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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null | null | null | dx.doi.org/10.17504/protocols.io.ecxbaxn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<strong>Viral Bioinformatic Resource Centre</strong>
<ul>
<li><strong>Provide databases of viral genomic information.</strong>
<ul>
<li>Please check the <strong><em>Organisms</em></strong> menu to see which viruses we support: we’re now focusing on large DNA viruses</li>
<li>The... | [] |
25,291 | Triple Anterograde Tracing | null | dx.doi.org/10.17504/protocols.io.4xjgxkn | null | Hongwei Dong | TITLE: Triple Anterograde Tracing
AUTHORS: Hongwei Dong
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"> Stereotaxic surgeries are performed to inject neural circuit tracers into different target regions in the brain. Animals are allowed one week to habituate following their arrival at the host viva... | ["Instruments are washed with soap, wiped down with alcohol, and autoclaved for the first surgery. Instruments are wiped down with alcohol and sterilized via a glass bead sterilizer in between surgeries.", "Animal is deeply anesthetized. The surgeries are performed under isoflurane anesthesia. Mice are initially anesth... |
null | null | null | dx.doi.org/10.17504/protocols.io.ibxcapn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Please contact Dr. Steven Wilhelm (wilhelm@utk.edu) for additional information regarding this protocol.</p>
<p> </p>
<p>Modified from J Mol Biol 13,269 (1965)</p>
[STEPS]
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97,016 | Ex vivo mouse brain patch clamp recordings combined with optogenetic stimulation | 4 | dx.doi.org/10.17504/protocols.io.5qpvokxp9l4o/v1 | https://www.protocols.io/view/ex-vivo-mouse-brain-patch-clamp-recordings-combine-dayy2fxw | Enrico Zampese, DeNard V Simmons | TITLE: Ex vivo mouse brain patch clamp recordings combined with optogenetic stimulation
AUTHORS: Enrico Zampese, DeNard V Simmons
[DESCRIPTION]
In this protocol we detail the steps to perform ex-vivo brain slice electrophysiology and optogenetic stimulation.
[BEFORE_START]
Please note that optogenetic experiments req... | ["[Prepare patch pipettes] Turn on the Sutter P-1000 puller and enter the desired pull protocol.", "[Prepare patch pipettes] Insert a thick-walled borosilicate glass capillary and press pull.", "[Prepare patch pipettes] Pipette resistance must be of 3 to 5 megaohms.", "[Setting up patch rig and environment] Turn on the... |
94,973 | Muconic acid isomers and aromatic compounds analyzed by UHPLC-DAD | 1 | dx.doi.org/10.17504/protocols.io.36wgqjjxyvk5/v2 | https://www.protocols.io/view/muconic-acid-isomers-and-aromatic-compounds-analyz-c8y5zxy6 | Sean P. Woodworth, Stefan J. Haugen, William E. Michener, Kelsey J. Ramirez, Gregg T. Beckham | TITLE: Muconic acid isomers and aromatic compounds analyzed by UHPLC-DAD
AUTHORS: Sean P. Woodworth, Stefan J. Haugen, William E. Michener, Kelsey J. Ramirez, Gregg T. Beckham
[DESCRIPTION]
An analysis method was developed to allow for quantitation of muconic acid isomers (cis, cis and cis, trans) and aromatic compou... | ["[Preparation of Standards] Calibration Curve", "[Analytical Quality Control] Multiple strategies are utilized when performing this analysis to ensure instrument stability and reproducibility.", "[Preparation of Standards] Standards\n\n This procedure for standard preparation is previously documented in our work publi... |
null | null | null | dx.doi.org/10.17504/protocols.io.c52y8d | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
Note: AmPure XP beads are normally used at 80:100 ratio* (beads:DNA) to remove fragments less than 100bp and retain all DNA above 100bp. If you lower that ratio. then DNA will not bind to the beads as efficiently (due to decreased amount of PEG present) and you will lose some of ... | [] |
97,857 | Baiting Pythium myriotylum from Infested Soil | 4 | dx.doi.org/10.17504/protocols.io.yxmvm3726l3p/v2 | https://www.protocols.io/view/baiting-pythium-myriotylum-from-infested-soil-dbs92nh6 | Nimalka Weerasuriya | TITLE: Baiting Pythium myriotylum from Infested Soil
AUTHORS: Nimalka Weerasuriya
[DESCRIPTION]
Baiting Pythium from seedlings in infested soil or infected hulls.
[STEPS]
SECTION: Preparation
1. Prep P5ARP Plates 1-2 days before plating.
Prepare working culture plates (CMA, PDA + amp) up to 1 week before plating.
... | ["[Preparation] Prep P5ARP Plates 1-2 days before plating.\nPrepare working culture plates (CMA, PDA + amp) up to 1 week before plating.", "[Transfer Culture] Check plates after 24-48 h.", "[Oospore Check] Check for \"gold coin\" oospores at plate edges to indicate Pythium myriotylum. \nUse CMA for oospore production\n... |
64,681 | Biotin-Labelling of Immunoprecipitated RNA (v1pre) | 1 | null | https://www.protocols.io/view/biotin-labelling-of-immunoprecipitated-rna-v1pre-cbehsjb6 | Steven Blue, Eric Van Nostrand, Gene Yeo | TITLE: Biotin-Labelling of Immunoprecipitated RNA (v1pre)
AUTHORS: Steven Blue, Eric Van Nostrand, Gene Yeo
[DESCRIPTION]
RNA binding proteins (RBPs) regulate a diverse array of RNA processing steps by binding RNAs through sequence and structural elements. The development of crosslinking and immunoprecipitation (CLI... | ["[Conjugate Antibody to Beads] For each 4M cell lysate, aliquot 25 μL of species-specific Dynabeads (e.g. ThermoFisher catalog # 11203D, 11202D, or equivalent)", "[Conjugate Antibody to Beads] Wash the beads twice in 500 μL cold Lysis Buffer.", "[Conjugate Antibody to Beads] Resuspend in 100 μL of Lysis Buffer.", "[Co... |
31,903 | Oyster Shell Processing Protocol | null | dx.doi.org/10.17504/protocols.io.bbd7ii9n | null | Benjamin Walther | TITLE: Oyster Shell Processing Protocol
AUTHORS: Benjamin Walther
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the procedure for sectioning oyster shells, micromilling to extract carbonate powder, and an overview of analyses at the UC Davis Stable Isotope Facility to obtai... | [] |
99,034 | Stereotactic injection of viral vectors | 0 | dx.doi.org/10.17504/protocols.io.6qpvr8dbplmk/v1 | https://www.protocols.io/view/stereotactic-injection-of-viral-vectors-dcx22xqe | William S Conrad, Lucie Oriol | TITLE: Stereotactic injection of viral vectors
AUTHORS: William S Conrad, Lucie Oriol
[DESCRIPTION]
Here we describe stereotactic injection of AAV into ventral tegmental area (VTA) of mice.
[STEPS]
SECTION: A. Pre-surgery Preparation
1. Pull pipettes and cut at 9.0 mm from start of glass bend with microdissection ... | ["[A. Pre-surgery Preparation] Pull pipettes and cut at 9.0 mm from start of glass bend with microdissection scissors.", "[A. Pre-surgery Preparation] Wash hands and put on clean lab coat and gloves", "[A. Pre-surgery Preparation] Turn on glass bead sterilizer, heating pads (for operation and recovery), stereotac... |
76,019 | Chronic Vagus-Nerve Activity with Carbon Nanotube Sensors in Freely Moving Rodents | 1 | dx.doi.org/10.17504/protocols.io.4r3l273x3g1y/v1 | https://www.protocols.io/view/chronic-vagus-nerve-activity-with-carbon-nanotube-cngtvbwn | Grant Mccallum, Joseph Marmerstein, Dominique Durand | TITLE: Chronic Vagus-Nerve Activity with Carbon Nanotube Sensors in Freely Moving Rodents
AUTHORS: Grant Mccallum, Joseph Marmerstein, Dominique Durand
[DESCRIPTION]
This study presents the first chronic recording and decoding of activity in the vagus nerve of freely moving animals. The majority of vagal afferent fibe... | ["[Protocol for CNTY Electrode Manufacture:] Carbon nanotube yarns (CNTYs) were manufactured at Case Western Reserve University using a previously described method (https://doi.org/10.1038/s41598-017-10639-w).", "[Protocol for CNTY Electrode Manufacture:] CNTYs were connected to 35NLT®-DFT® wire using silver conductive... |
null | null | null | dx.doi.org/10.17504/protocols.io.fabbian | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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51,808 | snmCAT_V2 | 1 | null | https://www.protocols.io/view/snmcat-v2-bwt8perw | Bang-An Wang, Chongyuan Luo, Hanqing Liu, Anna Bartlett, Rosa Castanon, Joseph Ecker | TITLE: snmCAT_V2
AUTHORS: Bang-An Wang, Chongyuan Luo, Hanqing Liu, Anna Bartlett, Rosa Castanon, Joseph Ecker
[DESCRIPTION]
To comprehensively assess the molecular phenotypes of single cells in tissues, we devised single-nucleus methylCytosine, Chromatin accessibility and Transcriptome sequencing (snmCAT-seq) ... | ["[Background] This protocol is based on the original protocol named as snmC2T-seq from the BioRxiv paper (ChongyuanLuo, et al. BioRxiv 2019) https://www.biorxiv.org/content/10.1101/2019.12.11.873398v1 and SMART-seq3 (Hagemann-Jensen, et al.Nat Biotechnol 2020, https://www.protocols.io/view/smart-seq3-protocol-bcq4ivy... |
50,886 | Microparticle delivery of CRISPR-Cas9 ribonucleoprotein to Isochrysis galbana for gene editing of URA3 gene. | 4 | dx.doi.org/10.17504/protocols.io.bvxen7je | https://www.protocols.io/view/microparticle-delivery-of-crispr-cas9-ribonucleopr-bvxen7je | Andrea Highfield, Glen Wheeler | TITLE: Microparticle delivery of CRISPR-Cas9 ribonucleoprotein to Isochrysis galbana for gene editing of URA3 gene.
AUTHORS: Andrea Highfield, Glen Wheeler
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a method for gene editing in Isochrysis galbana. It uses a ribonucleoprotein (RNP) appro... | ["[Prepare Isochryis galbana CCMP 1323 cells]\nPrepare 50% salinity F/2; 1 % (w/v) agar plates in advance. These can be stored for up to a month at 4oC. Ensure plates are dried in a sterile hood before use.", "[Prepare Isochryis galbana CCMP 1323 cells]\nGrow Isochrysis galbana cells in 50% salinity F/2 liquid media u... |
null | null | null | dx.doi.org/10.17504/protocols.io.jazcif6 | null | null | TITLE: No Title
AUTHORS:
[STEPS] | [] |
45,134 | Single cell CUT and Tag on 10x genomics platform | 4 | dx.doi.org/10.17504/protocols.io.bqbnmsme | https://www.protocols.io/view/single-cell-cut-and-tag-on-10x-genomics-platform-bqbnmsme | Marek Bartosovic, Goncalo Castelo-Branco | TITLE: Single cell CUT and Tag on 10x genomics platform
AUTHORS: Marek Bartosovic, Goncalo Castelo-Branco
[DESCRIPTION]
scCU&Tag on 10x platform uses scCUT&Tag protocol from Steven Henikoff's lab (Kaya-Okur et al., 2019), and scATAC-seq chromium platform (10x Genomics) to perform single-cell barcoding. The method can ... | ["[Nuclei preparation and primary antibody incubation] Dissociate your tissue/ cell line into a single-cell (single-nuclei) suspension and count your cells using manual counting chamber. We generally use between 150,000-250,000 cells as input from fresh samples and up to 500,000 nuclei extracted from frozen tissue.\n\n... |
72,729 | Goga Lab RT-qPCR protocol: QuantStudio6 Machine | 4 | null | https://www.protocols.io/view/goga-lab-rt-qpcr-protocol-quantstudio6-machine-ci9zuh76 | Jeremy.williams | TITLE: Goga Lab RT-qPCR protocol: QuantStudio6 Machine
AUTHORS: Jeremy.williams
[DESCRIPTION]
Guidelines for preparing RT-qPCR samples for QuantStudio 6 located in HSW7 lab space.
[BEFORE_START]
*Thaw on ice (leave time!) and keep all reagents on ice through preparation. Prepare the plate on ice.
[GUIDELINES]
*star... | ["Use 'GogaLab-RTqPCR-Preparation' Excel spreadsheet to input your sample number and calculate reagent volumes.", "Mix your forward and reverse primer pairs together, to a final dilution of 10uM forward and 10uM reverse. For example, add 10uL each of forward and reverse primers to 80uL PCR-quality DI for 100uL final vo... |
73,453 | Single nucleotide polymorphism in vitamin D receptor gene and dental caries | 1 | null | https://www.protocols.io/view/single-nucleotide-polymorphism-in-vitamin-d-recept-cjymupu6 | Sudhir Varma | TITLE: Single nucleotide polymorphism in vitamin D receptor gene and dental caries
AUTHORS: Sudhir Varma
[DESCRIPTION]
Ubiquitous nature of dental caries in all the populations globally, varies in between and in populations due to its complex nature. The fact that it cannot be prevented and its onset may be at any poi... | ["[Single nucleotide polymorphism in vitamin D receptor gene and dental caries] 5ml of unstimulated salivary samples were collected and analyzed for salivary Vitamin D and LL-37 levels. Salivary DNA isolation was done and PCR RFLP was conducted for VDR gene SNP’s Taq1,Apa1 and Bsm1", "[Single nucleotide polymorphism in... |
11,703 | Field-adapted PPRV whole genome MinION library build | 1 | dx.doi.org/10.17504/protocols.io.pnxdmfn | https://www.protocols.io/view/field-adapted-pprv-whole-genome-minion-library-bui-pnxdmfn | Emeli Torsson, Emeli Torsson, Oskar Karlsson Lindsjö | TITLE: Field-adapted PPRV whole genome MinION library build
AUTHORS: Emeli Torsson, Emeli Torsson, Oskar Karlsson Lindsjö
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Peste-des-petit-ruminants virus is currently the focus of a control and eradication program launched by the FAO and OIE. One of th... | ["[Amplicon preparation]\nSet up the following reaction AB1Random hexamers (50 ng/µl)1 µl2dNTP mix (10 mM)1 µl 3RNA1 - 11 µl4DEPCto reach 13 µl5Total 13 µlMix and centrifuge, then heat to anneal primers\nAB1Random hexamers (50 ng/µl)1 µl2dNTP mix (10 mM)1 µl 3RNA1 - 11 µl4DEPCto reach 13 µl5Total 1... |
null | null | null | dx.doi.org/10.17504/protocols.io.k7qczmw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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42,608 | Axy Prep 质粒DNA小量提取 | 4 | null | https://www.protocols.io/view/axy-prep-dna-bmuqk6vw | 张 雪 | TITLE: Axy Prep 质粒DNA小量提取
AUTHORS: 张 雪
[STEPS]
?. 取菌液于2ml圆底EP管中，12000rcf，1min，弃上清
?. 加入250µl Buffer S1（细菌悬浮液，已加RNase A，4°C储存），振荡器悬浮细菌沉淀
?. 裂解：加入250µl Buffer S2（细菌裂解液），温和翻转4-6次，静置至形成透亮液体（不超过5min）
?. 中和：加入350µl Buffer S3（中和液），温和翻转6-8次，12000rcf，10min
?. 取上清于制备管（置于配套的2ml离心管中），12000rcf，1min，弃滤液
?. 结合：加入500µl Buffer W1（洗涤液）... | ["取菌液于2ml圆底EP管中，12000rcf，1min，弃上清", "加入250µl Buffer S1（细菌悬浮液，已加RNase A，4°C储存），振荡器悬浮细菌沉淀", "裂解：加入250µl Buffer S2（细菌裂解液），温和翻转4-6次，静置至形成透亮液体（不超过5min）", "中和：加入350µl Buffer S3（中和液），温和翻转6-8次，12000rcf，10min", "取上清于制备管（置于配套的2ml离心管中），12000rcf，1min，弃滤液", "结合：加入500µl Buffer W1（洗涤液），12000rcf，1min，弃滤液", "洗涤：加入700µl Buffer W2（去盐液，已加... |
87,814 | Cell line information | 1 | dx.doi.org/10.17504/protocols.io.rm7vz82o8vx1/v4 | https://www.protocols.io/view/cell-line-information-czzex73e | Philippa R Kennedy, Melissa Khaw, Amanda Russell | TITLE: Cell line information
AUTHORS: Philippa R Kennedy, Melissa Khaw, Amanda Russell
[DESCRIPTION]
An amalgamation of cell line data in the lab. Its origin and standard culture conditions.
[STEPS]
SECTION: Overview
1. All cells are maintained in humidified incubators at 37°C, 5% CO2, unless otherwise specified.
... | ["[Overview] All cells are maintained in humidified incubators at 37°C, 5% CO2, unless otherwise specified. \n\nAll cells are routinely tested for mycoplasma infection using a PCR-based test (Universal Mycoplasma Detection Kit, ATCC Cat. No. 30-1012K)\n\nDates of purchase are provided. Aliquots of purchased cells lines... |
25,512 | Clostridia cultivation | 1 | dx.doi.org/10.17504/protocols.io.yxmvm76eov3p/v1 | https://www.protocols.io/view/clostridia-cultivation-46ggzbw | Eva Petrova, Roey Angel | TITLE: Clostridia cultivation
AUTHORS: Eva Petrova, Roey Angel
[DESCRIPTION]
adopted from Dr Tomasz Grenda (2018)
Pictures of C. perfringens strains grown on Willis – Hobbs agar:
http://www.medycynawet.edu.pl/images/stories/pdf/pdf2018/00-artwait/2019016161.pdf
Pictures of C. botulinum type A (proteolytic) strain o... | ["[Cultivation] Inoculate about 1 g of sample into two tubes with preregenerated (by thermal deoxygenation or conditioning in anaerobic conditions) TPGY broth. \nSubmit half of inoculated tubes to pasteurisation process at 70°C for 15 min and then incubate all of them in an anaerobic jar/chamber at 30°C or 37°C (optio... |
28,023 | U Michigan - DNA Extraction for Illumina 16S rRNA Extraction | null | dx.doi.org/10.17504/protocols.io.7kxhkxn | null | Vincent Young | TITLE: U Michigan - DNA Extraction for Illumina 16S rRNA Extraction
AUTHORS: Vincent Young
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">This protocol is for the submission of tissue/fecal samples for DNA extraction... | ["Briefly centrifuge the PowerMag Glass Bead plate to collect beads at the bottom of the well. In a clean hood, add a maximum of 0.25g or 250 uL of sample to the PowerMag Glass Bead plate and seal with mat. Reserve at least three wells in the bead plate for controls. Maximum number of samples per plate is 93. Clear... |
45,973 | Expression analysis about cell lines in CCLE | 5 | dx.doi.org/10.17504/protocols.io.bq5vmy66 | https://www.protocols.io/view/expression-analysis-about-cell-lines-in-ccle-bq5vmy66 | Keita Fukuyama, iwaisako | TITLE: Expression analysis about cell lines in CCLE
AUTHORS: Keita Fukuyama, iwaisako
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Cancer cell lines are widely used in basic research to study cancer development, growth, invasion, or metastasis. They are also used for the development and screenin... | ["[Cell line comparison]\n1 Data acquisitionmRNA expression data (CCLE_Expression.Arrays_2013-03-18.tar.gz) and annotation files (CCLE_Expression.Arrays.sif_2012-10-18.txt) were downloaded from the CCLE (https://portals.broadinstitute.org/ccle). The Catalogue of Somatic Mutations in Cancer (COSMIC) data were downloaded... |
90,467 | MBA DToL DNA barcoding of macroalgae and marine protists, fungi and lichens – detailed Standard Operating Procedure | 1 | dx.doi.org/10.17504/protocols.io.4r3l22y53l1y/v1 | https://www.protocols.io/view/mba-dtol-dna-barcoding-of-macroalgae-and-marine-pr-c4kbyusn | Helen Jenkins, Rebekka Uhl, Joanna Harley, Susan Wharam | TITLE: MBA DToL DNA barcoding of macroalgae and marine protists, fungi and lichens – detailed Standard Operating Procedure
AUTHORS: Helen Jenkins, Rebekka Uhl, Joanna Harley, Susan Wharam
[DESCRIPTION]
Version 1.5
Purpose: This SOP outlines the method used to DNA barcode macroalgae and marine protists (microalgae), f... | ["Sequence generation\nNote: the method has evolved during the project, and has therefore varied between\nsamples. Initially, DNA was extracted from samples prior to PCR. Later,\ntissue-direct, Phire PCR was used to improve throughput and potentially lessen\nthe impacts of inhibiters in samples. Both methods generate r... |
61,838 | Quantification of the SARS-CoV-2 using Nanotrap Particles®, the QIAcuity™ Digital PCR System, and GT-Digital SARS-CoV-2 Wastewater Surveillance Assay | 4 | dx.doi.org/10.17504/protocols.io.e6nvwk8b2vmk/v1 | https://www.protocols.io/view/quantification-of-the-sars-cov-2-using-nanotrap-pa-b8mnru5e | Solana Narum, Thibault Stalder, Erik Coats, Eva Top | TITLE: Quantification of the SARS-CoV-2 using Nanotrap Particles®, the QIAcuity™ Digital PCR System, and GT-Digital SARS-CoV-2 Wastewater Surveillance Assay
AUTHORS: Solana Narum, Thibault Stalder, Erik Coats, Eva Top
[DESCRIPTION]
This protocol was developed in an effort to serve as a timely and efficient method f... | ["[Sample Collection] Composite primary influent samples are collected (grab samples, flow composite, or time composite)", "[Sample Collection] 50 mL sub-samples are collected in 50 mL sterile conical tubes. The samples are stored at 4 °C until further processing.", "[Concentration of Viral Fraction]", "[Concentration ... |
33,276 | Smart-seq3 Protocol | null | dx.doi.org/10.17504/protocols.io.bcq4ivyw | null | Michael Hagemann-Jensen, Christoph Ziegenhain, Ping Chen, Daniel Ramsköld, Gert-Jan Hendriks, Anton J.M Larsson, Omid R. Faridani, Rickard Sandberg | TITLE: Smart-seq3 Protocol
AUTHORS: Michael Hagemann-Jensen, Christoph Ziegenhain, Ping Chen, Daniel Ramsköld, Gert-Jan Hendriks, Anton J.M Larsson, Omid R. Faridani, Rickard Sandberg
[STEPS]
?. [Before starting]
This protocol should be carried out in a clean environment. Use ethanol, RNAseZAP, DNA-OFF, or similar to ... | ["[Before starting]\nThis protocol should be carried out in a clean environment. Use ethanol, RNAseZAP, DNA-OFF, or similar to prepare work bench before start.Work quickly and preferably on .Prepare master-mixes right before use.Use multichannel pipettes, liquid dispensers etc. to dispense the master-mixes. Avoid pipe... |
28,329 | qPCR Assay | 1 | null | https://www.protocols.io/view/qpcr-assay-7whhpb6 | Kokila Shankar, Olivier George | TITLE: qPCR Assay
AUTHORS: Kokila Shankar, Olivier George
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is for running qPCR assays using previously generated cDNA. This protocol has been adapted from ThermoFisher (</span><a href="https://www.thermofisher.com/document-connect/do... | ["Make cDNA and H2O master mix by combining cDNA with enough H2O for a total of , and multiplying these values by the number of wells needed. Samples should be run in at least duplicate, but preferably triplicate.\n20 ng\n4.5 µl\nMake sure to account for pipetting error and make slightly more master mix than needed (... |
92,697 | MOLECULAR ANALYSES | 1 | dx.doi.org/10.17504/protocols.io.j8nlkoyzdv5r/v1 | https://www.protocols.io/view/molecular-analyses-c6rzzd76 | Marco A. de Oliveira, Lilian H. Florentino, Thais T. Sales, Rayane N. Lima, Luciana R. C. Barros, Cintia G. Limia, Mariana S. M. Almeida, Maria L. Robledo, Leila M. G. Barros, Eduardo O. Melo, Daniela M. Bittencourt, Stevens K. Rehen, Martín H. Bonamino, Elibio Rech | TITLE: MOLECULAR ANALYSES
AUTHORS: Marco A. de Oliveira, Lilian H. Florentino, Thais T. Sales, Rayane N. Lima, Luciana R. C. Barros, Cintia G. Limia, Mariana S. M. Almeida, Maria L. Robledo, Leila M. G. Barros, Eduardo O. Melo, Daniela M. Bittencourt, Stevens K. Rehen, Martín H. Bonamino, Elibio Rech
[DESCRIPTION]
Thi... | ["[Primer design ● Timing 1d] Select approximately 20 nucleotides both upstream and downstream of the core region of each att site formed in the reporter plasmid after recombination takes place.", "[Primer design ● Timing 1d] Use an online oligo design tool to define the best forward primers annealing to promoter seque... |
51,346 | T4PNK end-healing of RNA samples | 1 | dx.doi.org/10.17504/protocols.io.bwdspa6e | https://www.protocols.io/view/t4pnk-end-healing-of-rna-samples-bwdspa6e | Jonathan Howard | TITLE: T4PNK end-healing of RNA samples
AUTHORS: Jonathan Howard
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Resolution of 5' and 3' ends of sample RNA prior to library preparation.</div></div>
[STEPS]
?. [PNK treatment and cleanup]
Set up the following reaction components in a sterile PCR tube... | ["[PNK treatment and cleanup]\nSet up the following reaction components in a sterile PCR tube: 4 μl 5 × PNK pH 6.5 buffer 0.5 μl PNK 0.5 μl RNasin 5 μl Plus-AlkB/Minus-AlkBRNA sample To 20 μL with Nuclease-free Water", "[PNK treatment and cleanup]\nPut reaction at 37C for 30 mins. This can be done in... |
66,458 | Expression and purification MBP-ATG9 Constructs | 4 | null | https://www.protocols.io/view/expression-and-purification-mbp-atg9-constructs-cc52sy8e | Adam Yokom | TITLE: Expression and purification MBP-ATG9 Constructs
AUTHORS: Adam Yokom
[DESCRIPTION]
Expression and purification from HEK cells of ATG13, ATG101 and FOLDON-ATG9A proteins
[STEPS]
SECTION: Expression
1. Transfect HEK GNTI cells at concentration of 2 × 106 cells/ml
SECTION: Purification
8. Resuspended pellet i... | ["[Expression] Transfect HEK GNTI cells at concentration of 2 × 106 cells/ml", "[Purification] Resuspended pellet in lysis buffer (25 mM HEPES pH 7.5, 200 mM NaCl, 2 mM MgCl2, 1 mM TCEP, 5 mM EDTA, 10% Glycerol) with 1% Triton X-100 and protease inhibitor cocktail (Thermo Scientific, Waltham, MA)", "[Expression] Dilute... |
12,968 | Nucleic acids preparations | null | dx.doi.org/10.17504/protocols.io.qwgdxbw | null | Adriana Alberti, Julie Poulain, Stefan Engelen, Karine Labadie, Sarah Romac, Isabel Ferrera, Guillaume Albini, Jean-Marc Aury, Caroline Belser, Alexis Bertrand, Corinne Cruaud, Corinne Da Silva, Carole Dossat, Frédéric Gavory, Shahinaz Gas, Julie Guy, Maud Haquelle, E'krame Jacoby, Olivier Jaillon, Arnaud Lemainque, E... | TITLE: Nucleic acids preparations
AUTHORS: Adriana Alberti, Julie Poulain, Stefan Engelen, Karine Labadie, Sarah Romac, Isabel Ferrera, Guillaume Albini, Jean-Marc Aury, Caroline Belser, Alexis Bertrand, Corinne Cruaud, Corinne Da Silva, Carole Dossat, Frédéric Gavory, Shahinaz Gas, Julie Guy, Maud Haquelle, E'krame J... | ["Please select nucleic acids extraction method.Euk_ DNA_RNA_extDNA/RNA extractions from size fractions 0.8–5 μm (or 0.8–3 μm), 0.8–2000 μm, 5–20 μm (or 3–20 μm), 3–2000 μm, 20–180 μm and 180–2000 μmDNA/RNA extractions from size fractions 0.2–1.6 μmgirus_DNA_extDNA extractions from sizData availability e fractions 0.2–... |
22,888 | SPARC Serotonin (5-HT) Immunohistochemistry Protocol in Rat Tissues Labeled with Cholera Toxin B-fragment | null | dx.doi.org/10.17504/protocols.io.2kggctw | null | Elisa Gonzalez-Rothi, Yasin Seven, Latoya Allen, Marissa Ciesla, Gordon Mitchell | TITLE: SPARC Serotonin (5-HT) Immunohistochemistry Protocol in Rat Tissues Labeled with Cholera Toxin B-fragment
AUTHORS: Elisa Gonzalez-Rothi, Yasin Seven, Latoya Allen, Marissa Ciesla, Gordon Mitchell
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the immunofluorescent lab... | ["Day 1: primary antibodies required:5-HT: Rabbit anti-5-HT (Immunostar #20080)Cholera toxin B-fragment: Goat anti-CT-B (Millipore #227040)", "Place 40um transverse spinal cord sections into 1xPBS-Triton (0.1%) in 12 well cell culture plates", "5x washes in 1xPBS-Triton (0.1%) for 5 minutes each at room temperature", ... |
66,879 | Preparation of ATP13A2 cryo-EM grids | 6 | dx.doi.org/10.17504/protocols.io.q26g74eb9gwz/v1 | https://www.protocols.io/view/preparation-of-atp13a2-cryo-em-grids-cdi7s4hn | Sue Sim, eunyong_park | TITLE: Preparation of ATP13A2 cryo-EM grids
AUTHORS: Sue Sim, eunyong_park
[DESCRIPTION]
Preparing cryo-EM grids using purified ATP13A2 samples
[STEPS]
SECTION: Preparing samples
1. Spin purified and concentrated ATP13A2 sample (5-7 mg/mL) after SEC at 17000 x g, 10 min, 4 °C
SECTION: Preparing samples
2. Keep p... | ["[Preparing samples] Spin purified and concentrated ATP13A2 sample (5-7 mg/mL) after SEC at 17000 x g, 10 min, 4 °C", "[Preparing samples] Keep protein on ice", "Plasma clean grids", "Used gold holey carbon grids (Quantifoil R 1.2/1.3, 400 mesh) and PELCO easiGlow Glow Discharge Cleaning System (0.39 mBar, 25-30 mA, 4... |
92,524 | Visium Direct Mount FFPE v2 -- University of Minnesota TMCs | 1 | dx.doi.org/10.17504/protocols.io.kxygx3qpkg8j/v2 | https://www.protocols.io/view/visium-direct-mount-ffpe-v2-university-of-minnesot-c6kkzcuw | Laura J Niedernhofer, David A Bernlohr | TITLE: Visium Direct Mount FFPE v2 -- University of Minnesota TMCs
AUTHORS: Laura J Niedernhofer, David A Bernlohr
[DESCRIPTION]
The Visium Spatial Gene Expression for FFPE is designed to measure mRNA in tissue sections derived
from formalin fixed & paraffin embedded (FFPE) tissue samples and requires a Visium Spatial... | ["[Deparaffinization, H&E Staining, Imaging & Decrosslinking]", "[Library Preparation & Sequencing]", "[FASTQ Generation] BCL data from Illumina sequencer is demultiplexed and converted into FASTQ format using bcl2fastq software version 2.20.0"] |
69,926 | Immunofluorescence on paraffin sections | 4 | dx.doi.org/10.17504/protocols.io.rm7vzbn62vx1/v1 | https://www.protocols.io/view/immunofluorescence-on-paraffin-sections-cgietube | miquel.vila | TITLE: Immunofluorescence on paraffin sections
AUTHORS: miquel.vila
[DESCRIPTION]
Immunofluorescence protocol on paraffin-embedded rat brain sections
[STEPS]
SECTION: 1. Deparaffinization and hydratation :
1. Put the slides 30 min in the incubator at 60ºC
SECTION: 1. Deparaffinization and hydratation :
2. Wash 3x3 m... | ["[1. Deparaffinization and hydratation :] Put the slides 30 min in the incubator at 60ºC", "[1. Deparaffinization and hydratation :] Wash 3x3 min in xylene", "[1. Deparaffinization and hydratation :] Wash 1x10 min in ethanol 100%", "[1. Deparaffinization and hydratation :] Wash 1x10 min in ethanol 95%", "[1. Deparaffi... |
null | null | null | dx.doi.org/10.17504/protocols.io.gg4btyw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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15,782 | Example of two-path protocol | null | dx.doi.org/10.17504/protocols.io.tneembe | null | Cleyde Helena | TITLE: Example of two-path protocol
AUTHORS: Cleyde Helena
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is an example of a protocol that have a common first steps, then forks into two different ones.</div></div>
[STEPS]
?. [Amount]
Add of Solution A into a beacker
10 µl
?. [Concentration]
P... | ["[Amount]\nAdd of Solution A into a beacker\n10 µl", "[Concentration]\nPrepare of 0.9% NaClAdd of PBS\n100 ml\n20 ml\n[(adjust pH to 7)]", "[Incubation]\nMix Steps 1 and 2 at for", "[Incubation]\nIncubate an extra", "[Incubation]\nLet it cool down and store in a freezer", "[Incubation]\nproceed with the experiment by... |
100,075 | Clinical features and management of VEXAS syndrome in critical care: a scoping review protocol | 0 | null | https://www.protocols.io/view/clinical-features-and-management-of-vexas-syndrome-ddyj27un | Kasumi Satoh, Yasushi Tsujimoto, Daisuke Kasugai, Kazuki Okura, Takao Ono, Yuki Miyamoto, Tasuku Matsuyama, Taketo Watase, Hajime Nakae, Tadahiro Goto | TITLE: Clinical features and management of VEXAS syndrome in critical care: a scoping review protocol
AUTHORS: Kasumi Satoh, Yasushi Tsujimoto, Daisuke Kasugai, Kazuki Okura, Takao Ono, Yuki Miyamoto, Tasuku Matsuyama, Taketo Watase, Hajime Nakae, Tadahiro Goto
[DESCRIPTION]
Objective: This study aims to understand th... | ["[Introduction] Vacuoles, E1 enzyme, X-linked, Autoinflammatory, Somatic (VEXAS) syndrome is an acquired autoinflammatory disorder that primarily affects men over 50 years of age and was identified in 2020 as a new disease concept associated with mutations in the Ubiquitin-like modifier activating enzyme 1 (UBA1) gene... |
47,510 | Polyelectrolyte-chain-at-equilibrium | 1 | dx.doi.org/10.17504/protocols.io.bsmwnc7e | https://www.protocols.io/view/polyelectrolyte-chain-at-equilibrium-bsmwnc7e | Mike Edwards | TITLE: Polyelectrolyte-chain-at-equilibrium
AUTHORS: Mike Edwards
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>By means of the density functional theory framework (DFT) as well as the molecular dynamic simulations (MD), a polyelectrolyte chain (PE) in the good solvent conditions at therma... | [] |
59,613 | FLASH-seq UMI protocol | 4 | dx.doi.org/10.17504/protocols.io.bp2l619rdvqe/v2 | https://www.protocols.io/view/flash-seq-umi-protocol-b6f5rbq6 | Simone Picelli, Vincent Hahaut | TITLE: FLASH-seq UMI protocol
AUTHORS: Simone Picelli, Vincent Hahaut
[DESCRIPTION]
The single-cell RNA-sequencing (scRNA-seq) field has evolved tremendously since the first paper was published back in 2009. While the first methods analysed just a handful of cells, the throughput and performance rapidly increased o... | ["[Prepare lysis mix] Prepare the following lysis mix:\n ReagentReaction concentrationVolume (µl)384-well plateTriton-X100 (10% v/v)0.2%0.0208.448dNTP mix (25 mM each)6 mM0.240101.376STRT-P1-T31 oligo (100 µM)1.8 mM0.0187.603RNAse inhibitor (40 U/µl)1.2 U/µl0.03012.672DTT (100 mM)1.2 mM0.0125.069dCTP (100 µM)9 mM0.0... |
77,393 | Virome DNA extraction with phenol-chloroform | 1 | dx.doi.org/10.17504/protocols.io.ewov1oxdklr2/v1 | https://www.protocols.io/view/virome-dna-extraction-with-phenol-chloroform-cptrvnm6 | Adair Borges | TITLE: Virome DNA extraction with phenol-chloroform
AUTHORS: Adair Borges
[DESCRIPTION]
This protocol details high-molecular-weight DNA extraction from bacteriophages using phenol-chloroform. This protocol can be performed on a virome harvested from a microbial community, or a single phage amplified in the lab.
[STE... | ["[Degradation of host nucleic acids] To degrade any non-encapsulated nucleic acids, treat the concentrated phage lysate with 10 µg/mL RNase A (NEB T3018) and 10 µg/mL DNase I (NEB M0303). Digest for 1 h at room temperature or 4 °C overnight. Store phage at 4 °C.", "[Phage DNA extraction (using phenol-chloroform)] Stri... |
41,142 | ELISA for quantification of IL-20 in human serum or plasma. | 6 | dx.doi.org/10.17504/protocols.io.bkewktfe | https://www.protocols.io/view/elisa-for-quantification-of-il-20-in-human-serum-bkewktfe | Angel Justiz-Vaillant | TITLE: ELISA for quantification of IL-20 in human serum or plasma.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Interleukins (IL) are a type of cytokine first thought to be expressed by leukocytes alone but have later been found to be produced by many other bod... | ["An anti-human IL-20 coating antibody is adsorbed onto the microwells by incubation overnight at 4°C.", "Add 50 µl of human serum. Human IL-20 present in the serum sample binds to antibodies adsorbed to the microwells.", "The microplate is blocked with 3% non-fat milk-PBS buffer and later wash to remove unbound protei... |
30,790 | Flex-T™ Tetramer and Cell Staining Protocol | null | dx.doi.org/10.17504/protocols.io.babeiaje | null | Sam Li | TITLE: Flex-T™ Tetramer and Cell Staining Protocol
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Using UV-induced peptide exchange, MHC/peptide monomers can be generated with conditional Flex-T™ monomers that harbor peptides of interest in their binding grooves. These new MHC monom... | ["[Peptide Exchange:]\nBring all reagents to 0°C by putting them on ice.", "[Peptide Exchange:]\nDilute 10mM stock solutions of peptides of choice to 400µM by mixing 5µl of peptide stock solution with 120µl PBS, and keep on ice.", "[Peptide Exchange:]\nAdd 20µl diluted peptide (400µM) and 20µl peptide Flex-T™ monomer U... |
null | null | null | dx.doi.org/10.17504/protocols.io.cdjs4m | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is the PCR protocol for Phusion® High-Fidelity DNA Polymerase (M0530)
[BEFORE_START]
Annealing temperatures should be determined using the <a href="http://tmcalculator.neb.com/#!/" target="_blank">NEB Annealing Temp Calculator</a>.
[GUIDELINES]
<strong>OVERVIEW</... | [] |
92,232 | Mycoplasma Removal Treatment Protocols | 1 | dx.doi.org/10.17504/protocols.io.kxygx34pkg8j/v1 | https://www.protocols.io/view/mycoplasma-removal-treatment-protocols-c6bgzajw | Carolina Lopez | TITLE: Mycoplasma Removal Treatment Protocols
AUTHORS: Carolina Lopez
[DESCRIPTION]
This protocol describes three mycoplasma removal procedures to be utilized depending on need. The protocols are described from milder/maintenance to the harshest option to be used in extreme cases of contamination when it is not possib... | ["[Mycoplasma Treatment Protocols] NOTES for effective treatment\n\nA. All treatment antibiotics should be added directly to the media at time of use. They should not be diluted or stored in media.\n\nB. For the most effective treatment, the cells should be trypsinized when the media is changed to release any mycoplas... |
64,030 | UroMOCA and StimPod Daily Testing | 3 | dx.doi.org/10.17504/protocols.io.261gen84yg47/v1 | https://www.protocols.io/view/uromoca-and-stimpod-daily-testing-car6sd9e | Dennis Bourbeau | TITLE: UroMOCA and StimPod Daily Testing
AUTHORS: Dennis Bourbeau
[DESCRIPTION]
Protocol for daily stimulation using StimPods
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.n4tdgwn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Purpose</strong></p>
<p>To describe the LN34 real-time RT-PCR assay procedure used for the qualitative detection of lyssavirus RNA in whole RNA extracted from brain tissue samples. The assay detects RNA from diverse lyssaviruses at varying concentrations [1]. </p>
[B... | [] |
86,277 | IGVF Liver nuclei isolation protocol | 4 | null | https://www.protocols.io/view/igvf-liver-nuclei-isolation-protocol-cyhdxt26 | Elisabeth Rebboah | TITLE: IGVF Liver nuclei isolation protocol
AUTHORS: Elisabeth Rebboah
[DESCRIPTION]
This protocol describes isolation of nuclei from 10 week old whole mouse livers from 8 founder strains (B6J, AJ, 129S1J, NZOJ, WSBJ, NODJ, PWKJ, and CASTJ), preparation of a single nucleus suspension, and fixation for single nucleus R... | [] |
64,417 | Simpli Keto + ACV Gummies – Shocking Scam Alert! Read Customer Reviews | 3 | dx.doi.org/10.17504/protocols.io.3byl4b1n2vo5/v1 | https://www.protocols.io/view/simpli-keto-acv-gummies-shocking-scam-alert-read-c-ca59sg96 | JosephDHedberg | TITLE: Simpli Keto + ACV Gummies – Shocking Scam Alert! Read Customer Reviews
AUTHORS: JosephDHedberg
[DESCRIPTION]
Simpli ACV Keto Gummies are easily purchased from online stores. You need to visit the official website of manufacturers and producers who deliver high-quality and affordable keto candies to potential ... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.qq6dvze | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is used to clarity the process of total DNA extration for our Betta splendens genome.</p>
[STEPS]
?.
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23,767 | Cultivating Melanized Fungi from Biological Soil Crust and Rock Surfaces | null | dx.doi.org/10.17504/protocols.io.3fxgjpn | null | Tania Kurbessoian | TITLE: Cultivating Melanized Fungi from Biological Soil Crust and Rock Surfaces
AUTHORS: Tania Kurbessoian
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">As the interest to understand melanized fungi becomes more of a focus due to pathological diseases, there needs to be a clearer method to isolate... | ["of sample (either biocrust, soil or rock surface can be used) placed in microcentrifuge tube.\n0.1 g", "Vortex (on highest setting) sample for 10 minutes until solution becomes a slurry.\nRock surface samples may not become a slurry.", "Preparing the Serial DilutionPrepare 3 other microcentrifuge tubes with .\n[ste... |
60,465 | HuBMAP | GE/ University of Washington Cell DIVE™ Modality Overview | 1 | dx.doi.org/10.17504/protocols.io.3byl4bwmzvo5/v1 | https://www.protocols.io/view/hubmap-ge-university-of-washington-cell-dive-modal-b7arrid6 | Liz McDonough | TITLE: HuBMAP | GE/ University of Washington Cell DIVE™ Modality Overview
AUTHORS: Liz McDonough
[DESCRIPTION]
This is an overview of all protocols currently in use for the GE/University of Washington Cell DIVE collaboration for the Human BioMolecular Atlas Program (HuBMAP). It includes links to each of the individu... | ["Prepare paraffin blocks and FFPE sections from tissue samples.\n\nHuBMAP Tissue Preservation Protocol", "Deparaffinize and rehydrate slides.\n\nCell DIVE™ Platform | Slide Clearing and Antigen Retrieval", "Characterize antibodies (primary/secondary, direct conjugates, and zenon labelled antibodies) and determine any ... |
74,417 | MinION Sequencing protocol for Rabies virus of Arctic lineage | 4 | dx.doi.org/10.17504/protocols.io.3byl4jzb8lo5/v1 | https://www.protocols.io/view/minion-sequencing-protocol-for-rabies-virus-of-arc-ckwruxd6 | pramadaprasad, Harsha P.K., Chitra Pattabiraman | TITLE: MinION Sequencing protocol for Rabies virus of Arctic lineage
AUTHORS: pramadaprasad, Harsha P.K., Chitra Pattabiraman
[DESCRIPTION]
An ONT MinION-based sequencing protocol to retrieve whole genomes of Rabies virus of the Artic lineage. Primers were selected using PrimalScheme (https://primalscheme.com/) and th... | ["[RNA Extraction] Extract and purify RNA from Brain tissue homogenate using .", "[Amplicon PCR] Primers are designed using Primal Scheme. Resuspend the lyophilized oligos fully in Nuclease free water / 1X TE to a concentration of 100µM, vortex thoroughly,Nuclease-free, and spin down.", "[Amplicon PCR] Separate odd an... |
16,171 | Species delimitation of Ophiothrix using bPTP | null | dx.doi.org/10.17504/protocols.io.t2jeqcn | null | Renata Alitto, Michela Borges, Letícia Dias de Oliveira, Karin Regina Seger, Luciana Bolsoni Lourenço | TITLE: Species delimitation of Ophiothrix using bPTP
AUTHORS: Renata Alitto, Michela Borges, Letícia Dias de Oliveira, Karin Regina Seger, Luciana Bolsoni Lourenço
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This test adds Bayesian support (BS) values to the nodes of the input tree and delimit s... | ["[Phylogenetic tree]\nThe phylogenetic tree generated by the Bayesian Inference was submitted to the Bayesian Poisson Tree Processes - bPTP [56] to test species boundaries.", "[Analyses]\nThe analyses were conducted on the web server (available at http://species.h-its.org/ptp/). The parameters for the run were 500000 ... |
69,097 | Data and script to reproduce the analysis in 'Changes in methodological study characteristics in psychology between 2010-2021' | 5 | dx.doi.org/10.17504/protocols.io.j8nlkk775l5r/v1 | https://www.protocols.io/view/data-and-script-to-reproduce-the-analysis-in-39-ch-cfqhtmt6 | Ingmar Böschen | TITLE: Data and script to reproduce the analysis in 'Changes in methodological study characteristics in psychology between 2010-2021'
AUTHORS: Ingmar Böschen
[DESCRIPTION]
This protocol contains the R script and data files to reproduce the analysis presented in: Böschen, I. (2022).Changes in methodological stu... | ["Download the four data files and the R script provided at:\nhttps://www.protocols.io/workspaces/methodological-changes-in-psychology", "Open the script in R, set the working directory and run the analysis."] |
55,952 | Photolithography for microfluidics | 1 | null | https://www.protocols.io/view/photolithography-for-microfluidics-b2vqqe5w | Nadanai Laohakunakorn | TITLE: Photolithography for microfluidics
AUTHORS: Nadanai Laohakunakorn
[DESCRIPTION]
Photolithography for microfluidic mold fabrication, successfully tested at the Scottish Microelectronics Centre. Produces rounded flow layer using positive resist SPR 220-7 with ~12um features, and rectangular control layer using ne... | ["[Flow Layer] HMDS priming", "[Control layer] O2 plasma treatment", "[Flow Layer] Prebake", "[Flow Layer] Spin coat with SPR 220-7 (Megaposit)", "[Flow Layer] Softbake", "[Flow Layer] Exposure", "[Flow Layer] Post-exposure bake", "[Flow Layer] Develop with MF26A", "[Flow Layer] Reflow", "[Flow Layer] Prime a clean Si ... |
77,711 | Systematic literature review | 1 | dx.doi.org/10.17504/protocols.io.n92ldpjkol5b/v1 | https://www.protocols.io/view/systematic-literature-review-cp5pvq5n | Carlos Reis, Aloísio Santos Nascimento Filho, Ingrid WinKler | TITLE: Systematic literature review
AUTHORS: Carlos Reis, Aloísio Santos Nascimento Filho, Ingrid WinKler
[DESCRIPTION]
This protocol aims to ensure the reproducibility of the systematic literature review carried out on state-of-the-art models for developing strategies for professional administrations, with emphasis o... | ["[State-of-the-art model features] To identify the characteristics of the models on the formulation of strategies for schools and hospitals, a systematic literature review (SLR) was carried out using only contemporary data from the last five years to verify the frontier of knowledge in relation to the theme. A bibliog... |
85,876 | Example | 5 | dx.doi.org/10.17504/protocols.io.5jyl8pjm9g2w/v1 | https://www.protocols.io/view/example-cx4uxqww | Chasz Griego | TITLE: Example
AUTHORS: Chasz Griego
[DESCRIPTION]
abstract
[STEPS]
1. Step 1
2. 100 °C Heat up for 5 min
3.
| ["Step 1", "100 °C Heat up for 5 min"] |
25,093 | RNA Isolation from Plant Tissue Protocol 5: pBIOZOL Method | null | dx.doi.org/10.17504/protocols.io.4rdgv26 | null | null | TITLE: RNA Isolation from Plant Tissue Protocol 5: pBIOZOL Method
AUTHORS:
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Implemented by: Beijing Genomics Institute</div><div class = "text-block"><span>This protocol is part of a collection of eighteen protocols used to isolate total RNA from plant... | ["Grind tissue to a powder in liquid nitrogen.", "Add of cold () pBIOZOL Reagent for up to of frozen, ground tissue.\n1.3 ml\n4 °C\n100 mg", "Incubate the tube for at .\n20 °C\nLay the tube down horizontally to maximize surface area during RNA extraction.", "Centrifuge for at .", "Add of NaCl to the extract.\n100... |
37,137 | Validation of Selected RNA Extraction Method | 1 | null | https://www.protocols.io/view/validation-of-selected-rna-extraction-method-bghrjt56 | Ariel Cerda, Catalina Ibarra-Henriquez, Valentina Sebastian, Grace Armijo, Liliana Lamig, Carolina Miranda, Marcela Lagos, Sandra Solari, Ana María Guzmán, Teresa Quiroga, Susan Hitschfeld, Eleodoro Riveras, Marcela Ferres, Rodrigo A. Gutiérrez, Patricia García, Aniela Wozniak | TITLE: Validation of Selected RNA Extraction Method
AUTHORS: Ariel Cerda, Catalina Ibarra-Henriquez, Valentina Sebastian, Grace Armijo, Liliana Lamig, Carolina Miranda, Marcela Lagos, Sandra Solari, Ana María Guzmán, Teresa Quiroga, Susan Hitschfeld, Eleodoro Riveras, Marcela Ferres, Rodrigo A. Gutiérrez, Patricia Garc... | ["[Biological Samples]\nObtain nasopharyngeal swabs in Universal Transport Medium (UTM) from 50 patients that attend outpatient services at Red Salud UC-CHRISTUS (Santiago, Chile) because of suspected coronavirus infection.\nTwo types of biological samples were used:For preliminary evaluation of the RNA extraction meth... |
71,085 | Plasmid Miniprep for 2022 | 1 | dx.doi.org/10.17504/protocols.io.dm6gpjwdpgzp/v1 | https://www.protocols.io/view/plasmid-miniprep-for-2022-chnmt5c6 | Team Fudan iGEM | TITLE: Plasmid Miniprep for 2022
AUTHORS: Team Fudan iGEM
[DESCRIPTION]
Plasmid extraction and purification, based on Vazyme Mini-prep Kit manual.
[STEPS]
1. Pellet bacteria culture in a 1.6mL centrifugation tube at 13,000rpm for 1 minute. Decant supernatant. The pellet in the tube can be stored in -20 freezer if tim... | ["Pellet bacteria culture in a 1.6mL centrifugation tube at 13,000rpm for 1 minute. Decant supernatant. The pellet in the tube can be stored in -20 freezer if time not enough for the following steps.", "Add 250uL of resuspension solution (P1 with RNase) and vortex. After adding RNase into the P1, P1 is stored in 4 degr... |
51,905 | Library Construction Protocols | 1 | dx.doi.org/10.17504/protocols.io.bww9pfh6 | https://www.protocols.io/view/library-construction-protocols-bww9pfh6 | Graham J Etherington, Darren Heavens, David Baker, Ashleigh Lister, Rose McNelly, Gonzalo Garcia, Bernardo Clavijo, Iain Macaulay, Wilfried Haerty, Federica Di Palma | TITLE: Library Construction Protocols
AUTHORS: Graham J Etherington, Darren Heavens, David Baker, Ashleigh Lister, Rose McNelly, Gonzalo Garcia, Bernardo Clavijo, Iain Macaulay, Wilfried Haerty, Federica Di Palma
[DESCRIPTION]
Amplification Free Paired End Library Construction Protocol.
[STEPS]
SECTION: PCR-free Illu... | ["[PCR-free Illumina 2500] A total of 600 ng of DNA was sheared in a 60 µL volume on a Covaris S2 (Covaris, Massachusetts, USA) for 1 cycle of 40 s with a duty cycle of 5%, cycles per burst of 200 and intensity of 3.", "[PCR-free Illumina 2500] The fragmented molecules were then end repaired in 100 µL volume using the ... |
44,870 | Versatile Cell-Free Protein Synthesis Systems Based on Chinese Hamster Ovary Cells | 4 | dx.doi.org/10.17504/protocols.io.bp3emqje | https://www.protocols.io/view/versatile-cell-free-protein-synthesis-systems-base-bp3emqje | Lena Thoring, Stefan Kubick | TITLE: Versatile Cell-Free Protein Synthesis Systems Based on Chinese Hamster Ovary Cells
AUTHORS: Lena Thoring, Stefan Kubick
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">We present an alternative production platform for the synthesis of complex proteins. Apart from conventionally applied protei... | ["[3.1 Biomass Production]\nInitially culture CHO -K1 cells in shake flask starting with a density between 0.5 and 0.7 × 106 cells/mL. Cultivation conditions are set to a temperature of , a CO2 concentration of 5% and a shaking speed of 100 RPM.\n37 °C", "[3.1 Biomass Production]\nFor biomass production, the stirred ta... |
null | null | null | dx.doi.org/10.17504/protocols.io.s9reh56 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Learn the basic commands to navigate in a command-line terminal.</p>
[BEFORE_START]
<p><strong>For Windows users :</strong></p>
<p>You will need to install a shell, I personnaly recommand Cygwin. To install Cygwin, go to <a href="https://www.cygwin.com/install.html" target="... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.hvgb63w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Milliplex Cytokine/Chemokine 7-plex manufacturer's protocol</p>
[STEPS]
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?.
?. | [] |
21,871 | Plate assay for identification of salt stress induced changes in Arabidopsis thaliana's Root System Architecture | null | dx.doi.org/10.17504/protocols.io.zkpf4vn | null | Magdalena Julkowska | TITLE: Plate assay for identification of salt stress induced changes in Arabidopsis thaliana's Root System Architecture
AUTHORS: Magdalena Julkowska
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocols is a fairly simple method to study the developmental changes in Root System Architecture... | [] |
94,651 | 1. PERFF-seq: Cell and Nuclei Preparation | 4 | dx.doi.org/10.17504/protocols.io.14egn3k6ql5d/v1 | https://www.protocols.io/view/1-perff-seq-cell-and-nuclei-preparation-c8n3zvgn | Tsion Abay, Robert Stickels, Meril Takizawa, Ronan Chaligne, Caleb Lareau | TITLE: 1. PERFF-seq: Cell and Nuclei Preparation
AUTHORS: Tsion Abay, Robert Stickels, Meril Takizawa, Ronan Chaligne, Caleb Lareau
[DESCRIPTION]
This protocol can be used for preparation of Cells and Fresh-Frozen and Formalin-Fixed Paraffin-Embedded (FFPE) Tissue Derived Nuclei. This protocol should be followed by "... | ["[Nuclei Preparation from Formalin Fixed Paraffin Embedded (FFPE) Tissue (using S2 Genomics Singulator)] ISOLATION", "[Nuclei Preparation from Fresh Frozen Tissue] FIXATION AND PERMEABILIZATION", "[Nuclei Preparation from Fresh Frozen Tissue] Weight tissue to determine the volume of fixation buffer needed. \n2 mL fixa... |
null | null | null | dx.doi.org/10.17504/protocols.io.riid4ce | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Infiltration of leaves with various herbicides, targetting photosynthetic electron transport, were utilized to mimic changes in redox state (otherwise caused by changes in light irradiance) of photosynthetic electron transport components and study the response of APX2. </p>
<... | [] |
73,188 | Senescence Cocktail | 3 | dx.doi.org/10.17504/protocols.io.4r3l24xmxg1y/v2 | https://www.protocols.io/view/senescence-cocktail-cjqcumsw | Sakthikumar Mathivanan | TITLE: Senescence Cocktail
AUTHORS: Sakthikumar Mathivanan
[DESCRIPTION]
Modeling age-related neurodegenerative disorders with human stem cells is difficult due to the embryonic nature of stem cell derived neurons. We developed a chemical cocktail to induce senescence of iPSC-derived neurons to address this challenge.... | [] |
41,529 | Highfield Diagnostics COVID19 LFA Protocol | 2 | dx.doi.org/10.17504/protocols.io.bkszkwf6 | https://www.protocols.io/view/highfield-diagnostics-covid19-lfa-protocol-bkszkwf6 | peijun he | TITLE: Highfield Diagnostics COVID19 LFA Protocol
AUTHORS: peijun he
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Highfield Diagnositc`s has developed a COVID-19 rapid diagnostic test (RDT), which is a lateral flow immunochromatographic assay (LFA), that detects nucleoproteinin nasal swab specime... | [] |
71,476 | Invertebrate bulk sample metabarcoding protocol collection | 2 | dx.doi.org/10.17504/protocols.io.j8nlkw4n6l5r/v4 | https://www.protocols.io/view/invertebrate-bulk-sample-metabarcoding-protocol-co-ch2ut8ew | Dominik Buchner | TITLE: Invertebrate bulk sample metabarcoding protocol collection
AUTHORS: Dominik Buchner
[DESCRIPTION]
This is a collection of protocols currently used in the LeeseLab to perform invertebrate bulk sample metabarcoding. Feel free to contact us if any questions arise.
[STEPS] | [] |
99,452 | AAV Craniotomy | 0 | dx.doi.org/10.17504/protocols.io.5jyl829q7l2w/v1 | https://www.protocols.io/view/aav-craniotomy-ddc422yw | Santiago Unda, Roberta Marongiu, Mihaela Stavarache, Michael G. Kaplitt | TITLE: AAV Craniotomy
AUTHORS: Santiago Unda, Roberta Marongiu, Mihaela Stavarache, Michael G. Kaplitt
[DESCRIPTION]
This protocol is for injection of AAV into a mouse brain using a stereotactic frame and Hamilton syringe.
[GUIDELINES]
Note that sterile technique must be followed during this procedure to avoid health... | ["[Anesthesia] Weigh mice.", "[Anesthesia] Administer intraperitoneal mixture of ketamine (ButlerAnimal Health Supply) and xylazine (Lloyd Laboratories) at concentrations of 110 and 10 mg/kg of body weight, respectively.", "[Anesthesia] Confirm induction of anesthesia.", "[Injection] Place mouse into stereotactic frame... |
45,577 | Swallowing Study Using Water-soluble Contrast Agents Increases Aspiration Sensitivity and Antedates Oral Feeding without Respiratory and Drug Complications: A Prospective, Observational, Case-control Trial | 1 | dx.doi.org/10.17504/protocols.io.bqrhmv36 | https://www.protocols.io/view/swallowing-study-using-water-soluble-contrast-agen-bqrhmv36 | Chang Ho Hwang | TITLE: Swallowing Study Using Water-soluble Contrast Agents Increases Aspiration Sensitivity and Antedates Oral Feeding without Respiratory and Drug Complications: A Prospective, Observational, Case-control Trial
AUTHORS: Chang Ho Hwang
[STEPS]
SECTION: Materials
2.
1. Based on their medical conditions and aspirat... | ["[Materials]", "Based on their medical conditions and aspiration risk, patients undergoing the swallowing study were assigned to iohexol 350 (Omnipaque® [osmolarity 541 mOsm/L, viscosity 10.4 centipoise at 37°C, specific gravity of 1.406], GE Healthcare, USA)19 or barium sulfate (BaSO4 40% [osmolarity 233 mOsm/L, visc... |
76,131 | Ultra-Competent Cells Preparation | 4 | dx.doi.org/10.17504/protocols.io.q26g7yd48gwz/v1 | https://www.protocols.io/view/ultra-competent-cells-preparation-cnkbvcsn | jorge.fernandez | TITLE: Ultra-Competent Cells Preparation
AUTHORS: jorge.fernandez
[DESCRIPTION]
Adaptation of the Inoue protocol for competent cells preparation.
Expected transformation efficiency of 108 colonies per μg of plasmidic DNA.
Original Source: doi:10.1101/pdb.prot101196
[STEPS]
SECTION: Preparation of Transformation ... | ["[Preparation of Transformation Buffer & Reagents] Prepare a buffer with the following composition", "[Preparation of Transformation Buffer & Reagents] Prepare Stock of PIPES 0.5 M\n\nMeasure 7.56 g and dissolve it in 40 mL using a small beaker. Set a magnetic stirrer in the beaker and start stirring. Then,... |
77,480 | Differentiation of human cortical neurons (CNs) from induced pluripotent stem cells (iPSCs) and their coculture with rat astrocytes | 1 | dx.doi.org/10.17504/protocols.io.j8nlkw6rwl5r/v1 | https://www.protocols.io/view/differentiation-of-human-cortical-neurons-cns-from-cpwgvpbw | Quyen Do, Bryan Ng, Richard Wade-Martins | TITLE: Differentiation of human cortical neurons (CNs) from induced pluripotent stem cells (iPSCs) and their coculture with rat astrocytes
AUTHORS: Quyen Do, Bryan Ng, Richard Wade-Martins
[DESCRIPTION]
This protocol described the production of human cortical neurons from induced pluripotent stem cells in cocultured... | ["[Differentiation of iPSCs into Neuronal Progenitor Cells (NPCs)] Day -2: Preparing plates for replating\nTwo days before intending on starting the differentiation (Day -2), add 1 mL/well in a 6-well plate of Geltrex one day prior to replating the iPSCs to begin the differentiation.", "[Differentiation of iPSCs into N... |
43,651 | PCR for amplification of bark beetles or fungal DNA | 3 | dx.doi.org/10.17504/protocols.io.bnvbme2n | https://www.protocols.io/view/pcr-for-amplification-of-bark-beetles-or-fungal-dn-bnvbme2n | Demian F Gomez, You Li, Caroline Storer | TITLE: PCR for amplification of bark beetles or fungal DNA
AUTHORS: Demian F Gomez, You Li, Caroline Storer
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The purpose of this protocol is to conduct PCR of bark beetles or fungal DNA.</div><div class = "text-block"><span>This protocol is part of the ... | [] |
31,279 | Body Asymmetry | 1 | dx.doi.org/10.17504/protocols.io.baspiedn | https://www.protocols.io/view/body-asymmetry-baspiedn | Cristina Zogmaister, Federica Durante, Silvia Mari, Franca Crippa, Chiara Volpato | TITLE: Body Asymmetry
AUTHORS: Cristina Zogmaister, Federica Durante, Silvia Mari, Franca Crippa, Chiara Volpato
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes a measure of asymmetry of images of body shapes.</div><div class = "text-block">Two judges have separately measured... | [] |
50,954 | Ligated intestinal loop mouse model protocol. | 4 | dx.doi.org/10.17504/protocols.io.bvzin74e | https://www.protocols.io/view/ligated-intestinal-loop-mouse-model-protocol-bvzin74e | Pablo Castro-Córdova, Maria José Mendoza-León, Daniel Paredes-Sabja | TITLE: Ligated intestinal loop mouse model protocol.
AUTHORS: Pablo Castro-Córdova, Maria José Mendoza-León, Daniel Paredes-Sabja
[DESCRIPTION]
In the present protocol, we provide a step-by-step protocol with all the critical information to perform an intestinal ligated loop in a mouse model. Using this technique, we... | ["[Surgery] Depth anesthesia was induced in ~3 min with 4 % (v/v) and a flow of 0.6L/min of with an isoflurane induction chamber.", "[Surgery] Take out the mouse from the isoflurane induction chamber, put the mouse prone into the surgery tray, and put the snout (nose and mouth) into the isoflurane mask. The surgery ... |
41,889 | Colorimetric RT-LAMP Research group SARS-COV-2 detection protocol | 1 | dx.doi.org/10.17504/protocols.io.bk59ky96 | https://www.protocols.io/view/colorimetric-rt-lamp-research-group-sars-cov-2-det-bk59ky96 | Teodor Emilov Mentov | TITLE: Colorimetric RT-LAMP Research group SARS-COV-2 detection protocol
AUTHORS: Teodor Emilov Mentov
[STEPS]
?. [vortex swab sample]
Vortex swab sample in Viral transport medium
?. [vortex swab sample]
Take 200µl and transfer to 1,5ml microtube
?. [vortex swab sample]
Add 500ul of ethanol reconstituted lysis buffer... | ["[vortex swab sample]\nVortex swab sample in Viral transport medium", "[vortex swab sample]\nTake 200µl and transfer to 1,5ml microtube", "[vortex swab sample]\nAdd 500ul of ethanol reconstituted lysis buffer incubate 10 minutes. Vortex or shake after", "[vortex swab sample]\nAdd solubilization buffer, and wait 2 min... |
54,146 | E. coli growth curve assay in BG-11 + sucrose | 4 | dx.doi.org/10.17504/protocols.io.by5apy2e | https://www.protocols.io/view/e-coli-growth-curve-assay-in-bg-11-sucrose-by5apy2e | sanjana | TITLE: E. coli growth curve assay in BG-11 + sucrose
AUTHORS: sanjana
[DESCRIPTION]
To obtain growth curves of KJK01 and pCSCX-KJK01 in BG-11 + sucrose and to characterize their growth. This also serves to estimate sucrose consumption and butanol production over time.
This can be adapted for any other bacteria as w... | ["[Primary culture] Inoculate 1 colony of E. coli KJK01 in 5 mL of 1X LB", "[Primary culture] Inoculate 1 colony of E. coli pCSCX-KJK01 in 5 mL of 1X LB with 5 µL Kan50 and 5 µL Amp100", "[Primary culture] Leave both cultures in a shaker incubator at 37 °C and", "[Secondary culture] The next morning, inoculate 900... |
75,108 | LEGACY01: STUDY MANAGEMENT | 1 | null | https://www.protocols.io/view/legacy01-study-management-cmkcu4sw | Katrina M Pollock, Calliope Dendrou | TITLE: LEGACY01: STUDY MANAGEMENT
AUTHORS: Katrina M Pollock, Calliope Dendrou
[DESCRIPTION]
This protocol details study management in an experimental medicine study of seasonal influenza vaccination responses in Lymph nodE single-cell Genomics in AnCestrY (LEGACY01).
[GUIDELINES]
STUDY MANAGEMENT
The day-to-day man... | [] |
51,333 | Single-cell ATAC sequencing | 4 | dx.doi.org/10.17504/protocols.io.bwddpa26 | https://www.protocols.io/view/single-cell-atac-sequencing-bwddpa26 | Klaus H. Kaestner Lab, Suzanne Shapira | TITLE: Single-cell ATAC sequencing
AUTHORS: Klaus H. Kaestner Lab, Suzanne Shapira
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Interrogating cell-type specific chromatin accessibility can reveal cis-regulatory elements linked to downstream gene expression patter... | ["[Steps in pre-processing]\n1. Transfer handpicked islets (approximately 5,000 IEQs) into conical tube. 2. Add of 1xPBS w/o Ca2+, Mg2+ (Rockland, MB-008). Centrifuge for 2 min at RT, 180 xg. Aspirate the supernatant.3. Add of warm ( ) 0.05% Trypsin (Invitrogen, 25300054) to the islets. Pipette up and down with p100... |
102,049 | Perfusion/ Fixation for cryostat slicing for HHC | 0 | dx.doi.org/10.17504/protocols.io.j8nlk8dk5l5r/v1 | https://www.protocols.io/view/perfusion-fixation-for-cryostat-slicing-for-hhc-dfv93n96 | louis-eric.trudeau | TITLE: Perfusion/ Fixation for cryostat slicing for HHC
AUTHORS: louis-eric.trudeau
[DESCRIPTION]
This protocol details the Perfusion and Fixation for cryostat slicing for HHC.
[STEPS]
SECTION: Cryostat slicing
1. Weight the animal.
SECTION: Cryostat slicing
2. Anesthetize the animal with sodium pentobarbital (100 m... | ["[Cryostat slicing] Weight the animal.", "[Cryostat slicing] Anesthetize the animal with sodium pentobarbital (100 mg/kg et 7 mg/ml) by i.p. injection with a 27G needle.", "[Cryostat slicing] Confirm the absence of pain reflex (paw pinch).", "[Cryostat slicing] Perfuse the animal with 50 mL of PBS followed by 50 mL ... |
53,844 | Transformation | 4 | dx.doi.org/10.17504/protocols.io.bytupwnw | https://www.protocols.io/view/transformation-bytupwnw | Shuning Guo | TITLE: Transformation
AUTHORS: Shuning Guo
[DESCRIPTION]
This protocol is used to transform plasmid DNA into competent cells by chemical method or electroporation.
[BEFORE_START]
Do not place the competent cells on the the ice for too long time before start.
[STEPS]
1. Choose one transformation method depending o... | ["Choose one transformation method depending on your requirement of transformation efficiency.", "Wash the 0.1 or 0.2 cm electroporation cuvette (store in 75% ethanol)by tap water for one time and ddH2O for two times and dry in the oven.", "Place the electroporation cuvette on the ice and use UV to disinfect for 20 min... |
70,878 | An experimental approach on dynamic Occlusal Fingerprint Analysis to simulate use-wear development and localisation on stone tools | 1 | dx.doi.org/10.17504/protocols.io.261ge346dl47/v1 | https://www.protocols.io/view/an-experimental-approach-on-dynamic-occlusal-finge-chf6t3re | Hannah Rausch, Ottmar Kullmer, Joao Marreiros, Lisa Schunk, Walter Gneisinger, Ivan Calandra | TITLE: An experimental approach on dynamic Occlusal Fingerprint Analysis to simulate use-wear development and localisation on stone tools
AUTHORS: Hannah Rausch, Ottmar Kullmer, Joao Marreiros, Lisa Schunk, Walter Gneisinger, Ivan Calandra
[DESCRIPTION]
Occlusal Fingerprint Analysis (OFA) was applied to four sets of ... | ["[Sample Documentation] Documentation\n\nBefore and after each experiment, the tool samples and contact material are documented. Note that the contact materials are not documented before the experiment because their surface is featureless. \n\nAcetone is applied to the edge of the tool samples with a cotton swab for i... |
91,118 | S-5 SOIL SHIPPING | 4 | dx.doi.org/10.17504/protocols.io.36wgq3y7ylk5/v1 | https://www.protocols.io/view/s-5-soil-shipping-c48nyzve | REDI-NET Consortium | TITLE: S-5 SOIL SHIPPING
AUTHORS: REDI-NET Consortium
[DESCRIPTION]
This protocol describes soil shipping.
[GUIDELINES]
OBJECTIVE
To outline steps for proper packaging and shipping of preserved soil samples from a REDI-NET Silver Lab to a REDI-NET Gold Lab.
SUMMARY/SCOPE
The overarching aim of the REDI-NET is to d... | ["[SAMPLE PREPARATION] Primary holding sample holding containers must be leak-proof. Samples should be preserved in appropriate preservative, if applicable (REDI-NET Soil Processing SOP S-2). Ensure that the lids are tightly closed to prevent leaking of storage media while in transit.", "[SAMPLE PREPARATION] Pack vials... |
92,535 | Autopsy and Brain Collection and Fixation | 4 | dx.doi.org/10.17504/protocols.io.n92ldm6nnl5b/v1 | https://www.protocols.io/view/autopsy-and-brain-collection-and-fixation-c6kxzcxn | Yaping.Chu, Scott Muller, Jeffrey Kordower | TITLE: Autopsy and Brain Collection and Fixation
AUTHORS: Yaping.Chu, Scott Muller, Jeffrey Kordower
[DESCRIPTION]
Protocol for autopsy and brain collection and fixation in the Kordower Laboratory.
[STEPS]
SECTION: Autopsy
1. Everyone present for autopsy must don Personal Protective Equipment (impermeable gown, shoe ... | ["[Autopsy] Everyone present for autopsy must don Personal Protective Equipment (impermeable gown, shoe covers, hair cover, N95 respirator, face shield, two pairs of nitrile gloves).", "[Autopsy] Place body on table in dorsal recumbency.", "[Autopsy] Place absorbent pads under head and over face. Place head block under... |
96,788 | Endophytic fungal DNA extraction from seeds using Qiagen DNeasy Plant Mini | 0 | dx.doi.org/10.17504/protocols.io.5qpvokxxzl4o/v1 | https://www.protocols.io/view/endophytic-fungal-dna-extraction-from-seeds-using-daru2d6w | Eve Kenny | TITLE: Endophytic fungal DNA extraction from seeds using Qiagen DNeasy Plant Mini
AUTHORS: Eve Kenny
[DESCRIPTION]
This protocol was modified from the QIAGEN Plant Mini Kit Handbook to extract fungal DNA from within the seed coat of small (<1mm diameter) seeds. It can be followed by amplification with fungal specific ... | ["[Surface sterilization and lysis] Rinse seeds in microcentrifuge tube with ddH20 and finger vortex for 1 minute. Replace water and repeat two more times. Move seeds to screw cap tubes and add a large spatula scoop of mini beads (~100 μg).", "[Surface sterilization and lysis] Add 400 μg Buffer AP1 to each tube and us... |
101,946 | SynGO analysis | 0 | dx.doi.org/10.17504/protocols.io.x54v92r94l3e/v1 | https://www.protocols.io/view/syngo-analysis-dfs23nge | Chuyu Chen | TITLE: SynGO analysis
AUTHORS: Chuyu Chen
[DESCRIPTION]
synapse function and gene enrichment analysis
[STEPS]
SECTION: SynGO analysis
1. Convert mouse Gene ID to human genes symbols with ID conversion tool
SECTION: SynGO analysis
2. Copy converted genes symbols to the SynGO input section, select background as brain ... | ["[SynGO analysis] Convert mouse Gene ID to human genes symbols with ID conversion tool", "[SynGO analysis] Copy converted genes symbols to the SynGO input section, select background as brain expressed, and name the experiment in the description", "[SynGO analysis] Start analysis and export data to Excel files", "[SynG... |
17,045 | ChroDrip - IMAC | null | dx.doi.org/10.17504/protocols.io.uvvew66 | null | David Frommholz, Nadine Stefanczyk, Alexandra Ehl | TITLE: ChroDrip - IMAC
AUTHORS: David Frommholz, Nadine Stefanczyk, Alexandra Ehl
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Purification Guide for the Isolation of Histidine-tagged Proteins with ChroDrip Columns by DALEX Biotech.</span></div><div class = "text... | ["[Equilibration]\nIf you start with a dry column, add 5 column volumes deionized water (bed volume is written on the column) and wait until it has drained. Add 0.5 column volumes of nickel or cobalt solution, let the solution drain and add another 5 column volumes of deionized water.When starting with a column which h... |
63,135 | Yeast cells live fluorescence imaging | 4 | dx.doi.org/10.17504/protocols.io.n92ldzqjnv5b/v1 | https://www.protocols.io/view/yeast-cells-live-fluorescence-imaging-b9v7r69n | Florian Wilfling, Fabian Fiedler, Anna Bieber, Cristina Capitanio | TITLE: Yeast cells live fluorescence imaging
AUTHORS: Florian Wilfling, Fabian Fiedler, Anna Bieber, Cristina Capitanio
[DESCRIPTION]
Protocol for sample preparation and live fluorescence imaging of yeast cells.
[STEPS]
SECTION: Yeast cell culture in low fluorescence medium
1. Grow yeast cells overnight in Low... | ["[Yeast cell culture in low fluorescence medium] Grow yeast cells overnight in Low Fluorescence (LoFlo) medium.", "[Yeast cell culture in low fluorescence medium] In the morning dilute cells in LoFlo to OD 0.1.", "[Yeast cell culture in low fluorescence medium] Grow until mid-log phase (0.5–0.8 OD).", "[Pre-treat micr... |
null | null | null | dx.doi.org/10.17504/protocols.io.dsz6f5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
QIAgen's DNeasy Blood & Tissue kit (cat#69504 or 69506) for cultured cells
[BEFORE_START]
<strong>Preparation of buffer AW1 and AW2</strong><br />Add ethanol to AW1 and AW2 as directed on bottle. Stable for one year.<br /><br />If buffer AL has precipitates, warm to 56C unt... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.crqv5v | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?. | [] |
30,660 | Immunofluorescent Staining of Foxp3 in Frozen Sections | null | dx.doi.org/10.17504/protocols.io.97ch9iw | null | Sam Li | TITLE: Immunofluorescent Staining of Foxp3 in Frozen Sections
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">T regulatory cells (also known as Tregs or Regulatory T cells) are essential cells in the immune system that suppress immune responses of other cells, designed to limit exces... | ["Thaw frozen sections in a sealed environment to avoid damage by frozen water crystals (Approximately 1 hour).", "Fix for 5 minutes in acetone (-20°C). Note: Do not use more often than 5 times.", "Dry for 10 minutes at room temperature.", "Incubate sections in TBS-T (50 mM Tris, 150 mM NaCl, adjust pH with HCl to 7.6 ... |
27,826 | Bead-free long fragment LSK109 library preparation | null | dx.doi.org/10.17504/protocols.io.7eshjee | null | John Tyson | TITLE: Bead-free long fragment LSK109 library preparation
AUTHORS: John Tyson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Bead-Free LSK109 ligation prep for ultra-long DNA</span></div><div class = "text-block"><span>The use of AMPureXP beads for reaction cleanup... | ["of HMW genomic DNA in of EB was either used unsheared or sheared (see previous protocols).\n10 µg\n51 µl", "Quantify of the DNA sample using the Qubit DNA HS kit to confirm DNA recovery and then set up the following End-Prep reaction: DNA sample Ultra II End-Prep Buffer (NEB) Ultra II End-Prep Enzyme mix (NEB)\n1 µ... |
94,839 | Staining protocol for Imaging Mass Cytometry | 1 | dx.doi.org/10.17504/protocols.io.n2bvj34bblk5/v1 | https://www.protocols.io/view/staining-protocol-for-imaging-mass-cytometry-c8uxzwxn | Vijayakumar R Kakade, Tifanny Budiman, Lloyd Cantley | TITLE: Staining protocol for Imaging Mass Cytometry
AUTHORS: Vijayakumar R Kakade, Tifanny Budiman, Lloyd Cantley
[DESCRIPTION]
In Imaging Mass Cytometry (IMC), a high-resolution laser is combined with a mass cytometer that permits mass spectrometry-based, spatially reserved high-dimensional analysis of intact formali... | ["[Staining Tissue Sections] Bake the slides at 60°C. Ensure that all visible wax has been removed", "[Staining Tissue Sections] Dewax the slides in xylenes in the fume hood for 10 min", "[Staining Tissue Sections] Repeat step 2 and dewax the slides in fresh xylene in the fume hood for 10 min", "[Staining Tissue Sect... |
98,065 | One-pot native barcoding of amplicons v4 (LoCost) | 1 | dx.doi.org/10.17504/protocols.io.kxygxebydv8j/v2 | https://www.protocols.io/view/one-pot-native-barcoding-of-amplicons-v4-locost-dbzr2p56 | Josh Quick, Lauren Lansdowne | TITLE: One-pot native barcoding of amplicons v4 (LoCost)
AUTHORS: Josh Quick, Lauren Lansdowne
[DESCRIPTION]
This one-pot native barcoding protocol was developed in conjunction with Oxford Nanopore Technologies, New England Biolabs and BCCDC.
[STEPS]
1. In a new PCR strip-tube/plate set up the following reaction for ... | ["In a new PCR strip-tube/plate set up the following reaction for each sample:", "Incubate at room temperature for 15 min \nIncubate at 65 °C for 15 min \nIncubate on ice for 1 min", "In a new PCR strip-tube/plate set up the following reaction for each sample:", "Incubate at room temperature for 20 min \nIncubate at 6... |
106,296 | USDA LTAR Common Experiment measurement: Aboveground biomass | 0 | dx.doi.org/10.17504/protocols.io.bp2l62zmkgqe/v1 | https://www.protocols.io/view/usda-ltar-common-experiment-measurement-abovegroun-dj2y4qfw | Brook Wilke, Lori J. Abendroth, Stacey VanderWulp | TITLE: USDA LTAR Common Experiment measurement: Aboveground biomass
AUTHORS: Brook Wilke, Lori J. Abendroth, Stacey VanderWulp
[DESCRIPTION]
The most important ecosystem service from agriculture is the provision of food, fiber, feed, and fuel. These outputs from the system are almost always a function of the amount of... | ["[Overview] This protocol describes methods for collecting whole plant samples taken by hand from random or predetermined sampling areas in plots and fields. These samples constitute the collection of all plant material (including non-crop species). Following the collection process, the individual will then separate t... |
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