% hyd... |
28,865 | Creatinine Clearance by HPLC | null | dx.doi.org/10.17504/protocols.io.8e9hth6 | null | Kumar Sharma | TITLE: Creatinine Clearance by HPLC
AUTHORS: Kumar Sharma
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">This protocol describes the procedures for collecting, preparing and performing the DiaComp Creatinine Clearance... | ["[Collection of timed mouse urines.]\nGeneral procedure using the Nalgene Diuresis Cage (650-0322): a clean cage is prepared for use by lightly spraying the (1) metal mouse screen, (2) the mesh support grid and (3) the conical mouse funnel with silicone spray. Wipe off any excessive silicone and allow it to sit on ben... |
106,631 | PFF seeding in U2OS cells | 0 | dx.doi.org/10.17504/protocols.io.q26g717bqgwz/v1 | https://www.protocols.io/view/pff-seeding-in-u2os-cells-dkdf4s3n | Isabel Lam, Alain Ndayisaba, Vikram Khurana | TITLE: PFF seeding in U2OS cells
AUTHORS: Isabel Lam, Alain Ndayisaba, Vikram Khurana
[DESCRIPTION]
PFF seeding in U2OS cells
[STEPS] | [] |
33,325 | Brooks Lab Western Blotting Protocol | null | dx.doi.org/10.17504/protocols.io.bcsmiwc6 | null | Brooks Lab University of California, Eva Robinson, Alison Tang | TITLE: Brooks Lab Western Blotting Protocol
AUTHORS: Brooks Lab University of California, Eva Robinson, Alison Tang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a Western Blotting Protocol for Brooks Lab, Department of Biomolecular Engineering, University of California, Santa Cruz.</div>... | ["[RIPA Lysis Buffer]\nMake , cover, and freeze in 10 ml aliquots at . ORUse pre-made Pierce RIPA buffer, 100 ml, which is aliquoted in aliquots and stored in\n[RIPA w/o protease inhibitor]\n-20 °C\n10 ml\n-20 °C", "[RIPA Lysis Buffer]\nBefore use, thaw and add 1 tablet of protease inhibitor (PI) per 10 ml aliquot. (... |
66,461 | Purification and Crystallization of ATG9 HDIR-ATG101:ATG13 complex | 4 | dx.doi.org/10.17504/protocols.io.dm6gpbkdjlzp/v1 | https://www.protocols.io/view/purification-and-crystallization-of-atg9-hdir-atg1-cc55sy86 | Adam Yokom, Xuefeng Ren | TITLE: Purification and Crystallization of ATG9 HDIR-ATG101:ATG13 complex
AUTHORS: Adam Yokom, Xuefeng Ren
[DESCRIPTION]
Purification and Crystallization of ATG9 HDIR (828-839) fused ATG101 (1-198):ATG13 (1-197)
[STEPS]
SECTION: Crystallization
19. ATG9 HDIR-ATG101:ATG13 complex at 6 mg/ml in 25 mM HEPES pH 7.5, 1... | ["[Crystallization] ATG9 HDIR-ATG101:ATG13 complex at 6 mg/ml in 25 mM HEPES pH 7.5, 150mM NaCl, 1mM MgCl2, 1mM TCEP was used as the protein stock", "[Crystallization] Crystallization was carried out by sitting-drop vapor diffusion using an automated liquid-handling system (Mosquito, TTP LabTech, UK) at 288 K in 96-we... |
15,198 | SN medium | null | dx.doi.org/10.17504/protocols.io.s36egre | null | Roscoff Culture Collection | TITLE: SN medium
AUTHORS: Roscoff Culture Collection
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Used for some cyanobacteria in particular </span><span style = "font-style:italic;">Synechococcus</span><span style = "font-style:italic;">.</span></div></div>
[STEPS]
?. Autoclave and filter ... | ["Autoclave and filter aged seawaterWork under laminar flow hood.Add to 800mL of seawater the following nutriments that have been autoclaved beforehand (except vitamin) Quantity\n Compound\n Stock Solution\n 2,0 mL\n EDTA disodium salt dihydrate (Na2EDTA-2H2O)\n 2,8 g/L\n 2,0 mL\n Sodium carbonat... |
null | null | null | dx.doi.org/10.17504/protocols.io.u73ezqn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol results in the isolation of single nucleated zoospores from a culture of Aurantiochytrium limacinum. The point is to recover single nucleus colonies rather than single cell colonies (which may contain varying nuclei - particularly following transformation).
[STEP... | ["[Prepare Culture] Inoculate 500 ul GPY media (microcentrifuge tube) with toothpick scrape of a colony. If inoculating a zeocin resistant colony, add 5 ul zeocin (for 100 ug/ml). Vortex/ resuspend cells. Pipette 4.5 ml of GPY into a 15 ml glass culture tube. Add 500 ul inoculum. Incubate at 28 C, 170 rpm for 48 h, or ... |
null | null | null | dx.doi.org/10.17504/protocols.io.ibbcain | null | null | TITLE: No Title
AUTHORS:
[BEFORE_START]
<p>-Sterile polypropylene tubes (15 or 50 ml); sterile Oak Ridge-tubes</p>
<p> </p>
<p>-Steel forceps </p>
<p> </p>
<p>-Scissors</p>
<p> </p>
<p>-glass rod with rounded end</p>
<p> </p>
<p>-95% Ethanol for sterilization</p>
<p> </p>
<p>-Sterile lysis buffer (10 mM Tris, 100 mM ... | [] |
51,686 | Test protocol II | 1 | null | https://www.protocols.io/view/test-protocol-ii-bwqepdte | Abby Moore | TITLE: Test protocol II
AUTHORS: Abby Moore
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a test protocol</div></div>
[STEPS]
?. Use 80:20 MeOH:H2O for this step. This is not easy to access by machine.
?. If you haven't already, make a solution with the following components:
?. If you hav... | ["Use 80:20 MeOH:H2O for this step. This is not easy to access by machine.", "If you haven't already, make a solution with the following components:", "If you haven't already, make a solution with the following components:", "Use this piece of equipment:"] |
71,137 | Colony PCR | 1 | dx.doi.org/10.17504/protocols.io.dm6gpjwx8gzp/v1 | https://www.protocols.io/view/colony-pcr-chp9t5r6 | Georgina Elisa Diego Macías, Ana Belem García González, Irán Alessandra Chaparro Rodríguez, Jair Alexis Gardea Sáenz | TITLE: Colony PCR
AUTHORS: Georgina Elisa Diego Macías, Ana Belem García González, Irán Alessandra Chaparro Rodríguez, Jair Alexis Gardea Sáenz
[DESCRIPTION]
Protocol for a PCR from a colony
[STEPS]
1. Dissolve one colony in 20 µL of nuclease-free water and heat at 80°C for 10 minutes.
2. Prepare the following 50 uL... | ["Dissolve one colony in 20 µL of nuclease-free water and heat at 80°C for 10 minutes.", "Prepare the following 50 uL reaction in a 0.2mL PCR tube on ice:", "Gently mix the reaction and spin down in the microcentrifuge", "Cycling conditions for a routine PCR:"] |
26,190 | DIFFERENTIATION OF i3LMNS (Basic Protocol 7) | null | dx.doi.org/10.17504/protocols.io.5tng6me | null | Michael S. Fernandopulle, Ryan Prestil, Christopher Grunseich, Chao Wang, Li Gan, Michael E. Ward | TITLE: DIFFERENTIATION OF i3LMNS (Basic Protocol 7)
AUTHORS: Michael S. Fernandopulle, Ryan Prestil, Christopher Grunseich, Chao Wang, Li Gan, Michael E. Ward
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describes the rapid and robust differentiation of hiPSCs into lower motor... | ["[Day 0]\nPrepare a sufficient amount of hNIL-iPSC for differentiation.\nApproximately two wells of a 6-well dish at 80 % confluency are sufficient to begin the differentiation of a 10-cm dish, and cell numbers may be scaled by well surface area.Typically, hNIL lines proliferate for longer than hNGN2 lines, and this p... |
9,378 | Heterologous expression and affinity purification of Strep-tagged (KaiC) proteins | null | dx.doi.org/10.17504/protocols.io.meac3ae | null | Anika Wiegard, Christin Köbler, Katsuaki Oyama, Anja K. Dörrich, Chihiro Azai, Kazuki Terauchi, Annegret Wilde, Ilka Maria Axmann | TITLE: Heterologous expression and affinity purification of Strep-tagged (KaiC) proteins
AUTHORS: Anika Wiegard, Christin Köbler, Katsuaki Oyama, Anja K. Dörrich, Chihiro Azai, Kazuki Terauchi, Annegret Wilde, Ilka Maria Axmann
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol can be use... | ["[heterologous protein expression in E.coli]\ntransformation", "[heterologous protein expression in E.coli]\npre-culture:inoculate LB medium containing 75-100 µg ampicillin ml-1 (optional: plus 30 µg chloramphenicol ml-1) with resulting transformants (use e.g. 200 ml LB)incubate over night at 37 °C and 200-250 r.p.m."... |
71,070 | Nanopore sequencing data analysis using Microsoft Azure cloud computing service | 5 | dx.doi.org/10.17504/protocols.io.x54v9dj7pg3e/v1 | https://www.protocols.io/view/nanopore-sequencing-data-analysis-using-microsoft-chm6t49e | Linh Truong | TITLE: Nanopore sequencing data analysis using Microsoft Azure cloud computing service
AUTHORS: Linh Truong
[DESCRIPTION]
This protocol provides instruction to set up the analytic pipeline to process raw data from Oxford Nanopore Sequencing. This pipeline leverages the computing resources available in Microsoft Azure ... | ["[Section 1: Generation of data on-site] Load the multiplexed HLA library pool consisting of 48 individuals onto a MinION flow cell. The data is acquired using MinKNOW software for 16 hours using default settings. \n \n960 min", "[Section 1: Generation of data on-site] The raw FAST5 files are stored in a local folder ... |
null | null | null | dx.doi.org/10.17504/protocols.io.nupdevn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?. | [] |
27,302 | Coulter Method for the detection of Physiological parameters | null | dx.doi.org/10.17504/protocols.io.6wehfbe | null | Xiaohua Du, Xia Liu, Mawolo James Blackar, Yingjie Zhou, Haifeng Wang, Fayang Liu, Zhiqing He | TITLE: Coulter Method for the detection of Physiological parameters
AUTHORS: Xiaohua Du, Xia Liu, Mawolo James Blackar, Yingjie Zhou, Haifeng Wang, Fayang Liu, Zhiqing He
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Instrument</span></div><div class = "text-block... | [] |
107,048 | Astrocyte generation | 0 | dx.doi.org/10.17504/protocols.io.bp2l62e5dgqe/v1 | https://www.protocols.io/view/astrocyte-generation-dksg4wbw | Patricia López García | TITLE: Astrocyte generation
AUTHORS: Patricia López García
[DESCRIPTION]
Protocol to generate astrocytes from cortical NPCs using a comercial media (AM)
[STEPS]
SECTION: NPC generation
1. To prepare the iPSC’s for neural induction, iPSCs need to grow to 90 - 100% confluence.
SECTION: NPC generation
2. As soon as the... | ["[NPC generation] To prepare the iPSC’s for neural induction, iPSCs need to grow to 90 - 100% confluence.", "[NPC generation] As soon as the cells reach 90% confluence mTeSR media is switched to neural induction media (N2B27 supplemented with 10uM SB431542 and 1uM Dorsomorphin).", "[NPC generation] Neural induction me... |
92,392 | noesypr1d_metab.nan | 5 | dx.doi.org/10.17504/protocols.io.x54v9p21pg3e/v4 | https://www.protocols.io/view/noesypr1d-metab-nan-c6ggzbtw | NAN KB, John Glushka, Mario Uchimiya, Saraa Al Jawad, Christopher Esselman, Leandro I Ponce, Laura Morris, Arthur Edison | TITLE: noesypr1d_metab.nan
AUTHORS: NAN KB, John Glushka, Mario Uchimiya, Saraa Al Jawad, Christopher Esselman, Leandro I Ponce, Laura Morris, Arthur Edison
[DESCRIPTION]
This is a protocol for running the Bruker pulse program "noesypr1d".
[BEFORE_START]
This protocol assumes your sample is loaded, locked, tuned, and... | ["[Create a new dataset]", "[Create a new dataset] On the menu bar on TopSpin, click on\nStart → Create Dataset", "[Create noesypr1d experiment file] When Lock, Tune, Shim are complete proceed to the specific protocol for your desired pulseprogram(s).", "[Create a new dataset] A new window opens. On the right top bar, ... |
null | null | null | dx.doi.org/10.17504/protocols.io.grwbv7e | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.jqwcmxe | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?. | [] |
44,420 | Live Cell Quantification using Image Analysis | 1 | dx.doi.org/10.17504/protocols.io.bpmcmk2w | https://www.protocols.io/view/live-cell-quantification-using-image-analysis-bpmcmk2w | Minjung Song, Florian Merkle | TITLE: Live Cell Quantification using Image Analysis
AUTHORS: Minjung Song, Florian Merkle
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Purpose</span></div><div class = "text-block">This protocol describes image-based quantification of human pluripotent stem cell... | ["[Cell culture and staining: Cell plating]\nCoat plate with appropriate substrate to prepare cells for plating.\nWe have found the 24-well black μ-Plate from Ibidi allows good cell growth and is compatible with high-content imaging systems.", "[Cell culture and staining: Cell plating]\nWhen plating cells for culture, ... |
69,505 | PCR amplicon next generation sequencing | 1 | dx.doi.org/10.17504/protocols.io.36wgq64olk57/v3 | https://www.protocols.io/view/pcr-amplicon-next-generation-sequencing-cf49tqz6 | Susanne Kreutzer, Lilly van de Venn, Charles Yeh, Mark DeWitt | TITLE: PCR amplicon next generation sequencing
AUTHORS: Susanne Kreutzer, Lilly van de Venn, Charles Yeh, Mark DeWitt
[DESCRIPTION]
Preparation of Amplicons for deep sequencing is based on two PCR steps. The genomic loci of interest is enriched in a first PCR including a stubber sequence to both ends of the molecule.... | ["[Extract genomic DNA from edited cells using QuickExtract solution] Resuspend cell pellet to ≥2,500 cells/µL in QuickExtract solution. Vortex or pipette-mix to resuspend thoroughly.\n \n\nMake sure to check whether QuickExtract is appropriate for your sample and application. Take a look at \n\nfor a more extensive li... |
42,327 | Unlocking Spatial Molecular & Cellular Relationships of SARS-CoV-2 in Archived Human Tissue | 3 | dx.doi.org/10.17504/protocols.io.bmjxk4pn | https://www.protocols.io/view/unlocking-spatial-molecular-amp-cellular-relations-bmjxk4pn | Sam Pattle, Jenna Gregory, Fergal M Waldron | TITLE: Unlocking Spatial Molecular & Cellular Relationships of SARS-CoV-2 in Archived Human Tissue
AUTHORS: Sam Pattle, Jenna Gregory, Fergal M Waldron
[DESCRIPTION]
The true prevalence of SARS-CoV-2 infection in the UK population remains unknown. Phylogenetic diversity estimates derived from genomic sequence trac... | [] |
42,342 | Copy of Lab 1 Notebook | 3 | null | https://www.protocols.io/view/copy-of-lab-1-notebook-bmkek4te | Kamron Mojabe | TITLE: Copy of Lab 1 Notebook
AUTHORS: Kamron Mojabe
[STEPS] | [] |
77,698 | The monocyte-derived dendritic cell (MoDC) assay – an in vitro assay for testing the immunogenicity of cellular therapies | 4 | dx.doi.org/10.17504/protocols.io.8epv5jmqdl1b/v2 | https://www.protocols.io/view/the-monocyte-derived-dendritic-cell-modc-assay-an-cp5avq2e | Annabel J Curle, Sarah Howlett, Joanne Jones | TITLE: The monocyte-derived dendritic cell (MoDC) assay – an in vitro assay for testing the immunogenicity of cellular therapies
AUTHORS: Annabel J Curle, Sarah Howlett, Joanne Jones
[DESCRIPTION]
The monocyte-derived dendritic cell (MoDC) assay can be used to test, in vitro, the immunogenicity of potential regenerati... | ["[Cell preparations and moDC differentiation - Day 0-7] Make PBMCs using preferred method from whole blood", "[Cell preparations and moDC differentiation - Day 0-7] Take whole PBMCs and enrich for CD14+ cells using magnetic activated cell sorting (MACS) with CD14+ microbeads", "[Cell preparations and moDC differentiat... |
28,285 | MojoSort™ Nanobeads Protocol - 1 | null | dx.doi.org/10.17504/protocols.io.7u5hny6 | null | Sam Li | TITLE: MojoSort™ Nanobeads Protocol - 1
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 either selected or depleted by incubating... | ["Prepare cells from your tissue of interest or blood without lysing erythrocytes. Kits for human samples have been optimized for PBMCs, please prepare the cells using a suitable method.", "In the final wash of your sample preparation, resuspend the cells in MojoSort™ Buffer by adding up to 4mL in a 5 mL (12 x 75 mm) p... |
26,381 | Microbiome Assay | null | dx.doi.org/10.17504/protocols.io.5zmg746 | null | Priota Islam | TITLE: Microbiome Assay
AUTHORS: Priota Islam
[STEPS]
?. Preparing worms Chunk N2s on 3-4 plates on Wednesday, also book the hood for next Wednesday morning to dry the seeded plates Bleach the N2s on Friday and keep the tube in the rotator inside the 20C incubator On Monday refeed the arrested L1s to be young adults o... | ["Preparing worms Chunk N2s on 3-4 plates on Wednesday, also book the hood for next Wednesday morning to dry the seeded plates Bleach the N2s on Friday and keep the tube in the rotator inside the 20C incubator On Monday refeed the arrested L1s to be young adults on Thursday (Tracking Day1), do the same on Tuesday for t... |
44,260 | test 1 v3 | 1 | null | https://www.protocols.io/view/test-1-v3-bpgcmjsw | 611 | TITLE: test 1 v3
AUTHORS: 611
[STEPS]
?. test | ["test"] |
null | null | null | dx.doi.org/10.17504/protocols.io.dzr755 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
The following continued adaptation of Hennes et al. (1995) is a result of FLVP assay optimizations for the <em>Vibrio alginolyticus</em> PWH3a-phage P1 phage-host system (PHS) for use with SYBR Green I stain. Novices to microscopy would benefit from reading Wen et al. (2004) for... | [] |
87,957 | A computational pipeline to quantify perinuclear lysosomes in fibroblasts using CellProfiler | 5 | dx.doi.org/10.17504/protocols.io.81wgbxrw3lpk/v1 | https://www.protocols.io/view/a-computational-pipeline-to-quantify-perinuclear-l-cz5vx866 | Ebsy Jaimon, Suzanne R Pfeffer | TITLE: A computational pipeline to quantify perinuclear lysosomes in fibroblasts using CellProfiler
AUTHORS: Ebsy Jaimon, Suzanne R Pfeffer
[DESCRIPTION]
Here we present a CellProfiler software pipeline to quantify the distribution of lysosomes in MEF cells. The lysosomes were stained using anti-LAMP1 antibody, and nu... | ["[Import files into CellProfiler and extract metadata] A. Select the Images module, drag and drop the maximum intensity projected .TIF files as indicated\n\nB. Select the Metadata module\n\nIn the Metadata module: \n\nExtract metadata? Yes.\n\nMetadata extraction method: Extract from file/folder names\n\nMetadata so... |
93,094 | Culture of human epithelial cells (skin, cornea, thymus) on 3T3J2 feeder layer cells | 4 | dx.doi.org/10.17504/protocols.io.14egn31ezl5d/v3 | https://www.protocols.io/view/culture-of-human-epithelial-cells-skin-cornea-thym-c66ezhbe | Pierluigi Giuseppe Manti | TITLE: Culture of human epithelial cells (skin, cornea, thymus) on 3T3J2 feeder layer cells
AUTHORS: Pierluigi Giuseppe Manti
[DESCRIPTION]
Despite several protocols having been published in the past in a fragmented way,
this protocol represents a harmonious recollection and reorganization of those,
which proves to be... | ["[3T3J2 Growth Medium] Open DMEM bottle (ThermoFisher Scientific).", "[3T3J2 Growth Medium] Add 8 % (v/v) of bovine serum (ThermoFisher Scientific) (DO NOT use fetal calf serum!).", "Set up one flask at low density to maintain the line (5*10^5 cells at early passages, 10^5 cells at late passages). This flask should r... |
74,817 | ARTIC-like Bacillus anthracis MLVA amplicon sequencing protocol for MinION | 4 | dx.doi.org/10.17504/protocols.io.3byl4jzozlo5/v1 | https://www.protocols.io/view/artic-like-bacillus-anthracis-mlva-amplicon-sequen-cma9u2h6 | Ágnes Nagy, Gábor Tóth | TITLE: ARTIC-like Bacillus anthracis MLVA amplicon sequencing protocol for MinION
AUTHORS: Ágnes Nagy, Gábor Tóth
[DESCRIPTION]
Multiple-Locus Variable Number of Tandem Repeats (VNTR) Analysis (MLVA) is one of the gold standard strain-level subtyping methods for outbreak-related Bacillus anthracis strains. The repeat... | ["[Primer pool preparation] If required resuspend lyophilised primers at a concentration of 100µM each. Primer names, characteristics, concentrations and volumes required for primer stocks are listed in the table below.", "[Primer pool preparation] Generate 500 µL primer Pool 1 stock by adding 7 µL, 13.5 µL or 15.5 µL ... |
41,873 | Fluorescent-Reporter Based Assay | 4 | dx.doi.org/10.17504/protocols.io.bk5rky56 | https://www.protocols.io/view/fluorescent-reporter-based-assay-bk5rky56 | Piyush Jain, Long T Nguyen, Santosh Rananaware | TITLE: Fluorescent-Reporter Based Assay
AUTHORS: Piyush Jain, Long T Nguyen, Santosh Rananaware
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The CRISPR-Enhance SARS-CoV-2 detection kit has been designed to detect fragments of the Nucleocapsid (“N”) gene and Envelope gene (E) of SARS-CoV-2. An in... | ["[RT-LAMP Master Mix Preparation]\nLabel a new microcentrifuge tube for each target ( N, E and RP) and prepare a RT-LAMP Master Mix consisting of the WarmStart®Colorimetric LAMP 2X Master Mix with UDG.and the appropriate 10x Primer Mix using the recipe in Table 1 below. Make enough of each master mix for all samples ... |
43,254 | BGISEQ-500 WGS library construction | 1 | null | https://www.protocols.io/view/bgiseq-500-wgs-library-construction-bngwmbxe | Jie Huang, Xinming Liang, Yuankai Xuan, Chunyu Geng, Yuxiang Li, Haorong Lu, Shoufang Qu, Xianglin Mei, Hongbo Chen, Ting Yu, Nan Sun, Junhua Rao, Jiahao Wang, Wenwei Zhang, Ying Chen, Sha Liao, Hui Jiang, Xin Liu, Zhaopeng Yang, Feng Mu, Shangxian Gao | TITLE: BGISEQ-500 WGS library construction
AUTHORS: Jie Huang, Xinming Liang, Yuankai Xuan, Chunyu Geng, Yuxiang Li, Haorong Lu, Shoufang Qu, Xianglin Mei, Hongbo Chen, Ting Yu, Nan Sun, Junhua Rao, Jiahao Wang, Wenwei Zhang, Ying Chen, Sha Liao, Hui Jiang, Xin Liu, Zhaopeng Yang, Feng Mu, Shangxian Gao
[DESCRIPTION]
... | ["[Overview]", "[DNA fragmentation]\n1) Input genomic DNA sampleGenomic DNA Sample Recommendation AB1Nucleic Acid\n*High-quality genomic DNA\n2Molecular Weight\n>23k bp\n3Amount\n1μg\n4Concentration\n≥12.5ng/μL\n5Purity\nOD260/OD280=1.8~2.0\n*High-quality genomic DNA should be free of salt or organics. It could run... |
86,194 | TMT labelling | 4 | null | https://www.protocols.io/view/tmt-labelling-cyesxtee | Louise Uoselis | TITLE: TMT labelling
AUTHORS: Louise Uoselis
[DESCRIPTION]
TMT labelling
[STEPS]
1. Reconstitute lyophilised peptides in 25 µL by vortexing each sample for ~10 s, and then leaving to sit at Room temperature for 15 min. Each sample was then sonicated for 5 min in a waterbath sonicator in an ice slurry.
2. Determine ... | ["Reconstitute lyophilised peptides in 25 µL by vortexing each sample for ~10 s, and then leaving to sit at Room temperature for 15 min. Each sample was then sonicated for 5 min in a waterbath sonicator in an ice slurry.", "Determine the peptide concentration of each sample spectroscopically", "Aliquot10 µg of peptides... |
61,884 | Immunostaining of Bodo saltans | 4 | null | https://www.protocols.io/view/immunostaining-of-bodo-saltans-b8n4rvgw | Ewa Chrostek, Mastaneh Ahrar, Gregory Dd Hurst | TITLE: Immunostaining of Bodo saltans
AUTHORS: Ewa Chrostek, Mastaneh Ahrar, Gregory Dd Hurst
[DESCRIPTION]
This protocol is used in our Laboratory in Liverpool to perform IF on Bodo saltans cells.
[STEPS]
SECTION: Culture conditions
1. Bodo saltans was cultured in a cerophyl-based medium enriched with 3.5 mM s... | ["[Culture conditions] Bodo saltans was cultured in a cerophyl-based medium enriched with 3.5 mM sodium phosphate dibasic (Na2HPO4)1. Cultures were incubated at 22 °C in T25 tissue culture flasks containing 20 ml of media bacterized with Klebsiella pneumoniae subsp. Pneumoniae (ATCC® 700831).", "[Immunostaining] Please... |
43,379 | A Simple Multistep Protocol for Differentiating Human Induced Pluripotent Stem Cells into Functional Macrophages | 1 | dx.doi.org/10.17504/protocols.io.bnktmcwn | https://www.protocols.io/view/a-simple-multistep-protocol-for-differentiating-hu-bnktmcwn | Chandrayana Mukherjee, Christine Hale, Subhankar Mukhopadhyay | TITLE: A Simple Multistep Protocol for Differentiating Human Induced Pluripotent Stem Cells into Functional Macrophages
AUTHORS: Chandrayana Mukherjee, Christine Hale, Subhankar Mukhopadhyay
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Macrophages differentiated from human induced pluripotent ste... | ["[General Considerations]\nHuman iPSCs are delicate and more difficult to maintain in culture compared to most other conventional human cell lines. They show a natural tendency to spontaneously differentiate into fibroblast like cells. Cytokines and growth factors present in the medium allow them to be kept in pluripo... |
71,010 | Participant Registration Form For Mapping the Early Childhood Gut Across Ancestry, Geography, and Environment (Gut-AGE) | 1 | dx.doi.org/10.17504/protocols.io.6qpvr4d3zgmk/v1 | https://www.protocols.io/view/participant-registration-form-for-mapping-the-earl-chkat4se | Fatima Zulqarnain, Stephanie Regis, elsy.ngwa, Asra Usmani, jason.boisvert, Arg7Ef, Sana Syed, Jocelyn Silvester, jay.thiagarajah | TITLE: Participant Registration Form For Mapping the Early Childhood Gut Across Ancestry, Geography, and Environment (Gut-AGE)
AUTHORS: Fatima Zulqarnain, Stephanie Regis, elsy.ngwa, Asra Usmani, jason.boisvert, Arg7Ef, Sana Syed, Jocelyn Silvester, jay.thiagarajah
[DESCRIPTION]
The gastrointestinal (GI) system has a... | ["[To be filled out by the study team] PARTICIPANT REGISTRATION FORM \n\nThe first part of the form collects registration information from each participant. The purpose of this section is to ensure that the study team has all relevant participant information for accessing participant health records at their site of car... |
77,406 | HYPROP soil sample collection | 1 | dx.doi.org/10.17504/protocols.io.261ge3jedl47/v1 | https://www.protocols.io/view/hyprop-soil-sample-collection-cpt6vnre | marshall.bennett | TITLE: HYPROP soil sample collection
AUTHORS: marshall.bennett
[DESCRIPTION]
Procedure developed using information gathered from the following sources:
Shokrana, M. S. B., & Ghane, E. (2020, February 22). Measurement of soil water characteristic curve using hyprop2. Measurement of soil water characteristic curve usi... | ["Gather tools needed for HYPROP sample ring collection.", "Identify sampling locations. Collect and record all appropriate field data (GPS coordinates, soil texture information, weather, etc.).", "Clear the surface of the soil to remove excess plant cover or debris. DO NOT DISTURB THE SOIL It is important to note that... |
75,388 | Insert Alignment ELYRA7 | 1 | null | https://www.protocols.io/view/insert-alignment-elyra7-cmu4u6yw | Rafael Camacho | TITLE: Insert Alignment ELYRA7
AUTHORS: Rafael Camacho
[DESCRIPTION]
Alignment of the stage insert to ensure that the sample is perpendicular to the optical axis. This protocol is based on material provided by ZEISS' application specialists.
What is needed before to start:
- This protocol was designed for the EL... | ["[Find sample plane via the eye pieces] ZEN black -> Locate Tab,\n \nand set an imaging protocol for transmitted light so you can see the sample via the eye pieces.", "[Find sample plane via the eye pieces] Change the objective to the lowest magnification, typically 10X", "[Find sample plane via the eye pieces] Place... |
83,281 | Sectioning of Mouse Brain by Microtome | 1 | dx.doi.org/10.17504/protocols.io.81wgbxd91lpk/v1 | https://www.protocols.click/view/sectioning-of-mouse-brain-by-microtome-cvjrw4m6 | Maryana Nissan | TITLE: Sectioning of Mouse Brain by Microtome
AUTHORS: Maryana Nissan
[DESCRIPTION]
This protocol describes how to use the microtome to prepare and slice mouse brain sections for Immunohistochemistry
[STEPS]
SECTION: Preparation Methods
1. While preparing the microtome, make sure the blade is covered. The microtome ... | ["[Preparation Methods] While preparing the microtome, make sure the blade is covered. The microtome used in the lab is from Leica Microsystems.", "[Preparation Methods] Slide the plate into the stage and secure it by tightening it with a screw.", "[Preparation Methods] Orient the plate so that it is centered.", "[Prep... |
99,811 | 4% PFA + 2.5% Glutaraldehyde Fixative | 1 | dx.doi.org/10.17504/protocols.io.dm6gpr15dvzp/v3 | https://www.protocols.io/view/4-pfa-2-5-glutaraldehyde-fixative-ddqb25sn | Allen Institute for Brain Science | TITLE: 4% PFA + 2.5% Glutaraldehyde Fixative
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
This protocol is used to prepare 4% Paraformaldehyde (PFA) + 2.5% Glutaraldehyde Fixative. This is utilized to fix the tissue after electrophysiology recordings.
Note: Research reported in this publication was suppo... | [] |
21,563 | UC Davis - Vertical Sleeve Gastrectomy | null | dx.doi.org/10.17504/protocols.io.za3f2gn | null | Kristin Evans | TITLE: UC Davis - Vertical Sleeve Gastrectomy
AUTHORS: Kristin Evans
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">
Vertical sleeve Gastrectomy (VSG) is a common surgical treatment of obesity, type-2 diabetes, and oth... | ["Preparation: 1. Animals should be fasted overnight to ensure that their stomach and intestines are as empty as possible. 2. Weight prior to surgery to calculate drugs (Meloxicam and Baytril dosing) 3. Autoclave all supplies and tools needed for the surgery, start the bead sterilizer for sterilizing instruments. 4. Pr... |
108,247 | Collection of Selected Behavioural Assessment Methods in the Tropical Marine Amphipod, Parhyale hawaiensis | 0 | dx.doi.org/10.17504/protocols.io.eq2lywrowvx9/v1 | https://www.protocols.io/view/collection-of-selected-behavioural-assessment-meth-dmxx47pn | Ibrahim Lawan | TITLE: Collection of Selected Behavioural Assessment Methods in the Tropical Marine Amphipod, Parhyale hawaiensis
AUTHORS: Ibrahim Lawan
[DESCRIPTION]
This is a collection of some selected protocols for Behavioural Assessment Methods in the Tropical Marine Amphipod, Parhyale hawaiensis
[STEPS] | [] |
82,483 | U54 SCENT Normal Lung Surgical Tissue Collection Procedure | 1 | null | https://www.protocols.click/view/u54-scent-normal-lung-surgical-tissue-collection-p-custwwen | Carolyn Glass, andrew.nixon, Matthew Hartwig, Nancy McGreal, SSCRS, Mary Jordan* | TITLE: U54 SCENT Normal Lung Surgical Tissue Collection Procedure
AUTHORS: Carolyn Glass, andrew.nixon, Matthew Hartwig, Nancy McGreal, SSCRS, Mary Jordan*
[DESCRIPTION]
This document outlines the required criteria for inclusion and collection of lung tissue obtained by surgical resection at Duke University Hospital t... | ["[Inclusion and Exclusion Criteria] Inclusion Criteria: \n • Any age \n • All sexes \n • Grossly normal lung obtainable through surgical pathology\n\nExclusion Criteria:\n • No recent treatment with chemotherapy (recent <1 year) \n • No recent treatment with radiation (recent <1 year) \n • No history... |
21,615 | CUT&RUN: Targeted in situ genome-wide profiling with high efficiency for low cell numbers | null | dx.doi.org/10.17504/protocols.io.zcpf2vn | null | Derek Janssens, Steven Henikoff | TITLE: CUT&RUN: Targeted in situ genome-wide profiling with high efficiency for low cell numbers
AUTHORS: Derek Janssens, Steven Henikoff
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>We previously described a novel alternative to Chromatin Immunoprecipitation, Cleavage Under Targets & Relea... | ["[Binding cells to beads (~30 min)]\nHarvest fresh culture(s) at room temperature and count cells. The same protocol can be used for up to 500,000 mammalian cells per sample and/or digestion time point.\nCRITICAL STEP: All steps prior to the addition of antibody are performed at room temperature to minimize stress on ... |
103,197 | Immunohistochemistry on mouse brain sections | 0 | dx.doi.org/10.17504/protocols.io.j8nlk8m4xl5r/v1 | https://www.protocols.io/view/immunohistochemistry-on-mouse-brain-sections-dgz53x86 | Shiyi Wang | TITLE: Immunohistochemistry on mouse brain sections
AUTHORS: Shiyi Wang
[DESCRIPTION]
Immunohistochemistry on mouse brain sections
[STEPS]
1. **Anesthesia and Perfusion**
1.1. - Anesthetize mice with 200 mg/kg Avertin.
1.2. - Perform transcardial perfusion using TBS/Heparin followed by 4% paraformaldehyde (PFA).
2. *... | ["**Anesthesia and Perfusion**", "- Anesthetize mice with 200 mg/kg Avertin.", "- Perform transcardial perfusion using TBS/Heparin followed by 4% paraformaldehyde (PFA).", "**Brain Collection and Post-Fixation**", "- Remove the brain and post-fix it in 4% PFA overnight at 4°C.", "**Cryoprotection and Storage**", "- Cry... |
50,273 | Coral Carbohydrate Assay for 96-well plates | 1 | dx.doi.org/10.17504/protocols.io.bvb9n2r6 | https://www.protocols.io/view/coral-carbohydrate-assay-for-96-well-plates-bvb9n2r6 | Colleen Bove, Justin Baumann | TITLE: Coral Carbohydrate Assay for 96-well plates
AUTHORS: Colleen Bove, Justin Baumann
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><ol style = "list-style-type: decimal;"></ol></div><div class = "text-block">1. Masuko T, Minami A, Iwasaki N, Majima T, Nishimura S, Lee YC. Carbohydrate analysis... | ["[Carbohydrate Assay]\nPull desired coral slurries from the -80 freezer to thaw at room temperature", "[Carbohydrate Assay]\nCollect test tubes and label (10 for the standard + the number of samples running)", "[Carbohydrate Assay]\nMake the standards and blank as shown below Tube IDConcentration (mg/mL)Vol water (uL)... |
45,087 | Quantitative Assessment of Islet Viability upon Arrival to HIPP by Staining with Trypan Blue Dye | 4 | dx.doi.org/10.17504/protocols.io.bp97mr9n | https://www.protocols.io/view/quantitative-assessment-of-islet-viability-upon-ar-bp97mr9n | IIDP-HIPP | TITLE: Quantitative Assessment of Islet Viability upon Arrival to HIPP by Staining with Trypan Blue Dye
AUTHORS: IIDP-HIPP
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;font-style:italic;">This Standard Operating Procedure (SOP) is based on the Vanderbilt Human Isl... | ["[Procedures]\nDispersion of islets into single cell suspension", "[Procedures]\nPrepare 2 aliquots of approximately 100 handpicked islets in tubes to determine viability of islets. Note: This is important especially for islet preparations with lower purity where cell death in the contaminating exocrine compartment ma... |
32,975 | 3.7% Paraformaldehyde solution | null | dx.doi.org/10.17504/protocols.io.bcfpitmn | null | Institute of Medical Biotechnology | TITLE: 3.7% Paraformaldehyde solution
AUTHORS: Institute of Medical Biotechnology
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for preparing a 3.7% Paraformaldehyde (PFA) solution. 3.7% PFA solution can be used to fix tissues. </div></div>
[STEPS]
?. For , add to a glass beaker on a st... | ["For , add to a glass beaker on a stir plate.\n[3.7% Formaldehyde]\n[1X DPBS]\nBe sure to work under a ventilated fume hood.", "Heat while stirring to approximately .\n55 °C", "Add to the heated DPBS solution.\n[paraformaldehyde powder]", "Keep stirring until all PFA powder is dissolved.\nTake care that the solution... |
null | null | null | dx.doi.org/10.17504/protocols.io.h4kb8uw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?. | [] |
21,241 | Impact of preventive oral health interventions during the prenatal care on preterm delivery, an integrative review protocol. | null | dx.doi.org/10.17504/protocols.io.yyzfxx6 | null | Cristina Dutra Vieira, Andreza Nayla de Assis Aguiar, Camila Aparecida Silva de Oliveira Lima, Zilma Reis | TITLE: Impact of preventive oral health interventions during the prenatal care on preterm delivery, an integrative review protocol.
AUTHORS: Cristina Dutra Vieira, Andreza Nayla de Assis Aguiar, Camila Aparecida Silva de Oliveira Lima, Zilma Reis
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Backg... | ["Search strategyThe search strategy was performed using the following keyword combination for the composition of key-words and descriptors of health: Health Education; Health Education, Dental; Health Promotion; Pregnant Women; Pregnancy Outcome; Infant, Low Birth Weight; Premature Birth; Infant, Small for Gestational... |
48,666 | Genome-wide quantification of TF binding at single DNA molecule resolution | 1 | dx.doi.org/10.17504/protocols.io.btr2nm8e | https://www.protocols.io/view/genome-wide-quantification-of-tf-binding-at-single-btr2nm8e | Rozemarijn Kleinendorst, guido.barzaghi , Mike L. Smith, Judith B. Zaugg, Arnaud Krebs | TITLE: Genome-wide quantification of TF binding at single DNA molecule resolution
AUTHORS: Rozemarijn Kleinendorst, guido.barzaghi , Mike L. Smith, Judith B. Zaugg, Arnaud Krebs
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Precise control of gene expression requires the coordinated act... | [] |
91,933 | HyDrop-RNA v1.0 | 1 | dx.doi.org/10.17504/protocols.io.dm6gpwqjjlzp/v3 | https://www.protocols.io/view/hydrop-rna-v1-0-c5z5y786 | Florian De Rop, Suresh Poovathingal, Stein Aerts | TITLE: HyDrop-RNA v1.0
AUTHORS: Florian De Rop, Suresh Poovathingal, Stein Aerts
[DESCRIPTION]
Step-by-step protocol for performing HyDrop-RNA. The duration of each step assumes an experienced protocol user. For a first-time user, we recommend doubling the expected time for each step.
[STEPS]
SECTION: Microfluidics P... | ["[Microfluidics Preparation] Setting up the Microfluidic Framework\nThese steps need to happen in advance before the run can be started, as time between the preparation of the cell resuspension in RT mix and actual encapsulation needs to be minimised to preserve cell viability.", "[Microfluidics Preparation] Boot up ... |
47,189 | Protocol for assembling SARS-Cov-2 runs with s-aligner | 5 | dx.doi.org/10.17504/protocols.io.bsbvnan6 | https://www.protocols.io/view/protocol-for-assembling-sars-cov-2-runs-with-s-ali-bsbvnan6 | Juanjo Bermúdez | TITLE: Protocol for assembling SARS-Cov-2 runs with s-aligner
AUTHORS: Juanjo Bermúdez
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a protocol for using Contignant s-aligner to de-novo assemble SARS-Cov-2 genomes. S-aligner outperforms common open-source software for de novo-assembly of ... | ["[Indexing and fast-testing]", "[Indexing and fast-testing]\nresults/your-run-id-500.fa should have the largest contig bigger than 1.200bp and at least one of the files containing aligned reads to form a contig should look like that:", "[Indexing and fast-testing]", "Trim your data and start again.", "[Indexing and fa... |
98,706 | RNA extraction using the PureLink® RNA Mini Kit | 0 | dx.doi.org/10.17504/protocols.io.261ge54r7g47/v1 | https://www.protocols.io/view/rna-extraction-using-the-purelink-rna-mini-kit-dcms2u6e | Enrico Bagnoli, Miratul Muqit | TITLE: RNA extraction using the PureLink® RNA Mini Kit
AUTHORS: Enrico Bagnoli, Miratul Muqit
[DESCRIPTION]
This Protocol details the extraction of total RNA using the PureLink® RNA Mini Kit.
[STEPS]
SECTION: Prepare lysates from ≤5 × 106 monolayer cells:
1. Remove the growth medium from the cells.
SECTION: Prep... | ["[Prepare lysates from ≤5 × 106 monolayer cells:] Remove the growth medium from the cells.", "[Prepare lysates from ≤5 × 106 monolayer cells:] Using RNase-free pipette tips, add the appropriate volume of lysis buffer prepared with 2-mercaptoethanol to sample.", "[Prepare lysates from ≤5 × 106 monolayer cells:] Proceed... |
25,239 | RNA Isolation from Plant Tissue Protocol 1: Qiagen RNeasy Plant Mini Kit | null | dx.doi.org/10.17504/protocols.io.4vxgw7n | null | Jim Leebens-Mack, Charlotte Carrigan | TITLE: RNA Isolation from Plant Tissue Protocol 1: Qiagen RNeasy Plant Mini Kit
AUTHORS: Jim Leebens-Mack, Charlotte Carrigan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol implemented by: Jim Leebens-Mack and Charlotte Carrigan </div><div class = "text-block"><span>The first protocol used... | [] |
59,959 | Detection of recombinant and endogenous LPPR3 by western blot | 1 | dx.doi.org/10.17504/protocols.io.81wgb6z2olpk/v2 | https://www.protocols.io/view/detection-of-recombinant-and-endogenous-lppr3-by-w-b6sxrefn | cristina.kroon | TITLE: Detection of recombinant and endogenous LPPR3 by western blot
AUTHORS: cristina.kroon
[DESCRIPTION]
This is a protocol for detection of overexpressed and endogenous LPPR3 from N1E-115 cells and primary hippocampal neurons.
[STEPS]
SECTION: Sample preparation
1. N1E cells for detection of recombinant LPPR3
... | ["[Sample preparation] N1E cells for detection of recombinant LPPR3\n\nDIV 0: N1E cells were plated at a density of 150 000 cells/well (6-well plates) and grown overnight in DMEM medium (Gibco) with 10% FCS and 1% penicillin/streptomycin. \nDIV 1: The cells were transfected with 1 µg of DNA using Lipofectamine 2000 (Th... |
82,749 | Live imaging and analysis to investigate phase separation properties of NEMO during mitophagy | 1 | dx.doi.org/10.17504/protocols.io.j8nlkw7rxl5r/v1 | https://www.protocols.io/view/live-imaging-and-analysis-to-investigate-phase-sep-cu25wyg6 | OLIVIA HARDING, Erika L.F. Holzbaur | TITLE: Live imaging and analysis to investigate phase separation properties of NEMO during mitophagy
AUTHORS: OLIVIA HARDING, Erika L.F. Holzbaur
[DESCRIPTION]
Phase condensation of biomolecular particles is increasingly examined for its relevance in physiological contexts. When we observed formation of NEMO puncta as... | ["[Replace Standard Media with Imaging Media and Induce Mitophagy] Wait until imaging chamber is heated to 37 °C.", "[Replace Standard Media with Imaging Media and Induce Mitophagy] Aspirate media from sample.", "[Replace Standard Media with Imaging Media and Induce Mitophagy] Repeat the following two steps for a total... |
null | null | null | dx.doi.org/10.17504/protocols.io.scneave | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol outlines our preparation of single-nuclei suspension from surgically acquired fresh human adult brain tissue.</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
33,743 | MicroRNA Affymetrix microarray probe labeling from ocular fluids | 1 | dx.doi.org/10.17504/protocols.io.bc7pizmn | https://www.protocols.io/view/microrna-affymetrix-microarray-probe-labeling-from-bc7pizmn | Zeljka Smit-Mcbride | TITLE: MicroRNA Affymetrix microarray probe labeling from ocular fluids
AUTHORS: Zeljka Smit-Mcbride
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Sample collection, isolation of miRNAs, and quality control </span></div><div class = "text-block"><span>Aqueous and ... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.pxidpke | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is the protocol for the PhireKit touchdown PCR assay</p>
[BEFORE_START]
<p>The assay has been optimized and validated for the Bio-rad C1000 Touch Thermocycler.</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.f9tbr6n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocol modified for <em>Puccinia striiformis</em> f. sp <em>tritici</em> (<em>Pst</em>), based on:</p>
<p>Michielse, C. B., Hooykaas, P. J., van den Hondel, C. A., & Ram, A. F. (2008). Agrobacterium-mediated transformation of the filamentous fungus Aspergillus awamori. ... | [] |
69,101 | Roadmap to the bioinformatic study of gene and protein phylogeny and evolution - a practical guide | 5 | dx.doi.org/10.17504/protocols.io.36wgq77e3vk5/v2 | https://www.protocols.io/view/roadmap-to-the-bioinformatic-study-of-gene-and-pro-cfqmtmu6 | florian.jacques, Paulina Bolivar, Kristian Pietras, Emma Hammarlund | TITLE: Roadmap to the bioinformatic study of gene and protein phylogeny and evolution - a practical guide
AUTHORS: florian.jacques, Paulina Bolivar, Kristian Pietras, Emma Hammarlund
[DESCRIPTION]
We present a compilation of nucleic acid and protein databases and bioinformatic tools for phylogenetic reconstructions a... | ["[Phylogenetic analysis] Option 1: Maximum parsimony\n\nMaximum parsimony is a classic and simple method, that calculates the minimum number of evolutionary steps, including nucleotide insertions, deletions or substitutions, between species.\n\nHowever, this method ignores hidden mutations and does not take into accou... |
76,690 | S. O. C. medium | 4 | null | https://www.protocols.io/view/s-o-c-medium-cn5svg6e | Andreas Sagen | TITLE: S. O. C. medium
AUTHORS: Andreas Sagen
[DESCRIPTION]
S.O.C. Medium is used in the final step of bacterial cell transformation to obtain maximal transformation efficiency ofE. coli. S.O.C.
[STEPS]
SECTION: 500 mL 1 M Glucose solution
1. Fill the bottle with 400 mL distilled water
SECTION: 500 mL 1 M Glucose sol... | ["[500 mL 1 M Glucose solution] Fill the bottle with 400 mL distilled water", "[500 mL 1 M Glucose solution] Measure 90.08 g Glucose\n\nMaterials:", "[500 mL 1 M Glucose solution] Add distilled water to a total of 500 mL", "[500 mL 1 M Glucose solution] Filter sterilize with a 0.2 µm filter", "[1 000 mL S. O. B. medium... |
41,088 | Doctor Vida Pocket - COVID-19 assay - Instructions for Use | 4 | dx.doi.org/10.17504/protocols.io.bkc8kszw | https://www.protocols.io/view/doctor-vida-pocket-covid-19-assay-instructions-for-bkc8kszw | goncalo.doria | TITLE: Doctor Vida Pocket - COVID-19 assay - Instructions for Use
AUTHORS: goncalo.doria
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Instruction of use for Doctor Vida pocket - COVID-19 assay</div></div>
[STEPS]
?. [Preparation setup]
Turn on Dr. Vida Pocket device - by plugging the Dr. Vida P... | ["[Preparation setup]\nTurn on Dr. Vida Pocket device - by plugging the Dr. Vida Pocket device's power supply into a suitable power plug (120V/240V AC) and connecting the micro-usb plug into the Dr. Vida Pocket device.\nWhen turned on, the device will emit a short bip.", "[Start new assay]\nPress \"Start new assay\" in... |
null | null | null | dx.doi.org/10.17504/protocols.io.qz7dx9n | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
91,120 | CAR T cell characterization by flow cytometry | 4 | null | https://www.protocols.io/view/car-t-cell-characterization-by-flow-cytometry-c48qyzvw | Andrea R Daniel | TITLE: CAR T cell characterization by flow cytometry
AUTHORS: Andrea R Daniel
[DESCRIPTION]
Flow cytometry of tumor tissue and blood from mice with human tumors. Mice bearing HCC1954 tumors were euthanized at days 3 and 19 post CAR T cel delivery. This protocol describes methods for preparing input CAR T cells and tum... | ["[Tissue collection] Place mice under deep isoflurane anesthesia (5% isoflurane, minimum of 15 minutes)", "[Tissue collection] Spray the abdomen of the mouse with 70% ethanol, this is to avoid fur contamination of samples", "[Tissue collection] Perform a bilateral thoracotomy, cut the right atrium of the heart.", "[Ti... |
55,929 | Manual Nanotrap Concentration and RNA Extraction for SARS-CoV-2 Viral Capture | 4 | dx.doi.org/10.17504/protocols.io.b2uzqex6 | https://www.protocols.io/view/manual-nanotrap-concentration-and-rna-extraction-f-b2uzqex6 | Matthew Cavallo, Stephen P Hilton, Jamie VanTassell, Julia Raymond, Marlene K Wolfe, Pengbo Liu, Christine Moe | TITLE: Manual Nanotrap Concentration and RNA Extraction for SARS-CoV-2 Viral Capture
AUTHORS: Matthew Cavallo, Stephen P Hilton, Jamie VanTassell, Julia Raymond, Marlene K Wolfe, Pengbo Liu, Christine Moe
[DESCRIPTION]
This protocol details a method for SARS-CoV-2 capture and concentration through the use of Na... | ["[Concentration Procedure] Place a 50 mL conical tube in a tube rack.", "[Concentration Procedure] Vigorously shake the sample to re-suspend solids. Immediately move on to Step 3.", "[Concentration Procedure] Add 50 mL of wastewater to the conical tube inside the biosafety cabinet.", "[Concentration Procedure] Transfe... |
67,414 | https://www.facebook.com/PureKanaKetoGummiesShop/ | 3 | dx.doi.org/10.17504/protocols.io.e6nvwk3pwvmk/v1 | https://www.protocols.io/view/https-www-facebook-com-purekanaketogummiesshop-cd3ws8pe | antoniocsmith | TITLE: https://www.facebook.com/PureKanaKetoGummiesShop/
AUTHORS: antoniocsmith
[DESCRIPTION]
These gummies are herbal weight reduction supplements that is to help you trim down your weight naturally without any unfavourable effects on your health.
[STEPS] | [] |
57,781 | Amplifying the target genomic region by PCR | 4 | dx.doi.org/10.17504/protocols.io.b4nvqve6 | https://www.protocols.io/view/amplifying-the-target-genomic-region-by-pcr-b4nvqve6 | Hanqin Li, Yogendra Verma, Dirk Hockemeyer, Frank Soldner | TITLE: Amplifying the target genomic region by PCR
AUTHORS: Hanqin Li, Yogendra Verma, Dirk Hockemeyer, Frank Soldner
[DESCRIPTION]
This protocol describes a procedure for amplifying targeted genomic regions using a PCR reaction
[STEPS]
1. For a 150bp paired-end or single-read sequencing experiment, design primers ... | ["For a 150bp paired-end or single-read sequencing experiment, design primers in a way that the region of interest, like CRISPR cutting site or specific mutations, locates within 130bp from at least one of the primers", "Add NGS adapters to 5’ end of primers following the instructions of your local NGS facility", "20 µ... |
98,168 | Mo'orea Surf Tourism Research Protocol | 0 | dx.doi.org/10.17504/protocols.io.kqdg3258qv25/v1 | https://www.protocols.io/view/mo-39-orea-surf-tourism-research-protocol-db4y2qxw | Flynn Ryan Dartland | TITLE: Mo'orea Surf Tourism Research Protocol
AUTHORS: Flynn Ryan Dartland
[DESCRIPTION]
This protocol describes a method of understanding the attitudes of Mo'orea locals towards the development of surf tourism on the island of Mo'orea, French Polynesia. The research involves interviewing local surfers, residents,... | ["[Interviewing Surfers] The first step is to identify surf breaks on Mo’orea. To locate surf breaks, you can use a map to identify reef passes where waves break, the Surfline app, the internet, and/or ask locals in the area about where surf breaks are located.", "[Interviewing Surfers] Paddle, kayak, or boat out to a ... |
39,102 | Two-Bottle Choice Protocol | 1 | null | https://www.protocols.io/view/two-bottle-choice-protocol-bie6kbhe | Marcella Hughes, Olivier George | TITLE: Two-Bottle Choice Protocol
AUTHORS: Marcella Hughes, Olivier George
[STEPS]
?. [24-Hour Two Bottle Choice Procedure]
Record weekly body weights of animals for calculation of solution intake as mg/kg
?. [24-Hour Two Bottle Choice Procedure]
Mix and fill required solutions in bottles
?. [24-Hour Two Bottle Choice... | ["[24-Hour Two Bottle Choice Procedure]\nRecord weekly body weights of animals for calculation of solution intake as mg/kg", "[24-Hour Two Bottle Choice Procedure]\nMix and fill required solutions in bottles", "[24-Hour Two Bottle Choice Procedure]\nRecord weight of all bottles prior to drinking session", "[24-Hour Two... |
null | null | null | dx.doi.org/10.17504/protocols.io.hmgb43w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>We recently developed a continuous flow system to transform microorganisms in high throughput in a microfluidic device (Garcia et al., 2017). This system employs microfluidic channels that contain a bilateral constriction between the inlet and outlet electrode connections (<e... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.j7hcrj6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>INTRODUCTION: </strong>Blindness is and, apparently always has been, a problem in Egypt. Corneal blindness is a major public health problem worldwide according to the World Health Organization (WHO), which estimated that in every year, about 1.5–2.0 million new cases ... | [] |
77,215 | DeRisi Lab RNA Library Prep 96-well Protocol on Echo 550 | 1 | dx.doi.org/10.17504/protocols.io.n2bvj8jrngk5/v1 | https://www.protocols.io/view/derisi-lab-rna-library-prep-96-well-protocol-on-ec-cpm7vk9n | Madeline Y Mayday, Miriam R Simon, Lillian M Khan, Eric D. Chow, Matt S Zinter, Joseph Derisi | TITLE: DeRisi Lab RNA Library Prep 96-well Protocol on Echo 550
AUTHORS: Madeline Y Mayday, Miriam R Simon, Lillian M Khan, Eric D. Chow, Matt S Zinter, Joseph Derisi
[DESCRIPTION]
Preparation of high-quality sequencing libraries is a costly and time-consuming component of metagenomic next generation sequencing (mNGS... | ["Spin plate of sample RNA in vacuum evaporator at the appropriate temperature and time settings to dry completely (approximately 37-38ºC for 1 hour, depending on number of samples and machine used).", "[GeneVac] Warming up GeneVac: Turn to \"aqueous\" setting and set temperature to ~40-42ºC and let run for ~30min befo... |
91,462 | jres_metab.nan | 5 | dx.doi.org/10.17504/protocols.io.e6nvwd27wlmk/v1 | https://www.protocols.io/view/jres-metab-nan-c5jey4je | NAN KB, John Glushka, Mario Uchimiya, Saraa Al Jawad, Christopher Esselman, Leandro I Ponce, Laura Morris, Arthur Edison | TITLE: jres_metab.nan
AUTHORS: NAN KB, John Glushka, Mario Uchimiya, Saraa Al Jawad, Christopher Esselman, Leandro I Ponce, Laura Morris, Arthur Edison
[DESCRIPTION]
This is a protocol for running the Bruker pulse program "jresgpprqf".
[BEFORE_START]
This protocol assumes your sample is loaded, locked, tuned, and shi... | ["[Create a new dataset]", "[Create noesypr1d experiment file] When Lock, Tune, Shim are complete proceed to the specific protocol for your desired pulseprogram(s).", "[Create a new dataset] On the menu bar on TopSpin, click on\nStart → Create Dataset", "[Create a new dataset] Enter\nNAME: Name of a set of datasets (e.... |
28,349 | Viral metagenomics using SMART-9n amplification and nanopore sequencing | null | dx.doi.org/10.17504/protocols.io.7w5hpg6 | null | Ingra Claro Morales, Josh Quick | TITLE: Viral metagenomics using SMART-9n amplification and nanopore sequencing
AUTHORS: Ingra Claro Morales, Josh Quick
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a SMART-Seq (Switch Mechanism at the 5′ End of RNA Templates) protocol developed to use random 9n priming and be compatible ... | ["[Centrifugal filtration]\nTransfer up to sample directly onto a Ultrafree-MC Centrifugal Filter column\n500 µl", "[Centrifugal filtration]\nSpin at for\nCentrifuge: 5000 34", "[Centrifugal filtration]\nRecover filtrate into Eppendorf tube\n1.5 ml", "[Centrifugal filtration]\nRemove basket and discard", "[Centrifuga... |
103,467 | Human Neuronal Nucleus Isolation for Single-Nucleus Transcriptomic Profiling (10x Genomics) | 0 | dx.doi.org/10.17504/protocols.io.4r3l2q3p4l1y/v1 | https://www.protocols.io/view/human-neuronal-nucleus-isolation-for-single-nucleu-dhaj32cn | Satoshi Ishishita, Allan-Hermann Pool | TITLE: Human Neuronal Nucleus Isolation for Single-Nucleus Transcriptomic Profiling (10x Genomics)
AUTHORS: Satoshi Ishishita, Allan-Hermann Pool
[DESCRIPTION]
Protocol generating suspensions of neuronal nuclei (NeuN+) from human central nervous system tissue for single-nucleus transcriptomics.
[STEPS]
SECTION: Equip... | ["[Equipment and Reagents] Equipment\nKimble Dounce Kontes tissue-grinder set (DWK 885300-0000)\n50 ml Oakridge tubes (#0556214D)\n15 mL Falcon tubes (Fisher #352097)\n50 mL Falcon tubes (Fisher #352070)\n1.5mL LoBind Eppendorf Tubes\n70-micron Corning Cell Strainer (#431751)\nFire polished glass Pasteur pipettes (VWR ... |
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