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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35,369 | SARS-CoV-2 Enrichment Sequencing by Spiked Primer MSSPE method | null | dx.doi.org/10.17504/protocols.io.beshjeb6 | null | Jessica E. Manning, Jennifer Bohl, Sreyngim Lay, Sophana Chea, Vida Ahyong, Erik Karlsson | TITLE: SARS-CoV-2 Enrichment Sequencing by Spiked Primer MSSPE method
AUTHORS: Jessica E. Manning, Jennifer Bohl, Sreyngim Lay, Sophana Chea, Vida Ahyong, Erik Karlsson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left">This protocol was used to enrich f... | ["[Sample Collection]\nNasopharyngeal and oropharyngeal swabs (combined into one tube) were collected from a symptomatic patient meeting case definition for possible infection with SARS-CoV-2.", "[RNA extraction]\nExtraction of viral nucleic acids from clinical sample was performed with a QIAamp Viral RNA Mini Kit (Qia... |
43,578 | Transfer of RNA from Acrylamide Gels onto Membranes | 4 | dx.doi.org/10.17504/protocols.io.bns2mege | https://www.protocols.io/view/transfer-of-rna-from-acrylamide-gels-onto-membrane-bns2mege | Jonathan Houseley, Cristina Cruz | TITLE: Transfer of RNA from Acrylamide Gels onto Membranes
AUTHORS: Jonathan Houseley, Cristina Cruz
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Over the past decade a plethora of noncoding RNAs (ncRNAs) have been identified, initiating an explosion in RNA research. Although RNA sequencing metho... | ["[Transfer of RNA from Acrylamide Gels onto Membranes]\nPaper and membrane: cut two pieces of Whatman paper and one piece of membrane to the size of the gel, a maximum of 9 × 9 cm. Cut a corner and label the membrane with pencil.\nCutting a corner of the membrane helps to keep track of the orientation of the gel once ... |
97,185 | Fabrication of laser inscribed graphene (LIG) 3-electrode plug-and-play chip | 0 | dx.doi.org/10.17504/protocols.io.dm6gpze1dlzp/v1 | https://www.protocols.io/view/fabrication-of-laser-inscribed-graphene-lig-3-elec-da592g96 | Lisseth Casso-Hartmann, Geisianny AM Moreira, Yifan Tang, Diana Vanegas, Eric S McLamore | TITLE: Fabrication of laser inscribed graphene (LIG) 3-electrode plug-and-play chip
AUTHORS: Lisseth Casso-Hartmann, Geisianny AM Moreira, Yifan Tang, Diana Vanegas, Eric S McLamore
[DESCRIPTION]
Laser inscribed graphene (LIG) is a versatile material that is commonly used to prepare electrochemical sensors (Moreira et... | ["Step 1) Fabrication of USB-A Adapter \nHeat the soldering iron, and prepare a wet sponge and solder wick. \nSee the following for an introduction to soldering techniques (link)\nSolder one 28AWG jumper wire to each of the two outer contacts in the USB-A adapter. \nCreate an electrical connection (i.e., “jump”) the tw... |
81,907 | Motor Behavior Assays (Mouse) | 4 | dx.doi.org/10.17504/protocols.io.q26g7yo4kgwz/v1 | https://www.protocols.io/view/motor-behavior-assays-mouse-ct8twrwn | Kelsey Barcomb, Beatriz E Nielsen, Christopher Ford | TITLE: Motor Behavior Assays (Mouse)
AUTHORS: Kelsey Barcomb, Beatriz E Nielsen, Christopher Ford
[DESCRIPTION]
This protocol describes motor behavioral assays used to assess motor function in different models of Parkinson's disease.
These assays include open field, pole, rotarod, cylinder, balance beam tests.
It incl... | ["[Open Field Test] Required materials\nOpen field chambers - either clear 25 cm diameter cylinders or gray 50 cm x 50 cm square boxes (if chambers are open ended on both sides, use gray silicone mats underneath)\nOverhead mounted camera\nVideo analysis software", "[Pole Test] Required materials\n50-60 cm pole with att... |
92,448 | Immunohistochemistry | 4 | dx.doi.org/10.17504/protocols.io.bp2l6xzrklqe/v1 | https://www.protocols.io/view/immunohistochemistry-c6h8zb9w | Peter Kilfeather | TITLE: Immunohistochemistry
AUTHORS: Peter Kilfeather
[DESCRIPTION]
This protocol describes the immunohistochemistry protocol.
[GUIDELINES]
This protocol needs prior approval by the users' Institutional Animal Care and Use Committee (IACUC)
[STEPS]
SECTION: Tissue Collection and Storage
4. Dissect and extract the br... | ["[Tissue Collection and Storage] Dissect and extract the brain.", "[Tissue Collection and Storage] Store the brain in 4 % PFA at 4 °C overnight.", "[Dehydration] Slice each brain into 3 mm coronal sections (approximately).", "[Dehydration] Pass each section through graded alcohol solutions (50, 70, 80, 95, 100, 100 an... |
39,443 | Lessons learned from the resilience of public health systems, hospitals and their personnel to the COVID-19 pandemic: a scoping review protocol. | 1 | dx.doi.org/10.17504/protocols.io.birtkd6n | https://www.protocols.io/view/lessons-learned-from-the-resilience-of-public-heal-birtkd6n | Lola Traverson, Isadora Mathevet, Amanda Paes, Karla Paz, Andrea Andrade, Katarina Ost, Kate Zinszer, Valery Ridde | TITLE: Lessons learned from the resilience of public health systems, hospitals and their personnel to the COVID-19 pandemic: a scoping review protocol.
AUTHORS: Lola Traverson, Isadora Mathevet, Amanda Paes, Karla Paz, Andrea Andrade, Katarina Ost, Kate Zinszer, Valery Ridde
[STEPS]
?. [Title and author identificati... | ["[Title and author identification]\nLessons learned from the resilience of public health systems, hospitals and their personnel to the COVID-19 pandemic: a scoping review of empirical literature.Lola Traverson1, Isadora Mathevet1, Amanda Correia2, Karla Paz2, Andrea Andrade2, Katarina Ost3, Kate Zinszer3,4, Valéry Ri... |
19,434 | Monthly Quality Control | null | dx.doi.org/10.17504/protocols.io.w8ifhue | null | Lukas Snoek, H.Steven Scholte, Tinka Beemsterboer | TITLE: Monthly Quality Control
AUTHORS: Lukas Snoek, H.Steven Scholte, Tinka Beemsterboer
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The monthly quality control is a more extensive quality check of our 3T MRI system but also the other computers in the operator room. </div><div class = "text-blo... | ["[Virus scan ]\nVirus scan (~1 hour)Start a full virus scan of the MRI computer as follows:Right click virus scan icon in the bottom right corner; click “VirusScan Console”Select “Full scan”, right click, and click “start”You can do the calibration procedure during the virus scan.", "[Delete eyetracker-files]\nDelete ... |
54,661 | Populating NCBI template for submissions using BioNumerics v7.6 | 1 | null | https://www.protocols.io/view/populating-ncbi-template-for-submissions-using-bio-bzmdp426 | Ruth Timme, Maria Balkey, Julie Haendiges | TITLE: Populating NCBI template for submissions using BioNumerics v7.6
AUTHORS: Ruth Timme, Maria Balkey, Julie Haendiges
[DESCRIPTION]
PURPOSE: to define the standard operating procedure for collecting isolate metadata using BioNumerics for submission of food/environmental isolates to NCBI.
SCOPE: to provide a ... | ["Metadata SampleSheet preparation \n\nBefore uploading your sequencing run or linking NCBI sequencing records at the BioNumerics platform make sure to fill out the metadata spreadsheet form. \n\nPlease download the template and guidelines included in the file 'GT_BioNumerics_spreadsheet_v2.xlsx'. \n\nCreate the fiel... |
74,050 | Assembly: Chronic recoverable Neuropixels in mice | 1 | null | https://www.protocols.io/view/assembly-chronic-recoverable-neuropixels-in-mice-ckjauuie | Emily A Aery Jones | TITLE: Assembly: Chronic recoverable Neuropixels in mice
AUTHORS: Emily A Aery Jones
[DESCRIPTION]
This protocol collection explains how to build a low-cost, lightweight system to implant Neuropixels 1.0 probes into mice, record during freely moving behavior, then recover the probe for future use. This protocol explai... | ["[3D print components] Build a print file for the following pieces per mouse: 1 each of body piece, back and front flex cable holders, and dome, plus 2 wings. Print 1 headstage holder per recording rig. To re-use explanted probes, print everything except for the body piece, which is permanently affixed to the probe. F... |
null | null | null | dx.doi.org/10.17504/protocols.io.ecqbavw | 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... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.pz7dp9n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>In agro-ecosystems, pollinators are essential for orchard, oilseed crop, horticultural and forage production, as well as the production of seed for many root and fibre crops. Pollinators such as bees, birds and bats affect 35 percent of the world’s crop production, increasing... | [] |
50,785 | A-Z of ancient DNA protocols for shotgun Illumina Next Generation Sequencing | 2 | dx.doi.org/10.17504/protocols.io.bvt9n6r6 | https://www.protocols.io/view/a-z-of-ancient-dna-protocols-for-shotgun-illumina-bvt9n6r6 | James Fellows Yates, Franziska Aron, Gunnar Neumann, Irina Velsko, Eirini Skourtanioti, Eleftheria Orfanou, Zandra Fagernäs, Raphaela Stahl, Aida Andrades Valtuena, Christina Warinner, Wolfgang Haak, Guido Brandt | TITLE: A-Z of ancient DNA protocols for shotgun Illumina Next Generation Sequencing
AUTHORS: James Fellows Yates, Franziska Aron, Gunnar Neumann, Irina Velsko, Eirini Skourtanioti, Eleftheria Orfanou, Zandra Fagernäs, Raphaela Stahl, Aida Andrades Valtuena, Christina Warinner, Wolfgang Haak, Guido Brandt
[DESCRIPTION]... | [] |
48,073 | LC-MS/MS Label-Free Proteomic Data Acquisition | 1 | dx.doi.org/10.17504/protocols.io.bs7hnhj6 | https://www.protocols.io/view/lc-ms-ms-label-free-proteomic-data-acquisition-bs7hnhj6 | Danielle Gutierrez, Jamie Allen, Zach Jenkins, Jeff Spraggins | TITLE: LC-MS/MS Label-Free Proteomic Data Acquisition
AUTHORS: Danielle Gutierrez, Jamie Allen, Zach Jenkins, Jeff Spraggins
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Description of settings used to acquire LC-MS/MS data from label-free proteomic samples.</div></div>
[STEPS]
?. Label-free pro... | ["Label-free proteomic samples were analyzed on a Thermo Scientific Orbitrap Fusion Tribrid mass spectrometer in line with an EvoSep One HPLC system.", "Samples,1 µL at a 1 µg/µL, were loaded onto EvoTips and diluted with 19 µL of mobile phase A (100% water, 0.1% formic acid). Samples were processed on tip according to... |
null | null | null | dx.doi.org/10.17504/protocols.io.c6azad | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?. | [] |
51,048 | Assembling of Synoecnema hirsutum mitochondrial genome | 4 | dx.doi.org/10.17504/protocols.io.bv4gn8tw | https://www.protocols.io/view/assembling-of-synoecnema-hirsutum-mitochondrial-ge-bv4gn8tw | Elena S Ivanova, Boris D. Efeykin, Sergei E Spiridonov | TITLE: Assembling of Synoecnema hirsutum mitochondrial genome
AUTHORS: Elena S Ivanova, Boris D. Efeykin, Sergei E Spiridonov
[DESCRIPTION]
Synoecnemahirsutum Timm, 1959 (Ungellidae, Drilonematoidea) found in the body cavity of the pheretimoid earthworm at the border of Laos and Vietnam was redescribed and illus... | ["DNA from the frozen nematodes samples was isolated using the QiAmp Micro Kit (Qiagen) according to a standard protocol.", "DNA library preparation was implemented using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA).", "DNA quality was checked with Qubit 3.0, final libr... |
56,229 | PotatoMASH library construction | 4 | dx.doi.org/10.17504/protocols.io.e6nvw53zdvmk/v1 | https://www.protocols.io/view/potatomash-library-construction-b26dqha6 | Maria de la O Leyva Perez, Lea Vexler, Dan Milbourne | TITLE: PotatoMASH library construction
AUTHORS: Maria de la O Leyva Perez, Lea Vexler, Dan Milbourne
[DESCRIPTION]
We have developed PotatoMASH (Potato Multi-Allele Scanning Haplotags), a novel low cost, genome-scanning marker platform. We designed a panel of 339 multi-allelic regions placed at 1 Mb intervals througho... | ["[Organize your samples in 96 well plates, quantitate template DNA, and normalize at 20ng/uL.] Quantification with PicoGreen\nIn the preparation for the library construction, the first step is to quantify the template DNA. We used Quant-iT™ PicoGreen ® dsDNA assay kit (Invitrogen, P7589)as detailed below: \n\nThe Quan... |
57,361 | Production of α-synuclein preformed fibrils (PFF) | 4 | dx.doi.org/10.17504/protocols.io.dm6gpbw28lzp/v1 | https://www.protocols.io/view/production-of-synuclein-preformed-fibrils-pff-b39rqr56 | Tae-In Kam, Rong Chen, Valina L. Dawson, Ted Dawson | TITLE: Production of α-synuclein preformed fibrils (PFF)
AUTHORS: Tae-In Kam, Rong Chen, Valina L. Dawson, Ted Dawson
[DESCRIPTION]
This protocol outlines the procedure to produce preformed fibrils (PFF).
It has been adapted from Volpicelli-Daley et al., 2014
[STEPS]
SECTION: Generation of α-synuclein monomer
1. Tran... | ["[Generation of α-synuclein monomer] Transform α-synuclein plasmids (full length human α-synuclein cloned into pRK172 vector) into ClearColiTM BL21-competent E. coli, that have been genetically modified so that LPS does not trigger LPS-mediated immune response. From the small scale culture in LB medium, make a bacteri... |
92,532 | Minibulk v2 (modified Prime-seq) | 1 | dx.doi.org/10.17504/protocols.io.kxygx34qog8j/v1 | https://www.protocols.io/view/minibulk-v2-modified-prime-seq-c6kuzcww | Daniel V Brown | TITLE: Minibulk v2 (modified Prime-seq)
AUTHORS: Daniel V Brown
[DESCRIPTION]
Cost-efficient library generation by early barcoding has been central in propelling single-cell RNA sequencing. Here, we optimize and validate prime-seq, an early barcoding bulk RNA-seq method. We show that it performs equivalently to TruSeq... | ["[Preparation] Clean all surfaces and pipettes with PCR clean wipes", "[Preparation] Thaw frozen buffers and primers on ice", "[Preparation] Prepare fresh 80% EtOH", "Input to minibulk v2 is extracted RNA or sorted cells.\nIt is essential, however, that the samples either have the same input or that they are normalize... |
null | null | null | dx.doi.org/10.17504/protocols.io.mhkc34w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is a protocol optimized from Oxford Nanopore Technology 1D native barcoding genomic DNA (with EXP-NBD103 and SQK-LSK108) for sequencing amplicons of fungal marker genes (ITS, EF1a) using PCR.</p>
<p> </p>
<p>Thanks to Dr. Benjamin Schwesinger for his suggestions about th... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.e5nbg5e | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<p>A genetic transformation method has been established in <em>Perkinsus marinus</em> using the Amaxa Nucleofector system (Fernández-Robledo et al. 2008, Sakamoto et al. 2016). We tried to optimize the transformation conditions for <em>P. marinus</em> using the Gene Pulser Xcell ... | [] |
44,049 | Contact tracing and health inequalities during disease outbreaks : a rapid review protocol. | 1 | dx.doi.org/10.17504/protocols.io.bn9rmh56 | https://www.protocols.io/view/contact-tracing-and-health-inequalities-during-dis-bn9rmh56 | Isadora Mathevet, Katarina Ost, Lola Traverson, Kate Zinszer, Valery Ridde | TITLE: Contact tracing and health inequalities during disease outbreaks : a rapid review protocol.
AUTHORS: Isadora Mathevet, Katarina Ost, Lola Traverson, Kate Zinszer, Valery Ridde
[STEPS]
?. [Title and authors identification]
Contact tracing and health inequities during disease outbreaks: a rapid review of empiri... | ["[Title and authors identification]\nContact tracing and health inequities during disease outbreaks: a rapid review of empirical literature. Isadora Mathevet1, Katarina Ost2, Lola Traverson1, Kate Zinszer2,3, Valéry Ridde11. CEPED, Institute for Research on Sustainable Development, IRD-Université de Paris, ERL INSERM... |
30,642 | A lexical learning task for English and Italian participants | null | dx.doi.org/10.17504/protocols.io.96sh9ee | null | Chiara Valeria Marinelli, Pierluigi Zoccolotti, Cristina Romani | TITLE: A lexical learning task for English and Italian participants
AUTHORS: Chiara Valeria Marinelli, Pierluigi Zoccolotti, Cristina Romani
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>“Lexical learning” is the ability to set up stable and accurate mental representations of words in the le... | [] |
59,053 | RNA Extraction and RT-qPCR | 4 | dx.doi.org/10.17504/protocols.io.b5wmq7c6 | https://www.protocols.io/view/rna-extraction-and-rt-qpcr-b5wmq7c6 | Haley Geertsma | TITLE: RNA Extraction and RT-qPCR
AUTHORS: Haley Geertsma
[DESCRIPTION]
This protocol is used to extract RNA from mouse brain tissue and quantify with RT-qPCR.
[STEPS]
1. Homogenize hemibrain in 3mL 1X PEPI buffer using a dounce homogenizer.
1X PEPI Buffer: 5mM EDTA + 1X protease inhibitor in 1X phosphate buffered ... | ["Homogenize hemibrain in 3mL 1X PEPI buffer using a dounce homogenizer.\n1X PEPI Buffer: 5mM EDTA + 1X protease inhibitor in 1X phosphate buffered saline (PBS)", "Take 3% of homogenate and add 1mL TRIzol Reagent and follow their user guide.", "Synthesize cDNA with 5X All-In-One RT Master Mix Kit then perform qPCR.\nqP... |
38,762 | Cryopreservation of organoid cultures | 1 | dx.doi.org/10.17504/protocols.io.bh4ij8ue | https://www.protocols.io/view/cryopreservation-of-organoid-cultures-bh4ij8ue | Emily Souster, Hazel Rogers, Laura Letchford, Sara Vieira, Maria Garcia-Casado, Mya Fekry-Troll, Charlotte Beaver, Rachel Nelson, Hayley Francies, Mathew Garnett | TITLE: Cryopreservation of organoid cultures
AUTHORS: Emily Souster, Hazel Rogers, Laura Letchford, Sara Vieira, Maria Garcia-Casado, Mya Fekry-Troll, Charlotte Beaver, Rachel Nelson, Hayley Francies, Mathew Garnett
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol defines the procedure ... | ["[Process diagram]", "[Protocol]\nUsing a P1000 pipette, or a cell-scraper, detach BME2 drops from as many wells as required (generally 1 well into 1 cryovial- we recommend aiming for a density of 1x106 cells per cryovial).\nIf you plan to bank a specific number of cells, be sure to take a cell count at Step 7.The cou... |
39,643 | Supplemental Resources for You Can’t Hide Your Lying Eyes: Honesty Oaths and Misrepresentation | 3 | dx.doi.org/10.17504/protocols.io.bix3kfqn | https://www.protocols.io/view/supplemental-resources-for-you-can-t-hide-your-lyi-bix3kfqn | J Jobu Babin, Haritima Chauhan, Feng Liu | TITLE: Supplemental Resources for You Can’t Hide Your Lying Eyes: Honesty Oaths and Misrepresentation
AUTHORS: J Jobu Babin, Haritima Chauhan, Feng Liu
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Abstract</div><div class = "text-block">Lying about personal qualifications for a job or in college ... | [] |
88,664 | Primer stock preparation | 4 | null | https://www.protocols.io/view/primer-stock-preparation-c2tyyepw | Brian Lovett, Kristen Pierce | TITLE: Primer stock preparation
AUTHORS: Brian Lovett, Kristen Pierce
[DESCRIPTION]
General protocol for preparation of lyophilized primer stocks from IDT.
[GUIDELINES]
Recommended: When you receive your lyophilized primers, check the name of the primer, primer sequence and the concentration listed on the tube. IDT p... | ["[Preparation of stock solution] Reconstitute lyophilized primers in required volume of molecular grade water (i.e., RNase/DNase free) to 100 micromolar (µM).", "[Preparation of working solution] Allow stock solution to thaw completely at Room temperature.", "[Use of primers] For a typical 25 µL PCR reaction, 1 µL of ... |
null | null | null | dx.doi.org/10.17504/protocols.io.kz3cx8n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is the general immunofluorescence protocol used in the Laboratory for Integrative Neuroscience at NIAAA. This protocol can be adapted for most primary antibodies but specific antibodies and concentrations need to be determined by the user and the protocol adapted accordi... | [] |
40,872 | Copy of Detection of total and faecal coliforms in the oysters | 4 | dx.doi.org/10.17504/protocols.io.bj6gkrbw | https://www.protocols.io/view/copy-of-detection-of-total-and-faecal-coliforms-in-bj6gkrbw | Sade Aisha Folashade John, Patrick E. Akpaka, Chandrashekhar Unakal, Arvind Kurhade, Angel Justiz-Vaillant | TITLE: Copy of Detection of total and faecal coliforms in the oysters
AUTHORS: Sade Aisha Folashade John, Patrick E. Akpaka, Chandrashekhar Unakal, Arvind Kurhade, Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Enterobacteriaceae the leading cause of gastroenteritis. These gra... | ["The meat (10 oysters per cup) of the unprepared oysters was blended with 25ml of sterile distilled water and 25ml of sterile peptone water using a sterilized blender (the blender was washed with antibacterial soap as well as bleach and rinsed with sterile distilled water along with 70% ethanol before autoclaving prio... |
77,093 | Passaging and plating A549 cells | 1 | null | https://www.protocols.io/view/passaging-and-plating-a549-cells-cpidvka6 | ATCC, Steven Walter | TITLE: Passaging and plating A549 cells
AUTHORS: ATCC, Steven Walter
[DESCRIPTION]
Volumes used in this protocol are for 75 cm2flask; proportionally reduce or increase amount of dissociation medium for culture vessels of other sizes. Corning T-75 flasks (catalog #430641) are recommended for subculturing this product.
... | ["[Splitting A549 in T-75] Remove and discard culture medium, by tipping dish carefully to one side and aspirating the media without disturbing the adherent cells", "[Splitting A549 in T-75] Briefly rinse the cell layer with 1.0 mL 0.05% (w/v) Trypsin - 53 mM EDTA solution to remove all traces of serum which contains t... |
62,423 | ViaKeto BHB Apple Gummies Reviews | 1 | dx.doi.org/10.17504/protocols.io.eq2lyn96mvx9/v1 | https://www.protocols.io/view/viaketo-bhb-apple-gummies-reviews-b87xrzpn | Apple Keto Gummies | TITLE: ViaKeto BHB Apple Gummies Reviews
AUTHORS: Apple Keto Gummies
[DESCRIPTION]
ViaKeto BHB Apple Gummies
[STEPS]
SECTION: ViaKeto BHB Apple Gummies
1. ViaKeto BHB Apple Gummies are the high level adaptation of the keto equation, which incorporates the interesting BHB parts to focus on the real reason for weigh... | ["[ViaKeto BHB Apple Gummies] ViaKeto BHB Apple Gummies are the high level adaptation of the keto equation, which incorporates the interesting BHB parts to focus on the real reason for weight gain. It is the progressive plan behind its creation. While none of the current recipes fulfills the longings, how should these ... |
null | null | null | dx.doi.org/10.17504/protocols.io.fi4bkgw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>mothur is a bioinformatics tool for analyzing 16S rRNA gene sequences, which can be used to process data generated by Sanger, PacBio, IonTorrent, 454, and Illumina (MiSeq/HiSeq). </p>
[BEFORE_START]
<p>Before starting, please visit the ECOGEO website for more information on... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ju3cnyn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><span style="font-weight: 400;">Angionesis </span><em><span style="font-weight: 400;">in vitro: </span></em><span style="font-weight: 400;">Es la formación </span><em><span style="font-weight: 400;">In vitro </span></em><span style="font-weight: 400;">de tubos capilares por c... | [] |
85,687 | Oxford Nanopore Technologies SQK-LSK114 library preparation on Hamilton NGS STAR SOP | 4 | dx.doi.org/10.17504/protocols.io.n2bvj36mnlk5/v1 | https://www.protocols.io/view/oxford-nanopore-technologies-sqk-lsk114-library-pr-cxwxxpfn | Laksh Malik, Maysa Abdelhalim, Breeana Baker, Cornelis Blauwendraat, Kimberley J Billingsley | TITLE: Oxford Nanopore Technologies SQK-LSK114 library preparation on Hamilton NGS STAR SOP
AUTHORS: Laksh Malik, Maysa Abdelhalim, Breeana Baker, Cornelis Blauwendraat, Kimberley J Billingsley
[DESCRIPTION]
LIbrary preparation for population-scale Oxford Nanopore long-read DNA sequencing SOP
At the NIH's Center for... | ["Part 1: Sample Preparation and Instrument Initialization\n\nNote: The CARD team has spent ~10 months optimizing this protocol for use with 48 brain or blood samples, so some optimizations may be specific to our samples and desired sequencing output. Therefore additional optimization is likely needed for new users.\n\... |
21,702 | Monitoring cell-surface expression of GPCR by ELISA | null | dx.doi.org/10.17504/protocols.io.zfef3je | null | Elie Besserer-Offroy, Rebecca L Brouillette, Jean-Michel Longpré, Philippe Sarret | TITLE: Monitoring cell-surface expression of GPCR by ELISA
AUTHORS: Elie Besserer-Offroy, Rebecca L Brouillette, Jean-Michel Longpré, Philippe Sarret
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Quantifying cell surface expression of G Protein-Coupled Receptors (GPCRs) can be exteremly important ... | ["[Day 1 - Cell Culture & Transfections]\nCoat 24-well plates with Poly-L-Lysine (this need to be done in a biological safety cabinet to ensure sterility).", "[Day 1 - Cell Culture & Transfections]\nAdd of Poly-L-Lysine solution in each well of the 24-well plate and incubate at .This can be done using a 300µL multic... |
null | null | null | dx.doi.org/10.17504/protocols.io.t5qeq5w | null | null | TITLE: No Title
AUTHORS:
[STEPS]
SECTION: Recovering skeletons
?.
SECTION: Rinsing
?.
SECTION: Cleaning
?.
SECTION: Cleaning
?.
SECTION: Diluting
?.
SECTION: Rinsing
?.
SECTION: Staining
?.
SECTION: Staining
?.
SECTION: Diluting
?.
SECTION: Rinsing
?.
SECTION: Preparing for imaging
?.
SECTION: Preparing fo... | ["[Recovering skeletons] After DNA extraction, recover skeleton from the eluted pellet under binoculars or inverted microscope. \n\nNote: During DNA extraction: dilute waste from the extraction procedure (i.e. pellet debris, containing the skeleton) in milliQ water and store skeletons at -20°C.", "[Rinsing] Rinse skele... |
41,131 | Preparation of bacterial cell lysate for proteomics (LC-MS) by freeze and thaw cycles | 4 | dx.doi.org/10.17504/protocols.io.bkejktcn | https://www.protocols.io/view/preparation-of-bacterial-cell-lysate-for-proteomic-bkejktcn | Alexandro Rodríguez-Rojas | TITLE: Preparation of bacterial cell lysate for proteomics (LC-MS) by freeze and thaw cycles
AUTHORS: Alexandro Rodríguez-Rojas
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify"><span style = "font-weight:bold;">Preparation of bacterial cell lysate f... | ["[Preparation of bacterial cell lysate for proteomics (LC-MS) by freeze and thaw cycles (developed by Alexandro Rodríguez-Rojas, FU Berlin, a.rojas@fu-berlin.de).]\nGrow the cells to an OD600of 0.4 (six tube per condition including control groups). Treat the cells with the desired conditions (typically 30 minutes).", ... |
101,900 | Mouse Stereotaxic Surgery for Alpha Synuclein Pre-formed Fibrils (PFFs) Injection in the Dorsal Striatum | 4 | dx.doi.org/10.17504/protocols.io.yxmvm33nbl3p/v2 | https://www.protocols.io/view/mouse-stereotaxic-surgery-for-alpha-synuclein-pre-dfrk3m4w | Saroj Kumar Sah, Thomas Biederer | TITLE: Mouse Stereotaxic Surgery for Alpha Synuclein Pre-formed Fibrils (PFFs) Injection in the Dorsal Striatum
AUTHORS: Saroj Kumar Sah, Thomas Biederer
[DESCRIPTION]
This protocol outlines the procedures for conducting stereotaxic surgery in mice for intracranial injections of PFFs into the dorsal striatum of the mo... | ["[Preparation of drugs for injection] Prepare drugs and sonicated PFFs", "[Preparation of surgery apparatus] Surgery room setup", "[Mouse preparation and anesthesia] Mouse anaesthesia", "[Pre-operative treatment and PFFs injection] Pre-operative treatment and surgery", "[Pre-operative treatment and PFFs injection] Dri... |
84,663 | Cell culture | 4 | dx.doi.org/10.17504/protocols.io.n2bvj3y5blk5/v1 | https://www.protocols.io/view/cell-culture-cwwxxffn | Elias Adriaenssens | TITLE: Cell culture
AUTHORS: Elias Adriaenssens
[DESCRIPTION]
This protocol describes routine cell culture maintenance.
[STEPS]
SECTION: Cell culture
1. Grow HeLa and HEK293T cells in Dulbecco Modified Eagle Medium (DMEM, Thermo
Fisher) supplemented with 10% (v/v) Fetal Bovine Serum (FBS, Thermo Fisher), 25 millimola... | ["[Cell culture] Grow HeLa and HEK293T cells in Dulbecco Modified Eagle Medium (DMEM, Thermo\nFisher) supplemented with 10% (v/v) Fetal Bovine Serum (FBS, Thermo Fisher), 25 millimolar (mM) HEPES (Thermo Fisher), 1% (v/v) non-essenMal amino acids (NEAA, Thermo Fisher), and 1% (v/v) Penicillin-Streptomycin (Thermo Fishe... |
77,120 | RADSeq protocol EFGL | 1 | dx.doi.org/10.17504/protocols.io.kqdg39bjqg25/v1 | https://www.protocols.click/view/radseq-protocol-efgl-cpi8vkhw | eaglefishgeneticslab | TITLE: RADSeq protocol EFGL
AUTHORS: eaglefishgeneticslab
[DESCRIPTION]
Modified from protocol of Sean O’Rourke and Mike Miller published in:
[STEPS]
SECTION: Day 1 - Ligation
10. Ligate adapters onto digested DNA
SECTION: Day 1 - Ligation
10.1. Thaw BestRAD adaptors (prepared in steps 1-4) and reagents for Li... | ["[Day 1 - Ligation] Ligate adapters onto digested DNA", "[Day 1 - Ligation] Thaw BestRAD adaptors (prepared in steps 1-4) and reagents for Ligation Master Mix (listed above)", "[Day 2 - Sonication] Prepping the Sonicator", "[DNA quantification <48 samples] Quantify DNA with Qubit", "[Day 1 - Digestion] Digest the n... |
69,593 | Primary neuronal cultures | 4 | dx.doi.org/10.17504/protocols.io.ewov1ojwklr2/v1 | https://www.protocols.io/view/primary-neuronal-cultures-cf7ztrp6 | Miguel Da Silva Padilha, Irina Dudanova, F. Ulrich Hartl, Itika Saha, Mark S. Hipp | TITLE: Primary neuronal cultures
AUTHORS: Miguel Da Silva Padilha, Irina Dudanova, F. Ulrich Hartl, Itika Saha, Mark S. Hipp
[DESCRIPTION]
This protocol describes the preparation of primary neuronal cultures from E15.5 CD-1 wild type mouse embryos. Experiments involving animal models must be performed in accordance wi... | ["Sacrifice pregnant female mice by cervical dislocation.", "Remove the uterus from the abdominal cavity and place into a 10 cm sterile Petri dish on ice containing dissection medium, consisting of Hanks’ balanced salt solution (HBSS) supplemented with 0.01 M HEPES, 0.01 M MgSO4 and 1% penicillin/streptomycin.", "Isola... |
84,245 | coloMOCA implantation protocol | 4 | dx.doi.org/10.17504/protocols.io.ewov1q8qogr2/v1 | https://www.protocols.io/view/colomoca-implantation-protocol-cwhvxb66 | Brett Hanzlicek, Dennis Bourbeau | TITLE: coloMOCA implantation protocol
AUTHORS: Brett Hanzlicek, Dennis Bourbeau
[DESCRIPTION]
This protocol describes the implantation of our bowel device (ColoMOCA) in pigs.
[STEPS]
SECTION: Anesthesia
1. Anesthetize/prep the animal for surgery.
Aseptic procedures by trained personnel are utilized during t... | ["[Anesthesia] Anesthetize/prep the animal for surgery.\n\n Aseptic procedures by trained personnel are utilized during the surgery. All tools are sterilized prior to insertion. Drapes will be used and personnel performing surgery will wear clean surgical scrubs, and sterile gowns/gloves and masks.", "[La... |
78,998 | Protocol for the Experimental and Bioinformatic Analysis for Gut Microbiota Profiling of Litopenaeus vannamei | 1 | dx.doi.org/10.17504/protocols.io.rm7vzbe32vx1/v1 | https://www.protocols.io/view/protocol-for-the-experimental-and-bioinformatic-an-crdwv27e | Luis Enrique Vazquez-Morado, Melany J Cervantes-Echeverría, Fernanda Cornejo-Granados, Luigui Gallardo-Becerra, Filiberto Sánchez-López, Adrian Ochoa-Leyva | TITLE: Protocol for the Experimental and Bioinformatic Analysis for Gut Microbiota Profiling of Litopenaeus vannamei
AUTHORS: Luis Enrique Vazquez-Morado, Melany J Cervantes-Echeverría, Fernanda Cornejo-Granados, Luigui Gallardo-Becerra, Filiberto Sánchez-López, Adrian Ochoa-Leyva
[DESCRIPTION]
The Pacific white shrim... | ["[Shrimp Gut Sample Extraction] Before beginning any sample collection, it is crucial to prepare the working environment properly. Start by rinsing the surgical forceps with a 10% chlorine solution, then rinse thoroughly with sterile Milli-Q water. Next, place 1.5 ml Eppendorf tubes with 1 mL of RNAlater or 20% glycer... |
null | null | null | dx.doi.org/10.17504/protocols.io.ep7bdrn | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<div><strong>GEL PREPARATIONS</strong></div>
<p><strong><br />Sample Recipe for Resolving Gel:<br /></strong></p>
<table>
<tbody>
<tr>
<td>12.5% acrylamide (40.0 mL volume)</td>
</tr>
<tr>
<td>16.7 mL 30% acrylamide solution</td>
</tr>
<tr>
<td>10.0 mL 4X resolving gel buffer</td... | [] |
12,404 | qPCR quantification of methanogens using general mcrA primers | null | dx.doi.org/10.17504/protocols.io.qcudsww | https://www.protocols.io/view/qpcr-quantification-of-methanogens-using-general-m-qcudsww | Roey Angel, Eva Petrova | TITLE: qPCR quantification of methanogens using general mcrA primers
AUTHORS: Roey Angel, Eva Petrova
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>General </span><span style = "font-style:italic;">mcrA</span><span> primers for quantifying methanogens using a SYBR Green-based assay.</span></... | ["[QPCR mixture]\nABCD1ReagentFinal conc.1 tube (25 μl)plate (25 μl x 100)2PCR H2O 2.852853qPCR master mix1x12.512504MgCl2 (25mM)*3.5 mM3.53505BSA (50 μg μl-1)0.8 μg μl-10.4406mlas-mod (25 μM)0.25 μM0.25257mrcA-rev (25 μM)0.25 μM0.25258Template 55 x 100 * Different master mixes vary in concentration of MgCl2 ... |
72,120 | SARS-CoV-2 inactivation and scRNAseq sample preparation protocol | 4 | dx.doi.org/10.17504/protocols.io.kqdg3999eg25/v1 | https://www.protocols.io/view/sars-cov-2-inactivation-and-scrnaseq-sample-prepar-cinyudfw | Raven M Osborn, Justin Leach, Michelle Zanche, John M. Ashton, ChinYi Chu, Juilee Thakar, Stephen Dewhurst, Sonia Rosenberger, Martin Pavelka, Gloria S Pryhuber, Thomas J. Mariani, Christopher Anderson | TITLE: SARS-CoV-2 inactivation and scRNAseq sample preparation protocol
AUTHORS: Raven M Osborn, Justin Leach, Michelle Zanche, John M. Ashton, ChinYi Chu, Juilee Thakar, Stephen Dewhurst, Sonia Rosenberger, Martin Pavelka, Gloria S Pryhuber, Thomas J. Mariani, Christopher Anderson
[DESCRIPTION]
Coronavirus disease (C... | ["[Lifting cells from tissue culture plate] Set up the biosafety cabinet according to your institution’s BSL3 biosafety cabinet setup standard operating procedure or the \"Basic Biosafety Cabinet Setup” supplied in this protocol.", "[Lifting cells from tissue culture plate] Transfer the tissue culture plates, in a seco... |
null | null | null | dx.doi.org/10.17504/protocols.io.rpud5nw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Objective:</strong> To characterize the lipid profile in vaginal discharge of women with vulvovaginal candidiasis, cytolytic vaginosis, or no vaginal infection or dysbiosis.</p>
<p><strong> </strong></p>
<p><strong>Design:</strong> Cross-sectional study.</p>
<p><stron... | [] |
50,838 | Protocol-IHC | 1 | dx.doi.org/10.17504/protocols.io.bvvwn67e | https://www.protocols.io/view/protocol-ihc-bvvwn67e | Klaus Hirschbühl | TITLE: Protocol-IHC
AUTHORS: Klaus Hirschbühl
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:center">Protocol-IHC to the paper:</div></div><div class = "text-block"><div class = "justify" style = "text-align:center"></div></div><div class = "text-block"><d... | [] |
50,512 | Data collection | 5 | null | https://www.protocols.io/view/data-collection-bvjqn4mw | Alise Ponsero | TITLE: Data collection
AUTHORS: Alise Ponsero
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocols aims to details the steps necessary to collect new data points for the "Database Justice League" project.</div></div>
[STEPS]
?. [Download data]
Once you have received the link to download y... | ["[Download data]\nOnce you have received the link to download your dataset, download the csv file locally.Make sure to save it on your computer in a convenient folder!In this protocol we will perform the data collection on a test dataset:", "[Download data]\nAs you can see in this test dataset, some preliminary inform... |
84,033 | Combinatorial selective ER-phagy remodels the ER during neurogenesis | 2 | dx.doi.org/10.17504/protocols.io.81wgbx13nlpk/v1 | https://www.protocols.io/view/combinatorial-selective-er-phagy-remodels-the-er-d-cwa9xah6 | Melissa Hoyer, Harper JW, Ian R. Smith, Julia C. Paoli, Yizhi Jiang, Joao A. Paulo | TITLE: Combinatorial selective ER-phagy remodels the ER during neurogenesis
AUTHORS: Melissa Hoyer, Harper JW, Ian R. Smith, Julia C. Paoli, Yizhi Jiang, Joao A. Paulo
[DESCRIPTION]
The endoplasmic reticulum (ER) has a vast proteomic landscape to perform many diverse functions including protein and lipid synthesis, ca... | [] |
44,946 | Nano-OTS | 4 | null | https://www.protocols.io/view/nano-ots-bp5smq6e | Ida Hoijer, Josefin Johansson, Sanna Gudmundsson, Chen-Shan Chin, Ignas Bunikis, Susana Häggkvist, Anastasia Emmanouilidou, Maria Wilbe, Marcel Den Hoed, Marie-Louise Bondeson, Lars Feuk, Ulf Gyllensten, Adam Ameur | TITLE: Nano-OTS
AUTHORS: Ida Hoijer, Josefin Johansson, Sanna Gudmundsson, Chen-Shan Chin, Ignas Bunikis, Susana Häggkvist, Anastasia Emmanouilidou, Maria Wilbe, Marcel Den Hoed, Marie-Louise Bondeson, Lars Feuk, Ulf Gyllensten, Adam Ameur
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>T... | ["[Shearing of genomic DNA]\nShear 5-10 µg of HMW genomic DNA to 20 kb using Megaruptor 2.", "[Shearing of genomic DNA]\nAdd 0.45x AMPure XP beads to the sample and incubate at 2000 rpm using a vortex mixer for 10 min.", "[Shearing of genomic DNA]\nPlace the tube on a magnetic rack until the beads collect on the side o... |
45,005 | Come importare identificatori OAI-PMH in OpenRefine | 1 | dx.doi.org/10.17504/protocols.io.bp7mmrk6 | https://www.protocols.io/view/come-importare-identificatori-oai-pmh-in-openrefin-bp7mmrk6 | Andrea Marchitelli | TITLE: Come importare identificatori OAI-PMH in OpenRefine
AUTHORS: Andrea Marchitelli
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocollo per importare in OpenRefine una lista di identificatori OAI-PMH per successive elaborazioni.</div></div>
[STEPS]
?. Aprire OpenRefine e scegliere "Crea p... | ["Aprire OpenRefine e scegliere \"Crea progetto\"", "Selezionare \"Indirizzo/i Web (URLs)\" come fonte dei dati del nuovo progetto e cliccare su \"Avanti\". Inserire la baseurl OAI-PMH del target individuato, scegliere il verbo ListIdentifiers e il metadataPrefix opportuno.Es. http://www.bibliotecheoggi.it/trends/oai?v... |
52,328 | SDS-PAGE | 4 | dx.doi.org/10.17504/protocols.io.5jyl85o7dl2w/v1 | https://www.protocols.io/view/sds-page-bxcgpitw | Anna Bird, Chiara Gandini | TITLE: SDS-PAGE
AUTHORS: Anna Bird, Chiara Gandini
[DESCRIPTION]
SDS-PAGE gels are used to visualize proteins. This protocol describes how to prepare all the buffers required for casting and running SDS-PAGE gels, as well as how to prepare whole cell samples.
[STEPS]
SECTION: Buffers
1. 4X Resolving Buffer (1.5 M T... | ["[Buffers] 4X Resolving Buffer (1.5 M Tris-HCl, pH 8.8)\nAdd 90.75 g to 400 mL DI water\nTitrate the solution with ~18% HCl to pH 8.8\nAdd water to a final volume of 500 mL \nStore at 4°C", "[Gel Casting] In an Eppendorf tube combine\n0.5 mL 30% Acrylamide: Bisacrylamide (29:1)\n0.5 mL DI water\n10 µL APS\n1 µLTEME... |
28,182 | Quick Protocol for Extraction and Purification of Genomic DNA | 1 | null | https://www.protocols.io/view/quick-protocol-for-extraction-and-purification-of-7rwhm7e | New England Biolabs | TITLE: Quick Protocol for Extraction and Purification of Genomic DNA
AUTHORS: New England Biolabs
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Genomic DNA Purification Consists of Two Stages:</div><div class = "text-block"><ul style = "list-style-type:disc;"><li style = "counter-reset:ol0;list-s... | ["[PART 1: SAMPLE LYSIS]\nPlease select the sample material that you want to use:Cultured CellsMammalian Whole Blood (non-nucleated)Nucleated Whole Blood (birds, reptiles)Animal Tissue", "[PART 1: SAMPLE LYSIS]\nStart with a cell pellet containing 1 x 104 – 5 x 106 cells (typical starting amount is 1 x 106 cells).Froze... |
57,408 | Effect of exercise and androgen deprivation therapy on prostate cancer: a meta-analysis | 1 | dx.doi.org/10.17504/protocols.io.b4a8qshw | https://www.protocols.io/view/effect-of-exercise-and-androgen-deprivation-therap-b4a8qshw | Wenjuan Shao, Hanyue Zhang, Qi Han, Yimin Zhang | TITLE: Effect of exercise and androgen deprivation therapy on prostate cancer: a meta-analysis
AUTHORS: Wenjuan Shao, Hanyue Zhang, Qi Han, Yimin Zhang
[DESCRIPTION]
Androgen deprivation therapy is a common treatment for prostate cancer. However, this therapy is associated with various adverse effects, such as i... | ["[Preliminary searches] We searched the PubMed, EMBASE, Web of Science, EBSCO, and Cochrane Library databases for reports that were published until October 22, 2021. The search terms generally focused on ‘exercise’, ‘training’, ‘physical activity’, ‘prostate cancer’, and ‘androgen deprivation therapy’.", "[Formal scre... |
93,102 | Autoclave Instructions for the BD FACS Aria Fusion Sheath Fluid Tank | 1 | null | https://www.protocols.io/view/autoclave-instructions-for-the-bd-facs-aria-fusion-c66nzhde | Jamie C Tijerina | TITLE: Autoclave Instructions for the BD FACS Aria Fusion Sheath Fluid Tank
AUTHORS: Jamie C Tijerina
[DESCRIPTION]
It is good practice to clean sheath tanks regularly to prevent biofilm formation, rust, and contamination of cytometers or sorters. The sheath tank is a common point of cytometer and cell sorter contamin... | ["[Autoclave Instructions] Wipe down the surface of a biosafety cabinet with 70% Ethanol or CaviWipes. Switch on the air flow.\n\n*Make sure that your biosafety cabinet is cleaned regularly, including underneath the grates and surface. You may need to lift these components out in order to do this. This should be done a... |
17,336 | Flavonol, Anthocyanin, and Chlorophyll Indices using a Force-A Dualiex Scientific+ | null | dx.doi.org/10.17504/protocols.io.u6yezfw | null | David LeBauer, Maria Newcomb, Matthew Herrit, Ebrahim Babaeian | TITLE: Flavonol, Anthocyanin, and Chlorophyll Indices using a Force-A Dualiex Scientific+
AUTHORS: David LeBauer, Maria Newcomb, Matthew Herrit, Ebrahim Babaeian
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocols describes the use of a hand-held sensor to estimate polyphenols and cholorp... | ["[Take measurements]\nFor each two row plot:For two subsamples per plot: Identify the 1-3 replicate plants per row to measure. For a standard 3 m row, this would be the plant closest to 1.5m from the end. For six subsamples / plot: Identify the center plant and two adjacent plants in each of the two rows", "[Identify ... |
92,993 | projectpr1d_metab.nan | 5 | dx.doi.org/10.17504/protocols.io.ewov1qkzkgr2/v1 | https://www.protocols.io/view/projectpr1d-metab-nan-c629zgh6 | NAN KB, John Glushka, Mario Uchimiya, Christopher Esselman, Saraa Al Jawad, Leandro I Ponce, Laura Morris, Arthur Edison | TITLE: projectpr1d_metab.nan
AUTHORS: NAN KB, John Glushka, Mario Uchimiya, Christopher Esselman, Saraa Al Jawad, Leandro I Ponce, Laura Morris, Arthur Edison
[DESCRIPTION]
This is a protocol for running the Bruker pulse program "projectpr1d".
This pulse program was originally proposed in:
[BEFORE_START]
This pr... | ["[Create a new dataset]", "[Create a new dataset] On the menu bar on TopSpin, click on\nStart → Create Dataset", "[Create noesypr1d experiment file] When Lock, Tune, Shim are complete proceed to the specific protocol for your desired pulseprogram(s).", "[Create a new dataset] A new window opens. On the right top bar, ... |
78,531 | Stern REHAB | 1 | null | https://www.protocols.io/view/stern-rehab-cqxbvxin | Abby Myers | TITLE: Stern REHAB
AUTHORS: Abby Myers
[DESCRIPTION]
Instructions for taking care of Stern's REHAB vials.
[STEPS]
SECTION: Adding stocks to Stern REHAB
1. When a vial looks sick, first check all other copies (including drobot copy) and if EVERY vial looks sick, consolidate all of the flies in a fresh food vial with m... | ["[Adding stocks to Stern REHAB] When a vial looks sick, first check all other copies (including drobot copy) and if EVERY vial looks sick, consolidate all of the flies in a fresh food vial with moist cotton roll", "If not all vials look sick, top off your sick vial with the other healthy copy", "Add vial with consolid... |
44,315 | Ligate 3′ RNA Adapter (On-Bead) | 4 | dx.doi.org/10.17504/protocols.io.bph3mj8n | https://www.protocols.io/view/ligate-3-rna-adapter-on-bead-bph3mj8n | Eric L. Van Nostrand, Thai B. Nguyen, Chelsea Gelboin-Burkhart, Ruth Wang, Steven M. Blue, Gabriel A. Pratt, Ashley L. Louie, Gene W. Yeo | TITLE: Ligate 3′ RNA Adapter (On-Bead)
AUTHORS: Eric L. Van Nostrand, Thai B. Nguyen, Chelsea Gelboin-Burkhart, Ruth Wang, Steven M. Blue, Gabriel A. Pratt, Ashley L. Louie, Gene W. Yeo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Profiling of RNA binding protein targets in vivo provides critical... | ["[Prepare RNA Adapter Ligation Master Mix]\nPrepare ; per sample: AB1H2O9 μL210× Ligase buffer (no DTT)3 μL30.1 M ATP0.3 μL4100% DMSO0.8 μL550% PEG 80009 μL6Murine RNase Inhibitor0.4 μL7High concentration T4 RNA Ligase2.5 μL\non ice\n25 µl\nAB1H2O9 μL210× Ligase buffer (no DTT)3 μL30.1 M ATP0.3 μL4100% DMSO0.8 μL550... |
81,627 | TS Spurrs - cell pellet (TM - 013) | 4 | dx.doi.org/10.17504/protocols.io.81wgb6jpolpk/v2 | https://www.protocols.io/view/ts-spurrs-cell-pellet-tm-013-ctx3wpqn | sandra.crameri | TITLE: TS Spurrs - cell pellet (TM - 013)
AUTHORS: sandra.crameri
[DESCRIPTION]
This method is used for conventional processing of cell pellets to Spurr's resin.
[GUIDELINES]
All time are minimum times, it is acceptable to go over time specified for any given step. Good place steps to leave overnight or at 70% ethano... | ["[HEADER] SAN:\n\n\nSPEC No:\n\n\nOPERATOR & STEPS:\n\n\nOPERATOR & STEPS:", "[CONVENTIONAL] 2.5 % volume for at least 40 min", "[CONVENTIONAL] Wash 0.1 Molarity (M) Sorenson's Phosphate Buffer pH 07.2 (300mosmol/kg) for 15 min", "[CONVENTIONAL] 1 % volume in buffer for 60 min", "[CONVENTIONAL] 70 % volume for a... |
56,398 | SARS-CoV-2 NCBI consensus submission protocol: GenBank | 1 | dx.doi.org/10.17504/protocols.io.b3bnqime | https://www.protocols.io/view/sars-cov-2-ncbi-consensus-submission-protocol-genb-b3bnqime | Ruth Timme, Emma Griffiths, Lee Katz, Duncan MacCannell, Michael Weigand | TITLE: SARS-CoV-2 NCBI consensus submission protocol: GenBank
AUTHORS: Ruth Timme, Emma Griffiths, Lee Katz, Duncan MacCannell, Michael Weigand
[DESCRIPTION]
This is a SARS-CoV-2 specific protocol that covers the steps needed to submit SARS-CoV-2 consensus sequence to GenBank.
If you need a pipeline for frequen... | ["["Ingredients" to have in place before starting your submissions] 1.1: Ensure you have a working NCBI user account\n1.2: Identify your NCBI submission user group or establish a new one if necessary. \n1.3: Bookmark the link to your submission portal\n1.4. BioSample + BioProject accessions in-hand\n\nAfter t... |
43,721 | UV Denaturation of Proteins Monitored by Circular Dichroism in the Far-UV Region (180–260 nm) | 1 | dx.doi.org/10.17504/protocols.io.bnxhmfj6 | https://www.protocols.io/view/uv-denaturation-of-proteins-monitored-by-circular-bnxhmfj6 | Rohanah Hussain, Charlotte S. Hughes, Giuliano Siligardi | TITLE: UV Denaturation of Proteins Monitored by Circular Dichroism in the Far-UV Region (180–260 nm)
AUTHORS: Rohanah Hussain, Charlotte S. Hughes, Giuliano Siligardi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">CD spectroscopy is the essential tool to quickly ascertain in the far-UV region the... | ["[The general protocol is as follows:]\nFor a cuvette (either cylindrical or rectangular cell) of 0.02 cm pathlength, at about is loaded into the cuvette.\n[protein solution]", "[The general protocol is as follows:]\nStandard data collection parameters in the far-UV region (180–260 nm) include 1 nm increments, 1 s i... |
95,208 | LUHMES culturing and differentiation protocol | 4 | dx.doi.org/10.17504/protocols.io.kxygx36ykg8j/v1 | https://www.protocols.io/view/luhmes-culturing-and-differentiation-protocol-c88gzztw | Mallory Wright, William J Buchser, ckremitz, jwaligor, bachman@wustl.edu | TITLE: LUHMES culturing and differentiation protocol
AUTHORS: Mallory Wright, William J Buchser, ckremitz, jwaligor, bachman@wustl.edu
[STEPS]
SECTION: LUHMES coating protocol
1.
0.1 mg/mL
50 µg/µL
SECTION: LUHMES Passaging (~ every 2-3 days)
20. Triturate cells only 1 or 2 times before seeding.
SECTION: LUHMES Pas... | ["[LUHMES coating protocol] 0.1 mg/mL\n50 µg/µL", "[LUHMES Passaging (~ every 2-3 days)] Triturate cells only 1 or 2 times before seeding.", "[LUHMES Passaging (~ every 2-3 days)] Discard the supernatant and resuspend in 1mL and use a 5mL pipette", "[LUHMES Passaging (~ every 2-3 days)] Transfer cells to 15mL tube and ... |
26,303 | LIVE IMAGING OF i3NEURONS (Support Protocol 5) | null | dx.doi.org/10.17504/protocols.io.5w7g7hn | null | Michael S. Fernandopulle, Ryan Prestil, Christopher Grunseich, Chao Wang, Li Gan, Michael E. Ward | TITLE: LIVE IMAGING OF i3NEURONS (Support Protocol 5)
AUTHORS: Michael S. Fernandopulle, Ryan Prestil, Christopher Grunseich, Chao Wang, Li Gan, Michael E. Ward
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Live imaging permits visualization of molecular and organellar dynamics within the n... | [] |
46,077 | Extraction and qPCR of Environmental Surveillance samples for the detection of Salmonella Typhi | 4 | null | https://www.protocols.io/view/extraction-and-qpcr-of-environmental-surveillance-bq85mzy6 | Dilip Abraham, Nicola Elviss, Nicholas Feasey, Nick Grassly, Jacob John, Gagandeep Kang, John Scott Meschke, Venkata Raghava Mohan, Satheesh Nair, Jonathan Rigby, Rajan Srinivasan, Catherine Troman, Christopher Uzzell, Nicolette Zhou | TITLE: Extraction and qPCR of Environmental Surveillance samples for the detection of Salmonella Typhi
AUTHORS: Dilip Abraham, Nicola Elviss, Nicholas Feasey, Nick Grassly, Jacob John, Gagandeep Kang, John Scott Meschke, Venkata Raghava Mohan, Satheesh Nair, Jonathan Rigby, Rajan Srinivasan, Catherine Troman, Chr... | ["[DNA Extraction] For extraction from Moore swabs, empty the contents of a PowerBead tube provided in the extraction kit into the PowerBead tube used for storing the filter.\n\nFor the pellet from membrane filtration, resuspend the pellet in 800µl CD1 from the first step of the DNA extraction protocol, then transfer t... |
90,665 | Nutil Data Integration | 4 | dx.doi.org/10.17504/protocols.io.3byl4qrz8vo5/v1 | https://www.protocols.io/view/nutil-data-integration-c4shywb6 | Michael X. Henderson | TITLE: Nutil Data Integration
AUTHORS: Michael X. Henderson
[DESCRIPTION]
This protocol describes Nutil data integration from segmentation and registration of mouse brain data.
[STEPS]
SECTION: Nutil Data Quantification
1. Open Nutil and find operation tab.
SECTION: Nutil Data Quantification
2. Find the 3 folders ... | ["[Nutil Data Quantification] Open Nutil and find operation tab.", "[Nutil Data Quantification] Find the 3 folders you created at the beginning of this workflow and populated during the workflow and populate them into their corresponding list above. (segmentation is your input folder, brain atlas map folder is your atl... |
null | null | null | dx.doi.org/10.17504/protocols.io.h83b9yn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>A hallmark of legume plants is their ability to establish mutualistic symbioses with <em>Rhizobium</em> bacteria and arbuscular mycorrhizal fungi (<em>Rhizophagus irregularis</em>). These symbionts help in providing nutritional benefits to the host plants. Herein, we provide ... | [] |
73,156 | Bariatric Apps Final.pdf | 1 | dx.doi.org/10.17504/protocols.io.kxygx9ykzg8j/v1 | https://www.protocols.io/view/bariatric-apps-final-pdf-cjpcumiw | Irma Hellbrecht, Nadja Könsgen, Alina Weise, Jessica Breuing | TITLE: Bariatric Apps Final.pdf
AUTHORS: Irma Hellbrecht, Nadja Könsgen, Alina Weise, Jessica Breuing
[DESCRIPTION]
Please find detailed information on our protocol in the attached PDF file.
[STEPS] | [] |
27,675 | MojoSort™ Streptavidin Nanobeads Column Protocol - Negative Selection | null | dx.doi.org/10.17504/protocols.io.693hh8n | null | Kelsey Miller, Sam Li | TITLE: MojoSort™ Streptavidin Nanobeads Column Protocol - Negative Selection
AUTHORS: Kelsey Miller, Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>BioLegend MojoSort™ nanobeads work in commonly used separation columns, based on our internal research as well as validation by external t... | ["Prepare cells from your tissue of interest or blood without lysing erythrocytes.", "In the final wash of your sample preparation, resuspend the cells in MojoSort™ Buffer by adding up to 4 mL in a 5 mL (12 x 75 mm) polypropylene tube.Note: Keep MojoSort™ Buffer on ice throughout the procedure.", "Filter the cells with... |
88,734 | OT-2 Media dispensing and culture inoculation protocol | 5 | dx.doi.org/10.17504/protocols.io.q26g7yb3kgwz/v2 | https://www.protocols.io/view/ot-2-media-dispensing-and-culture-inoculation-prot-c2v6ye9e | Ana Mariya Anhel, Lorea Alejaldre, Ángel Goñi-Moreno | TITLE: OT-2 Media dispensing and culture inoculation protocol
AUTHORS: Ana Mariya Anhel, Lorea Alejaldre, Ángel Goñi-Moreno
[DESCRIPTION]
This protocol is meant to distribute reactive(s) into well plates with a single channel pipette, and then transfer culture samples from source plate(s) to these plates with a multi-... | ["[Files Preparation] Preparing Customized Template\n\nPreparing the template (a .xlsx) with the specific variables for each experiment and a .pdf that contains the instructions on how to fill the template \n\nHere we attach one Excel with several sheets:\nGeneralVariables: variables related mainly to the labware that ... |
56,880 | Acetylation of lysines on affinity-purification matrices to reduce co-digestion of bead-bound ligands | 4 | dx.doi.org/10.17504/protocols.io.b3sqqndw | https://www.protocols.io/view/acetylation-of-lysines-on-affinity-purification-ma-b3sqqndw | David M. Hollenstein, Margarita Maurer, Thomas Gossenreiter, Natascha Hartl, Dorothea Anrather, Markus Hartl | TITLE: Acetylation of lysines on affinity-purification matrices to reduce co-digestion of bead-bound ligands
AUTHORS: David M. Hollenstein, Margarita Maurer, Thomas Gossenreiter, Natascha Hartl, Dorothea Anrather, Markus Hartl
[DESCRIPTION]
In mass-spectrometry-based interaction proteomics on-bead digestion protocols... | ["[Acetylation protocol] Wash beads 3x with 100µl Reaction buffer, using the magnetic rack. \nRemove supernatant after the final wash.", "[Acetylation protocol] Add 19 µl Reaction buffer and 1 µl Sulfo-NHS-Acetate (100 mM) to obtain a final concentration of 5 mM Sulfo-NHS-Acetate. \nIncubate 1h at room temperature with... |
60,145 | Shipping wastewater samples to FDA-CFSAN | 1 | dx.doi.org/10.17504/protocols.io.14egn797zv5d/v2 | https://www.protocols.io/view/shipping-wastewater-samples-to-fda-cfsan-b6yrrfv6 | Maria Balkey | TITLE: Shipping wastewater samples to FDA-CFSAN
AUTHORS: Maria Balkey
[DESCRIPTION]
This SOP provides guidance for shipping wastewater samples to the US FDA Center for Food Safety and Applied Nutrition (CFSAN), covering specific steps for registering samples with CFSAN and for the preparation of shipments (documenta... | ["[Submission of metadata] Fill out the BioSample custom wastewater template (extension of NCBI's Generic SARS-CoV-2: wastewater surveillance, v1.0 ) according to the NCBI submission protocol for SARS-Cov-2 protocol, once completed, send it to covidtrakr@fda.hhs.gov for registration. Successful registrations will rece... |
42,696 | total RNA抽提 | 4 | null | https://www.protocols.io/view/total-rna-bmxgk7jw | 张 雪 | TITLE: total RNA抽提
AUTHORS: 张 雪
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">在收集到生物材料之后，最好能即刻进行RNA制备工作。若需暂时储存，则应以液氮将生物材料急速冷冻后，储存于-80℃冷冻柜。在制备RNA时，将储存于冷冻柜的材料取出，立即以加入液氮研磨的方式打破细胞，不可以先行解冻，以避免RNase的作用。</div></div>
[STEPS]
?. 取材：收集10~40个所需时期的斑马鱼胚胎
?. 用1×PBS漂洗，5min×2
on ice
全程冰上操作，RNase-free枪头
?. 每管加入1m... | ["取材：收集10~40个所需时期的斑马鱼胚胎", "用1×PBS漂洗，5min×2\non ice\n全程冰上操作，RNase-free枪头", "每管加入1ml TRIZOL试剂，放置冰上反复吹打，4°C，12000 rcf，离心10min\non ice\n用力吹打的同时注意不要让液体溅出", "上清转移至新的EP管，冰上放置5min\non ice", "加入200µl 氯仿后，剧烈震荡15s，冰上静置3min\non ice", "4°C，12000rcf，离心15min", "将上层无色水相转移至新EP管中，加入等体积（约500µl）的异丙醇（RNA专用），混匀，-20°C静置20min\n-20 °C", "4°C，1... |
36,383 | Mitochondrial Isolation SOP (#10) | 1 | dx.doi.org/10.17504/protocols.io.bfr7jm9n | https://www.protocols.io/view/mitochondrial-isolation-sop-10-bfr7jm9n | Elena Pumbo, Kimberly Chapman | TITLE: Mitochondrial Isolation SOP (#10)
AUTHORS: Elena Pumbo, Kimberly Chapman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for mitochondrial isolation used by our group for assays needing intact and mitochondrial lysates.</div></div>
[STEPS]
?. [Tissue Prepration]
Tissue preparation
?... | ["[Tissue Prepration]\nTissue preparation", "[Tissue Prepration]\nFor 5 mL of 15-20 mg/mL of liver mitochondria protein we need 10-15 gm of frozen mouse liver tissue. If more of less protein needed scale these numbers up or down.", "[Tissue Prepration]\nCool down centrifuge and Rotor F-35-6-30 for 6 x 50 mL and 5 x 15 ... |
69,133 | Protocol for DNA Extraction from Cowpea | 4 | dx.doi.org/10.17504/protocols.io.81wgbyddqvpk/v1 | https://www.protocols.io/view/protocol-for-dna-extraction-from-cowpea-cfrmtm46 | Aparna Srinivasan, Magdalena M Julkowska | TITLE: Protocol for DNA Extraction from Cowpea
AUTHORS: Aparna Srinivasan, Magdalena M Julkowska
[DESCRIPTION]
Protocol to extract high quality DNA from Cowpea leaves using modified CTAB method.
[STEPS]
SECTION: Collection of leaf sample
1.
Collect 1 fully expanded leaf from Cowpea plants in a 50ml centrifuge tube c... | ["[Collection of leaf sample] Collect 1 fully expanded leaf from Cowpea plants in a 50ml centrifuge tube containing five sterile glass beads (5mm diameter) and freeze immediately in liquid nitrogen.", "[DNA Extraction] Add equal volume of Chloroform, and vortex well.\n \n \n\nCentrifuge at 14000 rpm for 15 min. Transfe... |
49,158 | Murine intestinal cell dissociation suitable for multi-omics single-cell assays | 4 | dx.doi.org/10.17504/protocols.io.bt9enr3e | https://www.protocols.io/view/murine-intestinal-cell-dissociation-suitable-for-m-bt9enr3e | Mackenzie White, Astrid Kosters, Luisa Cervantes-Barragan, Eliver Ghosn | TITLE: Murine intestinal cell dissociation suitable for multi-omics single-cell assays
AUTHORS: Mackenzie White, Astrid Kosters, Luisa Cervantes-Barragan, Eliver Ghosn
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Here we present an optimized protocol for the single-cell suspension of murine inte... | ["[Obtain Tissues]\nEuthanize mouse, open peritoneal cavity. Take out intestines from the stomach to rectum, and place directly into 10 cm petri-dish containing 10 mL def-RPMI/3%NBCS on ice.", "[Obtain Tissues]\nRemove connective tissue from intestinal tissue. Untangle as necessary.", "[Obtain Tissues]\nSeparate/cut th... |
86,089 | Mitophagy induction using Difereprone | 1 | null | https://www.protocols.io/view/mitophagy-induction-using-difereprone-cybhxsj6 | Louise Uoselis | TITLE: Mitophagy induction using Difereprone
AUTHORS: Louise Uoselis
[DESCRIPTION]
Mitophagy induction in HeLa cells using Difereprone (DFP)
[STEPS]
SECTION: Day 1
1. Seed cells, aiming for a confluency of 80-90% at the time of treatment the next day.
SECTION: Day 2
2. Feed cells for 60 min in an appropriate volume ... | ["[Day 1] Seed cells, aiming for a confluency of 80-90% at the time of treatment the next day.", "[Day 2] Feed cells for 60 min in an appropriate volume of standard growth media.", "[Day 2] During the feed, warm up the difereprone (DFP) stock aliquot in a 37 deg C waterbath. Centrifuge the stock tube after thawing to e... |
46,039 | BHI/LB + v2 salts media | 4 | dx.doi.org/10.17504/protocols.io.bq7xmzpn | https://www.protocols.io/view/bhi-lb-v2-salts-media-bq7xmzpn | Matthew Haines | TITLE: BHI/LB + v2 salts media
AUTHORS: Matthew Haines
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-style:italic;">Vibrio natriegens </span><span>grows well media containing v2 salts e.g. BHI + v2 and LBv2 (</span><a href="http://2018.igem.org/Team:Marburg/Results" style = "t... | ["[Prepare stock salt solutions]\nPrepare the following salt solutions at the given concentrations:\n[NaCl]\n[KCl]\n[MgCl2.6H2O]", "[Prepare media]\nDissolve or in ddH2O in a 1 L graduated bottle.\n[BHI dry medium]\n[LB Broth (Miller)]\n400 mL", "[Sterilise and combine]\nSterilise all solutions by autoclaving.", "... |
null | null | null | dx.doi.org/10.17504/protocols.io.kbwcspe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is a novel dual reporter assay for transfected tissue culture cells. It is based on the naturally secreted luciferase from <em>Gaussia princeps</em> as the main reporter protein and a secreted version of the red fluorescent protein mCherry as internal standard. After fir... | [] |
35,804 | PNGase F Protocol (Non-Denaturing Reaction Conditions) | 1 | dx.doi.org/10.17504/protocols.io.be74jhqw | https://www.protocols.io/view/pngase-f-protocol-non-denaturing-reaction-conditio-be74jhqw | New England Biolabs | TITLE: PNGase F Protocol (Non-Denaturing Reaction Conditions)
AUTHORS: New England Biolabs
[DESCRIPTION]
PNGase F is the most effective enzymatic method for removing almost all N-linked oligosaccharides from glycoproteins. PNGase F is an amidase, which cleaves between the innermost GlcNAc and asparagine residues of... | ["[Non-Denaturing Reaction Conditions:] Combine 1 µg - 20 µg, 2 µL and H2O (if necessary) to make a 20 µL total reaction volume.", "[Non-Denaturing Reaction Conditions:] Add 2 µL - 5 µL, mix gently.", "[Non-Denaturing Reaction Conditions:] Incubate reaction at 37 °C for 240 min - 1440 min.", "[Non-Denaturing Reaction C... |
86,462 | Protocol details for autopsy specimens (WUSTL) | 1 | dx.doi.org/10.17504/protocols.io.e6nvwdd92lmk/v1 | https://www.protocols.io/view/protocol-details-for-autopsy-specimens-wustl-cyn6xvhe | Reyka Jayasinghe | TITLE: Protocol details for autopsy specimens (WUSTL)
AUTHORS: Reyka Jayasinghe
[DESCRIPTION]
protocol details for autopsy specimens
[STEPS]
SECTION: Sample Collection Strategy
1. The tissue is transported on ice to the lab for processing and storage.
Larger samples are sectioned into small segments and placed int... | ["[Sample Collection Strategy] The tissue is transported on ice to the lab for processing and storage. \n\nLarger samples are sectioned into small segments and placed into 2 mL cryovial before dropping into liquid nitrogen. \n\nVials are immediately placed in -80° freezer"] |
null | null | null | dx.doi.org/10.17504/protocols.io.kb7csrn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Co-assembly using Megahit.</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
30,338 | Immunofluorescence and Cell Counting | 1 | null | https://www.protocols.io/view/immunofluorescence-and-cell-counting-9vah62e | Yingchao Xue, Xiping Zhan, Shisheng Sun, Senthilkumar S. Karuppagounder, Shuli Xia, Valina L Dawson, Ted M Dawson, John Laterra, Jianmin Zhang, Mingyao Ying | TITLE: Immunofluorescence and Cell Counting
AUTHORS: Yingchao Xue, Xiping Zhan, Shisheng Sun, Senthilkumar S. Karuppagounder, Shuli Xia, Valina L Dawson, Ted M Dawson, John Laterra, Jianmin Zhang, Mingyao Ying
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol explains Immunofluores... | ["[Immunofluorescence]\nFix cells in 4% paraformaldehyde in PBS .", "[Immunofluorescence]\nBlock cells in 5% normal goat serum and 0.2% Triton X-100.", "[Immunofluorescence]\nDilute primary antibodies in 5% normal goat serum. Primary antibodies are listed in the \"Guidelines\".", "[Immunofluorescence]\nIncubate samples... |
45,950 | Fixation of fluorescent E.coli by Mannik | 4 | null | https://www.protocols.io/view/fixation-of-fluorescent-e-coli-by-mannik-bq46myze | Elizabeth Fozo | TITLE: Fixation of fluorescent E.coli by Mannik
AUTHORS: Elizabeth Fozo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Per Jaana Mannik Communication, June 1st 2020:</div><div class = "text-block">For the fixation of FtsZ-mNG cels, we have been using a mix of paraformaldehyde (PFA) and glutaraldeh... | ["[Fixation of FtsZ-mNG E.coli cells]\nFix cells directly in growth medium by addition of paraformaldehyde (PFA) to final concentration 2.8% (vol/vol) and glutaraldehyde (GH) to 0.04% (vol/vol) for 15 minutes at RT (work with PFA and GH under the chemical hood!)", "[Fixation of FtsZ-mNG E.coli cells]\nTransfer the cell... |
86,711 | 51Cr Release Cytotoxicity Assay for murine CAR T cells | 4 | dx.doi.org/10.17504/protocols.io.n92ldmm2ol5b/v1 | https://www.protocols.io/view/51cr-release-cytotoxicity-assay-for-murine-car-t-c-cywxxxfn | Tamer B Shabaneh, Andrew R Stevens | TITLE: 51Cr Release Cytotoxicity Assay for murine CAR T cells
AUTHORS: Tamer B Shabaneh, Andrew R Stevens
[DESCRIPTION]
A standard cell-based assay to assess the function of murine CAR T cells, which we regularly perform at the end of the process of generating CAR T cells (see "Retroviral transduction of primary murin... | ["[Labeling target cells with 51Cr (day 0)] For each adherent tumor cell line, plate 5x105 cells / 3mL (previously growing in log phase) in one 6-well-plate well; Incubate cells for ~3hr to rest.", "[Labeling target cells with 51Cr (day 0)] In the Hot Lab, label the target cells with 50 μL 51Cr (vial <1wk old), 100μL (... |
null | null | null | dx.doi.org/10.17504/protocols.io.h4gb8tw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?. | [] |
30,666 | Anti-c-Myc Tag (9E10) Affinity Gel Protocol | null | dx.doi.org/10.17504/protocols.io.97ih9ke | null | Sam Li | TITLE: Anti-c-Myc Tag (9E10) Affinity Gel Protocol
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Catalog Number: </span><span>658502</span></div><div class = "text-block"><span style = "font-weight:bold;">Storage Temperature: </span><span>2°C-8°C</... | ["[Part I. Cell Lysate Preparation: Purifying c-Myc fusion proteins from crude E. coli extracts]\nGrow the bacteria cells under the condition that induce production of c-Myc fusion proteins.", "[Part I. Cell Lysate Preparation: Purifying c-Myc fusion proteins from crude E. coli extracts]\nHarvest the cells by centrifug... |
53,614 | Mycology media | 1 | dx.doi.org/10.17504/protocols.io.e6nvw536wvmk/v1 | https://www.protocols.io/view/mycology-media-byknpuve | Yin-Tse Huang | TITLE: Mycology media
AUTHORS: Yin-Tse Huang
[DESCRIPTION]
Mycology media
[STEPS]
1. WA+C agar
Water agar + chloramphenicol (氯黴素 kill bacteria): As an environmental isolating media
2. PDA+C agar
potato dextrose agar + chloramphenicol (氯黴素 kill bacteria): Use when WA+C agar is not working
3. Emerson YpSs Aga... | ["WA+C agar \nWater agar + chloramphenicol (氯黴素 kill bacteria): As an environmental isolating media", "PDA+C agar\npotato dextrose agar + chloramphenicol (氯黴素 kill bacteria): Use when WA+C agar is not working", "Emerson YpSs Agar: For chytrids", "10% Unclarified V8 Agar\nCombine 100 ml V8 juice and 900 ml of distilled ... |
96,106 | The knowledge and perception of the general public an young adults of Palliative Care - A systematic Review | 0 | dx.doi.org/10.17504/protocols.io.261gedymwv47/v1 | https://www.protocols.io/view/the-knowledge-and-perception-of-the-general-public-c94iz8ue | Yann-Nicolas Batzler | TITLE: The knowledge and perception of the general public an young adults of Palliative Care - A systematic Review
AUTHORS: Yann-Nicolas Batzler
[DESCRIPTION]
Background: As a result of demographic change, chronic and oncological diseases gain importance in the context of public health. Palliative care plays a crucial... | ["[Preparation] General screening of literature", "[Development of the search algorithm] Develop search string", "[Identification of inclusion and exclusion criteria] Using PICOS process", "[Preparation] Screening for suitable databases", "[Preparation] Identify lack of knowledge", "[Development of the search algorithm... |
61,924 | PNA Oligomer Synthesis | 6 | dx.doi.org/10.17504/protocols.io.bp2l613r1vqe/v1 | https://www.protocols.io/view/pna-oligomer-synthesis-b8qcrvsw | Cathy Miller | TITLE: PNA Oligomer Synthesis
AUTHORS: Cathy Miller
[DESCRIPTION]
PNA is a pseudo-peptide backbone instead of the ribonucleic acid-phosphate backbone, retaining the original 4 bases. Nielsen et al in Rose Laboratory of the University of Copenhagen used a simple computer DNA model to successfully design and synthesize... | [] |
41,041 | ELISA for quantification of IL-4 in human serum. | 6 | dx.doi.org/10.17504/protocols.io.bkbrksm6 | https://www.protocols.io/view/elisa-for-quantification-of-il-4-in-human-serum-bkbrksm6 | Angel Justiz-Vaillant | TITLE: ELISA for quantification of IL-4 in human serum.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>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 body ... | ["An anti-human IL-4 coating antibody is adsorbed onto the microwells by incubation overnight at 4°C with carbonate-bicarbonate buffer.", "Add 50 µl of human serum. Human IL-4 present in the serum sample binds to antibodies adsorbed into the microwells.", "The microplate is blocked with 3% non-fat milk-PBS buffer and l... |
87,322 | Sanger Tree of Life HMW DNA Extraction: Automated MagAttract v.1 | 4 | dx.doi.org/10.17504/protocols.io.x54v9p2z1g3e/v1 | https://www.protocols.io/view/sanger-tree-of-life-hmw-dna-extraction-automated-m-czh2x38e | Edel Sheerin, Filipa Sampaio, graeme oatley, Maja Todorovic, Michelle Strickland, Raquel Juliana Vionette do Amaral, Caroline Howard | TITLE: Sanger Tree of Life HMW DNA Extraction: Automated MagAttract v.1
AUTHORS: Edel Sheerin, Filipa Sampaio, graeme oatley, Maja Todorovic, Michelle Strickland, Raquel Juliana Vionette do Amaral, Caroline Howard
[DESCRIPTION]
This protocol describes the automated extraction of HMW DNA from multiple different tissue ... | ["[Sample lysis] Prepare a lysis buffer master mix:\n Phosphate buffered solution (PBS)200 µLProteinase K20 µLRNase A4 µLBuffer AL150 µL", "[Sample lysis] Set a heat block to 25 °C.", "[Sample lysis] For cryoprepped samples:\nTransfer 25 mg cryogenically disrupted sample into a 2 mL microcentrifuge tube, then hold on ... |
28,009 | Ligation Protocol with T4 DNA Ligase | null | dx.doi.org/10.17504/protocols.io.7khhkt6 | null | Alba Balletbó | TITLE: Ligation Protocol with T4 DNA Ligase
AUTHORS: Alba Balletbó
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The final step in the construction of a recombinant plasmid is connecting the insert DNA (gene or fragment of interest) into a compatibly digested vector backbone. This is accomplished ... | ["Thaw the T4 DNA Ligase Buffer and resuspended at room temperature. 'Pro-tip': Alicuote the 10x buffer less concentrated so when thawing the DTT gets soluble more easily.", "Set up the reaction in a microcentrifuge tube on ice (T4 DNA Ligase should be added last.): AB1COMPONENT20 μl REACTION2T4 DNA Ligase Buffer (10... |
19,945 | E. coli Plating Quantification | null | dx.doi.org/10.17504/protocols.io.xqhfmt6 | null | Kenneth Schackart, Kattika Kaarj | TITLE: E. coli Plating Quantification
AUTHORS: Kenneth Schackart, Kattika Kaarj
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describes how to serially dilute and plate cultured </span><span style = "font-style:italic;">E. coli </span><span>K-12 in suspension for quantification... | ["[Prepare Serial Dilutions]\nTransfer of stock solution to 2 mL centrifuge tube.\n100 µl", "[Prepare Serial Dilutions]\nAdd DI water to the same centrifuge tube to make a dilution that is one-tenth the concentration of the stock solution.\n900 µl", "[Prepare Serial Dilutions]\nUsing of the dilution you just made, make... |
21,132 | Extracting high molecular weight DNA from Halichondria panicea (Phylum: Porifera) | 1 | dx.doi.org/10.17504/protocols.io.yvkfw4w | https://www.protocols.io/view/extracting-high-molecular-weight-dna-from-halichon-yvkfw4w | Rasmus Dam Wollenberg, Brian Strehlow, Astrid Schuster | TITLE: Extracting high molecular weight DNA from Halichondria panicea (Phylum: Porifera)
AUTHORS: Rasmus Dam Wollenberg, Brian Strehlow, Astrid Schuster
[DESCRIPTION]
This protocol was used to extract high molecular weight DNA from the sponge (porifera) Halichondria panicea. This protocol contains slight modificatio... | ["Rinse sample in filter sterilized seawater three times. Use a mortar and pestle to finely grind approximately 1 gram of tissue in liquid nitrogen.", "Transfer homogenized sample into a 15 mL tube.", "Add 5 mL of buffer AP1 (QIAGEN, Germany) and mix with 50 µL of 100 mg/mL RNase A. Invert tube a couple of times to mix... |
40,580 | The Pair Test - a computerised measure of learning and memory | 1 | dx.doi.org/10.17504/protocols.io.bjvckn2w | https://www.protocols.io/view/the-pair-test-a-computerised-measure-of-learning-a-bjvckn2w | Sarah Buck | TITLE: The Pair Test - a computerised measure of learning and memory
AUTHORS: Sarah Buck
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The Pair Test offers improved diagnosis, with more precise indication on the nature of the memory deficit and the underlying processing impairment in patients with... | [] |
27,719 | MojoSort™ Isolation Kits Column Protocol - 4 | null | dx.doi.org/10.17504/protocols.io.7bfhijn | null | Sam Li | TITLE: MojoSort™ Isolation Kits Column Protocol - 4
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>BioLegend MojoSort™ nanobeads work in commonly used separation columns, based on our internal research as well as validation by external testing by academic labs. This simple pro... | ["Prepare cells from your tissue of interest or blood without lysing erythrocytes. Kits for human samples have been optimized for PBMCs, please prepare the cells using a suitable method.", "In the final wash of your sample preparation, resuspend the cells in MojoSort™ Buffer by adding up to 4 mL in a 5 mL (12 x 75 mm) ... |
34,602 | Appendix 1: Size Selection | 1 | dx.doi.org/10.17504/protocols.io.rm7vz8onrvx1/v1 | https://www.protocols.io/view/appendix-1-size-selection-bd2ii8ce | Dakota Betz | TITLE: Appendix 1: Size Selection
AUTHORS: Dakota Betz
[DESCRIPTION]
Any commonly used size selection technique (e.g., the double-sided size selection described here, or an electrophoretic
method) may be integrated into the KAPA HyperPlus library construction workflow. Size selection should preferably be
carried out a... | ["Perform the first (0.7X) size cut (to exclude library molecules larger than ~450 bp) by combining the\nfollowing:", "Mix thoroughly by vortexing and/or pipetting up and down multiple times.", "Incubate the plate/tube(s) at room temperature for 5 min– 15 minin to bind library molecules larger than ~450 bp to the beads... |
71,262 | Preparing Biolog Growth Plates | 1 | null | https://www.protocols.io/view/preparing-biolog-growth-plates-cht6t6re | Carlos Goller, Carly Sjogren | TITLE: Preparing Biolog Growth Plates
AUTHORS: Carlos Goller, Carly Sjogren
[DESCRIPTION]
Overview and Goals
Your bacterial isolate has been grown on agar plates. You practiced pipetting. Now, let’s learn about how your organism grows! What nutrients help your bacterium grow? We will use plates with ninety-six wells w... | ["[Activity 1-Multichannel pipetting] Set your p200 multichannel pipet to 100 µL", "[Activity 1-Multichannel pipetting] Load 8 tips onto each gasket of the multichannel pipet.", "[Activity 1-Multichannel pipetting] Press the plunger TO the first stop.", "[Activity 1-Multichannel pipetting] Submerge all 8 tips into the ... |
101,669 | PECO eDNA field sampling protocol | 0 | null | https://www.protocols.io/view/peco-edna-field-sampling-protocol-dfid3ka6 | Jennifer Sunday, Matt Lemay, Sue Velazquez, Margot hessing-lewis | TITLE: PECO eDNA field sampling protocol
AUTHORS: Jennifer Sunday, Matt Lemay, Sue Velazquez, Margot hessing-lewis
[DESCRIPTION]
This protocol summarizes field sampling techniques used by a network of partners that contribute to the Pacific eDNA Coastal Observatory. It includes information on water sample collection,... | ["[Day-of preparation] Print and bring datasheets.", "[Day-of preparation] Without removing them from their bags, find a bag of 5 unused sterivex filters labeled “PECOe-xxx” or \"PECOe-XXXX\". These will be the 5 sample names for your next site.", "[Day-of preparation] Label your 5 Nalgene bottles, from 1-4 and C for c... |
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