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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82,660 | GFP-ATG3 GUV Assay | 1 | dx.doi.org/10.17504/protocols.io.yxmvm2d5ng3p/v1 | https://www.protocols.click/view/gfp-atg3-guv-assay-cuycwxsw | lmstrong | TITLE: GFP-ATG3 GUV Assay
AUTHORS: lmstrong
[DESCRIPTION]
LC3 lipidation on GUVs
[STEPS]
1. GUV Preparation
SECTION: GUV Preparation
1.
1.1. Clean the coverglass
1.2. Coat cleaned coverslips with 100 μL 5% (w/w) polyvinyl alcohol (PVA) with a molecular weight of 145,000 (Millipore). Place the coated coverslip in a... | ["GUV Preparation", "[GUV Preparation]", "Clean the coverglass", "Coat cleaned coverslips with 100 μL 5% (w/w) polyvinyl alcohol (PVA) with a molecular weight of 145,000 (Millipore). Place the coated coverslip in a heating incubator at 60 °C to dry the PVA film for 30 min.", "Spread a lipid mixture at 1 mg/ml with a mo... |
null | null | null | dx.doi.org/10.17504/protocols.io.ix3cfqn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The task described here is that used in the PLoS ONE paper entitled 'Continuous Robust Sound Event Classification Using Time-Frequency Features and Deep Learning'. It builds upon the long established standard isolated sound evaluation task first described by Jonathan Dennis, ... | [] |
70,341 | Sample preparation for single molecule localisation microscopy and imaging. | 1 | dx.doi.org/10.17504/protocols.io.3byl4j77olo5/v1 | https://www.protocols.io/view/sample-preparation-for-single-molecule-localisatio-cgxdtxi6 | gurvir.virdi | TITLE: Sample preparation for single molecule localisation microscopy and imaging.
AUTHORS: gurvir.virdi
[DESCRIPTION]
This protocol describes the sample preparation to perform SMLM on midbrain dopaminergic neurons using phalloidin and a DNA aptamer in a combination of STORM and DNA-PAINT.
It also describes the exper... | ["[Fixation] For single molecule localisation microscopy (SMLM), neurons were grown on glass coated ibidi chambers.", "[Fixation] Once neurons reached the desired age, they were washed once in PBS", "[Fixation] They are then fixed for 15 min in 4% paraformaldehyde + 0.1% glutaraldehyde (both from Electron Microscopy S... |
19,094 | Login to UA HPC | null | dx.doi.org/10.17504/protocols.io.wvwfe7e | null | Ken Youens-Clark, Bonnie Hurwitz | TITLE: Login to UA HPC
AUTHORS: Ken Youens-Clark, Bonnie Hurwitz
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This describes setting up ssh keys and configuration to avoid having to use your NetID+ 2-factor authentication every time you log into the HPC. Windows users will need to install a free... | ["Sign up for NetID+ https://webauth.arizona.edu/netid-plus/", "Initial loginOpen a terminal and type 'ssh @hpc.arizona.edu'. Enter your NetID password and then follow the instructions for 2-factor authentication. You will be presented with a menu that says:===============HPC.ARIZONA.EDU===============Please select a ... |
51,776 | Custom eDNA High Throughput Sequencing with MinION (Oxford Nanopore Technologies) | 4 | null | https://www.protocols.io/view/custom-edna-high-throughput-sequencing-with-minion-bws8pehw | Luca Mirimin | TITLE: Custom eDNA High Throughput Sequencing with MinION (Oxford Nanopore Technologies)
AUTHORS: Luca Mirimin
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is a custom workflow to carry out High Throughput Sequencing (HTS) on environmental DNA samples using a MinION portable sequenc... | ["[MATERIALS REQUIRED]\nThe enzyme and PCR mix used can be changed as long as the enzyme used is efficient and/or recommended for environmental samples. In this case we used Platinum™ II Taq Hot-Start DNA Polymerase (Invitrogen™)", "[1-step PCR (amplicons and barcodes)]\n[Includes experimental design planning, sample p... |
91,941 | An NGS amplicon tiling protocol for HIV-1 drug resistance detection using Illumina® COVIDSeq™ Assay Kit | 4 | dx.doi.org/10.17504/protocols.io.n92ldmq4ol5b/v2 | https://www.protocols.io/view/an-ngs-amplicon-tiling-protocol-for-hiv-1-drug-res-c52dy8a6 | Noah C. Hull, Eugene Yeboah, laura.j.tsaknaridis, Vanda Makris | TITLE: An NGS amplicon tiling protocol for HIV-1 drug resistance detection using Illumina® COVIDSeq™ Assay Kit
AUTHORS: Noah C. Hull, Eugene Yeboah, laura.j.tsaknaridis, Vanda Makris
[DESCRIPTION]
Summary
Human immunodeficiency virus (HIV) is the pathogen responsible for acquired immunodeficiency syndrome (AIDS) and... | ["Sample Extraction\n\nHIV-1 subtype B positive culture\ncontrol ZeptoMetrix (Part #v0801032CF), was extracted via the Qiagen Advanced XL DSP kit on the EZ1 extractor and serially diluted to the following concentration: 10ᶺ(-1), 10ᶺ(-2), 10ᶺ(-3), 10ᶺ(-4), 10ᶺ(-5), and 10ᶺ(-6), Undiluted control (1.74*10^10 IU/mL or 2.0... |
63,945 | Via Keto Gummies Reviews Advanced Formula | 1 | dx.doi.org/10.17504/protocols.io.ewov1nmj2gr2/v1 | https://www.protocols.io/view/via-keto-gummies-reviews-advanced-formula-caphsdj6 | viaketoengage | TITLE: Via Keto Gummies Reviews Advanced Formula
AUTHORS: viaketoengage
[DESCRIPTION]
This is definitively what the new and progressive Via Keto Gummies Reviews is about. It's a ketogenic supplement planned explicitly to assist you with arriving at ketosis faster. At the end of the day, the ideal answer for anybody ... | [] |
97,093 | USDA LTAR Common Experiment measurement: PhenoCam for Green Chromatic Coordinate | 0 | dx.doi.org/10.17504/protocols.io.ewov19j77lr2/v1 | https://www.protocols.io/view/usda-ltar-common-experiment-measurement-phenocam-f-da3d2gi6 | Dawn M. Browning, Nicanor Z. Saliendra, Craig W. Whippo | TITLE: USDA LTAR Common Experiment measurement: PhenoCam for Green Chromatic Coordinate
AUTHORS: Dawn M. Browning, Nicanor Z. Saliendra, Craig W. Whippo
[DESCRIPTION]
Phenology is the study of seasonal dynamics and how environmental conditions such as temperature and rainfall influence it over different time periods. ... | ["[Protocol] Camera installation, operation, and maintenance", "[Protocol] A Stardot camera (model NetCam-SC-IR) is installed at meteorological and flux tower locations at an appropriate height above the vegetation canopy, facing north to minimize sun angle effects throughout the year.", "[Protocol] When selecting the ... |
null | null | null | dx.doi.org/10.17504/protocols.io.ea2bage | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Guide for reagent/buffer preparation for protocol to separate chloroplasts from diatom cells using ammonium fluoride to permeate the silica frustrule and a percoll gradient to separate the plastid from other cellular components.
[GUIDELINES]
Buffers and reagents can be mixed up... | [] |
31,283 | Western Blot CTB | null | dx.doi.org/10.17504/protocols.io.bastieen | null | Arindam Naha | TITLE: Western Blot CTB
AUTHORS: Arindam Naha
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify"><span>For studying intracellular accumulation of CTB subunits in </span><span style = "font-style:italic;">E coli</span><span>, bacteria were grown up to ... | [] |
88,511 | Plasmid Construction Protocol | 4 | null | https://www.protocols.io/view/plasmid-construction-protocol-c2n7ydhn | Xuefeng Ren, Annan SI Cook | TITLE: Plasmid Construction Protocol
AUTHORS: Xuefeng Ren, Annan SI Cook
[DESCRIPTION]
This protocol details plasmid construction in general terms for the insertion of genes into the pCAG mammalian expression vector.
[STEPS]
SECTION: Design Plasmid Constructs
1. This protocol uses the pCAG vector and NEB restriction ... | ["[Design Plasmid Constructs] This protocol uses the pCAG vector and NEB restriction enzymes and Gibson Assembly kits.", "[Design Plasmid Constructs] Obtain the DNA sequences for the genes of interest from your preferred DNA synthesis vendor.", "[Digestion or Gibson Assembly] Decide whether to use restriction digestion... |
89,304 | Highway carbon unlocking efficiency study based on super-efficiency SBM-Malmquist | 1 | dx.doi.org/10.17504/protocols.io.8epv5xx7jg1b/v2 | https://www.protocols.io/view/highway-carbon-unlocking-efficiency-study-based-on-c3fyyjpw | Yun Chen, qi luo, machongsen | TITLE: Highway carbon unlocking efficiency study based on super-efficiency SBM-Malmquist
AUTHORS: Yun Chen, qi luo, machongsen
[DESCRIPTION]
Carbon Neutrality goals and Sustainable Development Goals (SDGs), as new requirements for global development at this stage, have raised higher requirements for achieving the coor... | [] |
86,066 | Wet Aggregate Stability in Soil | 6 | null | https://www.protocols.io/view/wet-aggregate-stability-in-soil-cyasxsee | susan.siragusa | TITLE: Wet Aggregate Stability in Soil
AUTHORS: susan.siragusa
[DESCRIPTION]
The wet sieving technique measures the percentage of water-stable aggregates in soils. It is a soil quality assessment analysis.
[STEPS]
1.
Weigh and record the weights of numbered (use permanent marker) weigh dishes. I recommend settin... | ["Weigh and record the weights of numbered (use permanent marker) weigh dishes. I recommend setting up small trays as follows: 2 mm in front, 1-2mm in middle, and 0.5-1.0mm in back.\n Weigh up the appropriate amount of Aggregate Fractioned soil (refer to the chart for sample amounts). Tare out the plastic weigh dish ... |
60,060 | A real-time PCR method to genotype mutant mouse models with altered affinity for cardiotonic steroids on the Na,K-ATPase | 4 | dx.doi.org/10.17504/protocols.io.rm7vzym2rlx1/v2 | https://www.protocols.io/view/a-real-time-pcr-method-to-genotype-mutant-mouse-mo-b6v4re8w | Peter W W Chomczynski, Kianna M Vires, Michal Rymascewski, Judith A. Heiny | TITLE: A real-time PCR method to genotype mutant mouse models with altered affinity for cardiotonic steroids on the Na,K-ATPase
AUTHORS: Peter W W Chomczynski, Kianna M Vires, Michal Rymascewski, Judith A. Heiny
[DESCRIPTION]
The highly conserved, cardiotonic steroid binding site (also termed ouabain binding sit... | ["[Pre-experiment preparation] In the interest of time and consistency, it is recommended that certain stock solutions and buffers be prepared ahead.", "[Pre-experiment preparation] Prepare a 10X stock solution of Tail Lysis Buffer and store in freezer.", "[Pre-experiment preparation] Prepare assay mixes.\nPrimers and ... |
53,545 | Private project from Hassan Hooo Hooo Ho (Meow) | 1 | dx.doi.org/10.17504/protocols.io.byihpub6 | https://www.protocols.io/view/private-project-from-hassan-hooo-hooo-ho-meow-byihpub6 | hassansammoer | TITLE: Private project from Hassan Hooo Hooo Ho (Meow)
AUTHORS: hassansammoer
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">private message from hassan meow</div></div>
[STEPS]
?. MeoooooowHi
?. | ["MeoooooowHi"] |
20,220 | HybISS: Hybridization-based In Situ Sequencing | null | dx.doi.org/10.17504/protocols.io.xy4fpyw | null | Daniel Gyllborg, Mats Nilsson | TITLE: HybISS: Hybridization-based In Situ Sequencing
AUTHORS: Daniel Gyllborg, Mats Nilsson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for multiplexed in situ sequencing in tissue sections as an image-based spatial transcriptomic method. This is the second iteration of In Situ Sequenc... | ["[Tissue Sample Preparation: Mouse Section]\n!!! Note: For human sections, proceed to Step 4 !!!Fresh frozen tissue samples are embedded in OCT (optimal cutting temperature) compound and stored at -80°C until cryosectioning. Tissue is cryosectioned at 10 μm thickness and collected on SuperFrost Plus adhesion slides an... |
41,535 | ELISA for quantification of macrophage-colony stimulating factor (M-CSF) in human serum or plasma. | 6 | dx.doi.org/10.17504/protocols.io.bks7kwhn | https://www.protocols.io/view/elisa-for-quantification-of-macrophage-colony-sti-bks7kwhn | Angel Justiz-Vaillant | TITLE: ELISA for quantification of macrophage-colony stimulating factor (M-CSF) in human serum or plasma.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. An anti-human macrophage-colony stimulating factor (M-CSF) coating antibody is adsorbed onto the microwells by inc... | ["An anti-human macrophage-colony stimulating factor (M-CSF) coating antibody is adsorbed onto the microwells by incubation overnight at 4°C with carbonate-bicarbonate buffer.", "Add 50 µl of human serum or plasma. M-CSF present in the serum sample binds to antibodies adsorbed into the microwells.", "The microplate is ... |
36,115 | When Misreporting the Value of Labor Benefits a Just Cause | null | dx.doi.org/10.17504/protocols.io.bfhtjj6n | https://www.protocols.io/view/when-misreporting-the-value-of-labor-benefits-a-ju-bfhtjj6n | J Jobu Babin | TITLE: When Misreporting the Value of Labor Benefits a Just Cause
AUTHORS: J Jobu Babin
[STEPS] | [] |
20,075 | U Mass - Chronic/acute phloridzin treatment | null | dx.doi.org/10.17504/protocols.io.xujfnun | null | Jason Kim | TITLE: U Mass - Chronic/acute phloridzin treatment
AUTHORS: Jason Kim
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">Phloridzin is a potent inhibitor of renal glucose reabsorption and may be used to lower serum glucose... | ["For chronic phloridzin treatment: 1. Anesthetize mice with an intraperitoneal injection of ketamine (100 mg/kg body weight) and xylazine (10 mg/kg body weight). 2. Shave hair at the incision site on the back. 3. Make an incision (~0.5 cm) using sterilized scalpel between the scapulae. 4. Subcutaneously insert an Alze... |
null | null | null | dx.doi.org/10.17504/protocols.io.pcudiww | null | null | TITLE: No Title
AUTHORS:
[STEPS]
SECTION: Water Collection
?.
SECTION: Discrete Sample Collection
?.
SECTION: Sample processing
?.
SECTION: References
?. | ["[Water Collection] Seawater is collected with a 3x rinsed (in seawater) bucket that is lowered with a rope to the water. The rinsed bucket is used to collect water to triple rinse a 2L polycarbonate bottle, a 1L cod-end, and an acid washed 30mL syringe. Then water is collected in the bucket and the syringe for the di... |
28,605 | Western Blot (Tank-Blot) | null | dx.doi.org/10.17504/protocols.io.765hrg6 | null | iGEM Dusseldorf | TITLE: Western Blot (Tank-Blot)
AUTHORS: iGEM Dusseldorf
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Blotting Buffer:</div><div class = "text-block"><ul style = "list-style-type:disc;"><li style = "counter-reset:ol0;list-style-type:disc;">100mL 10x SDS running buffer </li><li style = "counter-re... | [] |
57,661 | Extraction of RNA/DNA from Dried Blood on Filter Papers after Long-Term Storage | 1 | dx.doi.org/10.17504/protocols.io.dm6gpbbr5lzp/v1 | https://www.protocols.io/view/extraction-of-rna-dna-from-dried-blood-on-filter-p-b4i5qug6 | Gabriela Ulloa Urizar | TITLE: Extraction of RNA/DNA from Dried Blood on Filter Papers after Long-Term Storage
AUTHORS: Gabriela Ulloa Urizar
[DESCRIPTION]
Modified protocol from the manufacturer's protocol (Qiagen Quick-Start Protocol AllPrep DNA/RNA Mini Kit)
[STEPS]
SECTION: Dilute the sample for extraction
2. Add 600 µLof RLT Plus Buffe... | ["[Dilute the sample for extraction] Add 600 µLof RLT Plus Buffer to the 1.5 mL microtube with the blood sample on filter paper cut into small pieces (in 3 mm circles, equivalent to 50ul of whole blood), spin for 15 sat 10000 rpm.\n\nSpanish: Añadir 600 ul de Buffer RLT Plus al microtubo de 1.5mL con la muestra de sang... |
43,708 | Microbiome and eDNA sampling of sediment | 1 | dx.doi.org/10.17504/protocols.io.kxygxpp6zl8j/v1 | https://www.protocols.io/view/microbiome-and-edna-sampling-of-sediment-bnw4mfgw | Daniel S Read | TITLE: Microbiome and eDNA sampling of sediment
AUTHORS: Daniel S Read
[DESCRIPTION]
Protocol for field based sampling of bacterial biomass or environmental DNA (eDNA) in freshwater sediment.
[STEPS]
SECTION: Sample collection
1. To collect the sediment sample, you will require a sampling pole with a 50 mL falcon tub... | ["[Sample collection] To collect the sediment sample, you will require a sampling pole with a 50 mL falcon tube slot on the end, a 50 mL falcon tube, and a pair of gloves.", "[Sample collection] Attach the falcon tube to the end of the sampling pole by placing it in the slot, and make sure it is secure.", "[Sample coll... |
63,604 | K1 Keto Pills | Is It Really Fake Or Trusted?More Useful Than Other Products! | 3 | dx.doi.org/10.17504/protocols.io.5jyl89kb9v2w/v1 | https://www.protocols.io/view/k1-keto-pills-is-it-really-fake-or-trusted-more-us-cacusaww | thomsalonzo | TITLE: K1 Keto Pills | Is It Really Fake Or Trusted?More Useful Than Other Products!
AUTHORS: thomsalonzo
[DESCRIPTION]
K1 keto Life advanced weight loss true ingredients to help you get into ketosis without having to go on a strict ketogenic diet for days. (Buy Now)=>> https://reviewbylogix.online/... | [] |
37,990 | Chiaro Nanoindentation and Data Analysis | 1 | null | https://www.protocols.io/view/chiaro-nanoindentation-and-data-analysis-bhcej2te | Mariana A G Oliva | TITLE: Chiaro Nanoindentation and Data Analysis
AUTHORS: Mariana A G Oliva
[STEPS]
?. [Set-up and choosing the tip ]
To choose the right tip, refer to the advised stiffness range table below (Table1).
?. [Set-up and choosing the tip ]
Centre the probe into the optical axis (so that you can see it in the screen) Start ... | ["[Set-up and choosing the tip ]\nTo choose the right tip, refer to the advised stiffness range table below (Table1).", "[Set-up and choosing the tip ]\nCentre the probe into the optical axis (so that you can see it in the screen) Start software in laptop: PIUMA v2", "[Set-up and choosing the tip ]\nInsert tip first in... |
66,122 | GoKeto Gummies - An Introduction With Ingredients | 1 | dx.doi.org/10.17504/protocols.io.x54v9y4nmg3e/v1 | https://www.protocols.io/view/goketo-gummies-an-introduction-with-ingredients-cctiswke | orgtruketo | TITLE: GoKeto Gummies - An Introduction With Ingredients
AUTHORS: orgtruketo
[DESCRIPTION]
Agony and aggravation, especially persistent torment and irritation are extremely normal everywhere, and this GoKeto Gummies audit will be exceptionally useful to people who are experiencing it. Client assessments and overview... | [] |
103,856 | Eating Freely: assessing the feasibility of an online group intervention to improve emotional eating amongst adults with lived experience of obesity. | 0 | dx.doi.org/10.17504/protocols.io.kxygxyoywl8j/v1 | https://www.protocols.io/view/eating-freely-assessing-the-feasibility-of-an-onli-dhnq35dw | Dawn Power, Emma Murphy, Jamie Matu, Gemma Traviss-Turner, Louisa Ells | TITLE: Eating Freely: assessing the feasibility of an online group intervention to improve emotional eating amongst adults with lived experience of obesity.
AUTHORS: Dawn Power, Emma Murphy, Jamie Matu, Gemma Traviss-Turner, Louisa Ells
[DESCRIPTION]
This protocol describes the planned delivery and analysis of the Eat... | ["[Introduction] 1.0 Introduction\n\n \nEmotional eating has been identified as a potential target in weight management interventions due to its link to poorer outcomes in weight loss interventions (1; 2). People who emotionally eat are half as likely to achieve the 10% weight loss targets of standard interventions and... |
62,894 | Nanopore amplicon sequencing | 4 | dx.doi.org/10.17504/protocols.io.8epv5zrodv1b/v4 | https://www.protocols.io/view/nanopore-amplicon-sequencing-b9nnr5de | Yoshiyuki Matsuo | TITLE: Nanopore amplicon sequencing
AUTHORS: Yoshiyuki Matsuo
[DESCRIPTION]
The two-step PCR method allows us to perform nanopore amplicon sequencing with a user-defined inner primer set combined with barcoded outer primers provided by Oxford Nanopore Technologies, taking advantage of rapid adapter attachment chemist... | ["[Workflow]", "[1st PCR with inner primers] Prepare the PCR master mix.\n \n\nInner primers (user-supplied)", "[1st PCR with inner primers] Perform PCR.", "[1st PCR with inner primers] Analyze 2 µL of the PCR products by gel electrophoresis to verify successful amplification.", "[2nd PCR with barcoded outer primers] P... |
106,617 | Western Blots with S. rosetta lysate (version 1) | 0 | dx.doi.org/10.17504/protocols.io.3byl4987zgo5/v1 | https://www.protocols.io/view/western-blots-with-s-rosetta-lysate-version-1-dkcz4sx6 | Fredrick leon | TITLE: Western Blots with S. rosetta lysate (version 1)
AUTHORS: Fredrick leon
[DESCRIPTION]
This protocol utilizes the preferential lysis of S. rosetta to obtain choanoflagellate-specific proteins from co-culture with feeder bacteria. Protein concentrations are normalized by total protein stain, and the use of LICOR ... | ["[Prepare lysis buffer] The following recipe and protocol is based entirely on the preferential lysis of S. rosetta. Modifications have been made to remove all nucleic acids, and to remove unnecessary components.", "[Count, Harvest, and Lyse cells] Follow the lysis steps of the preferential lysis protocol.", "[Determi... |
81,151 | 2. Taxon Group: Bivalvia | 4 | dx.doi.org/10.17504/protocols.io.14egn2kd6g5d/v1 | https://www.protocols.io/view/2-taxon-group-bivalvia-ctg7wjzn | Patrick Adkins, Chris Fletcher, Inez Januszczak | TITLE: 2. Taxon Group: Bivalvia
AUTHORS: Patrick Adkins, Chris Fletcher, Inez Januszczak
[DESCRIPTION]
This is part of the collection "DToL Taxon-specific Standard Operating Procedures (SOPs) for Marine Metazoa", lead by the Other Metazoa Working Group. The SOP collection contains guidance on how to process the variou... | [] |
40,342 | ISOLATING CELLS IN LOUPE BROWSER | 3 | null | https://www.protocols.io/view/isolating-cells-in-loupe-browser-bjmwkk7e | Sumeet Gupta | TITLE: ISOLATING CELLS IN LOUPE BROWSER
AUTHORS: Sumeet Gupta
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:center"><span style = "font-weight:bold;:UNDERLINE;">ISOLATING CELLS IN LOUPE BROWSER</span></div></div></div>
[STEPS] | [] |
46,739 | DPP4 | 3 | dx.doi.org/10.17504/protocols.io.brvtm66n | https://www.protocols.io/view/dpp4-brvtm66n | thananda | TITLE: DPP4
AUTHORS: thananda
[STEPS] | [] |
21,298 | DNA Barcoding in a Field Setting | null | dx.doi.org/10.17504/protocols.io.y2sfyee | null | Aaron Pomerantz, Mrinalini Watsa, Stefan Prost, Gideon Erkenswick | TITLE: DNA Barcoding in a Field Setting
AUTHORS: Aaron Pomerantz, Mrinalini Watsa, Stefan Prost, Gideon Erkenswick
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol was used in the 2018 Genomics in the Jungle field course held at the Inkaterra Green Lab in the Madre de Dios Department of... | ["[PCRMixes]\n1We used a master mix (See below) to set up PCR reactionsButterfly rDNA (Total vol = )each of the forward and reverse primer set l water DNA q5 MasterMixMammal rDNA (Total vol = )each of the forward and reverse primer set l water DNA q5 MasterMixPlant rDNA (Total vol = )each of the forward and reverse pr... |
null | null | null | dx.doi.org/10.17504/protocols.io.k6sczee | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Replicate measurements are critical for quantitative Western blot (QWB) analysis. The purpose of QWB is to monitor changes in the relative abundance or modification of a target protein within a group of samples. Does the experimental treatment cause an increase or decrease in... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.u32eyqe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol describes the steps used to analyze shotgun sequences deposited in in Integrated Microbial Genomes and Microbiomes (IMG/M ) by using functional anotation evidences. KEGG orthology terms and pathways are used as evidence.The abundance of each of the corresponding b... | ["[Find metagenomes in the database] {\"blocks\":[{\"key\":\"cjq4i\",\"text\":\"\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[]},{\"key\":\"2thvd\",\"text\":\" Dataset\\nIntegrated Microbial Genomes and Microbiomes\\n\",\"type\":\"atomic\",\"depth\":0,\"inlineStyleRanges\":... |
78,798 | Anterograde tracing of spinal afferent innervation in rat stomach flat-mounts | 4 | dx.doi.org/10.17504/protocols.io.rm7vzb9dxvx1/v1 | https://www.protocols.io/view/anterograde-tracing-of-spinal-afferent-innervation-cq7nvzme | Jichao Ma, Duyen Nguyen, Jazune Madas, Andrew Kwiat, Zulema Toledo, Ariege Bizanti, Nicole Kogut, Anas Mistareehi, Kohlton Bendowski, Yuanyuan Zhang, Jin Chen, Terry Powley, John Furness, Zixi Jack Cheng | TITLE: Anterograde tracing of spinal afferent innervation in rat stomach flat-mounts
AUTHORS: Jichao Ma, Duyen Nguyen, Jazune Madas, Andrew Kwiat, Zulema Toledo, Ariege Bizanti, Nicole Kogut, Anas Mistareehi, Kohlton Bendowski, Yuanyuan Zhang, Jin Chen, Terry Powley, John Furness, Zixi Jack Cheng
[DESCRIPTION]
This p... | ["[Animals] Four to five-month-old male rats (n = 20) were housed in an animal room at which the dark/light cycle was set to 12/12 hours and water and food were supplied ad libitum. All procedures were carried out under the ethical guidelines of the University of Central Florida and approved by the University of Cent... |
null | null | null | dx.doi.org/10.17504/protocols.io.pkvdkw6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol provides a standardized methodolgy for a single-nucleotide polymorphism (SNP) at position -173 (-173*G/C) of the MIF gene. It also includes a standarized methodology to amplify a 207 bp (CATT<sub>5</sub>) segment of the MIF promoter region (MIF-794*CATT<sub>5-8 ... | [] |
45,987 | Experiment Data Depot (EDD) Study Creation | 1 | dx.doi.org/10.17504/protocols.io.n2bvjxn4xlk5/v1 | https://www.protocols.io/view/experiment-data-depot-edd-study-creation-bq6bmzan | Jennifer Gin, Christopher J Petzold | TITLE: Experiment Data Depot (EDD) Study Creation
AUTHORS: Jennifer Gin, Christopher J Petzold
[DESCRIPTION]
This protocol details how to create studies in the Experiment Data Depot. Data can be shared with collaborators via exported CSV files or through the REST API.
For more information about the EDD visit: Experim... | ["Go to the appropriate EDD for your project (e.g., public-edd.agilebiofoundry.org). Login with your username and credentials.", "Click on the New Study button on the top right.", "In the Add New Study pop-up window, type in your Study Name and Contact. Click Add Study button.", "On the Overview page, click on the E... |
77,583 | Human Islet Isolation Media Preparation | 1 | dx.doi.org/10.17504/protocols.io.5jyl8nnpdl2w/v3 | https://www.protocols.io/view/human-islet-isolation-media-preparation-cpzpvp5n | James Lyon, Aliya F Spigelman, Jocelyn E Manning Fox, Patrick E Macdonald | TITLE: Human Islet Isolation Media Preparation
AUTHORS: James Lyon, Aliya F Spigelman, Jocelyn E Manning Fox, Patrick E Macdonald
[DESCRIPTION]
This protocol describes the preparation of various media formulations required for the isolation and culture of human islets, as performed by the Alberta Diabetes Institute Is... | ["[HBSS (perfusion, rinse, priming solution), M199 (wash solution) and EMEM (dilution solution)]", "[Prepare and pH the HBSS, M199 and EMEM solutions] Prepare the HBSS, M199, and EMEM solutions outlined in step 1 of the Stock Media Preparation table using the following directions:\nDispense 9 L of Milli-Q (18mΩ) water... |
93,408 | MULTI-Seq Barcoding and Library Preparation | 4 | dx.doi.org/10.17504/protocols.io.kxygx3xzkg8j/v1 | https://www.protocols.io/view/multi-seq-barcoding-and-library-preparation-c7f8zjrw | Annika Martin, Hanqin Li, Dirk Hockemeyer | TITLE: MULTI-Seq Barcoding and Library Preparation
AUTHORS: Annika Martin, Hanqin Li, Dirk Hockemeyer
[DESCRIPTION]
This protocol describes MULTI-Seq barcoding of hESCs and library preparation, it is based on McGinnis et. al. 2019. PMID: 31209384 and the 10x Genomics user guide “Chromium Next GEM Single Cell 3ʹ Reagen... | ["[Oligonucleotides] Oligonucleotides (store in -20°C for large term storage):\n50 µM Anchor and Co-Anchor \n10 µM Barcode Oligos \n10 µM MULTI-seq additive primer \n10 µM Universal I5 primer \n10 µM TruSeq RPI primers \n\nAnchor LMO:\t\t 5’-TGGAATTCTCGGGTGCCAAGGgtaacgatccagctgtcact-{Lipid}-3’\nCo-Anchor LMO:\t 5’-{L... |
null | null | null | dx.doi.org/10.17504/protocols.io.qt5dwq6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The diverse applications of mutant and recombinant adenoviruses demand facile methods for their generation. This protocol allows the user to rapidly assemble customized adenoviral genomes from high-copy plasmids in a two-step isothermal reaction. Following <em>in vitro</em> a... | [] |
41,806 | Open Isothermal Platform Protocal | 4 | dx.doi.org/10.17504/protocols.io.bk3nkyme | https://www.protocols.io/view/open-isothermal-platform-protocal-bk3nkyme | Andrew Buultjens, Koen Vandelannoote, Tim Stinear | TITLE: Open Isothermal Platform Protocal
AUTHORS: Andrew Buultjens, Koen Vandelannoote, Tim Stinear
[STEPS]
?. Place strips in FABL-8
?. Cap all wells
?. Add 5ml of positive control in well 8.
?. Add 5ml of H2O in negative control well 7.
?. Transfer 5ml of extracted RNA to pre-aliquoted LAMP mix. Mix by pipetting up... | ["Place strips in FABL-8", "Cap all wells", "Add 5ml of positive control in well 8.", "Add 5ml of H2O in negative control well 7.", "Transfer 5ml of extracted RNA to pre-aliquoted LAMP mix. Mix by pipetting up and down 5 times.", "Extract RNA as per dx.doi.org/10.17504/protocols.io.bkynkxve", "LAMP reaction (can refer ... |
43,369 | Protocol for Extraction of Viral RNA with added DNase treatment | 4 | dx.doi.org/10.17504/protocols.io.bnkhmct6 | https://www.protocols.io/view/protocol-for-extraction-of-viral-rna-with-added-dn-bnkhmct6 | Megan Folkerts, Ashlyn Pfeiffer, mnguyen , Danielle Vazquez, Amber Jones | TITLE: Protocol for Extraction of Viral RNA with added DNase treatment
AUTHORS: Megan Folkerts, Ashlyn Pfeiffer, mnguyen , Danielle Vazquez, Amber Jones
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is modified from the MagMAX MVP II protocol from Thermo Fisher, and the MagMAX mirVa... | ["[RNA extraction using MVP II kit and Kingfisher]\nAliquot 5 ul of proteinase k to each sample well of a 96-well deep-well plate to be used for extraction.", "[RNA extraction using MVP II kit and Kingfisher]\nAdd 50ul sample to wells\nThis can be increased to as much as 200ul if sufficient sample volume is available",... |
null | null | null | dx.doi.org/10.17504/protocols.io.phmdj46 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
99,145 | Wake Forest University Health Sciences Manual of Procedures Biospecimen Collection and Processing V4 | 1 | dx.doi.org/10.17504/protocols.io.ewov19n4ylr2/v1 | https://www.protocols.io/view/wake-forest-university-health-sciences-manual-of-p-dc3h2yj6 | Kim Kennedy, Heather Gregory | TITLE: Wake Forest University Health Sciences Manual of Procedures Biospecimen Collection and Processing V4
AUTHORS: Kim Kennedy, Heather Gregory
[DESCRIPTION]
This includes the methods associated with obtaining muscle, blood, and urine along with demographic, clinical, health, and functional data from younger and old... | [] |
14,506 | MALE CIRCUMCISION FOR PREVENTION OF HETEROSEXUAL TRANSMISSION OF HIV IN ADULT MALES IN SOWETO, what do indicators and incidence rates show?untitled protocol | null | dx.doi.org/10.17504/protocols.io.seiebce | null | Hillary Mukudu, Neil Martinson, Benn Sartorius | TITLE: MALE CIRCUMCISION FOR PREVENTION OF HETEROSEXUAL TRANSMISSION OF HIV IN ADULT MALES IN SOWETO, what do indicators and incidence rates show?untitled protocol
AUTHORS: Hillary Mukudu, Neil Martinson, Benn Sartorius
[DESCRIPTION]
<p><strong>Background</strong></p>
<p>The biomedical prevention of HIV transmission t... | [] |
44,759 | PMN- 01a - Isolation of Human PMN from Buffy Coat | 4 | dx.doi.org/10.17504/protocols.io.bpxxmppn | https://www.protocols.io/view/pmn-01a-isolation-of-human-pmn-from-buffy-coat-bpxxmppn | Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino | TITLE: PMN- 01a - Isolation of Human PMN from Buffy Coat
AUTHORS: Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Separation of Human Neutrophils (PMN) from Buffy Coat: list of publ... | ["Place of venus blood from BUFFY COAT into 10 ml volume centrifuge tube.\n5 mL", "Add of SOLUTION- 03 and mix well drawing in and out of a pipette.\n2 mL", "Incubate in the DARK for at\n37 °C", "Place of Fycoll-HyPaque media solution into a 10 ml volume centrifuge tube.\n3 mL", "Slowly and carefully layer the supe... |
97,359 | Proteomic Analysis of Human Ovarian Cortex and Medulla Secretome Using Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) Acquisition by Data-Independent Acquisition (DIA) on an Orbitrap Eclipse Tribrid Mass Spectrometer | 0 | dx.doi.org/10.17504/protocols.io.n92ld83bnv5b/v1 | https://www.protocols.io/view/proteomic-analysis-of-human-ovarian-cortex-and-med-dbbp2imn | Joanna Bons, J P Rose, M A Watson, B Schilling | TITLE: Proteomic Analysis of Human Ovarian Cortex and Medulla Secretome Using Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) Acquisition by Data-Independent Acquisition (DIA) on an Orbitrap Eclipse Tribrid Mass Spectrometer
AUTHORS: Joanna Bons, J P Rose, M A Watson, B Schilling
[DESCRIPTION]
Ovaries from h... | ["[Conditioned Media Concentration with Amicon Ultra Centrifugal Filters] dx.doi.org/10.17504/protocols.io.e6nvw1px7lmk/v1", "[Protein Digestion with S-trap Spin Columns using Conditioned Concentrated Media] dx.doi.org/10.17504/protocols.io.x54v928eml3e/v1", "[Proteolytic Peptide Desalting with C18 HLB Cartridges] dx.d... |
104,920 | Immunohistochemistry Protocol | 0 | dx.doi.org/10.17504/protocols.io.kqdg32y61v25/v1 | https://www.protocols.io/view/immunohistochemistry-protocol-dipy4dpw | Livia Hecke Morais, Jenny Ji | TITLE: Immunohistochemistry Protocol
AUTHORS: Livia Hecke Morais, Jenny Ji
[DESCRIPTION]
Protocol has been approved by the California Institute of Technology’s Institutional Animal Care
and Use Committee (IACUC).
[STEPS]
SECTION: Brain Extraction
1. Mice were anesthetized with 150 uL pentobarbital (Euthasol), and the... | ["[Brain Extraction] Mice were anesthetized with 150 uL pentobarbital (Euthasol), and their hearts were punctured.", "[Brain Extraction] Mice were perfused with ice-cold phosphate-buffered saline (PBS) and 4% paraformaldehyde (PFA).", "[Brain Extraction] Brains were extracted and preserved in 4% PFA for 48 hours while ... |
null | null | null | dx.doi.org/10.17504/protocols.io.gakbscw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is a collection of Bioline protocols for the <span style="color: #000000; font-family: Arial; font-size: 13px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: left; text-i... | [] |
82,325 | MLi-2 treatment of astrocytes | 3 | dx.doi.org/10.17504/protocols.io.j8nlkwzzwl5r/v1 | https://www.protocols.io/view/mli-2-treatment-of-astrocytes-cumvwu66 | Shiyi Wang | TITLE: MLi-2 treatment of astrocytes
AUTHORS: Shiyi Wang
[DESCRIPTION]
LRRK2 inhibitor MLi-2 treatment of astrocytes
[STEPS] | [] |
53,898 | Colorimetric determination of urea | 6 | dx.doi.org/10.17504/protocols.io.byvipw4e | https://www.protocols.io/view/colorimetric-determination-of-urea-byvipw4e | noah.langenfeld , Laurenpayne , Bruce Bugbee | TITLE: Colorimetric determination of urea
AUTHORS: noah.langenfeld , Laurenpayne , Bruce Bugbee
[DESCRIPTION]
This protocol measures the absorbance of urea in solution in complexation with diacetyl monoxime at 520 nm and is linearly proportional to concentration up to 5 mM urea.
[BEFORE_START]
Ensure a lab coat, l... | ["[Mixed Acid Reagent Preparation] Dissolve 2.5 mg ferric chloride (97% purity) in 45 mL deionized water in a 250 mL volumetric flask.", "[Mixed Acid Reagent Preparation] Add 80 µL of 14.8 Molarity (M) concentrated phosphoric acid (85 wt. % phosphoric acid in water).", "[Mixed Acid Reagent Preparation] Prepare 4.7 Mo... |
20,279 | U Mass - Insulin tolerance test | null | dx.doi.org/10.17504/protocols.io.x2xfqfn | null | Jason Kim | TITLE: U Mass - Insulin tolerance test
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">
Insulin tolerance test measures systemic clearance of glucose followin... | ["Mice are fasted for 5 hours prior to the start of experiment.", "Collect plasma sample (20 µl) before the start of experiment (basal-0 min) to measurebasal insulin and glucose levels.", "Administer intraperitoneal injection of insulin (0.5 or 0.75 unit/kg body weight) using aninsulin syringe.", "Collect plasma sample... |
43,973 | MAPS image analysis | 5 | dx.doi.org/10.17504/protocols.io.bn7dmhi6 | https://www.protocols.io/view/maps-image-analysis-bn7dmhi6 | jessechao | TITLE: MAPS image analysis
AUTHORS: jessechao
[STEPS]
?. [Setting up required environment and packages]
Navigate to https://github.com/jessecanada/MAPS, download the repository.
?. [Setting up required environment and packages]
The following commands assume that you are using conda (or Anaconda) to manage your python... | ["[Setting up required environment and packages]\nNavigate to https://github.com/jessecanada/MAPS, download the repository.", "[Setting up required environment and packages]\nThe following commands assume that you are using conda (or Anaconda) to manage your python packages and that you are on a Unix type system (Linux... |
71,268 | Bacterial Genomic DNA Isolation | 1 | null | https://www.protocols.io/view/bacterial-genomic-dna-isolation-chuct6sw | Carly Sjogren, Carlos Goller | TITLE: Bacterial Genomic DNA Isolation
AUTHORS: Carly Sjogren, Carlos Goller
[DESCRIPTION]
Overview and Goals
Your bacterial isolate has been grown on agar plates. We now need to lyse open the bacteria and isolate only the genomic DNA for sequencing. For this, we need to gently lyse the bacteria with the enzyme lysozy... | ["[Activity 1: Bacterial Lysis] Preheat two Eppendorf Thermal mixers with 1.5 mL blocks to 37 °C and 55 °C", "[Activity 1: Bacterial Lysis] Use a sterile cotton swab to obtain bacterial colonies and resuspend in 300 µL of cold PBS or Tris buffer.", "[Activity 1: Bacterial Lysis] Centrifuge each microtube of the samp... |
33,849 | Hydroxyl Radical-scavenging Activity | null | dx.doi.org/10.17504/protocols.io.bdazi2f6 | null | Jing Xu | TITLE: Hydroxyl Radical-scavenging Activity
AUTHORS: Jing Xu
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The scavenging of hydroxyl radicals were determined by Guo et al. The reactions were performed in 0.3 ml of 20 mM sodium salicylate, 2.0 ml of 1.5 nM FeSO</span><span style = "vertical-... | [] |
28,650 | Sigmoid fitting in Excel (Excel Solver Add-In) | null | dx.doi.org/10.17504/protocols.io.78ihrue | null | Kenji Ohgane | TITLE: Sigmoid fitting in Excel (Excel Solver Add-In)
AUTHORS: Kenji Ohgane
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol covers how to fit sigmoidal curve to data within Excel, and allows rapid estimation of EC50/IC50 values from experimental dose-response data. Although R or other ... | ["Download the following excel file. Copy the excel sheet into your excel file if needed.The file contains a sheet set up for sigmoidal fitting with an example data set, for which you can test the fitting procedure.", "Open the excel file, and enter your data in the \"x\" and \"y\" column. Delete unnecessary data.\nThe... |
48,932 | document 7.4 1 | 3 | null | https://www.protocols.io/view/document-7-4-1-bt2cnqaw | Mariia Guliakina | TITLE: document 7.4 1
AUTHORS: Mariia Guliakina
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Sudden she seeing garret far regard. By hardly it direct if pretty up regret. Ability thought enquire settled prudent you sir. Or easy knew sold on well come year. Something consulted age extremely end pr... | [] |
82,349 | Measuring shoal cohesion from video frames in ImageJ using the Interfish Distance plugin | 1 | dx.doi.org/10.17504/protocols.io.j8nlkwz7wl5r/v1 | https://www.protocols.io/view/measuring-shoal-cohesion-from-video-frames-in-imag-cunmwvc6 | Matheus Gallas-Lopes, Daniela Varisco Müller, Amanda Patelli Alves, Angelo Piato, Ana P Herrmann | TITLE: Measuring shoal cohesion from video frames in ImageJ using the Interfish Distance plugin
AUTHORS: Matheus Gallas-Lopes, Daniela Varisco Müller, Amanda Patelli Alves, Angelo Piato, Ana P Herrmann
[DESCRIPTION]
This protocol presents a practical ImageJ workflow, built around the Interfish Distance plugin, for qua... | ["[Installing the plugin] To install the plugin, first you have to download the ImageJ software, and then the Inter sh distance PLUGIN.ijm archive \n\nImageJ software download link: https://imagej.nih.gov/ij/download.html\nPlugin download: \nImportant: The inter sh distance plugin must be dowloaded in the ImageJ's ma... |
88,321 | Fast-scan cyclic voltammetry to assess dopamine release in ex vivo mouse brain slices | 1 | dx.doi.org/10.17504/protocols.io.4r3l271zxg1y/v2 | https://www.protocols.io/view/fast-scan-cyclic-voltammetry-to-assess-dopamine-re-c2g9ybz6 | Katherine Brimblecombe, Stephanie J Cragg | TITLE: Fast-scan cyclic voltammetry to assess dopamine release in ex vivo mouse brain slices
AUTHORS: Katherine Brimblecombe, Stephanie J Cragg
[DESCRIPTION]
This protocol is to assess whether a drug changes the dopamine concentration released following a single pulse (1p) electrical stimulation.
[BEFORE_START]
Prio... | ["[Preparation of ex vivo mouse brain slices] Prepare HEPES buffer solution (see Materials), chill and oxygenate.", "[Preparation of ex vivo mouse brain slices] Prepare vibratome settings: 300 μm slices, 0.44 mm/s speed, Δ1.45 mm vibration. Chill plate and buffer tray in freezer, rinse razor blade in acetone.", "[Prepa... |
20,000 | U Mass - Basal glucose metabolism | null | dx.doi.org/10.17504/protocols.io.xr8fm9w | null | Jason Kim | TITLE: U Mass - Basal glucose metabolism
AUTHORS: Jason Kim
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">
Whole body glucose turnover and hepatic glucose production rates are measured at basal state using an intraven... | ["Survival surgery is performed to establish a chronic indwelling catheter at 5~6 days prior to experiment for intravenous infusion. (refer to M1023: Surgery-jugular vein cannulation)", "Mice are fasted overnight (~15 hours) or for 5 hours prior to the start of experiment.", "Place a mouse in a rat-size restrainer with... |
12,096 | Hornwort RNA extraction | null | dx.doi.org/10.17504/protocols.io.p28dqhw | null | Eftychis Frangedakis | TITLE: Hornwort RNA extraction
AUTHORS: Eftychis Frangedakis
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The same protocol used for DNA extraction is used for RNA extraction with the addition of an overnight RNA precipitation step with LiCl.</div></div>
[STEPS]
?. Grind 0.5-2 g of tissue using ... | ["Grind 0.5-2 g of tissue using mortar and pestle in the presence of liquid nitrogen until finely ground. Transfer frozen ground tissue to a 30 ml tube.", "Add 10 ml of 60 oC extraction buffer and 100 mg PVP-40/g tissue. Mix by inversion and incubate in 60 oC in a water bath for 30 min (or incubate on ice for 15 min).... |
76,247 | Nuclei isolation from frozen human brain samples for snRNA-seq | 4 | dx.doi.org/10.17504/protocols.io.j8nlkk9ydl5r/v2 | https://www.protocols.io/view/nuclei-isolation-from-frozen-human-brain-samples-f-cnpxvdpn | Marcos Nascimento | TITLE: Nuclei isolation from frozen human brain samples for snRNA-seq
AUTHORS: Marcos Nascimento
[DESCRIPTION]
Protocol to isolate nuclei from snap-frozen human brain samples for sn-RNAseq
[STEPS]
SECTION: Preparation
1. Check if the Rotor SW32Ti rotor is at 4°C
SECTION: Preparation
2. Clean your work area (bench and... | ["[Preparation] Check if the Rotor SW32Ti rotor is at 4°C", "[Preparation] Clean your work area (bench and pipettes) with RNAse Zap.", "[Preparation] Add RNAse inhibitor (Sigma cat.# 3335402001) to lysis buffer (LB) and wash and resuspension buffer (WRB) to a final concentration of 0.2U/ul.", "[Preparation] Put LB and ... |
28,876 | Ablation of ß-cells in Tg(ins:NTR-mCherry) transgenic zebrafish using metronidazole | null | dx.doi.org/10.17504/protocols.io.8fkhtkw | null | Sandra Rieger | TITLE: Ablation of ß-cells in Tg(ins:NTR-mCherry) transgenic zebrafish using metronidazole
AUTHORS: Sandra Rieger
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block"><span>To induce hyperglycemia in larval zebrafish, utili... | ["[Potential Pitfalls:]\n1. Ablation efficiency is low: MTZ might be old or only incompletely dissolved in the embryo medium. MTZ might alternatively be degraded if embryos were incubated in light, as MTZ is light sensitive.2. MTZ does not dissolve: DMSO and volume of initial solution is both crucial for dissolving the... |
78,929 | Descriptive analysis of patient involvement in the development of German clinical practice guidelines: A meta-research study | 1 | dx.doi.org/10.17504/protocols.io.8epv5j575l1b/v1 | https://www.protocols.io/view/descriptive-analysis-of-patient-involvement-in-the-crbrv2m6 | Stefanie Pfisterer-Heise, Clara Orduhan, Mai Nguyen, Käthe Gooßen, Jessica Breuing, Sebastian Von Peter, Corinna Schaefer, Dawid Pieper | TITLE: Descriptive analysis of patient involvement in the development of German clinical practice guidelines: A meta-research study
AUTHORS: Stefanie Pfisterer-Heise, Clara Orduhan, Mai Nguyen, Käthe Gooßen, Jessica Breuing, Sebastian Von Peter, Corinna Schaefer, Dawid Pieper
[DESCRIPTION]
Clinical practice guidelines... | ["Research team\nStefanie Pfisterer-Heise, Clara Orduhan, Mai Nguyen, Käthe Gooßen, Jessica Breuing, Sebastian von Peter, Corinna Schaefer, Dawid Pieper", "Objectives\nThe aims of this meta-research study are twofold: first, to investigate whether and how patients have been involved in the development of currently vali... |
33,839 | A membrane-enriched preparation of culture samples for mass spectrometry-based proteomics | null | dx.doi.org/10.17504/protocols.io.bdapi2dn | null | Gwendolyn Gallagher | TITLE: A membrane-enriched preparation of culture samples for mass spectrometry-based proteomics
AUTHORS: Gwendolyn Gallagher
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Purpose: </span><span>Preparation of culture samples for mass spectrometry-based proteomics<... | ["[Cell Lysis Protocol ]\nCell pellets resuspended in 333 uL wash solution and lysed with QSonica high power sonication (15 min, 1 sec pulse, Ampl 85%)\nAll samples were previously derived from 4.5 mL pure cultures spun down and flash frozen", "[Cell Lysis Protocol ]\nAfter sonication, the tubes were centrifuged (2500x... |
32,182 | Total RNA and DNA in microalgae: The extraction and quantification | 1 | null | https://www.protocols.io/view/total-rna-and-dna-in-microalgae-the-extraction-and-bbnwimfe | Yingyu Hu, Zoe V Finkel | TITLE: Total RNA and DNA in microalgae: The extraction and quantification
AUTHORS: Yingyu Hu, Zoe V Finkel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This assay protocol for total RNA and DNA is adapted from Berdalet E. et al. and Liefer J.D. et al.</div><div class = "text-block">RNA and DNA ar... | ["[RNA and DNA extraction]\nFreeze dry samples.\n\t\t\t\t\t\t\t .justify:after {\n\t\t\t\t\t\t\t content: \"\";\n\t\t\t\t\t\t\t display:inline-block;\n\t\t\t\t\t\t\t width: 100%;\n\t\t\t\t\t\t\t }\n\t\t\t\t\t\t\tFreeze-drying should be as short as possible to reduce sample degradation.\n\t\t\t\t\t\t\t .just... |
88,987 | FACS screening to detect regulators of ROS | 4 | dx.doi.org/10.17504/protocols.io.n2bvj32pwlk5/v1 | https://www.protocols.io/view/facs-screening-to-detect-regulators-of-ros-c253yg8n | Megan Lee, Neal Bennett, Ken Nakamura | TITLE: FACS screening to detect regulators of ROS
AUTHORS: Megan Lee, Neal Bennett, Ken Nakamura
[DESCRIPTION]
This protocol describes an adapted CRISPRi- and FACS- based genomic screen to identify genetic modulators of ROS. By incubating cells with ROS dyes that are then sorted with flow cytometry and sequenced, this... | ["[Culturing K562 Cells] Make K562 Media\n450 mL RMPI-1640 media (UCSF Media Core)\n50 mL 10% Fetal Bovine Serum\n5 mL 0.2 M glutamine\n5 mL PenStrep", "[Culturing K562 Cells] Transduce lentivirus containing your sgRNA library at an MOI < 1, lower for smaller libraries. We recommend a 2 hour spinfection at 32 degrees C... |
43,698 | Agarose Gel Electrophoresis | 4 | dx.doi.org/10.17504/protocols.io.bnwsmfee | https://www.protocols.io/view/agarose-gel-electrophoresis-bnwsmfee | Zhujun Wei | TITLE: Agarose Gel Electrophoresis
AUTHORS: Zhujun Wei
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The concentration of the agarose gel is 1%.</div></div>
[STEPS]
?. Weigh 0.20 g of agarose.
?. Add 20 ml of TAE 1X. Need to prepare 1X TAE with 50X TAE.
?. Heat up until the solution is homogeneou... | ["Weigh 0.20 g of agarose.", "Add 20 ml of TAE 1X. Need to prepare 1X TAE with 50X TAE.", "Heat up until the solution is homogeneous.", "Add 1 μl Gelred into solution and mix well.", "Put the solution into bed for polymerize, make sure \"comb\" is well placed and the solution is balanced.", "20 min later, use the gel."... |
28,112 | Q5 Polymerase PCR Cloning | null | dx.doi.org/10.17504/protocols.io.7pqhmmw | null | NUS iGEM | TITLE: Q5 Polymerase PCR Cloning
AUTHORS: NUS iGEM
[STEPS]
?. Prepare 6-reaction PCR mix by adding together deionized water, Q5 reaction buffer, dNTP mix, and Q5 DNA polymerase
244.2 µl
66 µl
6.6 µl
3.3 µl
?. Add 1 of template DNA and of primer pairs into specified PCR tube
1 µl
0.5 µl
?. Aliquot of PCR m... | ["Prepare 6-reaction PCR mix by adding together deionized water, Q5 reaction buffer, dNTP mix, and Q5 DNA polymerase\n244.2 µl\n66 µl\n6.6 µl\n3.3 µl", "Add 1 of template DNA and of primer pairs into specified PCR tube\n1 µl\n0.5 µl", "Aliquot of PCR mix into each PCR tube\n48 µl", "Load PCR tubes in therm... |
null | null | null | dx.doi.org/10.17504/protocols.io.dek3cv | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
For use in the "<a href="http://protocols.io/view/FASP-Kit-Protocol-ORNL-Developed-for-Bacteriophage-ddn25d" target="_blank">FASP Kit Protocol-ORNL Developed for Bacteriophage</a>"
[STEPS]
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.pcbdisn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Cell preservation and counting techniques for Monterey Wharf II monitoring and CA-HABMAP reporting.</p>
[STEPS]
?.
?.
?.
?.
?.
?. | [] |
49,865 | SPARC_Duke_Grill_OT2-OD025340_VagusNerve_IHC_ChAT | 1 | dx.doi.org/10.17504/protocols.io.buxhnxj6 | https://www.protocols.io/view/sparc-duke-grill-ot2-od025340-vagusnerve-ihc-chat-buxhnxj6 | J. Ashley Ezzell, Nicole A. Pelot, Kara A. Clissold, Warren M. Grill | TITLE: SPARC_Duke_Grill_OT2-OD025340_VagusNerve_IHC_ChAT
AUTHORS: J. Ashley Ezzell, Nicole A. Pelot, Kara A. Clissold, Warren M. Grill
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The protocol describes immunohistochemistry with anti-choline acetyltransferase, as it has been applied to cervical a... | ["[Immunohistochemistry]\nBake slides with sections of paraffin-embedded vagus nerve overnight at 50oC and then cool overnight.", "[Immunohistochemistry]\nDeparaffinize the slides and hydrate them to distilled water: xylene (2x 6 min), 100% ethanol (5 min), 95% ethanol (4 min), 70% ethanol (3 min), deionized water (2x ... |
100,675 | DNA Extraction from 0.22µm Sterivex Filters - Phenol-Chloroform | 1 | dx.doi.org/10.17504/protocols.io.14egn63oql5d/v1 | https://www.protocols.io/view/dna-extraction-from-0-22-m-sterivex-filters-phenol-dejb3cin | Colleen Kellogg | TITLE: DNA Extraction from 0.22µm Sterivex Filters - Phenol-Chloroform
AUTHORS: Colleen Kellogg
[DESCRIPTION]
This protocol is used to extract genomic DNA from 0.22μl sterivex filters using Phenol-Chlorophorm. As part of the Hakai Institute Ocean Observing Program, biomolecular samples have been collected weekly, from... | ["[LYSIS AND INCUBATION] Add 100 µL lysozyme (125 mg fully dissolved in 1000 μl 1 x TE) and 20µL RNase A (10 µg/ml: 1µL in 999µL 1 x TE) to each filter.\nReseal the top with Parafilm or a luer cap. \nIncubate Sterivex in a rotating incubator at 37°C for 1h (in labeled 50 ml falcon tubes).", "[LYSIS AND INCUBATION] Add... |
67,632 | SARS-CoV-2 Infection and Viral Replication of Human Lung Organoids | 1 | dx.doi.org/10.17504/protocols.io.j8nlkkepxl5r/v3 | https://www.protocols.io/view/sars-cov-2-infection-and-viral-replication-of-huma-ceaqtadw | Morris Baumgardt, Maren Hülsemann, Karen Hoffmann, Mirjana Kessler, Stefan Hippenstiel, Andreas C. Hocke, Katja Hönzke | TITLE: SARS-CoV-2 Infection and Viral Replication of Human Lung Organoids
AUTHORS: Morris Baumgardt, Maren Hülsemann, Karen Hoffmann, Mirjana Kessler, Stefan Hippenstiel, Andreas C. Hocke, Katja Hönzke
[DESCRIPTION]
This protocol describes the working steps to infect human alveolar-like organoids with SARS-CoV-2... | ["[Cultivation of human alveolar-like organoids] Grow your 3D model as described", "[Cell counting of human alveolar-like organoids] A specific cell number is needed to calculate the virus MOI (multiplicity of infection).\n\nCarefully remove organoid medium of one well.", "[Cell counting of human alveolar-like organoid... |
86,452 | Maintenance of the recording chamber for non-human primate (Chamber cleaning and dura scraping) | 1 | dx.doi.org/10.17504/protocols.io.5jyl8ppm9g2w/v1 | https://www.protocols.io/view/maintenance-of-the-recording-chamber-for-non-human-cynuxvew | Devin R Harsch, Daisuke Kase, Witold J Lipski, Robert S Turner | TITLE: Maintenance of the recording chamber for non-human primate (Chamber cleaning and dura scraping)
AUTHORS: Devin R Harsch, Daisuke Kase, Witold J Lipski, Robert S Turner
[DESCRIPTION]
Once a craniotomy has been done in the chamber, the inside of the chamber must be cleaned regularly (2-3 times per week) to preven... | ["[Daily maintenance of recording chamber (Chamber cleaning)] Wipe the desk with disposable disinfection wipes, then check if you have all items.", "[Daily maintenance of recording chamber (Chamber cleaning)] Open the chamber cleaning kit as instructed in the sub-steps below, and arrange the tools on the sterilization ... |
16,588 | Isolation of single nuclei from solid tissues | null | dx.doi.org/10.17504/protocols.io.ufketkw | null | Blue Lake, Kun Zhang | TITLE: Isolation of single nuclei from solid tissues
AUTHORS: Blue Lake, Kun Zhang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Nuclei can be readily isolated from frozen tissues with a combination of chemical and physical treatments that can circumvent the non-uniform or incomplete dissociation ... | ["[Prepare Reagents and Tissue]\nPrepare NEB-complete (NEB containing 5 ug/ml DAPI and 0.04 U/ul RNAse Inhibitor)chill on ice ABC1Final ConcentrationStockVolume (25 ml)220 mM Tris [pH 8]\n 320 mM sucrose \n 5 mM CaCl2 \n 3 mM MgAc2\n 0.1 mM EDTA\n 0.1% TritonX-100\n dH201M \n 1M \n 1M \n 1M \n 0.5M \n 10%\... |
58,576 | Keio Acute Single-Worm Tracking | 1 | dx.doi.org/10.17504/protocols.io.b5fqq3mw | https://www.protocols.io/view/keio-acute-single-worm-tracking-b5fqq3mw | Saul Moore | TITLE: Keio Acute Single-Worm Tracking
AUTHORS: Saul Moore
[DESCRIPTION]
In order to test how quickly C. elegans responds to the bacterial lawn, individual worms are gently picked onto 35mm petri plates a short distance away from the seeded lawn, and recording started immediately. Are there any differences between ... | ["[Preparing maintenance plates] Make 500mL normal Nematode Growth Media (NGM) agar, following the protocol", "[Preparing maintenance plates] Pour 15mL agar into each of 3 x 60mm Petri plates ('maintenance' plates) and 3.5mL agar into each of 30 x 35mm Petri plates ('imaging' plates)", "[Preparing maintenance plates] L... |
93,566 | Culturing of infective agents from infected wheat leaves | 4 | dx.doi.org/10.17504/protocols.io.6qpvr4rkpgmk/v2 | https://www.protocols.io/view/culturing-of-infective-agents-from-infected-wheat-c7k6zkze | Benjamin Schwessinger, Erin Hill, Peter Solomon | TITLE: Culturing of infective agents from infected wheat leaves
AUTHORS: Benjamin Schwessinger, Erin Hill, Peter Solomon
[DESCRIPTION]
This protocols is part of the ANU Biosecurity mini-research project #1 "Plant Pathogen Diagnostics: Visuals, subcultures, and genomics".
You will be provided four pots of 3-4 week ol... | ["[Week 2: Selection of representative leaf samples, surface sterilisation, and initial culturing.] Carefully, study the plants in each pot and select two leaves with symptoms of infected plants (if possible) and control leaves of uninfected plants. Select two leaves for each treatment group.", "[Week 2: Selection of r... |
null | null | null | dx.doi.org/10.17504/protocols.io.j3rcqm6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The crude extracts were obtained from orange wastes processed for juice. These crude extracts were concentrated by precipitation with ammonium sulfate. The lipases contained in the concentrated extracts were identified by zymography with the MUF-butyrate as substrate.</p>
[S... | [] |
47,315 | document 16/2 | 3 | null | https://www.protocols.io/view/document-16-2-bsftnbnn | Maria Guliakina | TITLE: document 16/2
AUTHORS: Maria Guliakina
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">One advanced diverted domestic sex repeated bringing you old. Possible procured her trifling laughter thoughts property she met way. Companions shy had solicitude favourable own. Which could saw guest man n... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.cviw4d | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
The Thermo Scientific Pierce Silver Stain Kit is a rapid and ultrasensitive silver stain system for protein detection in polyacrylamide gels. The stain performs consistently and reliably for both first-time and experienced users for high, low or gradient percentage gels in singl... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.fkrbkv6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This Agar medium can be used for the cultivation of Phytophthora infestans. It is particularly suitable for long term maintenaince of Phytophthora on plate.</p>
<p>To induce sporulation Rye B agar is recommended.</p>
<p> </p>
<p>This protocal has been copied from http://www.p... | [] |
27,825 | Size Selective Precipitation of DNA using PEG & Salt | null | dx.doi.org/10.17504/protocols.io.7erhjd6 | null | John Tyson | TITLE: Size Selective Precipitation of DNA using PEG & Salt
AUTHORS: John Tyson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Size Selective Precipitation of DNA using PEG & Salt</span></div><div class = "text-block">We and others have been thinking about the poss... | [] |
25,110 | RNA Isolation from Plant Tissue Protocol 10: TRIzol LS Reagent Method | null | dx.doi.org/10.17504/protocols.io.4rwgv7e | null | null | TITLE: RNA Isolation from Plant Tissue Protocol 10: TRIzol LS Reagent Method
AUTHORS:
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Implemented by: Michael Melkonian and Barbara Surek (algae) and Juan Carlos Villarreal (bryophytes)</div><div class = "text-block">This protocol follows the procedur... | ["Centrifuge at lowest speed to cause algae to form pellet.", "Homogenize each portion of pellet material to a powder in liquid nitrogen using mortar and pestle prechilled with liquid nitrogen.\n250 µl", "Add TRIzol LS to each of homogenized algal material.\n750 µl\n250 µl", "Homogenization is continued until the TR... |
95,837 | General Media Recipes: WA, PDA, LB, CMA, V8 | 4 | null | https://www.protocols.io/view/general-media-recipes-wa-pda-lb-cma-v8-c9t5z6q6 | rebecca.bennett, Nimalka Weerasuriya | TITLE: General Media Recipes: WA, PDA, LB, CMA, V8
AUTHORS: rebecca.bennett, Nimalka Weerasuriya
[DESCRIPTION]
These are current general media recipes for (acidified) water agar, (acidified) potato dextrose agar, LB broth, cornmeal agar, P5ARP/P10ARP, and clarified V8 juice agar.
[BEFORE_START]
Prepare the following... | ["[Making Media] Select media types from below:", "[Preparation] Autoclave liquid setting for 20 minutes to sterilize.", "[Preparation] Add stir bar and stir contents well. \nPlace a loose orange cap. Label cap with autoclave tape (1.5% WA) and date.", "[Preparation] Water Agar preparation:\n \n500 mL ~ 1.5 sleeves of ... |
36,420 | sci-RNA-seq 3 level protocol | 1 | dx.doi.org/10.17504/protocols.io.kqdg35w97v25/v1 | https://www.protocols.io/view/sci-rna-seq-3-level-protocol-bftcjniw | Beth Martin | TITLE: sci-RNA-seq 3 level protocol
AUTHORS: Beth Martin
[DESCRIPTION]
Single-cell combinatorial indexing RNA sequencing (sci-RNA-seq) is a powerful method for recovering gene expression data from an exponentially scalable number of individual cells or nuclei.
[STEPS]
SECTION: Nuclei Isolation ~2hours
1. Remember eve... | ["[Nuclei Isolation ~2hours] Remember everything is cold all the time. Prepare two ice buckets with wet ice, a bucket with crushed dry ice to hold your frozen tissues, and a thick, flat slab of dry ice for smashing tissues. Precool a centrifuge that will hold 50ml tubes, and a microfuge, to 4C.", "[Nuclei Isolation ~2h... |
90,420 | CportucalensisElectrocompetentCells | 4 | dx.doi.org/10.17504/protocols.io.kqdg3x7r7g25/v1 | https://www.protocols.io/view/cportucalensiselectrocompetentcells-c4iuyuew | Lev Tsypin, Dianne K Newman, Allen W Chen, Scott Saunders | TITLE: CportucalensisElectrocompetentCells
AUTHORS: Lev Tsypin, Dianne K Newman, Allen W Chen, Scott Saunders
[DESCRIPTION]
Protocol to prepare electrocompetent Citrobacter portucalensis MBL cells.
[STEPS]
SECTION: Large batch electrocompetent cells
1. Prepare 100 mL sterile LB in a 500 mL Erlenmeyer flask.
SECTION... | ["[Large batch electrocompetent cells] Prepare 100 mL sterile LB in a 500 mL Erlenmeyer flask.", "[Large batch electrocompetent cells] Prepare ice-cold 10 % glycerol and ultrapure water (both sterile).", "[Large batch electrocompetent cells] Two days prior to electroporation, streak out strain on LB agar and grow at 30... |
27,864 | Whole genome sequencing for de novo assembly: best practices | null | dx.doi.org/10.17504/protocols.io.7fyhjpw | null | Pacific Biosciences | TITLE: Whole genome sequencing for de novo assembly: best practices
AUTHORS: Pacific Biosciences
[STEPS]
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.knxcvfn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocol used to extract whole genome DNA from Nephila clavipes (Araneae: Araneidae) specimens.</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
83,185 | PARP inhibitors in colorectal malignancies: A 2023 update | 1 | dx.doi.org/10.17504/protocols.io.dm6gp3ey8vzp/v1 | https://www.protocols.click/view/parp-inhibitors-in-colorectal-malignancies-a-2023-cvgrw3v6 | NIKOLAOS SKOUTERIS, georgeipap | TITLE: PARP inhibitors in colorectal malignancies: A 2023 update
AUTHORS: NIKOLAOS SKOUTERIS, georgeipap
[DESCRIPTION]
Background: Colorectal carcinoma (CRC) is one of the most common malignancies in the Western world, and metastatic disease is associated with a dismal prognosis. Poly-ADp-ribose polymerase (PARP) inhi... | [] |
101,940 | Mitochondrial Antigen Presentation (MitAP) to 2CZ CD8+ T cell hybridoma | 0 | dx.doi.org/10.17504/protocols.io.5qpvok9j7l4o/v1 | https://www.protocols.io/view/mitochondrial-antigen-presentation-mitap-to-2cz-cd-dfsu3new | Alexandra Kazanova | TITLE: Mitochondrial Antigen Presentation (MitAP) to 2CZ CD8+ T cell hybridoma
AUTHORS: Alexandra Kazanova
[DESCRIPTION]
This protocol details the Mitochondrial Antigen Presentation (MitAP) to 2CZ CD8+ T cell hybridoma. Previously, quantification of the number of IL-2 producing 2cz hybridoma cells in an ELISPOT assay ... | ["[9 days prior to experiment] Collect bone marrow from femur of mice and start Bone Marrow Dendritic Cell (BMDC) culture with 20 1585 mrGM-CSF (according to BMDC protocol).", "[Three days prior to experiment (minimum)] Start 2CZ hybridoma from a frozen stock. Maintain the hybridomas in RPMI-1640 medium supplemented wi... |
46,092 | Protocols for "Linking gut microbiome to bone mineral density: a shotgun metagenomic dataset from 361 elderly women" | 2 | dx.doi.org/10.17504/protocols.io.bq9kmz4w | https://www.protocols.io/view/protocols-for-34-linking-gut-microbiome-to-bone-mi-bq9kmz4w | Qi Wang, Qiang Sun, Xiaoping Li, Zhefeng Wang, Haotian Zheng, Yanmei Ju, Ruijin Guo, Songlin Peng, Huijue Jia | TITLE: Protocols for "Linking gut microbiome to bone mineral density: a shotgun metagenomic dataset from 361 elderly women"
AUTHORS: Qi Wang, Qiang Sun, Xiaoping Li, Zhefeng Wang, Haotian Zheng, Yanmei Ju, Ruijin Guo, Songlin Peng, Huijue Jia
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Bone mass... | [] |
21,984 | Detection of bacterial pathogens and drug resistance markers using Rolling circle amplification | null | dx.doi.org/10.17504/protocols.io.zp8f5rw | null | Malte Kühnemund, Ivan Hernandez, Mohd Istiaq Sharif, Matteo Cornaglia, Martin A.M. Gijs, Mats Nilsson | TITLE: Detection of bacterial pathogens and drug resistance markers using Rolling circle amplification
AUTHORS: Malte Kühnemund, Ivan Hernandez, Mohd Istiaq Sharif, Matteo Cornaglia, Martin A.M. Gijs, Mats Nilsson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Here is described the protocol used to... | ["Dilute padlock probes to 10 nM. Is recommended to prepare a fresh dilution for each experiment.", "Denature extracted DNA from culture isolate or clinical sample by heating at.Put immediately on ice", "Prepare ligation mix for the total number of reactions you require ABCD1 Initial conc.Final conc.x1 reaction2Probe... |
73,291 | Electrochemical analysis of laser-inscribed graphene electrodes using cyclic voltammetry (ferri/ferrocyanide redox couple) | 6 | dx.doi.org/10.17504/protocols.io.4r3l27q7jg1y/v1 | https://www.protocols.io/view/electrochemical-analysis-of-laser-inscribed-graphe-cjtjunkn | Yifan Tang, Lisseth Casso Hartmann, David Bahamon Pinzon, Geisianny AM Moreira, Diana Vanegas, Eric S McLamore | TITLE: Electrochemical analysis of laser-inscribed graphene electrodes using cyclic voltammetry (ferri/ferrocyanide redox couple)
AUTHORS: Yifan Tang, Lisseth Casso Hartmann, David Bahamon Pinzon, Geisianny AM Moreira, Diana Vanegas, Eric S McLamore
[DESCRIPTION]
This protocol describes use of the cyclic voltammetry (... | ["[Preparation] Prepare LIG electrodes \nUse protocol for LIG fabrication to prepare a batch of electrodes (link here).\nFor quality control process to prepare large batches of LIG electrodes, contact the corresponding author (emclamo@clemson.edu). \n \n\nExpected results from step 1:\nFig 1 shows photographs of the in... |
33,646 | Repetitive element annotation protocol for the eastern banjo frog | 1 | dx.doi.org/10.17504/protocols.io.bc4niyve | https://www.protocols.io/view/repetitive-element-annotation-protocol-for-the-eas-bc4niyve | Qiye Li, Qunfei Guo, Yang Zhou, Huishuang Tan, Terry Bertozzi, Yuanzhen Zhu, Ji Li, Stephen Donnellan, Guojie Zhang | TITLE: Repetitive element annotation protocol for the eastern banjo frog
AUTHORS: Qiye Li, Qunfei Guo, Yang Zhou, Huishuang Tan, Terry Bertozzi, Yuanzhen Zhu, Ji Li, Stephen Donnellan, Guojie Zhang
[DESCRIPTION]
This pipeline is the repetitive element annotation by using homology-based, de novo predictions and Tandem... | ["The following sub-steps are the process for homology-based predictions to identify repetitive elements in the Limnodynastes dumerilii dumerilii genome assembly.", "Identify known repetitive elements by aligning the Limnodynastes dumerilii dumerilii genome sequences against the Repbase-derived RepeatMasker libraries ... |
75,835 | General subculture protocol for HEK-Blue cells | 4 | null | https://www.protocols.io/view/general-subculture-protocol-for-hek-blue-cells-cna3vagn | Andreas Sagen | TITLE: General subculture protocol for HEK-Blue cells
AUTHORS: Andreas Sagen
[DESCRIPTION]
HEK-Blue is a product from Invivogen, which provide reporter cells for endotoxin-testing among others. Here is a generalized protocol for culturing cells with reporter characteristics.
[BEFORE_START]
Prepare complete growth med... | ["[Complete growth medium (CCM)] For the HEK-Blue cells to work correctly, it has to contain a selective agent.", "[Complete growth medium (CCM)] In 450 mL DMEM, add 50 mL FBS, and selective antibiotics (cell line dependent; Remove equal volume DMEM/FBS):\n\nZeocin: 0.5 mL\nHEK-Blue selection: 2.0 mL\nBlasticidin: 1.5 ... |
38,789 | SOP for populating EBI submission templates (ENA) | 1 | dx.doi.org/10.17504/protocols.io.bh5dj826 | https://www.protocols.io/view/sop-for-populating-ebi-submission-templates-ena-bh5dj826 | Nabil-Fareed Alikhan, Emma Griffiths, Ruth Timme, Duncan MacCannell | TITLE: SOP for populating EBI submission templates (ENA)
AUTHORS: Nabil-Fareed Alikhan, Emma Griffiths, Ruth Timme, Duncan MacCannell
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Guidance on how to populate the extended PHA4GE metadata package for SARS-CoV-2 submissions, maximizing interoperabil... | ["[Three templates needed for NCBI SARS-CoV-2 submission]\nGuidance for populating the three templates for SARS-CoV-2 submission to EBI. This protocol helps to describe the fields needed to populate the ENA virus pathogen checklist, however, the primary PHA4GE guidance should be followed to ensure the controlled vocab... |
null | null | null | dx.doi.org/10.17504/protocols.io.u2ieyce | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Next Generation Sequencing technologies have enabled many advances across biology with microbial ecology benefiting primarily through expanded sample sizes. Although the cost of running sequencing instruments has decreased substantially over time, the price of library preparatio... | ["[Make primer working plates.] {\"blocks\":[{\"key\":\"8nngn\",\"text\":\"Resuspend lyophilized primers from 96-Well plates shipped from Integrated DNA Technologies (IDT) at 3nmol per well using the following protocol\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[]},{\"key\... |
63,296 | Rapid extraction of total lipids from microalgae | 1 | dx.doi.org/10.17504/protocols.io.dm6gpr9jdvzp/v4 | https://www.protocols.io/view/rapid-extraction-of-total-lipids-from-microalgae-b928r8hw | Yingyu Hu, Zoe V Finkel | TITLE: Rapid extraction of total lipids from microalgae
AUTHORS: Yingyu Hu, Zoe V Finkel
[DESCRIPTION]
In this protocol, total lipids from miroalgae is extracted with Folch solvent (2:1 chloroform-methanol v/v) and the addition of 5% water. Filter and cell debris is commonly removed by filtration, which is laborious... | ["[Collect microalgae samples] Precombust GFF filter at 450 °C for 240 min", "[Collect microalgae samples] Rinse forceps with 95% ethanol, air-dry.", "[Collect microalgae samples] Filter microalgae in liquid media onto precombusted GFF filters, using gentle vacuum pressure (5 inches Hg).", "[Collect microalgae samples... |
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