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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88,418 | Sea Water - Blue Treasure | 4 | dx.doi.org/10.17504/protocols.io.36wgq36b5lk5/v1 | https://www.protocols.io/view/sea-water-blue-treasure-c2kaycse | Willian Barela Costa | TITLE: Sea Water - Blue Treasure
AUTHORS: Willian Barela Costa
[DESCRIPTION]
Sea water production for microalgae cultivation using the Blue Treasure supplier.
25 - 35 Salinity
27 mg/mL
[STEPS]
SECTION: Salting process - 1 liter
1. 0.027 g/mL -> 27 g Sea Sal to 1 L
SECTION: Salting process - 1 liter
2. S... | ["[Salting process - 1 liter] 0.027 g/mL -> 27 g Sea Sal to 1 L", "[Salting process - 1 liter] Shake until diluted", "[Salting process - 1 liter] Make sure the salinity is within the desired range using the salinity refractometer. In this protocol, the focus is 27 salinity."] |
24,213 | Plague in Zimbabwe from 1974-2018 A Review Article | null | dx.doi.org/10.17504/protocols.io.3vvgn66 | null | AMON MUNYENYIWA, Moses Zimba, Tamuka Nhiwatiwa, Maxwell Barson | TITLE: Plague in Zimbabwe from 1974-2018 A Review Article
AUTHORS: AMON MUNYENYIWA, Moses Zimba, Tamuka Nhiwatiwa, Maxwell Barson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The protocol describes how literature was searched to write a review Article titled :Plague in Zimbabwe from 1974-2018.Lit... | ["Materials and Methods", "The literature review was conducted using the online databases PubMed, and HINARI; Hard copy textbooks with information relevant to plague were obtained from the University of Zimbabwe library.", "A thorough search of work was then undertaken in Zimbabwe from the first case of plague in 1974 ... |
91,536 | Isotopically labelled inorganic carbon delivered to algal cultures via bubbler bottle | 1 | dx.doi.org/10.17504/protocols.io.yxmvm3q8ol3p/v1 | https://www.protocols.io/view/isotopically-labelled-inorganic-carbon-delivered-t-c5mqy45w | Usha F Lingappa, Sunnyjoy Dupuis, Xavier Mayali, Sabeeha S. Merchant | TITLE: Isotopically labelled inorganic carbon delivered to algal cultures via bubbler bottle
AUTHORS: Usha F Lingappa, Sunnyjoy Dupuis, Xavier Mayali, Sabeeha S. Merchant
[DESCRIPTION]
This protocol describes a method for delivering labelled inorganic carbon as 13CO2 to algal cultures by bubbling air through a solutio... | ["[The purpose and problem of bubbling cultures] Bubbling air into algal cultures stimulates photosynthetic growth by ameliorating diffusion limitation for CO2 (fig. 1A-B). Stable isotope probing (SIP) experiments examining carbon fixation often involve 13C label introduced directly into the culture medium as a H13CO3-... |
45,825 | Standard Operating Procedure for Real-time PCR Detection and Identification of Bordetella pertussis, B. parapertussis, and B. holmesii using AB7500 | 1 | null | https://www.protocols.io/view/standard-operating-procedure-for-real-time-pcr-det-bqy9mxz6 | Adria D. Lee, Pamela K. Cassiday, Lucia C. Pawloski, Kathleen M. Tatti, Monte D. Martin, Elizabeth C. Briere, M. Lucia Tondella, Stacey W. Martin | TITLE: Standard Operating Procedure for Real-time PCR Detection and Identification of Bordetella pertussis, B. parapertussis, and B. holmesii using AB7500
AUTHORS: Adria D. Lee, Pamela K. Cassiday, Lucia C. Pawloski, Kathleen M. Tatti, Monte D. Martin, Elizabeth C. Briere, M. Lucia Tondella, Stacey W. Martin
[DESCRIPT... | ["Aliquot undiluted primers and probe and store for up to 6 months at -20ºC. Cover probe aliquot tubes with foil or use dark colored tubes.", "Prepare IS481 primers and probe: Prepare 30 μM (10X solution) concentrations of primers and 90 μM (10X solution) probe using sterile PCR grade water. Dispense 10X working concen... |
null | null | null | dx.doi.org/10.17504/protocols.io.e38bgrw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>High Quality Genomic DNA Extraction from Fungal Samples </p>
[GUIDELINES]
<p><strong>INTRODUCTION</strong></p>
<p>The OmniPrep™ for Fungus kit isolates high quality genomic DNA from fungal samples. The kit isolates high purity (A260/A280 ratios of 1.7 to 2) DNA between 100‐2... | [] |
52,178 | Genomic Signature Pattern Analysis of the HIV-1 Through Computational Approach | 4 | dx.doi.org/10.17504/protocols.io.bw7sphne | https://www.protocols.io/view/genomic-signature-pattern-analysis-of-the-hiv-1-th-bw7sphne | Sushanta Kumar Barik | TITLE: Genomic Signature Pattern Analysis of the HIV-1 Through Computational Approach
AUTHORS: Sushanta Kumar Barik
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify">).</div><style>
.justify:after {
content: "";
displ... | ["5", "6", "7"] |
71,185 | Microscopy-based evaluation of Parkin translocation and mitophagy in FBXO7-/- cell lines | 4 | dx.doi.org/10.17504/protocols.io.dm6gpjw28gzp/v1 | https://www.protocols.io/view/microscopy-based-evaluation-of-parkin-translocatio-chrrt556 | Felix Kraus | TITLE: Microscopy-based evaluation of Parkin translocation and mitophagy in FBXO7-/- cell lines
AUTHORS: Felix Kraus
[DESCRIPTION]
Microscopy-based evaluation of Parkin translocation and mitophagy in FBXO7-/- cell lines
[STEPS]
SECTION: Seeding of HeLa
1. Wash HeLa cells expressing GFP-Parkin with 1x PBS
SECTION: See... | ["[Seeding of HeLa] Wash HeLa cells expressing GFP-Parkin with 1x PBS", "[Seeding of HeLa] Add Trypsin to cells for 5 min and incubate at 37°C to dissociate cells from plastic well", "[Seeding of HeLa] Resuspend cells in 1 mL DMEM media", "[Seeding of HeLa] Count cells", "[Seeding of HeLa] Seed appropriate number of ce... |
null | null | null | dx.doi.org/10.17504/protocols.io.jsfcnbn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><span style="font-weight: 400;">Here we describe a procedure to make bacterial communication assays based on</span> 3OC6HSL and 3OC12HSL quorum sensing signaling. Strains that sense and response to these signals are plated on a permeable membrane printed with a hydrophobic gr... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.exmbfk6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Modified from Benjamin Schwessinger: High quality DNA from Fungi for long read sequencing e.g. PacBio. protocols.io</p>
<p>Optimized for DNA extraction from wheat stripe rust spores.</p>
<p>Buffers are best when fresh and not older than 3-6 months. <br />Buffered Phenol:Chlor... | [] |
107,212 | Brain Data Alchemy Project: Meta-Analysis of Re-Analyzed Public Transcriptional Profiling Data in the Gemma Database (v.2024) | 0 | dx.doi.org/10.17504/protocols.io.yxmvmejkng3p/v1 | https://www.protocols.io/view/brain-data-alchemy-project-meta-analysis-of-re-ana-dkxk4xkw | Megan Hagenauer, Duy Manh Nguyen, Elizabeth Flandreau, Eva Geoghegan, Sophie Mensch, Mubashshir Ra'eed Bhuiyan, Lakshmi Thirupatamma Chennupati, Sophia Espinoza, Ashlee Lewis, Anna Drozman, Brandon W. Hughes, M.S., Ph.D. | TITLE: Brain Data Alchemy Project: Meta-Analysis of Re-Analyzed Public Transcriptional Profiling Data in the Gemma Database (v.2024)
AUTHORS: Megan Hagenauer, Duy Manh Nguyen, Elizabeth Flandreau, Eva Geoghegan, Sophie Mensch, Mubashshir Ra'eed Bhuiyan, Lakshmi Thirupatamma Chennupati, Sophia Espinoza, Ashlee Lewis, An... | ["[Project Preparation: Environment Set-Up] Install R and RStudio", "[Project Preparation: Environment Set-Up] Install R", "[Project Preparation: Environment Set-Up] Install R Studio", "[Project Preparation: Environment Set-Up] Follow the Brain Data Alchemy code repository on Github", "[Project Preparation: Environment... |
92,331 | pH-Rodo pathogens to monitor phagocytosis in pMacs | 4 | dx.doi.org/10.17504/protocols.io.q26g7pn18gwz/v1 | https://www.protocols.io/view/ph-rodo-pathogens-to-monitor-phagocytosis-in-pmacs-c6ejzbcn | Rebecca Wallings | TITLE: pH-Rodo pathogens to monitor phagocytosis in pMacs
AUTHORS: Rebecca Wallings
[DESCRIPTION]
pH-Rodo pathogens to monitor phagocytosis in pMacs
[STEPS]
1. Once pMacs have adhered to plate, resuspend pHrodo‱ Green E. coli BioParticles‱ in Invitrogen‱ Live Cell Imaging Solution to a final concentration of 1mg/mL a... | ["Once pMacs have adhered to plate, resuspend pHrodo‱ Green E. coli BioParticles‱ in Invitrogen‱ Live Cell Imaging Solution to a final concentration of 1mg/mL and sonicate in bath sonicator for 10 minutes. \n\nAdd 100 μL of E. coli BioParticles solution to each well (96-well plate). \n\nPlace cells in a live imaging ch... |
39,699 | Antibody neutralization assay with SARS-CoV-2 and SARS-CoV pseudovirus | 4 | dx.doi.org/10.17504/protocols.io.biztkf6n | https://www.protocols.io/view/antibody-neutralization-assay-with-sars-cov-2-and-biztkf6n | Bei Wang, Wen-Hsin Sandy Lee, Cheng-I Wang | TITLE: Antibody neutralization assay with SARS-CoV-2 and SARS-CoV pseudovirus
AUTHORS: Bei Wang, Wen-Hsin Sandy Lee, Cheng-I Wang
[STEPS]
?. [Generation of pseudovirus particles]
Day 1: Transfection of HEK293T cells to generate pseudovirus.
?. [Generation of pseudovirus particles]
Dissociate the HEK293T cells with St... | ["[Generation of pseudovirus particles]\nDay 1: Transfection of HEK293T cells to generate pseudovirus.", "[Generation of pseudovirus particles]\nDissociate the HEK293T cells with StemPro Accutase Cell Dissociation Reagent and resuspend 5 x 106 cells in 9ml DMEM cell transfection medium.", "[Generation of pseudovirus pa... |
32,706 | Dirofilaria immitis and Brugia malayi emergence assay for individual or pools of mosquitoes | null | dx.doi.org/10.17504/protocols.io.bb7airie | null | Michael Povelones, Abigail McCrea | TITLE: Dirofilaria immitis and Brugia malayi emergence assay for individual or pools of mosquitoes
AUTHORS: Michael Povelones, Abigail McCrea
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This assay is for determining the number of infective third-stage (L3) larvae capable of emerging from individ... | ["As stated in the Abstract for this protocol, it is assumed that you already have groups of infected mosquitoes to examine. First, count and record the number of live and dead mosquitoes in each group and remove the dead ones. Count the total number of mosquitoes that will be assayed.\nIdeal group sizes will depend on... |
80,358 | Blacktip Reef Shark Aggression in Moorea | 1 | dx.doi.org/10.17504/protocols.io.6qpvr4nr3gmk/v1 | https://www.protocols.io/view/blacktip-reef-shark-aggression-in-moorea-csqewdte | jparadise | TITLE: Blacktip Reef Shark Aggression in Moorea
AUTHORS: jparadise
[DESCRIPTION]
On the island of Moorea, French Polynesia, tourism operators have engaged in consistent elasmobranch provisioning at specific sites since the 1990s, conditioning the area’s shark and ray populations to human feeding and developing profita... | ["[Observations] Preparation", "[Observations] Gather necessary materials: \nSnorkeling/diving gear (Mask, snorkel, fins, dive equipment, weight belt)\nUnderwater camera \nUnderwater notepad\nShark tagging equipment \nUnderwater watch or timekeeping equipment \nBag that attaches to weight-belt (optional, for storing it... |
20,715 | UC Davis - Creatinine Protocol | null | dx.doi.org/10.17504/protocols.io.ygjftun | null | Peter Havel | TITLE: UC Davis - Creatinine Protocol
AUTHORS: Peter Havel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">The method employed here is based on an enzymatic colorimetric determination of creatinine which largely elimi... | ["Add 3 µl of calibrator and sample to each well.", "Add 135 µl of R1 to each well. Incubate at 37°C for 5 minutes. Read at 550 nm.", "Add 45 µl of R2 to each well. Incubate at 37°C for 5 minutes. Read at 550 nm.", "Subtract blank readings from final readings. The assay will be linear so the unknown samples can be calc... |
72,873 | High-throughput 96-well assay to measure impact of polyphenolic compounds on fungal growth | 4 | dx.doi.org/10.17504/protocols.io.j8nlkwondl5r/v1 | https://www.protocols.io/view/high-throughput-96-well-assay-to-measure-impact-of-cjehujb6 | Megan Nickerson, Jana M U'Ren | TITLE: High-throughput 96-well assay to measure impact of polyphenolic compounds on fungal growth
AUTHORS: Megan Nickerson, Jana M U'Ren
[DESCRIPTION]
This protocol was developed to assess the growth of filamentous fungi in the presence of polyphenolic compounds--a class of secondary metabolites produced by plants wit... | ["[Media and Solution Preparation- Aspergillus nidulans Defined Media plus Carrageenan] Combine:\n- 900mL nanopure water\n-50mL 20X Sodium nitrate salts\n-1mL Trace elements", "[Media and Solution Preparation- Aspergillus nidulans Defined Media plus Carrageenan] Bring the pH to 6.5.", "[Media and Solution Preparation- ... |
null | null | null | dx.doi.org/10.17504/protocols.io.n6pdhdn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol details the methodology for processing environmental samples for Salmonella spp. detection.</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?. | [] |
25,391 | Predation assessment on fake caterpillars and leaf sampling: Protocol for partner schools | null | dx.doi.org/10.17504/protocols.io.42pgydn | null | Bastien Castagneyrol, Elena Valdés-Correcher, Michèle Kaennel Dobbertin, Martin Gossner | TITLE: Predation assessment on fake caterpillars and leaf sampling: Protocol for partner schools
AUTHORS: Bastien Castagneyrol, Elena Valdés-Correcher, Michèle Kaennel Dobbertin, Martin Gossner
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The '</span><span style = "font-style:italic;">Oak b... | [] |
66,220 | GST Bead pulldown Assay | 4 | null | https://www.protocols.io/view/gst-bead-pulldown-assay-ccwksxcw | Adam Yokom | TITLE: GST Bead pulldown Assay
AUTHORS: Adam Yokom
[DESCRIPTION]
GST Pulldown Assay for recruitment of bait proteins to GST labeled prey proteins. Prey proteins can be purified or from lysate.
[STEPS]
2. Equilibrate 30uL of Glutathione Sepharose beads (GE Healthcare) into pulldown buffer. To do this, pipette 60uL of... | ["Equilibrate 30uL of Glutathione Sepharose beads (GE Healthcare) into pulldown buffer. To do this, pipette 60uL of 50% slurry into a 1.7uL eppy. Add >500mL of wash buffer. Slow spin to pellet resin. ~1000rpm for 1 minute should be good. Repeat X3", "Add 1-10 μM purified protein (add buffer of 25 mM HEPES pH 7.5, 150mM... |
85,985 | Neural differentiation on EM grids - iNeurons sample preparation for cryo-ET and CLEM V2 | 4 | dx.doi.org/10.17504/protocols.io.dm6gp3j31vzp/v1 | https://www.protocols.io/view/neural-differentiation-on-em-grids-ineurons-sample-cx79xrr6 | Cristina Capitanio, Victoria Trinkaus, Melissa Hoyer | TITLE: Neural differentiation on EM grids - iNeurons sample preparation for cryo-ET and CLEM V2
AUTHORS: Cristina Capitanio, Victoria Trinkaus, Melissa Hoyer
[DESCRIPTION]
This is a protocol for differentiating AAVS1-TRE3G-NGN2 iPSCs and hESCs to iNeurons directly on EM grids for cryo-ET and cryo-CLEM. The protocol co... | ["[Starting the neural differentiation (Day 0-Day6)] We based our neural differentiation protocol, for both iPSCs and hESCs AAVS1-TRE3G-NGN2 cells, on: \n \nWe also refer to that protocol for a complete list of media and reagents. \n\nFollow the neural differentiation protocol until cell splitting on Day 6;\nOne well o... |
85,311 | Barcoding protocol for microalgae | 4 | dx.doi.org/10.17504/protocols.io.n92ldmzynl5b/v1 | https://www.protocols.click/view/barcoding-protocol-for-microalgae-cxi7xkhn | Elena L. Peredo | TITLE: Barcoding protocol for microalgae
AUTHORS: Elena L. Peredo
[DESCRIPTION]
Here I describe two methods for barcoding microalgae.
One starts with extracted DNA. In that case, I use Promega GoTaq, and so far, it has performed well. If I am only barcoding, I prefer using Phire Direct PCR. as it doesn't require DNA ... | ["[Regular PCR] PCR 18S/ITS\n\nUse 1 ul of the extracted DNA. \n\n PCR1XGoTaq® Green Master Mix (M712)10 ulPrimer F 10 uM0.4 ulPrimer R 10 uM0.4 ulDMSO1 ulWater 7.2 ulDNA1 ulTotal 20 ul\nRun the PCR program (I use a touchdown PCR, starting at 63 C as annelaing temperature and reducing 0.5 C each cycle for 12 cycles. T... |
56,057 | Modified Illumina DNA Prep (M) Tagmentation Library Preparation for cDNA amplicons from wastewater | 1 | dx.doi.org/10.17504/protocols.io.b2yzqfx6 | https://www.protocols.io/view/modified-illumina-dna-prep-m-tagmentation-library-b2yzqfx6 | Padmini Ramachandran, Tamara Walsky, Amanda Windsor, Maria Hoffmann, Chris Grim | TITLE: Modified Illumina DNA Prep (M) Tagmentation Library Preparation for cDNA amplicons from wastewater
AUTHORS: Padmini Ramachandran, Tamara Walsky, Amanda Windsor, Maria Hoffmann, Chris Grim
[DESCRIPTION]
This procedure outlines the protocol for sequencing of VarSkip Short SARS-CoV-2 cDNA amplicons using th... | ["[Dilute and Tagment Input DNA] Bring BLT (stored in refrigerator) and TB1 (stored in freezer) to room temperature. \n\nEnsure that BLT is stored upright at all times, so that the beads remain submerged in the\nbuffer", "[Dilute and Tagment Input DNA] Label a 96-well PCR plate with the Run ID.", "[Dilute and Tagment ... |
50,529 | The Innovation behind Customized Packaging with Logo | 1 | dx.doi.org/10.17504/protocols.io.bvj9n4r6 | https://www.protocols.io/view/the-innovation-behind-customized-packaging-with-lo-bvj9n4r6 | Customized Packaging | TITLE: The Innovation behind Customized Packaging with Logo
AUTHORS: Customized Packaging
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Customized Packaging, Printed Candle Packaging, Custom Cardboard Packaging, customized packaging, candle packaging, cardboard packaging, customized boxes, custom ... | ["The Innovation behind Customized Packaging with Logo", "For the most part, when a manufacturing business is getting started it needs many resources to keep on making it to the breakeven mark. The best way to deal with the customer queries is to understand the needs and requirements of the customers. It would not be p... |
34,696 | RNA Library Prep | 1 | dx.doi.org/10.17504/protocols.io.bp2l6nr9zgqe/v1 | https://www.protocols.io/view/rna-library-prep-bd5gi83w | Dakota Betz | TITLE: RNA Library Prep
AUTHORS: Dakota Betz
[DESCRIPTION]
This protocol is for RNA library prep with the KAPA mRNA HyperPrep Kit.
The kit contains all of the buffers and enzymes required for poly(A) mRNA capture and the rapid construction of stranded mrNA-Seq libraries from 50ng - 1ug of intact total RNA via the fol... | ["[Bead Washing] Before starting, equilibrate mRNA Capture Beads, mRNA Bead Binding Buffer, mRNA Bead Wash Buffer and Fragment, Prime and Elute Buffer (2X) to room temperature. Before use, beads must be washed with mRNA Bead Binding Buffer (purpose of this section).", "[Bead Washing] Resuspend the mRNA Capture Beads th... |
48,738 | Fixation/Dehydration Protocol for Organoids | 4 | null | https://www.protocols.io/view/fixation-dehydration-protocol-for-organoids-btuannse | Morrisey Lab | TITLE: Fixation/Dehydration Protocol for Organoids
AUTHORS: Morrisey Lab
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Fixation/Dehydration Protocol for Organoids</span></div></div>
[STEPS] | [] |
28,873 | E. coli and B. subtilis Colony PCR | null | dx.doi.org/10.17504/protocols.io.8fhhtj6 | null | iGEM Dusseldorf | TITLE: E. coli and B. subtilis Colony PCR
AUTHORS: iGEM Dusseldorf
[STEPS]
?. Prepare a PCR master mix for 9 reactions, as follows: ABC11x Reaction (Volume; µL)9x Reactions (Volume; µL)2Sterile MilliQ Water8723Red Taq 2x Master Mix(1.5 mM MgCl2)10904F Primer (10 µM)195R Primer (10 µM)196Total Volume20180
ABC11x... | ["Prepare a PCR master mix for 9 reactions, as follows: ABC11x Reaction (Volume; µL)9x Reactions (Volume; µL)2Sterile MilliQ Water8723Red Taq 2x Master Mix(1.5 mM MgCl2)10904F Primer (10 µM)195R Primer (10 µM)196Total Volume20180\nABC11x Reaction (Volume; µL)9x Reactions (Volume; µL)2Sterile MilliQ Water8723... |
18,380 | ATP assay | null | dx.doi.org/10.17504/protocols.io.v7ke9kw | null | Kiichi Hirota, Yoshiyuki Matsuo | TITLE: ATP assay
AUTHORS: Kiichi Hirota, Yoshiyuki Matsuo
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. Cells were seeded in 96-well plates and allowed to grow for indicated time periods.
?. CellTiter-Glo reagent (50 μl) was then added directly into each well and incubated for 10 min prior to reading the... | ["Cells were seeded in 96-well plates and allowed to grow for indicated time periods.", "CellTiter-Glo reagent (50 μl) was then added directly into each well and incubated for 10 min prior to reading the plate using an EnSpire® Multimode Plate Reader (PerkinElmer, Waltham, MA, USA).This detected the luminescence genera... |
54,560 | Zebrafish larvae dissociation for FACs sorting cells expressing fluorescent proteins | 4 | dx.doi.org/10.17504/protocols.io.yxmvmk819g3p/v1 | https://www.protocols.io/view/zebrafish-larvae-dissociation-for-facs-sorting-cel-bzh8p39w | Abigail Elliot, Yi Feng | TITLE: Zebrafish larvae dissociation for FACs sorting cells expressing fluorescent proteins
AUTHORS: Abigail Elliot, Yi Feng
[DESCRIPTION]
Large number of transgenic lines with cell/tissue specific expressing of fluorescent proteins are available in the zebrafish field. These tools provide an opportunity for isolating... | ["[Embryo Dissociation] Collect anaesthetised larvae in 2ml Eppendorf 5 min", "[Embryo Dissociation] Remove water and replace with 2ml Dissociation Solution with plastic pipette 5 min", "[Embryo Dissociation] Transfer larvae and solution to well of 12-well plate with plastic pipette. 2 min", "[Embryo Dissociation] Incu... |
109,398 | Sinai SCENT TMC - Human Colonoscopy Tissue Collection | 0 | dx.doi.org/10.17504/protocols.io.rm7vzjz4xlx1/v1 | https://www.protocols.io/view/sinai-scent-tmc-human-colonoscopy-tissue-collectio-dn3w5gpe | Ksenija Sabic, Colleen Chasteau, Judy Cho | TITLE: Sinai SCENT TMC - Human Colonoscopy Tissue Collection
AUTHORS: Ksenija Sabic, Colleen Chasteau, Judy Cho
[DESCRIPTION]
For this study we will utilize the world-renowned Inflammatory Bowel Disease program at MSSM, started by Dr. Burrill B. Crohn in the Division of Gastroenterology. Eminent physicians, surgeons, ... | ["[RECRUITMENT LOCATIONS] Mount Sinai School of Medicine and Medical Centers including affiliated sites within the Mount Sinai Health System such as Mount Sinai Queens, Mount Sinai Brooklyn, Beth Israel, Mount Sinai West, and Mount Sinai St. Luke’s. Endoscopy Center of New York, 201 East 93rd Street \nGastroenterolog... |
43,655 | General Assembly and Alignment in Geneious | 3 | dx.doi.org/10.17504/protocols.io.bnvfme3n | https://www.protocols.io/view/general-assembly-and-alignment-in-geneious-bnvfme3n | Andrew J. Johnson, Demian F Gomez | TITLE: General Assembly and Alignment in Geneious
AUTHORS: Andrew J. Johnson, Demian F Gomez
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The purpose of this protocol is to conduct general assembly and alignment of sequences in Geneious.</div><div class = "text-block"><span>This protocol is part ... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ingcdbw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Library building protocol for archival samples with single 8-nt adapters for Illumina platforms.</p>
[BEFORE_START]
<p>Calculate the DNA input and prepare the library adapters.</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.d7e9jd | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is a protocol for plasmid minipreps that does not involve any columns and uses commonly accessible reagents. <br />While it doesn't result in highly pure DNA, it can provide a sufficient quantity of plasmid for sequencing, restriction analysis, preparative digests.</p>
<... | [] |
83,875 | FixNCut v1.0 | 4 | dx.doi.org/10.17504/protocols.io.14egn3xjql5d/v1 | https://www.protocols.click/view/fixncut-v1-0-cv6bw9an | Laura Jiménez-Gracia, Domenica Marchese, Holger Heyn, Luciano G Martelotto | TITLE: FixNCut v1.0
AUTHORS: Laura Jiménez-Gracia, Domenica Marchese, Holger Heyn, Luciano G Martelotto
[DESCRIPTION]
This protocol details reversible fixation for cells and tissues for subsequent use in sc/snRNA, sc/snATAC or Multiome. Spatial-Omics compatibility is being validated. For more information check this pr... | ["[Preparation of DSP (Oz Soup) stock and working solutions] Equilibrate DSP vial at Room temperature for 30 min and then prepare 50x stock solution of DSP (50 mg/mL) in molecular biology grade dimethyl sulfoxide (Sigma, cat. no. D8418-50ML).", "[Preparation of DSP (Oz Soup) stock and working solutions] Dispense the st... |
null | null | null | dx.doi.org/10.17504/protocols.io.fhdbj26 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Purpose</strong>: To concentrate harvested phage lysate up to 20X - 40X. The Vivaflow device uses a peristaltic pump setup to recirculate the input sample over a 100,000 MWCO PES membrane, which allows the media filtrate to be diverted and the phage to remain in the s... | [] |
78,717 | ONT Sequencing IT/Compute Pop!_OS 22.04 Setup | 5 | dx.doi.org/10.17504/protocols.io.14egn7kzmv5d/v2 | https://www.protocols.io/view/ont-sequencing-it-compute-pop-os-22-04-setup-cq45vyy6 | Stephen Douglas Russell | TITLE: ONT Sequencing IT/Compute Pop!_OS 22.04 Setup
AUTHORS: Stephen Douglas Russell
[DESCRIPTION]
The IT requirements for processing MinION data should be carefully reviewed before purchasing a MinION device. You will want to go with a Linux system. System76 is really the primary/best vendor for laptops. Pay ... | ["[Preparing a new CPU for MinION Sequencing] The final setup I went with can be found below. It was expensive (around for the laptop in early 2022), but should be able to achieve live basecalling for two MinION devices at the same time. Overall specs of my laptop: \n\n \n\nMinimum IT requirements for MinION from O... |
82,369 | Nuclear cytoplasmic fractionation | 4 | dx.doi.org/10.17504/protocols.io.ewov1oejylr2/v1 | https://www.protocols.click/view/nuclear-cytoplasmic-fractionation-cun9wvh6 | Narayana Yadavalli, Shawn M. Ferguson | TITLE: Nuclear cytoplasmic fractionation
AUTHORS: Narayana Yadavalli, Shawn M. Ferguson
[DESCRIPTION]
This protocol describes nuclear cytoplasmic fractionation.
[STEPS]
SECTION: Nuclear cytoplasmic fractionation
1. Treat 500,000 BMDM’s with DMSO or 50 nanomolar (nM) MLi-2 for 360 min.
SECTION: Nuclear cytoplasmic fra... | ["[Nuclear cytoplasmic fractionation] Treat 500,000 BMDM’s with DMSO or 50 nanomolar (nM) MLi-2 for 360 min.", "[Nuclear cytoplasmic fractionation] After the treatment, wash the cells 3X in PBS.", "[Nuclear cytoplasmic fractionation] Harvest the cells in 500 µL of ice-cold hypotonic buffer.", "[Nuclear cytoplasmic frac... |
40,210 | Avast antivirus | 1 | null | https://www.protocols.io/view/avast-antivirus-bjhskj6e | George more | TITLE: Avast antivirus
AUTHORS: George more
[STEPS] | [] |
62,238 | Xp Keto Gummies | 1 | dx.doi.org/10.17504/protocols.io.e6nvwko6dvmk/v1 | https://www.protocols.io/view/xp-keto-gummies-b8z6rx9e | Pure Keto | TITLE: Xp Keto Gummies
AUTHORS: Pure Keto
[DESCRIPTION]
Xp Keto GummiesReview
Xp Keto Gummies Get Double The Fat Burn With This Formula!
XP Nutrition Keto Gummies are here to give both of you times the fat consume power from one item! Assuming you're tired of hauling around additional fat and you need to dispose of... | [] |
91,616 | Principles, Techniques, and Precautions in Transwell Migration and Invasion Assays for Cancer Cell Metastasis Research | 4 | dx.doi.org/10.17504/protocols.io.5qpvo3wn9v4o/v1 | https://www.protocols.io/view/principles-techniques-and-precautions-in-transwell-c5p8y5rw | Hussain Zubair | TITLE: Principles, Techniques, and Precautions in Transwell Migration and Invasion Assays for Cancer Cell Metastasis Research
AUTHORS: Hussain Zubair
[DESCRIPTION]
This article outlines a comprehensive procedure for conducting Transwell assays, a critical technique in cancer biology for assessing cell migration and in... | ["[I. Experimental Objective] To determine the migratory ability of cells.\nTo determine the invasive ability of cells.\nTo evaluate the efficacy of drugs that affect cell migration and invasion.", "[III. Introduction to the Principle of Transwell Assay] The Transwell experiment, also known as Transwell migration or in... |
91,133 | circRNA-producing gene function enrichment analysis | 5 | dx.doi.org/10.17504/protocols.io.81wgbx9yylpk/v1 | https://www.protocols.io/view/circrna-producing-gene-function-enrichment-analysi-c485yzy6 | Xianjun Dong | TITLE: circRNA-producing gene function enrichment analysis
AUTHORS: Xianjun Dong
[DESCRIPTION]
This protocol describes the method to perform function enrichment analysis for the circRNA-producing genes.
[STEPS] | [] |
92,904 | A standard pipeline for processing short-read sequencing data from Littorina snails | 1 | dx.doi.org/10.17504/protocols.io.dm6gp3m21vzp/v2 | https://www.protocols.io/view/a-standard-pipeline-for-processing-short-read-sequ-c6ygzftw | James Reeve, Amin Ghane, Pierre Barry, Alfonso Balmori-de la Puente, Roger K. Butlin, Le Qin Choo, Alan Le Moan, Diego Garica Castillo, Ana-Maria Peris Tamayo, Sarah Kingston, Erica Leder, Sean Stankowski | TITLE: A standard pipeline for processing short-read sequencing data from Littorina snails
AUTHORS: James Reeve, Amin Ghane, Pierre Barry, Alfonso Balmori-de la Puente, Roger K. Butlin, Le Qin Choo, Alan Le Moan, Diego Garica Castillo, Ana-Maria Peris Tamayo, Sarah Kingston, Erica Leder, Sean Stankowski
[DESCRIPTION]
... | ["[Overview] Processing of short read sequencing data can be broken down into four major steps (Fig. 1): \n 1) read quality inspection and trimming\n 2) read mapping\n 3) variant calling \n 4) variant filtering\nThere are numerous sub-steps in between, which together have a plethora of different adj... |
82,367 | Brimblecombe, K.R. et al. (2023) Inhibition of striatal dopamine release by the L-type calcium channel inhibitor isradipine, co-varies with risk factors for Parkinson’s. | 2 | dx.doi.org/10.17504/protocols.io.4r3l27dxxg1y/v1 | https://www.protocols.click/view/brimblecombe-k-r-et-al-2023-inhibition-of-striatal-cun7wvhn | Katherine Brimblecombe, Stephanie J Cragg | TITLE: Brimblecombe, K.R. et al. (2023) Inhibition of striatal dopamine release by the L-type calcium channel inhibitor isradipine, co-varies with risk factors for Parkinson’s.
AUTHORS: Katherine Brimblecombe, Stephanie J Cragg
[DESCRIPTION]
This collection contains three protocols detailing methods used in Brimbleco... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.cccssv | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol corrects small RNAs deep sequencing biases caused by RNA ligases. The key modification is the use of pooled adapters with the sequences below. See the cited publication for further details.
[BEFORE_START]
5' adapter-4N: 5’GUUCAGAGUUCUACAGUCCGACGAUCNNNN
<br>3' adap... | [] |
38,180 | One enzyme reverse transcription qPCR using Taq DNA polymerase | 1 | null | https://www.protocols.io/view/one-enzyme-reverse-transcription-qpcr-using-taq-dn-bhicj4aw | Sanchita Bhadra, Andre Maranhao, Andrew Ellington | TITLE: One enzyme reverse transcription qPCR using Taq DNA polymerase
AUTHORS: Sanchita Bhadra, Andre Maranhao, Andrew Ellington
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Taq DNA polymerase, one of the first thermostable DNA polymerases to be discovered, has been typecast as a DNA-dependent DN... | ["[Preparing RT-qPCR reaction]\nRT-qPCR assays were assembled in a total volume of containing the indicated buffer at 1X strength (see Generation 6A buffer recipe in step 2)\n25 µl", "[Preparing RT-qPCR reaction]\nThe buffer was supplemented with , , , and 2.5 units of Taq DNA polymerase from indicated commercial v... |
62,615 | What the Oxford English Dictionary Doesn't Tell You About Via Keto Apple Gummies? | 1 | dx.doi.org/10.17504/protocols.io.n2bvj6ze5lk5/v1 | https://www.protocols.io/view/what-the-oxford-english-dictionary-doesn-39-t-tell-b9dxr27n | noxcav | TITLE: What the Oxford English Dictionary Doesn't Tell You About Via Keto Apple Gummies?
AUTHORS: noxcav
[DESCRIPTION]
Dragons Den Slimming Pills UK : Almost one-third population of the world seems to be struggling with overweight and obesity health issues because we don’t live a healthy and fit life. Weight lo... | ["[Via Keto Apple Gummies]"] |
29,153 | Transfection of Micromonas commoda CCMP2709 | null | dx.doi.org/10.17504/protocols.io.8p9hvr6 | null | Lisa Sudek, Alexandra Worden, Manny Ares | TITLE: Transfection of Micromonas commoda CCMP2709
AUTHORS: Lisa Sudek, Alexandra Worden, Manny Ares
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describes the transformation of the picoprasinophyte alga </span><span style = "font-style:italic;">Micromonas commoda</span><span>... | ["[Plasmid Preparation]\nThe Carrier DNA stock (pUC19) is purchased at a concentration of 20 µg µl-1 in 10 mM TrisHCl pH8, aliquoted in 100 µl volumes and stored at -20 °C.", "[Plasmid Preparation]\nThe reporter plasmid stock (in this case of plasmid RPS9proMco-eGFP) is prepared by transforming the purchased plasmid in... |
96,611 | Plasmid Sequence Analysis from Long Reads | 1 | dx.doi.org/10.17504/protocols.io.36wgq4n5yvk5/v9 | https://www.protocols.io/view/plasmid-sequence-analysis-from-long-reads-dakb2csn | David A Eccles | TITLE: Plasmid Sequence Analysis from Long Reads
AUTHORS: David A Eccles
[DESCRIPTION]
This protocol demonstrates how to assemble reads from plasmid DNA, and generate a circularised and non-repetitive consensus sequence.
For plasmid sample preparation for nanopore sequencing, see here. The most recent version of our ... | ["[Read file preparation] Demultiplex reads as per protocol Demultiplexing Nanopore reads with LAST.\n\nIf this has been done, then the following command should produce output without errors:\n\n \n\nExample output:\n\n \n\nIf the barcode_counts.txt file is missing, the output will look like this:\n\n \n\nIf one or mor... |
70,195 | DNA extraction from mouthwash samples using Qiagen DNeasy PowersoilPro Kit | 1 | dx.doi.org/10.17504/protocols.io.eq2ly7dyrlx9/v1 | https://www.protocols.io/view/dna-extraction-from-mouthwash-samples-using-qiagen-cgsttwen | Ahmed A Shibl, Anique Ahmad, Tsedenia Denekew, Mamon Abd AlBaqi, Aashish R Jha | TITLE: DNA extraction from mouthwash samples using Qiagen DNeasy PowersoilPro Kit
AUTHORS: Ahmed A Shibl, Anique Ahmad, Tsedenia Denekew, Mamon Abd AlBaqi, Aashish R Jha
[DESCRIPTION]
This protocol describes how to extract DNA from mouthwash samples.
[BEFORE_START]
Set centrifuge to 4ºC
Keep CD2 solution on ice or a... | ["Thaw the sample on ice for 30 min", "Centrifuge the transferred sample at maximum speed (17000 x g ) at 4°C for 10 min", "Transfer the desired sample volume 1-2 mL into a 1.5mL or 2mL eppendorf tube", "Discard the supernatant carefully without disturbing the pellet", "Repeat Step 1.1 if more volume is needed to see ... |
98,244 | BAF_Protocol_009 Metabolomics: Lipid Extraction | 0 | dx.doi.org/10.17504/protocols.io.kqdg325b7v25/v1 | https://www.protocols.io/view/baf-protocol-009-metabolomics-lipid-extraction-db7c2riw | Nicholas Sherman | TITLE: BAF_Protocol_009 Metabolomics: Lipid Extraction
AUTHORS: Nicholas Sherman
[DESCRIPTION]
This protocol uses a similar method to Protocol_008 but retains the chloroform phase containing lipids and other very hydrophobic molecules. Extractions are done in a way to make sure the final sample is mostly lipids. This... | ["[Liquid Samples: Urine, Plasma, Culture Media] To each sample containing 100 uL add 750 µL of -20°C cold Chloroform:methanol (2:1) mixture and vortex", "[Liquid Samples: Urine, Plasma, Culture Media] Shake tubes vigorously for 30 min at 4°C in temperature temperature-controlled thermal shaker", "[Liquid Samples: Urin... |
null | null | null | dx.doi.org/10.17504/protocols.io.rsxd6fn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Background</strong>: Aberrant DNA methylation occurs frequently in cancer. The aim of this study was to identify novel methylation markers in lung cancer in Xuanwei, China, through integrated genome-wide DNA methylation and gene expression studies.</p>
<p><strong>Meth... | ["[MeDIP-chip] {\"blocks\":[{\"key\":\"78iq0\",\"text\":\"Genomic DNA (gDNA)\\u00a0 were extracted and purified from lung cancer and paired noncancerous lung tissues using the QIAamp DNA Mini kit (Qiagen, Hilden, Germany) according to the manufacturer\\u2019s instructions.\",\"type\":\"unstyled\",\"depth\":0,\"inlineSt... |
22,863 | SPARC bilateral terminal phrenic neurophysiology preparation with moderate acute intermittent hypoxia | null | dx.doi.org/10.17504/protocols.io.2jpgcmn | null | Elisa Gonzalez-Rothi, Arash Tadjalli, Raphael Perim, Gordon Mitchell | TITLE: SPARC bilateral terminal phrenic neurophysiology preparation with moderate acute intermittent hypoxia
AUTHORS: Elisa Gonzalez-Rothi, Arash Tadjalli, Raphael Perim, Gordon Mitchell
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for conducting bilateral phrenic neurograms in anestheti... | ["Isoflurane induction: 2.5-3% in 100% O2 in a closed chamber for 3-5 minutes", "Transfer to nose cone and maintain at 3% in 100% 02. Confirm adequate plane of anesthesia via toe pinch", "Place intravenous line into tail vein for delivery of drugs/anesthesia/fluids (flush with heparinized saline)", "Measure body temper... |
22,499 | The Nanopore libraries preparation for the Scapharca broughtonii | null | dx.doi.org/10.17504/protocols.io.z8bf9sn | null | Chang-Ming Bai | TITLE: The Nanopore libraries preparation for the Scapharca broughtonii
AUTHORS: Chang-Ming Bai
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is used to outline the process of Nanopore library preparation for </span><span style = "font-style:italic;">Scapharca broughtonii </spa... | ["About 6 μg genomic DNA was fragmented using a Megaruptor (Diagenode, Seraing, Belgium) to obtain ~20kb frequments, and verified with Agilent Bioanalyzer 2100 system (Agilent Technologies, Palo Alto, CA, USA).\nThe sizes of the main fragments should >17 Kb.", "Fragments with size > 15 Kb were selected using BluePippi... |
19,451 | Detection of Human Rhinovirus by PCR following Sanger Sequencing | null | dx.doi.org/10.17504/protocols.io.w83fhyn | null | Talita Gagliardi | TITLE: Detection of Human Rhinovirus by PCR following Sanger Sequencing
AUTHORS: Talita Gagliardi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Reference for the method and primer sequences</div><div class = "text-block">“Lee W.-M., Lemanske R. F., Evans M., Vang F., Pappas T. E., Gangnon R., Jack... | ["Prepare the PCR reaction using 3ul of random cDNA; 10pM of the mixture of forward primers (B1, B2 and B3) and 10pM of the FR2 reverse primer.", "Run a Touch-down PCR following the cycling conditions suggested by the polymerase manufacturer although varying the annealing temperature from 68C to 52C (decreasing 2C a... |
67,417 | Keto Blast Gummies Shark Tank Reviews- Price or Ingredients | 1 | dx.doi.org/10.17504/protocols.io.3byl4bo22vo5/v1 | https://www.protocols.io/view/keto-blast-gummies-shark-tank-reviews-price-or-ing-cd3zs8p6 | health | TITLE: Keto Blast Gummies Shark Tank Reviews- Price or Ingredients
AUTHORS: health
[DESCRIPTION]
Keto Blast Gummies Reviews -Many users are convinced of the effectiveness of the Keto Blast Gummies. You are particularly enthusiastic about the ease of use and effect. Some buyers report that they have tried many diets ... | ["Keto Blast Gummies Reviews -Many users are convinced of the effectiveness of the Keto Blast Gummies. You are particularly enthusiastic about the ease of use and effect. Some buyers report that they have tried many diets in the past. This prevented them from reaching their dream weight. Keto Blast Gummies is definitel... |
40,874 | Isolation of Escherichia coli pathogens from oysters | 4 | dx.doi.org/10.17504/protocols.io.bj6ikrce | https://www.protocols.io/view/isolation-of-escherichia-coli-pathogens-from-oyste-bj6ikrce | Angel Justiz-Vaillant1, Arvind Kurhade1, Chandrashekhar Unakal1, Patrick E. Akpaka1, Sade Aisha Folashade John1 | TITLE: Isolation of Escherichia coli pathogens from oysters
AUTHORS: Angel Justiz-Vaillant1, Arvind Kurhade1, Chandrashekhar Unakal1, Patrick E. Akpaka1, Sade Aisha Folashade John1
[STEPS]
?. The filtered homogenate was streaked on MacConkey's agar using standardized loops, the loops were flamed periodically to ensure... | ["The filtered homogenate was streaked on MacConkey's agar using standardized loops, the loops were flamed periodically to ensure sterility. This was done in duplicate. The plates were then inverted and incubated at 34°C. After an overnight incubation at 34°C, the plate with the best significant and adequate colonies w... |
62,863 | Nuova Versione Protocollo di Conformità di Riviste Scientifiche all'Open Access | 1 | dx.doi.org/10.17504/protocols.io.n2bvj6qxnlk5/v1 | https://www.protocols.io/view/nuova-versione-protocollo-di-conformit-di-riviste-b9mpr45n | Giulia Caldoni, Bianca Gualandi, Mario Marino, Silvio Peroni | TITLE: Nuova Versione Protocollo di Conformità di Riviste Scientifiche all'Open Access
AUTHORS: Giulia Caldoni, Bianca Gualandi, Mario Marino, Silvio Peroni
[DESCRIPTION]
Questo protocollo è stato utilizzato per indagare, a distanza di 3 anni dalla prima indagine (svolta nel 2019), la legittimità della definizione “Op... | ["[Creazione tabella] Creazione di una tabella di spreadsheet in cui far confluire i dati raccolti durante l'analisi delle riviste.", "[Strutturazione tabella] Viene implementata la tabella di spreadsheet condivisa, formulata per la precedente analisi, in cui far confluire i dati raccolti tramite l'analisi delle rivist... |
null | null | null | dx.doi.org/10.17504/protocols.io.rabd2an | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>1) The primers and probes utilized were obtained from published research article as referenced in the text.</p>
<p>2) First, Dengue virus RNA was extracted from patient serum by using Qiagen </p>
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.huqb6vw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?. | [] |
100,701 | “Treated and untreated cows housed side by side in tie-stalls and their respective risk of harboring E. coli resistant to antimicrobials” | 0 | dx.doi.org/10.17504/protocols.io.j8nlk8ojxl5r/v1 | https://www.protocols.io/view/treated-and-untreated-cows-housed-side-by-side-in-dej53cq6 | Belinda Köchle, Véronique Bernier Gosselin, Heike Kaspar, Jens Becker | TITLE: “Treated and untreated cows housed side by side in tie-stalls and their respective risk of harboring E. coli resistant to antimicrobials”
AUTHORS: Belinda Köchle, Véronique Bernier Gosselin, Heike Kaspar, Jens Becker
[DESCRIPTION]
Parenteral antimicrobial
treatment results in the excretion of antimicrobial-resi... | ["Materials and equipment:", "Rectal swabs in transport tubes", "BROLAC agar (Biolab, Budapest, Hungary)", "MacConkey agar (Thermo Fisher Scientific, Basel, Switzerland)", "Chromogenic coliform agar (Merck, Darmstadt, Germany)", "Trypticase soy agar with 5% sheep blood (Becton Dickinson, Franklin Lakes, NJ, USA)", "Col... |
59,042 | LRRK2 microtubule sedimentation binding assay | 4 | dx.doi.org/10.17504/protocols.io.36wgq73b5vk5/v1 | https://www.protocols.io/view/lrrk2-microtubule-sedimentation-binding-assay-b5waq7ae | Andrea Dickey, Mariusz Matyszewski | TITLE: LRRK2 microtubule sedimentation binding assay
AUTHORS: Andrea Dickey, Mariusz Matyszewski
[DESCRIPTION]
Assay to determine LRRK2 protein binding to microtubules.
Original assay by Andrea Dickey. Adapted by Mariusz Matyszewski for protocols.io.
Assay originally used in Snead, Matyszewski, Dickey et al. 2022
... | ["[Microtubule preparation] Polymerize tubulin at around 2.5 mg/mL for 30 min at 37 °C . Add Taxol for stabilization and incubate for another 10 min at 37 °C .", "[Microtubule preparation] Remove free tubulin by ultracentrifugation. 108628 x g, 15 min, 37 °C through a 64 % volume .", "[Microtubule preparation] Resuspe... |
97,679 | FFPE Tissue Processing for Multimodal Imaging Assays (Phenocycler-Fusion + H&E) following Xenium In Situ Gene Expression | 0 | dx.doi.org/10.17504/protocols.io.q26g71rwqgwz/v1 | https://www.protocols.io/view/ffpe-tissue-processing-for-multimodal-imaging-assa-dbmp2k5n | Santhosh Sivajothi, Emily Soja, Shruti Bhargava, William F Flynn, Elise T Courtois | TITLE: FFPE Tissue Processing for Multimodal Imaging Assays (Phenocycler-Fusion + H&E) following Xenium In Situ Gene Expression
AUTHORS: Santhosh Sivajothi, Emily Soja, Shruti Bhargava, William F Flynn, Elise T Courtois
[DESCRIPTION]
Xenium In Situ Gene Expression assay from 10X Genomics enables multiplexed imagin... | ["[Tissue Processing for Xenium In Situ Gene Expression] FFPE tissue on Xenium slides is processed according to the protocols in 10X User Guides: \n\nPlease refer to the linked 10X User Guides for all materials and detailed instructions. The key steps are noted below:\n\nTissue deparaffinization: Step 1.2 of CG000580 (... |
55,512 | Protocol for micro-sheet pocket 1: Detailed operation manual of six requirements | 1 | dx.doi.org/10.17504/protocols.io.b2fyqbpw | https://www.protocols.io/view/protocol-for-micro-sheet-pocket-1-detailed-operati-b2fyqbpw | Keiichi Iwaya, H-Arai , Nanao Takatou, Yuka Morita, Rinko Ozeki, Hirofumi Nakaoka, Masaru Sakamoto, Tsutomu Kouno, Masayoshi Soma | TITLE: Protocol for micro-sheet pocket 1: Detailed operation manual of six requirements
AUTHORS: Keiichi Iwaya, H-Arai , Nanao Takatou, Yuka Morita, Rinko Ozeki, Hirofumi Nakaoka, Masaru Sakamoto, Tsutomu Kouno, Masayoshi Soma
[DESCRIPTION]
This protocol details micro-sheet pocket 1 and detailed operation manua... | ["[Average diameter of filter opening] Examine the average diameter of filter opening by referring to the catalog of the sheet.", "[Average diameter of filter opening] Confirm opening size by using scanning electron microscopy (SEM), if possible.", "[Chemical resistance] Cut in half the sheet in order to compare each o... |
18,844 | Determination of Effective Synaptic Conductances Using Somatic Voltage Clamp | null | dx.doi.org/10.17504/protocols.io.wm4fc8w | null | Songting Li, Nan Liu, Xiaohui Zhang, Douglas Zhou, David Cai | TITLE: Determination of Effective Synaptic Conductances Using Somatic Voltage Clamp
AUTHORS: Songting Li, Nan Liu, Xiaohui Zhang, Douglas Zhou, David Cai
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">By using dynamic clamp to generate synaptic inputs, we demonstrate the deficiency of the tradition... | ["Clamp the somatic voltage at various levels using voltage clamp, generate simultaneous E and I synaptic input currents using dynamic clamp on the dendrite, and measure the corresponding synaptic currents arriving at the soma. In this step, one shall exert a well control of the experimental condition such that the E a... |
75,933 | Production of Crude AAV Virus Extract | 1 | dx.doi.org/10.17504/protocols.io.yxmvmx7r9l3p/v5 | https://www.protocols.io/view/production-of-crude-aav-virus-extract-cnd5va86 | Allen Institute for Brain Science | TITLE: Production of Crude AAV Virus Extract
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
This protocol is used to produce crude preps of AAV of any serotype.
Note: Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Awa... | [] |
56,764 | Inorganic polyphosphate from microalgae: A DAPI-based estimation in microtiter plate | 1 | null | https://www.protocols.io/view/inorganic-polyphosphate-from-microalgae-a-dapi-bas-b3n4qmgw | Yingyu Hu, Zoe V Finkel | TITLE: Inorganic polyphosphate from microalgae: A DAPI-based estimation in microtiter plate
AUTHORS: Yingyu Hu, Zoe V Finkel
[DESCRIPTION]
The DAPI-based fluorometric estimation of polyphosphate from microalgae has been widely used in field samples since the method was published by Martin P. et al., where fluoresce... | ["[Sample collection] Filter microalgae in liquid media onto precombusted GFF filters, using gentle vacuum pressure (5 inches Hg).", "[Sample collection] Rinse sample with filtered seawater", "[Sample collection] Place sample filters in cryogenic vials", "[Sample collection] Filter blank media (without cells) through p... |
62,685 | Rapid extraction of total lipids from microalgae | 1 | null | https://www.protocols.io/view/rapid-extraction-of-total-lipids-from-microalgae-b9f5r3q6 | 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... |
69,789 | Spatial Multi-omics Sequencing for Fixed Tissue via DBiT-seq | 1 | dx.doi.org/10.17504/protocols.io.3byl4j2kolo5/v1 | https://www.protocols.io/view/spatial-multi-omics-sequencing-for-fixed-tissue-vi-cgd5ts86 | Graham Su, archibald.enninful, Yang Liu, Rong Fan | TITLE: Spatial Multi-omics Sequencing for Fixed Tissue via DBiT-seq
AUTHORS: Graham Su, archibald.enninful, Yang Liu, Rong Fan
[DESCRIPTION]
This protocol describes the use of Deterministic Barcoding in Tissue for spatial omics sequencing (DBiT-seq) platform to construct a multi-omics atlas on fixed frozen tissue samp... | ["[Fabricating the Silicon Wafer Device Mold] Prepare a high-resolution computer-aided-design (CAD) file with the desired microfluidics chip design. A CAD file is also available in the link provided. (https://ars.els-cdn.com/content/image/1-s2.0-S2666166721002392-mmc4.zip)", "[Fabricating the Silicon Wafer Device Mold]... |
86,468 | Fecal Water Content Assay | 1 | dx.doi.org/10.17504/protocols.io.kqdg3xx5zg25/v1 | https://www.protocols.io/view/fecal-water-content-assay-cypcxviw | Sabina Marciano, Roberta Marongiu | TITLE: Fecal Water Content Assay
AUTHORS: Sabina Marciano, Roberta Marongiu
[DESCRIPTION]
This test is used to check for signs of constipation
[STEPS]
1. Label, weight and record the weight of each Eppendorf tube
2. Collect 2 pellets from each mouse and weigh.
3. Dry the pellets in the oven at 60 degrees C for 24 h... | ["Label, weight and record the weight of each Eppendorf tube", "Collect 2 pellets from each mouse and weigh.", "Dry the pellets in the oven at 60 degrees C for 24 hrs", "Weigh the pellets again after drying", "Calculate fecal water content according to the equation: \n\n(fecal weight before drying − fecal weight after ... |
79,967 | High-throughput nanopore sequencing of cell-free DNA | 4 | dx.doi.org/10.17504/protocols.io.4r3l27rjxg1y/v1 | https://www.protocols.io/view/high-throughput-nanopore-sequencing-of-cell-free-d-csb7warn | Billy T Lau | TITLE: High-throughput nanopore sequencing of cell-free DNA
AUTHORS: Billy T Lau
[DESCRIPTION]
https://www.biorxiv.org/content/10.1101/2022.06.22.497080v1
Epigenetic characterization of cell-free DNA (cfDNA) is an emerging approach for detecting and characterizing diseases such as cancer. We developed a strategy usin... | ["[Multiplexed cfDNA library preparation (barcode ligation)] 25 µL of each (usually this is half of the extracted volume, in case of reaction failure) is diluted with 25 µL of water in a PCR strip tube or microtiter plate.", "[Multiplexed cfDNA library preparation (barcode ligation)] A master mix of end-repair and a-... |
40,085 | LC-MS/MS analysis | 3 | dx.doi.org/10.17504/protocols.io.bjdvki66 | https://www.protocols.io/view/lc-ms-ms-analysis-bjdvki66 | avinash.kale | TITLE: LC-MS/MS analysis
AUTHORS: avinash.kale
[STEPS] | [] |
98,422 | Longitudinal TSPO PET imaging with [18F] DPA-714 in PPMI (PPMI DPA-714 PET Imaging) | 0 | dx.doi.org/10.17504/protocols.io.x54v92mxql3e/v1 | https://www.protocols.io/view/longitudinal-tspo-pet-imaging-with-18f-dpa-714-in-dccw2sxe | David Standaert | TITLE: Longitudinal TSPO PET imaging with [18F] DPA-714 in PPMI (PPMI DPA-714 PET Imaging)
AUTHORS: David Standaert
[DESCRIPTION]
This protocol details the Longitudinal TSPO PET imaging with [18F] DPA-714 in PPMI (PPMI DPA-714 PET Imaging).
[GUIDELINES]
APPENDIX 1- PPMI DPA-714 PET Imaging Schedule of Activities
I... | ["[PURPOSE OF STUDY] The overall goal of this protocol is to investigate [18F]DPA-714 binding in prodromal and early manifest Parkinson’s Disease (PD) and to determine the baseline and change from baseline in [18F]DPA-714 binding in PD participants during a 24-month interval.", "[PURPOSE OF STUDY] Primary Objectives of... |
103,744 | Matrix-Assisted Laser Desorption/Ionization-Mass Spectrometric Imaging (MALDI-MSI)_V2.0 | 1 | dx.doi.org/10.17504/protocols.io.14egn84dyg5d/v2 | https://www.protocols.io/view/matrix-assisted-laser-desorption-ionization-mass-s-dhi834hw | Ian M. Tamayo, Brittney Gorman, Guanshi Zhang, Dusan Velickovic, Soumya Maity, Theodore Alexandrov, Christopher R Anderton, Kumar Sharma | TITLE: Matrix-Assisted Laser Desorption/Ionization-Mass Spectrometric Imaging (MALDI-MSI)_V2.0
AUTHORS: Ian M. Tamayo, Brittney Gorman, Guanshi Zhang, Dusan Velickovic, Soumya Maity, Theodore Alexandrov, Christopher R Anderton, Kumar Sharma
[DESCRIPTION]
Mass spectrometry imaging is a cutting-edge molecular technology... | ["[MALDI-15T-FTICR MS (Bruker Solarix) with SmartBeam II laser source– Spatial Lipidomics] Slide(s) is (are) removed from the HTX sprayer, remounted in the MTP slide Adapter II and loaded into MS instrument.", "[MALDI-15T-FTICR MS (Bruker Solarix) with SmartBeam II laser source– Spatial Lipidomics] External calibration... |
null | null | null | dx.doi.org/10.17504/protocols.io.snnedde | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>We have developed a multiplexed single molecule FISH protocol for use at the Institute. This protocol was optimized on human tissue, but will work on mouse tissue as well. It was adapted from Lyubimova et. al., Nature Protocols, 2013. </p>
[BEFORE_START]
<div>
<div>
<div>
<d... | [] |
24,387 | Ultracentrifugal separation of VLDL, LDL and HDL | null | dx.doi.org/10.17504/protocols.io.33bgqin | null | Daniel Teupser, Jan Breslow | TITLE: Ultracentrifugal separation of VLDL, LDL and HDL
AUTHORS: Daniel Teupser, Jan Breslow
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">This protocol is used to isolate the various lipid fractions from blood plasm... | ["Add 60 ul of plasma to Beckman ultracentrifugation tube (7 x 20 mm; thick walled; polyallomer; cat. # 343621).", "Layer 60 ul of PBS on top of the plasma and place tubes in a TLA100 rotor.", "Spin for 3 hours Beckman Optima TL tabletop ultracentrifuge at 70,000 rpm, 4°C.", "Using a 100 μl Hamilton syringe, carefully ... |
66,594 | Protocole of the pilot study : Adolescent screen time and unhealthy food consumption in the context of the digital development in New Caledonia | 1 | dx.doi.org/10.17504/protocols.io.x54v9ynz4g3e/v1 | https://www.protocols.io/view/protocole-of-the-pilot-study-adolescent-screen-tim-cdaas2ae | Akila Nedjar-Guerre, Guillaume Wattelez, Christophe Serra-Mallol, Stephane Frayon, Olivier GALY | TITLE: Protocole of the pilot study : Adolescent screen time and unhealthy food consumption in the context of the digital development in New Caledonia
AUTHORS: Akila Nedjar-Guerre, Guillaume Wattelez, Christophe Serra-Mallol, Stephane Frayon, Olivier GALY
[DESCRIPTION]
For several years, the Pacific Island Coun... | ["[Methodology] In this study, quantitative data were obtained from questionnaire responses. Our study was part of a community-based food culture project conducted in eight selected representative school sites in the three provinces (Northern Province, Southern Province and Loyalty Islands) of New Caledonia. The school... |
null | null | null | dx.doi.org/10.17504/protocols.io.h2kb8cw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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null | null | null | dx.doi.org/10.17504/protocols.io.hrpb55n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol provides the detailed methods of assembly and annotation of the R. crenulata genome.</p>
[BEFORE_START]
<p>Get raw sequencing data in Fastq format.</p>
[STEPS]
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50,702 | Denuded Oocyte Isolation from Human Ovarian Tissue | 4 | null | https://www.protocols.io/view/denuded-oocyte-isolation-from-human-ovarian-tissue-bvrnn55e | Andrea Jones, Jordan Machlin, Ariella Shikanov | TITLE: Denuded Oocyte Isolation from Human Ovarian Tissue
AUTHORS: Andrea Jones, Jordan Machlin, Ariella Shikanov
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines steps to obtain live denuded oocytes from fresh or cryopreserved human ovarian cortex. Here, we do not outline st... | ["[Preparations]\nPrepare enzymes: Dilute DNase I stock (2% w/v) to 2 mg/mL by combining 10 μL stock with 90 μL DPBS +/+. Mix well and store on ice for the duration of cell isolation. Collagenase stock at 100 mg/mL should be stored on ice for the duration of cell isolation.", "[Preparations]\nPre-weigh an empty 30 mm d... |
26,811 | hist | null | dx.doi.org/10.17504/protocols.io.6e3hbgn | null | Monika Hassan | TITLE: hist
AUTHORS: Monika Hassan
[STEPS]
?. [fds]
?. [fds] | ["[fds]", "[fds]"] |
48,450 | Confidentiality and disclaimer examples | 1 | null | https://www.protocols.io/view/confidentiality-and-disclaimer-examples-btjankie | Lenny Teytelman | TITLE: Confidentiality and disclaimer examples
AUTHORS: Lenny Teytelman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Yale's SalivaDirect protocol</span><span>: "“For diagnostic and screening purposes, only labs designated by Yale and that follow the Instructions ... | [] |
92,855 | Rodent Liver 2-Step Collagenase Perfusion and Digestion using VitaCyte | 4 | dx.doi.org/10.17504/protocols.io.q26g7p74qgwz/v1 | https://www.protocols.io/view/rodent-liver-2-step-collagenase-perfusion-and-dige-c6wxzffn | sai.chung, manmeet.sekhon, Xue-Zhong Ma, Justin Manuel, Michael L Cheng, Sonya MacParland, Ian McGilvray | TITLE: Rodent Liver 2-Step Collagenase Perfusion and Digestion using VitaCyte
AUTHORS: sai.chung, manmeet.sekhon, Xue-Zhong Ma, Justin Manuel, Michael L Cheng, Sonya MacParland, Ian McGilvray
[DESCRIPTION]
To obtain a viable single cell suspensions of total liver homogenate (TLH) that can be used for downstream experi... | ["[Buffers and Solutions] Solution 1 – EGTA, Ca2+Mg2+ Free\nMOUSE: Add 100µL of 50mM EGTA into 50mL of Ca2+Mg2+free HBSS. \nRAT: Add 500µL of 50mM EGTA into 250mL of Ca2+Mg2+free HBSS.", "[Buffers and Solutions] Dehydrate\nAdd 68.6µL of 1M CaCl solution into 50mL of Ca2+Mg2+free HBSS.", "[Buffers and Solutions] Solutio... |
35,702 | Gates lab qPCR protocol for Cladocopium and Durusdinium Symbiodiniaceae detection | 1 | dx.doi.org/10.17504/protocols.io.be4wjgxe | https://www.protocols.io/view/gates-lab-qpcr-protocol-for-cladocopium-and-durusd-be4wjgxe | Mariana Rocha De Souza, Shayle Matsuda, Jenna Dilworth, Crawford Drury, Ross Cunning | TITLE: Gates lab qPCR protocol for Cladocopium and Durusdinium Symbiodiniaceae detection
AUTHORS: Mariana Rocha De Souza, Shayle Matsuda, Jenna Dilworth, Crawford Drury, Ross Cunning
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The purpose of this protocol is to quantify </span><span st... | ["[Mastermix preparation]\nPrimer and Probe DilutionsPrimers usually come in lyophilized form. We recommend diluting them to a 100µM stock, then diluting the stock to get the desired concentration for the reactions. For the reacions, Forward primers should be 1μM and Reverse primers shold be 1.5 μM. Probes should be di... |
null | null | null | dx.doi.org/10.17504/protocols.io.ed9ba96 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol provides a method for assembly of metagenomic data using the Ray assembly toolkit and the subsequent analysis of contig statistics. Based on the publication: <br /><br />Hannigan, Geoffrey D., et al. "The Human Skin Double-Stranded DNA Virome: Topographical and Tem... | [] |
47,920 | Iodine staining of starch to determine amylose percentage | 6 | null | https://www.protocols.io/view/iodine-staining-of-starch-to-determine-amylose-per-bs2qngdw | Chris Berndsen | TITLE: Iodine staining of starch to determine amylose percentage
AUTHORS: Chris Berndsen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Starch is well known to complex with iodine producing strong absorbance between 500 and 750 nm. Two structures that compose structure, amylose and amylopectin comp... | ["[Preparing starch for spectroscopic measurement]\nObtain soluble starch or starch granule sample in sterile water", "[Preparing starch for spectroscopic measurement]\nWarm sample to in a water bath for\n95 °C\nStarch granules will gelatinize under these conditions. Do not cool the samples otherwise staining may not ... |
19,369 | Epidural stimulation mapping protocol | 1 | dx.doi.org/10.17504/protocols.io.w6hfhb6 | https://www.protocols.io/view/epidural-stimulation-mapping-protocol-w6hfhb6 | Charles Hubscher, Robert Hoey | TITLE: Epidural stimulation mapping protocol
AUTHORS: Charles Hubscher, Robert Hoey
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Current experiments are utilizing epidural stimulation, and the measurement of numerous systems, after either sham transection or full T9 transection. Transected Wistar... | ["After all relevant surgical procedures have been performed the animal is placed on the specially made surgical platform and all necessary attachments are connected.", "The rat is placed on their ventrum throughout testing. The hindlimbs are taped down to the platform as the electrical stimulation can cause motor move... |
null | null | null | dx.doi.org/10.17504/protocols.io.c5my45 | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<strong> Primers: </strong><br />GM3: AGA GTT TGA TCM TGG C These primers are for almost full-length 16s (8F/1492R) <br />GM4: TAC CTT GTT ACG ACT T <br /><br />
<table style="width: 250px; height: 250px;">
... | [] |
21,295 | 16S Metagenomics in a Field Setting | null | dx.doi.org/10.17504/protocols.io.y2pfydn | null | Gideon Erkenswick, Stefan Prost, Mrinalini Watsa, Aaron Pomerantz | TITLE: 16S Metagenomics in a Field Setting
AUTHORS: Gideon Erkenswick, Stefan Prost, Mrinalini Watsa, Aaron Pomerantz
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is was used to conduct DNA 16S metagenomics on FPI's Genomics in the Jungle - 2018 field course at the Green Lab, locate... | ["[Electrophoresis]\nEquipmentBlueGel system MiniOne systemCreate .8 - 1.0% agarose 1 gel with 13 combs Measure 1 g of agaroseMix agraose with 100 mL of 1xTBEMicrowave the mixture until agarose is completely dissolved (1-3 min)Pour the agarose gel into the tray with the comb in place. Allow the agarose gel to harden (2... |
null | null | null | dx.doi.org/10.17504/protocols.io.dfz3p5 | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<strong>Primers:<br /><br /></strong>381_Lysis_418_F: TGC CTG AAC GGC TTA GAG GTT TGC<strong><br /></strong>381_Lysis_418_R: AGC ACC AAT CGG CGT CTT CGT <br /><br />Putative Lysis gene product = 350 bp<br /><br /><strong><strong>Reaction Mix<br /><br /></strong></strong>
... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ey8bfzw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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70,247 | Soil DNA Extraction Modified Protocol for Dryland Agroecosystems | 1 | dx.doi.org/10.17504/protocols.io.eq2ly7domlx9/v1 | https://www.protocols.io/view/soil-dna-extraction-modified-protocol-for-dryland-cguftwtn | McKenzie L. Stock, Paul Gabriel, Jennifer J. Randall, Nicole Pietrasiak | TITLE: Soil DNA Extraction Modified Protocol for Dryland Agroecosystems
AUTHORS: McKenzie L. Stock, Paul Gabriel, Jennifer J. Randall, Nicole Pietrasiak
[DESCRIPTION]
The Qiagen DNEasy PowerLyzer PowerSoil Kit is widely used in DNA based sample processing and extraction procedures. However, dryland soils are typically... | ["[Sample Prep] Soil samples should be stored cold, at least -20 C (ideally at -80 C).", "[Homogenization] Fill a 12 ml homogenization vial approximately 2/3 full with soil (Spex SamplePrep 6133PC-T). Include three 6.35 mm diameter chrome steel beads (BioSpec Products Cat. No. 11079635c).", "[Homogenization] Homogeniz... |
null | null | null | dx.doi.org/10.17504/protocols.io.rjud4nw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Dimethoxypropane (DMP) is an organic compound that reacts with water under acidified conditions to form methanol and acetone. The compound can also be used in place of an ethanol series to dehydrate formalin-fixed plant tissues for serial sectioning.</p>
[BEFORE_START]
<p>Pr... | [] |
83,149 | Adhesive Removal Test to assess sensorimotor deficits in parksisonian mice | 1 | null | https://www.protocols.click/view/adhesive-removal-test-to-assess-sensorimotor-defic-cvfmw3k6 | natalia.lopezgonzalezdelrey, Elizabeth Phelan, Zachary Gaertner | TITLE: Adhesive Removal Test to assess sensorimotor deficits in parksisonian mice
AUTHORS: natalia.lopezgonzalezdelrey, Elizabeth Phelan, Zachary Gaertner
[DESCRIPTION]
This behavior is used to asses fine motor movements in a mouse parkinsonian model. It checks for correct paw and mouth sensitivity (time-to-contact) a... | ["[Adhesive Removal Test] Total duration: 4 days", "[Protocol] Place the animal cage in the testing room to allow the animals to acclimate. 60 min", "[Protocol] Acclimating mice to testing box. 1 min", "[Protocol] Apply the two adhesive tape strips with equal pressure on each animal paw so that they cover the hairless ... |
null | null | null | dx.doi.org/10.17504/protocols.io.vqie5ue | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Background: To improve the care and treatment of HIV-exposed children, early infant diagnosis (EID) using dried blood spot (DBS) sampling has been performed in Senegal since 2007, making molecular diagnosis accessible for patients living in decentralized settings. This study aim... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ek4bcyw | null | null | TITLE: No Title
AUTHORS:
[BEFORE_START]
You must determine the titer of your phage lysate before performing the experiment.
[GUIDELINES]
Note: one-step growth experiment instructions are for MOI=3.
[STEPS]
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null | null | null | dx.doi.org/10.17504/protocols.io.iencbde | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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null | null | null | dx.doi.org/10.17504/protocols.io.ejgbcjw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Reef-building corals comprise multipartite symbioses where the cnidarian animal is host to an array of eukaryotic and prokaryotic organisms, and the viruses that infect them. These viruses are critical elements of the coral holobiont, serving not only as agents of mortality, but... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.kz2cx8e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This collection contains the protocols and recipes for the preparation of cell-free RNAPT7 transcription/translation coupled reactions.</p>
<p>The crude extracts are obtained from IPTG-treated E.coli BL21 DE3 STAR cells. IPTG triggers RNAPT7 expression and accumulation in cel... | [] |
28,194 | Protocol for Exonuclease VII (NEB #M0379) | 1 | null | https://www.protocols.io/view/protocol-for-exonuclease-vii-neb-m0379-7sahnae | New England Biolabs | TITLE: Protocol for Exonuclease VII (NEB #M0379)
AUTHORS: New England Biolabs
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Exonuclease VII efficiently cleaves single-stranded DNA (ssDNA) from both 5´→3´ and 3´→5´ direction. This enzyme is not active on linear or circular dsDNA</div></div>
[STEPS... | ["Set-up the reaction as follows: AB1COMPONENTSReaction Volumes2 PCR Product5 μl3 Exonuclease VII 2 μl (20 units)\nAB1COMPONENTSReaction Volumes2 PCR Product5 μl3 Exonuclease VII 2 μl (20 units)", "Incubate the mix at for .\n37 °C", "Heat inactivate for prior to Sanger DNA se... |
28,475 | Metabolite Extraction and Derivatization of Plasma/ Serum Samples for High Resolution GC-MS- based Metabolomics | null | dx.doi.org/10.17504/protocols.io.723hqgn | null | Biswapriya Misra, Michael Olivier | TITLE: Metabolite Extraction and Derivatization of Plasma/ Serum Samples for High Resolution GC-MS- based Metabolomics
AUTHORS: Biswapriya Misra, Michael Olivier
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">This protocol provides details on preparation of human a... | ["[PROTOCOL OVERVIEW BASED ON Lisec et al., 2006, Fiehn , 2016]\nFreshly thawed aliquots of serum or plasma (30 µL) samples from non-human primate (i.e., baboons, vervets) are subjected to sequential solvent extraction once each with 1 mL of acetonitrile: isopropanol: water (3:3:2, v/v ratio) stord in -20 C and 500... |
45,485 | Leaf Protein Extraction for Immunoblot (Soybean, Cowpea, Tobacco) | 4 | dx.doi.org/10.17504/protocols.io.bqnmmvc6 | https://www.protocols.io/view/leaf-protein-extraction-for-immunoblot-soybean-cow-bqnmmvc6 | Steven Burgess | TITLE: Leaf Protein Extraction for Immunoblot (Soybean, Cowpea, Tobacco)
AUTHORS: Steven Burgess
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protein extraction protocol was developed for analysis of protein abundance in leaf tissue by immunoblot. It was optimized for dicot species including... | ["[Buffer Preparation]\nIncubate 4x PEB (if stored at 4 oC) at for to re-suspended precipitated SDS in buffer.\n50 °C", "[Buffer Preparation]\nMake 1x PEB per sample by diluting 4x stock with dH2O.\n500 µl\nIt is advised to make more 1x PEB than necessary to avoid running out.", "[Tissue Lysis]\nPre-cool components ... |
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