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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89,553 | Quantification of p62-positive inclusions | 4 | dx.doi.org/10.17504/protocols.io.8epv5x33ng1b/v1 | https://www.protocols.io/view/quantification-of-p62-positive-inclusions-c3prymm6 | Núria Peñuelas | TITLE: Quantification of p62-positive inclusions
AUTHORS: Núria Peñuelas
[DESCRIPTION]
Quantification of p62-positive inclusions in the rodent brain
[STEPS]
1. Scan the 5um sections immunostained with guineapig anti-p62 (1:500, Progen #GP62-C), mouse anti-α-synuclein (1:500, BD Biosciences #610786) and TH (1:1000, Ca... | ["Scan the 5um sections immunostained with guineapig anti-p62 (1:500, Progen #GP62-C), mouse anti-α-synuclein (1:500, BD Biosciences #610786) and TH (1:1000, Calbiochem #657012) using ZEISS LSM 980 with Airyscan 2.", "Visualize the images with ZEN 2011 software (Zeiss, Germany) and determine one representative coronal ... |
78,975 | Efficacy and safety of probiotics in the treatment of irritable bowel syndrome: a systematic review and meta-analysis of randomised clinical trials using ROME IV criteria | 1 | null | https://www.protocols.io/view/efficacy-and-safety-of-probiotics-in-the-treatment-crc7v2zn | Giorgos Konstantis, Efstathiou Stylianos, Chryssa Pourzitaki, Kitsikidou Elisavet, Germanidis Georgios, Chourdakis Michail | TITLE: Efficacy and safety of probiotics in the treatment of irritable bowel syndrome: a systematic review and meta-analysis of randomised clinical trials using ROME IV criteria
AUTHORS: Giorgos Konstantis, Efstathiou Stylianos, Chryssa Pourzitaki, Kitsikidou Elisavet, Germanidis Georgios, Chourdakis Michail
[DESCRIPT... | ["Systematic review\n\nReview title.\n\n\nEfficacy and safety of probiotics in the treatment of irritable bowel syndrome: a systematic review and meta-analysis of randomised clinical trials using ROME IV criteria\n\nAnticipated or actual start date.\n\n\n\n01 October 2021 \n\n\nAnticipated completion date.\n\n\nNovembe... |
31,407 | AAV Production in HEK293T Cells | null | dx.doi.org/10.17504/protocols.io.bawpifdn | null | Addgene the nonprofit plasmid repository | TITLE: AAV Production in HEK293T Cells
AUTHORS: Addgene the nonprofit plasmid repository
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is used for AAV production in HEK293T cells. To see the full abstract and additional resources, visit the </span><a href="https://www.addgene.o... | ["[Procedure]\nTrypsinize and resuspend the HEK293T packaging cells from 2 x T-150 flasks. Cells should be at ~80% confluence. For each T-150 flask:Aspirate culture media and rinse once with of PBS.Aspirate PBS and add of 0.05% Trypsin/EDTA. Wait ~.Neutralize trypsin by adding of HI-FBS.\n10 ml\n4 ml\n4 ml", "[Proce... |
53,590 | Quadro de trabalho para Revisões Sistemáticas e Quantitativas da Literatura (RSQL) | 1 | dx.doi.org/10.17504/protocols.io.byjwpupe | https://www.protocols.io/view/quadro-de-trabalho-para-revis-es-sistem-ticas-e-qu-byjwpupe | Daniel Vartanian | TITLE: Quadro de trabalho para Revisões Sistemáticas e Quantitativas da Literatura (RSQL)
AUTHORS: Daniel Vartanian
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Este protocolo foi criado para o programa de Revisões Sistemáticas e Quantitativas da Literatura (RSQL) científica do Grupo Interd... | ["[Método Pickering & Byrne]\nConheça o método de Revisões Sistemáticas e Quantitativas da Literatura (RSQL) de Pickering e Byrne\nEste programa utiliza o método desenvolvido por Catherine Pickering e Jason Byrne. A primeira coisa que você precisa fazer é obter um bom conhecimento sobre ele.", "[Método Pickering & Byrn... |
48,184 | Antioxidant activity by reduced glutathione (GSH) assay: in vitro protocol | 6 | dx.doi.org/10.17504/protocols.io.btaynifw | https://www.protocols.io/view/antioxidant-activity-by-reduced-glutathione-gsh-as-btaynifw | Adrieli Sachett, Matheus Gallas-Lopes, Greicy M M Conterato, Ana Herrmann, Angelo Piato | TITLE: Antioxidant activity by reduced glutathione (GSH) assay: in vitro protocol
AUTHORS: Adrieli Sachett, Matheus Gallas-Lopes, Greicy M M Conterato, Ana Herrmann, Angelo Piato
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left"><span>Considering the ro... | ["[Preparing the reagents]\nThe first step is to prepare the reagents to be used in this protocol;", "[Preparing the reagents]\nPotassium phosphate buffer : 1.1.1 Weigh of monobasic potassium phosphate (KH2PO4) in a beaker of appropriate size; 1.1.2 Dissolve the salt with of ultrapure water; 1.1.3 Transfer t... |
10,022 | Validity of daily self-pulse palpation over two weeks for screening for atrial fibrillation among patients 65 years of age and older seeking primary care | null | dx.doi.org/10.17504/protocols.io.m2ec8be | null | Faris Ghazal | TITLE: Validity of daily self-pulse palpation over two weeks for screening for atrial fibrillation among patients 65 years of age and older seeking primary care
AUTHORS: Faris Ghazal
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left"><span style = "font-... | ["Design and Selection", "Design: Cross sectional study.", "Study population: It was planned to include patients who, for any reason, were seeking care in the primary health care and who were 65 years of age or older. Patients with previously known atrial fibrillation or ongoing anticoagualtion treatment were exluded."... |
51,287 | Cross-cultural adaptation and validity of the Italian version of the Anterior Knee Pain Scale: a prospective multi-centre study | 1 | dx.doi.org/10.17504/protocols.io.bwbxpapn | https://www.protocols.io/view/cross-cultural-adaptation-and-validity-of-the-ital-bwbxpapn | Jacopo E. Rocchi, Pasquale Alessio Sauchelli, Sebastiano Nutarelli, Lorenzo Rum, Riccardo Ciatti | TITLE: Cross-cultural adaptation and validity of the Italian version of the Anterior Knee Pain Scale: a prospective multi-centre study
AUTHORS: Jacopo E. Rocchi, Pasquale Alessio Sauchelli, Sebastiano Nutarelli, Lorenzo Rum, Riccardo Ciatti
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Purpose: va... | [] |
48,346 | Single-cell suspension preparation from Human bronchial biopsies to perform scRNA-sequencing using 10x chromium | 4 | null | https://www.protocols.io/view/single-cell-suspension-preparation-from-human-bron-btf2njqe | Martijn Nawijn, Leonie Apperloo | TITLE: Single-cell suspension preparation from Human bronchial biopsies to perform scRNA-sequencing using 10x chromium
AUTHORS: Martijn Nawijn, Leonie Apperloo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol enables the dissociation of human bronchial biopsies into a single-cell suspen... | ["[Before you start]\nAll steps should be performed in a sterile environment. Prepare all the buffers and reagents at room temperature as described in the \"Materials\" section.", "[Before you start]\nFreshly prepare the tissue dissociation solution.Dilute the 10x RBCs lysis buffer to 1x.", "[Preparation of single-cel... |
67,451 | Wo Sie Diaetovita (Höhle Der Löwen und Dietavita Erfahrungen) jetzt auf der offiziellen Website kaufen können! | 1 | dx.doi.org/10.17504/protocols.io.14egn7d8mv5d/v1 | https://www.protocols.io/view/wo-sie-diaetovita-h-hle-der-l-wen-und-dietavita-er-cd43s8yn | forexcarter | TITLE: Wo Sie Diaetovita (Höhle Der Löwen und Dietavita Erfahrungen) jetzt auf der offiziellen Website kaufen können!
AUTHORS: forexcarter
[DESCRIPTION]
Produktname: Diaetovita (Höhle Der LöwenundDietavita Erfahrungen)
Nebenwirkung: Keine größeren Nebenwirkungen bekannt
Erwartete Ergebnisse: In 2 – 3 Monaten
Bewe... | ["[Wo Sie Diaetovita (Höhle Der Löwen und Dietavita Erfahrungen) jetzt auf der offiziellen Website kaufen können!]"] |
39,339 | Characterization | 1 | null | https://www.protocols.io/view/characterization-binjkdcn | Hung Liang Pai | TITLE: Characterization
AUTHORS: Hung Liang Pai
[STEPS]
?. [In vitro protein synthesis]
Add the reagents(on ice) for synthesis of mRFP into one well of the 384-well plate. Add the reagents from top to down. ABCD1OrderLocationReagentAmount21Upper-leftDNase/RNase free waterTill 30 μL32Upper-leftSolution A12μL43Lower-r... | ["[In vitro protein synthesis]\nAdd the reagents(on ice) for synthesis of mRFP into one well of the 384-well plate. Add the reagents from top to down. ABCD1OrderLocationReagentAmount21Upper-leftDNase/RNase free waterTill 30 μL32Upper-leftSolution A12μL43Lower-rightSolution B9μL54Lower-rightRNase inhibitor1.2μL65Lower... |
55,650 | SWAP mouse genotyping | 4 | null | https://www.protocols.io/view/swap-mouse-genotyping-b2kaqcse | Peter W W Chomczynski, Kianna M Vires, Michal Rymascewski, Judith A. Heiny | TITLE: SWAP mouse genotyping
AUTHORS: Peter W W Chomczynski, Kianna M Vires, Michal Rymascewski, Judith A. Heiny
[DESCRIPTION]
The highly-conserved, cardiotonic steroid (CTS) binding site (also termed ouabain binding site) on the primary α subunit of Na,K-ATPase (NKA) plays a receptor signaling role in a range o... | ["[Tail clip digestion] Briefly vortex and centrifuge the tubes to pellet insoluble material. DNA will remain in the supernatant.", "[Tail clip digestion] Create a 1:100 dilution of each sample in a new, labelled 1.5 mL microcentrifuge tube. Add 198 µL of TE buffer (or ddH2O) to each tube, then add 2.0 µL of supernatan... |
76,288 | Immunocytochemistry | 4 | dx.doi.org/10.17504/protocols.io.5qpvor7pdv4o/v1 | https://www.protocols.io/view/immunocytochemistry-cnq8vdzw | anita.adami | TITLE: Immunocytochemistry
AUTHORS: anita.adami
[DESCRIPTION]
This protocol describes how to perform immunocytochemistry on 2D fixed cells
[STEPS]
SECTION: Fixing
1. The cells were washed three times with DPBS (GIBCO) and fixed for 10 minutes with 4% paraformaldehyde (Merck Millipore), followed by three more rinses ... | ["[Fixing] The cells were washed three times with DPBS (GIBCO) and fixed for 10 minutes with 4% paraformaldehyde (Merck Millipore), followed by three more rinses with DPBS.", "[Blocking and permeabilisation] The cells were blocked for 60 min in blocking solution (KPBS 0.25% Triton X-100 (Fisher Scientific) and 5% norma... |
71,022 | Inductively coupled plasma mass spectrometry (ICP-MS) | 6 | dx.doi.org/10.17504/protocols.io.x54v9dj2pg3e/v1 | https://www.protocols.io/view/inductively-coupled-plasma-mass-spectrometry-icp-m-chknt4ve | An.Huang | TITLE: Inductively coupled plasma mass spectrometry (ICP-MS)
AUTHORS: An.Huang
[DESCRIPTION]
Inductively coupled plasma mass spectrometry (ICP-MS) can be used to detect metal elements existing in samples. Because we are not capable of conducting ICP-MS on our own, we must seek help from our advisors. This protocol is ... | ["Filter all samples to be tested using 0.22μm syringe filters.", "(Optional) Dilute the samples to 0-20ppb using nitric acid (2%) if it contains too much desired elements more than the measuring range of equipment.", "Asking an assistant for help in conducting ICP-MS. Obtain a standardized curve before starting to mea... |
null | null | null | dx.doi.org/10.17504/protocols.io.t5xeq7n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Oral cancer is one of the most significant cancers in the world; the most common of which is oral squamous cell carcinoma (OSCC) that makes up to 94% of oral malignances (Bernestein et al, 2013). Based on reports of the world Health Organization (WHO), OSCC occupied the sixth mo... | [] |
95,972 | BAF_Protocol_007 Solution Digest with Protein Precipitation | 0 | dx.doi.org/10.17504/protocols.io.bp2l6xjp5lqe/v1 | https://www.protocols.io/view/baf-protocol-007-solution-digest-with-protein-prec-c9ycz7sw | Nicholas Sherman | TITLE: BAF_Protocol_007 Solution Digest with Protein Precipitation
AUTHORS: Nicholas Sherman
[DESCRIPTION]
The protocol is a method to digest a protein mixture obtained from a cell lysis or tissue that is in solution. The protocol includes a precipitation step to clean up the proteins before digestion. The protein mix... | ["[Solution Tissue Digest with Precipitation] Add 5X (volume to mg tissue) of lysis buffer (1% SDS, 100mM AmBiC) to tissue and transfer to Bead Mill 24 reinforced tube with 5 stainless steel balls.", "[Solution Tissue Digest with Precipitation] Lyse the cells with Fisher Bead Mill 24 (speed: 5m/s, time: 20 sec, number... |
42,691 | Dispensing agar into multiwell plates | 1 | dx.doi.org/10.17504/protocols.io.bmxbk7in | https://www.protocols.io/view/dispensing-agar-into-multiwell-plates-bmxbk7in | Ida Barlow | TITLE: Dispensing agar into multiwell plates
AUTHORS: Ida Barlow
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Protocol for pouring agar into 96 well plates using Integra VIAFILL dispenser. Agar should be prepared in advance, and kept in 60</span><span style = "vertical-align:super;">o</span... | ["[Configure Integra VIAFILL]\nPrepare a 250ml bottle of hot milliQ water in the microwave and keep in the waterbath along with the agar. The water is important to have on hand in case of tubing blockages.", "[Configure Integra VIAFILL]\nInsert large cassette into the machine", "[Configure Integra VIAFILL]\nConfigure X... |
29,336 | TotalSeq™-A Antibodies Protocol with 10x Single Cell 3' Reagent Kit v2 | null | dx.doi.org/10.17504/protocols.io.8vyhw7w | null | Sam Li | TITLE: TotalSeq™-A Antibodies Protocol with 10x Single Cell 3' Reagent Kit v2
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Buyer is solely responsible for determining whether Buyer has all intellectual property rights that are necessary for Buyer's intended uses of the BioLege... | ["[I) Cell staining for Drop-seq or 10x Genomics platforms]\nCarefully count all cells to ensure accurate quantitation.Make note of cell viability (>95%) and also include dead cells in the total cell count.If high cell death is observed, live cell enrichment (e.g. by Flow Cytometry) is recommended.", "[I) Cell staining... |
95,641 | Fecal sample collection | 0 | dx.doi.org/10.17504/protocols.io.3byl4qp22vo5/v1 | https://www.protocols.io/view/fecal-sample-collection-c9mzz476 | daniel.dautan daniel, Per Svenningsson | TITLE: Fecal sample collection
AUTHORS: daniel.dautan daniel, Per Svenningsson
[DESCRIPTION]
Fecal sample collection from mice to use for gut microbiome sequencing analysis.
[STEPS]
1. Set up the experiment by arranging clean cages without food, water or bedding. It is advisable to label each cage to avoid confusion ... | ["Set up the experiment by arranging clean cages without food, water or bedding. It is advisable to label each cage to avoid confusion later on.", "In front of each cage, place a glass filled with dry ice and a 1.5ml Eppendorf tube to\nspeed up collection. Use plastic forceps each cage. Avoid using the same forceps to ... |
75,598 | Isolation of bacteria and fungi from cheese rind microbiomes | 1 | dx.doi.org/10.17504/protocols.io.rm7vzb7b4vx1/v1 | https://www.protocols.click/view/isolation-of-bacteria-and-fungi-from-cheese-rind-m-cm3nu8me | Emily C.P. Weiss | TITLE: Isolation of bacteria and fungi from cheese rind microbiomes
AUTHORS: Emily C.P. Weiss
[DESCRIPTION]
This protocol describes how to harvest and stock bacterial and fungal isolates from cheese rind microbial community samples.
[STEPS]
SECTION: Harvesting the cheese rind biofilm
2. Holding the cheese in one (glo... | ["[Harvesting the cheese rind biofilm] Holding the cheese in one (gloved) hand and a sterile razor blade in the other, gently scrape the surface of the cheese to remove the rind biofilm. Avoid applying too much pressure, as you will start to dig into the paste. Scrape the rind biofilm into a weigh boat or other contain... |
97,664 | 10x Protocols: Chromium Next GEM Single Cell 5' -- University of Minnesota TMCsTMCs (CG000331 Rev E) | 0 | dx.doi.org/10.17504/protocols.io.5qpvokn89l4o/v1 | https://www.protocols.io/view/10x-protocols-chromium-next-gem-single-cell-5-39-u-dbk82kzw | Laura J Niedernhofer, David A Bernlohr | TITLE: 10x Protocols: Chromium Next GEM Single Cell 5' -- University of Minnesota TMCsTMCs (CG000331 Rev E)
AUTHORS: Laura J Niedernhofer, David A Bernlohr
[DESCRIPTION]
Following single-cell dissociation or nuclei isolation, the Next GEM 5' assay uses microfluidics to partition and assign cell- or nuclei-specifi... | ["[Library Preparation]", "[FASTQ Generation] BCL data from Illumina sequencer is demultiplexed and converted into FASTQ format using bcl2fastq version 2.20.0", "[Tissue Preparation] Complete single cell or nuclei isolation prior to starting this protocol"] |
74,646 | 0.1% BSA media prep and flow | 4 | dx.doi.org/10.17504/protocols.io.x54v9d7zpg3e/v1 | https://www.protocols.io/view/0-1-bsa-media-prep-and-flow-ck5wuy7e | Olya Oppenheim | TITLE: 0.1% BSA media prep and flow
AUTHORS: Olya Oppenheim
[DESCRIPTION]
Fetal Bovine Serum contains traces of ligands of the BMP pathway which affect the flow experiments with the ibidi perfusion system.
replacing EGM2 with 2% with EGM2 with 0.1% BSA 4h prior to onset of flow (with same media) allows cells to respon... | ["[BSA 0.1% media prep] 50 mL EGM2 without FBS\n667 µL BSA 7.5% solution\nfiltrate through 0.22um yellow filter.\nAdd to slides 4h before starting flow.", "[Optional] adding BMP9/10 to flow experiment\nin order to obtain a final 0.5 ng/ml , add 1.4ul BMP9/10 of 10 ug/ml initial concentration per perfusion unit (volume ... |
34,133 | unexpected perturbations while walking in virtual reality environment | 1 | dx.doi.org/10.17504/protocols.io.bdjvi4n6 | https://www.protocols.io/view/unexpected-perturbations-while-walking-in-virtual-bdjvi4n6 | Uri Rosenblum, Lotem Kribus-Shmiel, Gabi Zeilig, Yotam Bahat, Shani Kimel-Naor, Itshak Melzer, Meir Plotnik | TITLE: unexpected perturbations while walking in virtual reality environment
AUTHORS: Uri Rosenblum, Lotem Kribus-Shmiel, Gabi Zeilig, Yotam Bahat, Shani Kimel-Naor, Itshak Melzer, Meir Plotnik
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Walking perturbations are a well-established tool to study... | ["[Recruit Participants]\nIclusion CriteriaParticipants can be included in the study if they are:* Usually healthy* age 18-90Exclusion criteria Participants cannot be included in the study if they present the following conditions:* obesity (body mass index (kg/m2)> 30 [1]) * orthopedic condition affecting gait and bala... |
88,153 | Optimized QIAGEN DNeasy Blood & Tissue kit Protocol for Environmental DNA Extraction | 4 | dx.doi.org/10.17504/protocols.io.8epv5xn66g1b/v1 | https://www.protocols.io/view/optimized-qiagen-dneasy-blood-amp-tissue-kit-proto-c2bzyap6 | Marion Chevrinais, Jade Larivière, Laury-Ann Dumoulin, Ariane Therien, Grégoire Cortial, Cloé Lepage, Eric Parent, Geneviève J. Parent | TITLE: Optimized QIAGEN DNeasy Blood & Tissue kit Protocol for Environmental DNA Extraction
AUTHORS: Marion Chevrinais, Jade Larivière, Laury-Ann Dumoulin, Ariane Therien, Grégoire Cortial, Cloé Lepage, Eric Parent, Geneviève J. Parent
[DESCRIPTION]
This document aims at providing a transparent method and detailin... | ["[Filter Preparation] Install all the material on the benchtop including 2 mL microtubes with Lyse&Spin baskets for extraction, pre-identified 2 mL Eppendorf Safe-Lock for back up, tweezers, scissors, nacelles, waste beaker, microtube opener, and gloves.", "[Filter Preparation] Above a clean nacelle, take a filter wit... |
41,694 | COVID19 RTLAMP Assay | 4 | dx.doi.org/10.17504/protocols.io.bkx6kxre | https://www.protocols.io/view/covid19-rtlamp-assay-bkx6kxre | matt , Eugene Joseph, Arun Manoharan Arunprimediscoveriescom | TITLE: COVID19 RTLAMP Assay
AUTHORS: matt , Eugene Joseph, Arun Manoharan Arunprimediscoveriescom
[STEPS]
?. [Sample Purification / Concentration]
Preheat the Heat Block or Water Bath
?. [RT-LAMP Reaction]
Prepare the qPCR instrument, have Ice on hand to prepare the master Assay mix. Calculate the amount of samples b... | ["[Sample Purification / Concentration]\nPreheat the Heat Block or Water Bath", "[RT-LAMP Reaction]\nPrepare the qPCR instrument, have Ice on hand to prepare the master Assay mix. Calculate the amount of samples being run and make sure to include the Positive Control and the H20.", "[Sample Lysis / Inactivation]\nCent... |
59,054 | 2D TEM CLEM (Correlative Light Microscopy and Electron Microscopy) | 4 | dx.doi.org/10.17504/protocols.io.261gend2jg47/v1 | https://www.protocols.io/view/2d-tem-clem-correlative-light-microscopy-and-elect-b5wnq7de | Pietro De Camilli, Yumei Wu | TITLE: 2D TEM CLEM (Correlative Light Microscopy and Electron Microscopy)
AUTHORS: Pietro De Camilli, Yumei Wu
[DESCRIPTION]
This protocol details the general procedure of Correlative Light Microscopy and Electron Microscopy (CLEM) with conventional chemical fixation and 2D Transmission Electron Microscopy (TEM) imagi... | ["[General preparation:] Culture cells on poly-d-lysine-coated 35 mm MatTek dish (P35G-1.5-14-CGRD) and transfect the cells with the plasmids of the interest.", "[General preparation:] Pre-fix the cells in 37 °C-warmed 4% PFA and 0.25% glutaraldehyde in the imaging buffer.", "[General preparation:] Wash in the same ima... |
94,272 | SOP for Flow cytometry after DSS-induced gut and brain injury | 4 | dx.doi.org/10.17504/protocols.io.bp2l6x6zklqe/v1 | https://www.protocols.io/view/sop-for-flow-cytometry-after-dss-induced-gut-and-b-c8a8zshw | Malu G Tansey | TITLE: SOP for Flow cytometry after DSS-induced gut and brain injury
AUTHORS: Malu G Tansey
[DESCRIPTION]
SOP for Flow cytometry after DSS-induced gut and brain injury
[STEPS]
1. Following isolation of brain and circulating immune cells with magnetic beads, cells were transferred to a V-bottom plate for surface epito... | ["Following isolation of brain and circulating immune cells with magnetic beads, cells were transferred to a V-bottom plate for surface epitope labeling.", "Samples were centrifuged at 300g for 5min at 4°C, washed once in PBS, re-pelleted, and resuspended in an antibody cocktail containing fluorophore-conjugated antibo... |
null | null | null | dx.doi.org/10.17504/protocols.io.jcdcis6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is an effective protocol for genotyping diatom exconjugants which we believe is readily applicable to any other genetically manipulated marine microeukaryote.</p>
[BEFORE_START]
<p>1. Your exconjugant colonies should be growing as small - ~300 µL - liquid cultures in th... | [] |
68,430 | Secondary Data Analysis - Creating a MycoMap Project from ONT Amplicon/Barcode Data | 5 | null | https://www.protocols.io/view/secondary-data-analysis-creating-a-mycomap-project-ce3ntgme | Stephen Douglas Russell | TITLE: Secondary Data Analysis - Creating a MycoMap Project from ONT Amplicon/Barcode Data
AUTHORS: Stephen Douglas Russell
[DESCRIPTION]
This protocol outlines many of the steps that can be taken after the primary data analysis to expedite the final analysis - turning your data into results.
Topics include c... | ["[Create a MycoMap Project] Login to MycoMap.com. If you are not a member: \n\nRegister for a username on MycoMap.com: https://mycomap.com/login\n\nThen:\n\nCreate a project at the following link: https://mycomap.com/projects/create\n\nFill out the fields below:\n\nName: The name of your project. Something like \"Myco... |
77,517 | A single guide to impregnate samples with Golgi-Cox solution within 24hr and represent results with a set of algorithm | 4 | dx.doi.org/10.17504/protocols.io.3byl4jdrolo5/v1 | https://www.protocols.io/view/a-single-guide-to-impregnate-samples-with-golgi-co-cpxmvpk6 | Avishek Roy, Binney Sharma | TITLE: A single guide to impregnate samples with Golgi-Cox solution within 24hr and represent results with a set of algorithm
AUTHORS: Avishek Roy, Binney Sharma
[DESCRIPTION]
Golgi-Cox staining is one of the old but relevant histological technique to identify neurons in superficial/ deep brain structures. The goal of... | ["[Transcardial perfusion] Perfusion setup was filled with 0.9 % NaCl (saline) 2-4 °C and the flow rate was set at a rate of 3ml/min", "[Transcardial perfusion] Rats were placed onto their back and heart was made visible by opening cardiac envelop followed by an access to plural cavity through incisions through diaphr... |
94,571 | Preparation and RNAscope-labeling of fresh mouse midbrain tissue | 1 | dx.doi.org/10.17504/protocols.io.eq2lyjynelx9/v1 | https://www.protocols.io/view/preparation-and-rnascope-labeling-of-fresh-mouse-m-c8kjzuun | William S Conrad | TITLE: Preparation and RNAscope-labeling of fresh mouse midbrain tissue
AUTHORS: William S Conrad
[DESCRIPTION]
Below we describe preparing and labeling coronal sections of mouse substantia nigra (SNc) and ventral tegmental area (VTA) for probes targeting the genes Slc17a6 (VGLUT2), Slc32a1 (VGAT), and Slc18a2 (VMAT2)... | ["[A.\tMouse brain extraction] Add approximately 50mL of isopentane in a beaker (cleaned with RNAseZap) and chill on dry ice.", "[A.\tMouse brain extraction] Anaesthetize mouse with pentobarbital (200 mg/kg i.p.).", "[A.\tMouse brain extraction] Decapitate mouse and extract brain from skull.", "[A.\tMouse brain extract... |
18,686 | Nutrient solution for rice hydroponics culture | 1 | dx.doi.org/10.17504/protocols.io.wg6fbze | https://www.protocols.io/view/nutrient-solution-for-rice-hydroponics-culture-wg6fbze | John Platten | TITLE: Nutrient solution for rice hydroponics culture
AUTHORS: John Platten
[DESCRIPTION]
This represents a heavily modified Yoshida's solution. Compared to Yoshida's formulation, this solution has almost the same concentration of macro and micronutrients, but the formulation has been simplified. Key advantages:
* T... | ["[Solution A, 1000× (Main macro and micronutrients)] Make this solution up as a SINGLE stock solution. For 1L of stock solution,\n* Start with ~600mL de-ionised water.\n* Weigh out and dissolve each component (except ferric chloride and citric acid) directly in the 600mL solution. Allow each to dissolve completely b... |
null | null | null | dx.doi.org/10.17504/protocols.io.unpevdn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Caenorhabditis elegans, a small (adults are ~1 mm long), free-living soil nematode that feeds on bacteria, is an ideal organism for applying various live microscopy techniques. The organism is transparent, thus it is possible to microscopically analyze and record the whole anima... | ["[Pre-Imaging set-up] Clean the rectangular glass plate with ethanol and lint free tissue\n Switch ON the rig \n Align the movable part till desired position and lock it by pressing ON (If you want to move it again press EMO, to lock again twist the EMO knob and press ON again)\n Log in to the 3 PCs (Password: BehavGe... |
71,945 | Solid fungal extraction and C8 reversed phase chromatography | 6 | dx.doi.org/10.17504/protocols.io.ewov1onpklr2/v1 | https://www.protocols.io/view/solid-fungal-extraction-and-c8-reversed-phase-chro-cihhub36 | Shara Van De Pas, Siouxsie Wiles | TITLE: Solid fungal extraction and C8 reversed phase chromatography
AUTHORS: Shara Van De Pas, Siouxsie Wiles
[DESCRIPTION]
Protocol for freeze-drying fungal cultures and preparing extracts using C8 reversed-phase chromatography.
[STEPS]
SECTION: Crude extraction of fungal compounds
1. Subculture fungus onto ~40 Petr... | ["[Crude extraction of fungal compounds] Subculture fungus onto ~40 Petri dishes of media of choice and seal the plates with parafilm. Grow at the appropriate growth temperature until the fungus reaches the required age or coverage.", "[Crude extraction of fungal compounds] Weigh a clean 500ml beaker and break up dry f... |
66,016 | Functionality test (DNA gel stain) | 4 | null | https://www.protocols.io/view/functionality-test-dna-gel-stain-ccp8svrw | Nadine Mowoh, Stephane Fadanka | TITLE: Functionality test (DNA gel stain)
AUTHORS: Nadine Mowoh, Stephane Fadanka
[DESCRIPTION]
After PCR amplification of DNA, agarose gel electrophoresis is run to separate the DNA based on their size.
The agarose gel consists of microscopic pores that act as a molecular sieve which separates molecules based on t... | ["[Functionality test of Thiazole Orange-DMSO based DNA gel stain] Preparing 1.5 % agarose gel (using the test DNA gel stain)\n\nPrepare a 1.5 % agarose gel for electrophoresis as follows:\n\n \n\n \n\n\nUse a weighing balance to weigh 0.375 gof agarose powder and pour into a 150 ml or any appropriate size glass beaker... |
26,565 | A rapid, sensitive, scalable method for Precision Run-On sequencing (qPRO-seq) | null | dx.doi.org/10.17504/protocols.io.57dg9i6 | https://www.protocols.io/view/a-rapid-sensitive-scalable-method-for-precision-ru-57dg9i6 | Julius Judd, Luke A. Wojenski, Lauren M. Wainman, Nathaniel D. Tippens, Edward J. Rice, Alexis Dziubek, Geno J. Villafano, Erin M. Wissink, Philip Versluis, Lina Bagepalli, Sagar R. Shah, Dig B. Mahat, Jacob M. Tome, Charles G. Danko, John T. Lis, Leighton J. Core | TITLE: A rapid, sensitive, scalable method for Precision Run-On sequencing (qPRO-seq)
AUTHORS: Julius Judd, Luke A. Wojenski, Lauren M. Wainman, Nathaniel D. Tippens, Edward J. Rice, Alexis Dziubek, Geno J. Villafano, Erin M. Wissink, Philip Versluis, Lina Bagepalli, Sagar R. Shah, Dig B. Mahat, Jacob M. Tome, Charles ... | ["[Cell Permeabilization]\nPrepare permeabilization buffer, wash buffer, and freeze buffer and place .\non ice\nCAUTION: DEPC is toxic and harmful!\nCRITICAL: Care should be taken to avoid nuclease contamination. Change gloves routinely and prepare/use nuclease-free reagents.\nCRITICAL: ALL steps should be carried out ... |
63,730 | Diabetic Code Protocol | 5 | dx.doi.org/10.17504/protocols.io.261genj8wg47/v1 | https://www.protocols.io/view/diabetic-code-protocol-cagssbwe | Carlos A Maldonado Virella | TITLE: Diabetic Code Protocol
AUTHORS: Carlos A Maldonado Virella
[DESCRIPTION]
installs of the cure
[STEPS]
1.
2.
3.
4.
| [] |
87,926 | Soil extract for cocultures host-parasites media | 1 | dx.doi.org/10.17504/protocols.io.rm7vzxkq2gx1/v1 | https://www.protocols.io/view/soil-extract-for-cocultures-host-parasites-media-cz4wx8xe | Roscoff Culture Collection, Estelle Bigeard, Laure Guillou | TITLE: Soil extract for cocultures host-parasites media
AUTHORS: Roscoff Culture Collection, Estelle Bigeard, Laure Guillou
[DESCRIPTION]
How to prepare soil extract
[BEFORE_START]
Please refer to our general recommendations to grow cultures :
https://www.protocols.io/private/A48906DC1374AD6281495CB86A8F092F
[STE... | ["[Preparation of the soil extract solution (25g/l)] Add 1200ml of MilliQ water to the soil. \nClose the erlenmeyer with a aluminium foil.", "[Preparation of the soil extract solution (25g/l)] Heat at 100°C with pemanent mixing during 1 hour to obtain an efficient boiling.\nAdjust this time depending on the volume (mor... |
null | null | null | dx.doi.org/10.17504/protocols.io.jh7cj9n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Set up ssh keys to make login to the HPC easy!</p>
[STEPS]
?.
?.
?.
?.
?.
?. | [] |
101,280 | Use of EcoFAB 2.0 for reproducible plant-microbe interaction experiments | 0 | dx.doi.org/10.17504/protocols.io.kxygxyydkl8j/v1 | https://www.protocols.io/view/use-of-ecofab-2-0-for-reproducible-plant-microbe-i-de583g9w | Vlastimil Novak, Eoghan King, Peter Andeer, John Vogel, Trent t Northen | TITLE: Use of EcoFAB 2.0 for reproducible plant-microbe interaction experiments
AUTHORS: Vlastimil Novak, Eoghan King, Peter Andeer, John Vogel, Trent t Northen
[DESCRIPTION]
We conducted a multi-laboratory experiment across five labs to demonstrate reproducible microbiome formation, metabolite production, and plant g... | ["[Materials and equipment] Materials sent by the organizing lab (LBNL)\nMaterial needed for 40 EcoFAB (See EcoFAB 2.0 assembly protocol)\nSterilization pouches\nMurashige & Skoog (MS) Basal Salts (Caisson Labs MSP01-1LT).\nMicropore tape (UV-treated)\n15 mL centrifuge tubes, sterile\n2 mL microcentrifuge tubes contain... |
28,925 | Protocol for Subculture of Differentiated Blood-Brain Barrier Endothelial Cells onto Plates and Filters | null | dx.doi.org/10.17504/protocols.io.8g5hty6 | null | Ethan Lippmann, Hannah Wilson, Emma Neal | TITLE: Protocol for Subculture of Differentiated Blood-Brain Barrier Endothelial Cells onto Plates and Filters
AUTHORS: Ethan Lippmann, Hannah Wilson, Emma Neal
[STEPS]
?. [Subculturing (Day 6)]
Please select between subculturing onto plates or filters.
?. [Subculturing (Day 6)]
Coat plates with ECM plate solution for... | ["[Subculturing (Day 6)]\nPlease select between subculturing onto plates or filters.", "[Subculturing (Day 6)]\nCoat plates with ECM plate solution for at least at . Volume depends on plate type (see Table): ABC1Plate type for subculture phaseVolume of ECM solution for coatingWorking volume of EC media for cell cultu... |
68,472 | Transforming E. coli | 4 | null | https://www.protocols.io/view/transforming-e-coli-ce4ytgxw | Brian Teague | TITLE: Transforming E. coli
AUTHORS: Brian Teague
[DESCRIPTION]
Transformation is the process of inducing chemically competent E. coli to take up a plasmid. We do this in order to use E. coli as a "DNA copier" -- the bacterium takes up the plasmid, then copies it as it copies its own genomic DNA. We can grow up as ... | ["[Transformation] Retrieve the two tubes of chemically competent E. coli cells from the -80 °C freezer and place them immediately on ice. Incubate the cells on ice 3-4 minutes to thaw.", "[Transformation] Add 1 µL of DNA from your ligation to a tube of cells. Immediately after adding the DNA to the tube, flick several... |
40,318 | Preparation of a protein-AG conjugated to horseradish peroxidase by the periodate method. | 6 | dx.doi.org/10.17504/protocols.io.bjk6kkze | https://www.protocols.io/view/preparation-of-a-protein-ag-conjugated-to-horsera-bjk6kkze | Angel Justiz-Vaillant | TITLE: Preparation of a protein-AG conjugated to horseradish peroxidase by the periodate method.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A recombinant protein that combines the IgG-binding domains of SpA and SpG was developed, and labelled to horseradish pero... | ["Horseradish peroxidase (500 µg in 50 µl NaCO3 , pH 9.6) is mixed with freshly made sodium periodate solution (1.71 mg/ml) followed by incubation in the dark for 2 h.", "Mix 500 µg of staphylococcal protein-A (SpA) with an equal amount (500 micrograms) of a mix of horseradish peroxidase-sodium periodate. On the other ... |
44,037 | Vivarium Population Spender: Immigration Module | 5 | dx.doi.org/10.17504/protocols.io.bn9dmh26 | https://www.protocols.io/view/vivarium-population-spender-immigration-module-bn9dmh26 | Camila Rangel Smith | TITLE: Vivarium Population Spender: Immigration Module
AUTHORS: Camila Rangel Smith
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Description of the steps followed by Vivarium Population Spenser library when running the Immigration module. </div></div>
[STEPS]
?. Get the total number of immigrant... | ["Get the total number of immigrants expected for that local authority on a year from a local authority level international migration table.", "Divide the number of total immigrants to be assigned by the number of steps existing in that year.", "For each time step:", "Add the fraction of immigrants to be assigned in on... |
53,999 | Glycerol stock preparation | 4 | dx.doi.org/10.17504/protocols.io.byyppxvn | https://www.protocols.io/view/glycerol-stock-preparation-byyppxvn | Ashwinuday | TITLE: Glycerol stock preparation
AUTHORS: Ashwinuday
[DESCRIPTION]
This protocol is for the preparation of 10% glycerol stocks of bacterial strains.
[STEPS]
1. From a streaked plate of the bacteria, pick one colony and inoculate into a test tube containing 10 mL 1X LB
2. Grow the culture till it reaches an OD ~ ... | ["From a streaked plate of the bacteria, pick one colony and inoculate into a test tube containing 10 mL 1X LB", "Grow the culture till it reaches an OD ~ 0.6", "Into cryo-vials add 1.6 mL culture and 0.4 mL 50% autoclaved glycerol.", "Flash freeze the tubes in liquid Nitrogen and store it at -80 °C"] |
76,285 | TaME-seq2 | 1 | dx.doi.org/10.17504/protocols.io.dm6gpjxy5gzp/v1 | https://www.protocols.io/view/tame-seq2-cnq5vdy6 | jean-marc, Milan Stosic, Alexander Hesselberg, trinro | TITLE: TaME-seq2
AUTHORS: jean-marc, Milan Stosic, Alexander Hesselberg, trinro
[DESCRIPTION]
Tagmentation-assisted multiplex PCR enrichment sequencing for viral genomic profiling (TaME-seq2). Viral genome and integration enrichment library preparation protocol.
Manuscript:
TaME-seq2: Tagmentation-assisted multiplex... | ["[Sample preparation] Prepare and normalize DNA/cDNA samples by measuring sample concentration and diluting in nuclease-free water if necessary. \n\nSample volume should be 15 µL \n\n50 ng input is recommended, but the protocol works with less and performance is more dependent on viral load.", "[Tagmentation] Prepare... |
100,178 | Bacterial genome annotation script using BLASTN | 5 | dx.doi.org/10.17504/protocols.io.dm6gpjrb1gzp/v3 | https://www.protocols.io/view/bacterial-genome-annotation-script-using-blastn-dd3s28ne | Ana Mariya Anhel, Lorea Alejaldre, Ángel Goñi-Moreno | TITLE: Bacterial genome annotation script using BLASTN
AUTHORS: Ana Mariya Anhel, Lorea Alejaldre, Ángel Goñi-Moreno
[DESCRIPTION]
This protocol uses a python based script and command-line BLASTn to annotate in a final table single-read sequencing results from genome amplifications, within other output files.
Its mai... | ["[Adquisition of files] Download reference genome file\n\nYou can download the genome of the organism that you want to compare to the reading sequences from different sources such as NCBI, GSA or even pages dedicated to the organism (for example pseudomonas.com).\n\nFor this script to work, genome files need to be in ... |
22,116 | Squalene Quantification using Nile Red Staining (Developmental) | null | dx.doi.org/10.17504/protocols.io.zucf6sw | null | Sebastian Triesch | TITLE: Squalene Quantification using Nile Red Staining (Developmental)
AUTHORS: Sebastian Triesch
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">This protocol is under development!</span></div><div class = "text-block">Nile Red is a fluorescent dye that stains sele... | ["[Culture Sampling]\nSample 1-2 ml Synechocystis culture, measure its OD at 750 nm and adjust it to 2 ml of OD (750 nm) = 0.5 in BG-11 media. Split your adjusted culture in 2x 1 ml. One portion will be stained with Nile Red, the other will serve as a negative control.", "[Staining]\nStain one portion of the previously... |
71,353 | Constant mood monitoring using WhatsApp for persons with depression: a pilot study | 2 | dx.doi.org/10.17504/protocols.io.8epv5jz46l1b/v1 | https://www.protocols.io/view/constant-mood-monitoring-using-whatsapp-for-person-chwzt7f6 | Maritta A Välimäki, Qing Long, Min Yang, Sau Fong | TITLE: Constant mood monitoring using WhatsApp for persons with depression: a pilot study
AUTHORS: Maritta A Välimäki, Qing Long, Min Yang, Sau Fong
[DESCRIPTION]
Background
Preliminary evidence suggests that social media could provide a convenient platform to monitor mood. It is still unknown whether WhatsApp mood mo... | [] |
81,176 | Simple TCA/acetone protein extraction protocol for proteomics studies. | 4 | dx.doi.org/10.17504/protocols.io.5jyl8j74dg2w/v1 | https://www.protocols.io/view/simple-tca-acetone-protein-extraction-protocol-for-cthywj7w | Angelo José Rinaldi | TITLE: Simple TCA/acetone protein extraction protocol for proteomics studies.
AUTHORS: Angelo José Rinaldi
[DESCRIPTION]
Protein extraction with TCA (trichloroacetic acid) and acetone is a widely used method to precipitate proteins from biological samples. This method is useful for obtaining proteins of interest for p... | ["Prepare a 20% TCA solution by adding 200g of TCA in 800ml of distilled water. Be sure to do this in a well-ventilated area, wearing gloves and eye protection, as TCA is corrosive.", "Add the biological sample (approximately 300 mg) to a 2 mL microcentrifuge tube.", "Add a small amount of detergent (10% SDS) to the sa... |
28,611 | Removal of gDNA out of totalRNA | null | dx.doi.org/10.17504/protocols.io.77bhrin | null | iGEM Dusseldorf | TITLE: Removal of gDNA out of totalRNA
AUTHORS: iGEM Dusseldorf
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Start</span></div><div class = "text-block">Calculate the volume required for 1 µg RNA</div><div class = "text-block"><span style = "font-weight:bold;">Di... | [] |
60,846 | H&E Staining for Pancreas or Eye Cryosections | 1 | dx.doi.org/10.17504/protocols.io.rm7vz3e6rgx1/v2 | https://www.protocols.io/view/h-amp-e-staining-for-pancreas-or-eye-cryosections-b7nnrmde | Diane Saunders, Angela Kruse, Jamie Allen, Carrie Romer, Danielle Gutierrez, Alvin Powers, Jeff Spraggins | TITLE: H&E Staining for Pancreas or Eye Cryosections
AUTHORS: Diane Saunders, Angela Kruse, Jamie Allen, Carrie Romer, Danielle Gutierrez, Alvin Powers, Jeff Spraggins
[DESCRIPTION]
This protocol for H&E staining can be applied to either fixed or unfixed frozen cryosections.
[STEPS]
1. Air dry sections for... | ["Air dry sections for 5 min .", "Incubate in 95% alcohol for 1 min , then wash, dipping until clear.", "Incubate in hematoxylin for 30 s , then wash until clear.", "Dip 3-4x in bluing solution, then wash for 30 s", "Dip 3-4x in 95% alcohol.", "Dip 1-2x in eosin.", "Dip 5-10x in 95% alcohol, then repeat using 2nd aliqu... |
33,152 | PROTOCOL FOR: LRP37 method | null | dx.doi.org/10.17504/protocols.io.bck8iuzw | null | Gaku Takahashi, Katsuya Inada | TITLE: PROTOCOL FOR: LRP37 method
AUTHORS: Gaku Takahashi, Katsuya Inada
[STEPS] | [] |
101,699 | CYToF Staining | 0 | dx.doi.org/10.17504/protocols.io.14egn69nml5d/v1 | https://www.protocols.io/view/cytof-staining-dfjb3kin | Meelad Amouzgar, Patricia Favaro, Daniel Ho, Trevor Bruce, Kausalia Vijayaragavan, Sean Bendall | TITLE: CYToF Staining
AUTHORS: Meelad Amouzgar, Patricia Favaro, Daniel Ho, Trevor Bruce, Kausalia Vijayaragavan, Sean Bendall
[DESCRIPTION]
CYToF has significantly advanced immunophenotyping, especially in exploratory settings where comprehensive characterization of immune populations is necessary but sample sizes ar... | ["[CyToF Staining] PFA Fixation:\nAdd 100 uL of 16% PFA per 1 mL of media and incubate cells for 10 minutes at room temperature.\nWash with 4mL of CSM 2x\nPellet the cells by centrifugation at 600xg for 5 min.\nStore fixed cells in 1mL of CSM at -80C", "[CyToF Staining] Barcoding protocol:\nTransfer cells to cluster t... |
18,474 | N. parisii infection of C. elegans | null | dx.doi.org/10.17504/protocols.io.waiface | null | Emily Troemel | TITLE: N. parisii infection of C. elegans
AUTHORS: Emily Troemel
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.frsbm6e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The Sequence Read Archive (SRA) is a database for biological sequence data and is maintained by the National Center for Biotechnology Information (NCBI). Sequence files can be obtained by using the SRA Toolkit. This protocol provides the steps necessary to use the SRA toolkit... | [] |
24,576 | Immunofluorescence Staining of Sea Urchin Embryos | null | dx.doi.org/10.17504/protocols.io.388grzw | null | David Booth | TITLE: Immunofluorescence Staining of Sea Urchin Embryos
AUTHORS: David Booth
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">In this lab, you will use immunofluroescence stainging to visualize the wondrous cellular transformations that occur throughout sea urchin development. The goals of this modu... | ["[Fix Cells]\nPrepare cells for fixation• Place 300 µl of embryos in filtered seawater in 1 well of a 96-well, round-bottom dish.", "[Add Primary Antibody]\nPrepare primary antibody• Dilute mouse anti-Tubulin antibody 1:500 in Block solution! Remember that you will need 200 µl of primary antibody per well", "[Block]\n... |
62,194 | Cholera Toxin Subunit B (CTB) Retrograde tracing from the mouse colon and bladder wall. | 1 | dx.doi.org/10.17504/protocols.io.x54v9y391g3e/v1 | https://www.protocols.io/view/cholera-toxin-subunit-b-ctb-retrograde-tracing-fro-b8ysrxwe | Andrea Harrington | TITLE: Cholera Toxin Subunit B (CTB) Retrograde tracing from the mouse colon and bladder wall.
AUTHORS: Andrea Harrington
[DESCRIPTION]
This protocol is used to label the neurons and their central terminals of the sensory neurons innervating the colon and bladder in an experimental adult male or female mouse. The pr... | ["[Preparation for surgery] Prepare cages for each mouse – place clean bedding, nesting material in cage and water bottle and food pellets in hopper ready for post-surgery", "[Anaesthesia] Place mouse in induction box, and turn on isoflurane to 5% and oxygen flow rate to 0.5-0.6L/min.", "[Preparation for surgery] Weigh... |
54,952 | DNA extraction from concrete | 1 | null | https://www.protocols.io/view/dna-extraction-from-concrete-bzwgp7bw | Anders Kiledal, Julia A Maresca | TITLE: DNA extraction from concrete
AUTHORS: Anders Kiledal, Julia A Maresca
[DESCRIPTION]
This is a protocol for extracting DNA from concrete, based on the protocol developed by L. S. Weyrich, et al. for extraction of DNA from ancient calcified dental plaque. We have scaled it up for larger sample sizes and made som... | ["[Sample Pre-Treatment (Day 1)] In a 50 mL conical tube, place 10 g pulverized concrete, 5 mL 0.5 M EDTA, 150 µL Proteinase K (20 mg/mL), 138 µL 20% SDS, and 0.2 mL glacial acetic acid. Incubate at 55°C overnight with gentle rotation.", "[DNA Extraction (Days 2 and 3)] Vortex at maximum speed on a platform vortexer fo... |
null | null | null | dx.doi.org/10.17504/protocols.io.utcewiw | null | null | TITLE: No Title
AUTHORS:
[BEFORE_START]
Thaw GeltrexTM Basement Membrane Matrix at 2-8°C overnight. Refrigerator temperatures may vary; therefore, thaw extract on ice in a refrigerator. Basement Membrane Matrix gels in 5-10 minutes above 15°C; therefore when working from a full 5 ml vial, it is unnecessary to keep it... | ["[Thawing of Geltrex, dilution in DMEM/F12 and aliquotting for storage at -20C] {\"blocks\":[{\"key\":\"cvdtr\",\"text\":\" \",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[{\"offset\":0,\"length\":1,\"key\":0}],\"data\":[]},{\"key\":\"9u3ma\",\"text\":\"Thaw one tube of Geltrex (1-5 mL)... |
23,758 | Determination of Glomerular Filtration Rate in Conscious Mice using FITC-inulin | null | dx.doi.org/10.17504/protocols.io.3fngjme | null | Zhonghua Qi, Matthew D. Breyer | TITLE: Determination of Glomerular Filtration Rate in Conscious Mice using FITC-inulin
AUTHORS: Zhonghua Qi, Matthew D. Breyer
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">This protocol describes the procedures for ... | ["Preparation of 5% FITC-inulin solution:1. 5% FITC-inulin is dissolved in two ml of 0.9% NaCl -- facilitated by heating the solution in boiling water. 2. To remove residual FITC not bound to inulin, the solution is filled into a 1000 Daltons cut-off dialysis membrane (Spectra/Pro 6, Spectrum Laboratories Inc., Rancho ... |
null | null | null | dx.doi.org/10.17504/protocols.io.fyzbpx6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div class="page" title="Page 1">
<div class="layoutArea">
<div class="column">
<p>The SensiFAST™ SYBR® & Fluorescein Kit uses a combination of the latest advances in buffer chemistry and enhancers, together with an antibody-mediated hot-start DNA polymerase system, to ensur... | [] |
78,808 | Compartmental Protein Extraction to Achieve Enrichment of Extracellular Matrix (ECM) Proteins | 4 | dx.doi.org/10.17504/protocols.io.kxygx94b4g8j/v1 | https://www.protocols.io/view/compartmental-protein-extraction-to-achieve-enrich-cq7yvzpw | James Considine, Ikram Isa, Alexandra Naba | TITLE: Compartmental Protein Extraction to Achieve Enrichment of Extracellular Matrix (ECM) Proteins
AUTHORS: James Considine, Ikram Isa, Alexandra Naba
[DESCRIPTION]
This protocol provides instructions on how to extract cellular components of tissues and enrich for ECM proteins to be later analyzed via immunoblotting... | ["[Tissue Homogenization] Homogenize 100 mg of tissue in 1 mL of Buffer CEB containing protease inhibitors using a tissue homogenizer until the tissue is completely disrupted and a homogenous suspension is obtained.", "[Sequential extraction of intracellular soluble proteins]", "[Sequential extraction of intracellula... |
23,884 | Neuropathy Phentoyping Protocols - Apoptag (Peroxidase) Sections on Slides | null | dx.doi.org/10.17504/protocols.io.3jkgkkw | null | Eva Feldman | TITLE: Neuropathy Phentoyping Protocols - Apoptag (Peroxidase) Sections on Slides
AUTHORS: Eva Feldman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block"><span style = "font-weight:bold;">Phenotyping of Rodents for the Pre... | ["[Preparation:]\n1. Thaw equilibration buffer, TdT, reaction buffer and stopwash on ice. 2. Prepare working strength TdT enzyme. 3. Thaw enough reaction buffer and TdT to cover 30 ul/well TdT: reaction buffer, 33 µl: 77 µl. 4. Prepare stopwash buffer, add 1 ml buffer to 34 ml of ddH²0. 5. Prepare a humidified chamber.... |
null | null | null | dx.doi.org/10.17504/protocols.io.te7ejhn | null | null | TITLE: No Title
AUTHORS:
[STEPS] | [] |
99,977 | Intraperitoneal Injection in an Adult Mouse | 1 | dx.doi.org/10.17504/protocols.io.5qpvo5w8dl4o/v2 | https://www.protocols.io/view/intraperitoneal-injection-in-an-adult-mouse-ddvh2636 | Allen Institute for Brain Science | TITLE: Intraperitoneal Injection in an Adult Mouse
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
This protocol describes the general procedure used for intraperitoneal injection in adult mice.
Note: Research reported in this publication was supported by the National Institute Of Mental Health of the Nation... | [] |
82,822 | An axenic plant culture system for Sporobolus alterniflorus | 4 | dx.doi.org/10.17504/protocols.io.x54v9d94qg3e/v1 | https://www.protocols.click/view/an-axenic-plant-culture-system-for-sporobolus-alte-cu5ewy3e | Elena L. Peredo, Suzanne M Thomas, Zoe Cardon | TITLE: An axenic plant culture system for Sporobolus alterniflorus
AUTHORS: Elena L. Peredo, Suzanne M Thomas, Zoe Cardon
[DESCRIPTION]
Sporobulus alterniflorus is a native grass that dominates intertidal salt marsh platforms along thousands of miles of the U.S. East and Gulf coasts. This grass exhibits tolerance to ... | ["[Seed storage and germination] The plant material in this protocol is seedlings germinated ex vitro. While optional, we recommend autoclaving the soil and completing surface sterilization of the seeds to minimize the contaminants in the samples. Alternatively, seeds can be germinated in open containers.", "[Seed stor... |
74,205 | Nano3P-seq Protocol | 4 | dx.doi.org/10.17504/protocols.io.3byl4j292lo5/v2 | https://www.protocols.io/view/nano3p-seq-protocol-ckp5uvq6 | Oguzhan Begik | TITLE: Nano3P-seq Protocol
AUTHORS: Oguzhan Begik
[DESCRIPTION]
Here, we develop Nanopore 3’ end-capture sequencing (Nano3P-seq), a novel method that relies on nanopore cDNA sequencing to simultaneously quantify RNA abundance, tail composition and tail length dynamics at per-read resolution. By employing a template sw... | ["[Without Barcoding] Materials and consumables required\n\n●Direct cDNA Sequencing Kit (ONT, SQK-DCS109)\n●Flow Cell Priming Kit (ONT, EXP-FLP001)\n●AMPure XP Reagent (Agencourt , A63881)\n●Blunt/TA Ligase Master Mix (NEB, M0367)\n●TGIRT™-III Enzyme (InGex)\n●RNase Inhibitor, Murine (NEB,M0314L)\n●RNase Cocktail Enzy... |
91,049 | Ex vivo mouse brain patch clamp recordings combined with uncaging and optogenetic stimulation | 4 | dx.doi.org/10.17504/protocols.io.rm7vzx1w2gx1/v2 | https://www.protocols.io/view/ex-vivo-mouse-brain-patch-clamp-recordings-combine-c46hyzb6 | enrico.zampese | TITLE: Ex vivo mouse brain patch clamp recordings combined with uncaging and optogenetic stimulation
AUTHORS: enrico.zampese
[DESCRIPTION]
In this protocol we detail the steps to perform ex-vivo brain slices electrophysiology and optogenetic stimulation and/or 2-photon uncaging recordings.
[BEFORE_START]
Please note ... | ["[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... |
35,684 | FACS Single Cell Sorting | null | dx.doi.org/10.17504/protocols.io.be4cjgsw | null | Allen Institute for Brain Science | TITLE: FACS Single Cell Sorting
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol provides step by step instructions for performing single-cell sorting by using BD FACSAria II machine or BD FACSAria Fusion machine and BD FACSDiva software.</div>... | [] |
27,208 | Toxicity assay for inducer compounds in Synechocystis sp. PCC 6803 | null | dx.doi.org/10.17504/protocols.io.6tghejw | null | Anna Behle, Pia Saake, Ilka Maria Axmann | TITLE: Toxicity assay for inducer compounds in Synechocystis sp. PCC 6803
AUTHORS: Anna Behle, Pia Saake, Ilka Maria Axmann
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Inducible promoters are an important tool for synthetic biology. They enable temporal control of gene expression, as well as con... | ["[Inoculation of pre-culture]\nInoculate an appropriate amount of BG11 with your cyanobacterial strain of choice. The inoculation volume depends on the number of concentrations to be tested. For example: 3 concentrations x 3 replicates x 30 mL = 270 mL of preculture. Since the culture will be diluted ~1:3 before start... |
44,614 | Automated high throughput viral concentration from wastewater using the KingFisher Flex platform | 4 | null | https://www.protocols.io/view/automated-high-throughput-viral-concentration-from-bptemnje | Smruthi Karthikeyan, Greg Humphrey | TITLE: Automated high throughput viral concentration from wastewater using the KingFisher Flex platform
AUTHORS: Smruthi Karthikeyan, Greg Humphrey
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Large-scale wastewater surveillance has the ability to greatly augment the tracking of infection dynami... | ["Aliquot of raw sewage (no pre-filtering step required) into two wells of the KingFisher 24 deep-well plate (Cat# 95040470, Thermo Fisher). Each well should have of the raw sewage sample. For instance, of sample PL09 should be filled in A1 of plate 1 and in A1 of plate 2.\n10 mL\n5 mL\n5 mL\n5 mL", "Add of t... |
54,436 | Step 1: Swab sample collection | 1 | null | https://www.protocols.io/view/step-1-swab-sample-collection-bzecp3aw | Peter H L Krijger, Tim A Hoek, Sanne Boersma, Lieke I P M Donders, Maaike M C Broeders, Mark Pieterse, Pim W Toonen, Ive Logister, Bram M P Verhagen, Marjon J A M Verstegen, Thomas W van Ravesteyn, Rene J T M Roymans, Francesca Mattiroli, Jo Vandesompele, Monique Nijhuis, Stefan Meijer, Anton van Weert, Edwin Dekker, F... | TITLE: Step 1: Swab sample collection
AUTHORS: Peter H L Krijger, Tim A Hoek, Sanne Boersma, Lieke I P M Donders, Maaike M C Broeders, Mark Pieterse, Pim W Toonen, Ive Logister, Bram M P Verhagen, Marjon J A M Verstegen, Thomas W van Ravesteyn, Rene J T M Roymans, Francesca Mattiroli, Jo Vandesompele, Monique Nijhuis, ... | ["[Sample collection] Person 1 scans the 2D barcode at the bottom of a 0.8 ml Micronic tube prefilled with 0.4 ml virus transport buffer ( InActiv Blue mixed with a spike-in control RNA) and places it in a Micronic tube rack (tube rack A).", "[Sample collection] Person 1 removes cap from the Micronic tube using the man... |
83,898 | NEBNext Ultra II FS DNA Module E7810 | 1 | dx.doi.org/10.17504/protocols.io.bp2l66xrlqe5/v2 | https://www.protocols.click/view/nebnext-ultra-ii-fs-dna-module-e7810-cv62w9ge | jbonnevie | TITLE: NEBNext Ultra II FS DNA Module E7810
AUTHORS: jbonnevie
[DESCRIPTION]
The NEBNext Ultra II FS DNA Module contains the enzymes and buffers required to convert a broad range of input amounts of intact DNA into fragmented DNA with 5´ phosphorylated 3´ dA-tailed ends. The module is optimized for use with the NEBNex... | ["[Fragmentation/End Prep] Fragmentation occurs during the 37 °C incubation step. Use the chart below to determine the incubation time required to generate the desired fragment sizes. Incubation time may need to be optimized for individual samples. See Figure 1 for a typical fragmentation pattern.\n \n Fragmentation ... |
83,014 | Astrocyte isolation and culturing | 4 | dx.doi.org/10.17504/protocols.io.e6nvwdp9wlmk/v1 | https://www.protocols.io/view/astrocyte-isolation-and-culturing-cvbew2je | Julia F Riley | TITLE: Astrocyte isolation and culturing
AUTHORS: Julia F Riley
[DESCRIPTION]
This protocol details steps for preparing an astrocyte monoculture from mouse pups. From dissection to plated samples ready to be transfected, treated, lysed, or imaged, the protocol takes 20-25 days.
[BEFORE_START]
The night before (could... | ["[Dissection] Sacrifice mouse pups postnatal day (P) 1-3 via isoflourane overdose.", "[Dissection] Decapitate pups and transfer heads to a dish with 100 % (v/v) EtOH. Swirl to clean.", "[Dissection] Transfer heads to a new 10cm dish and place whole dish in a cell culture dish with a wider diameter. The surrounding dis... |
57,738 | Seeding nucleofected hPSCs in 96-well plates using limited dilution | 4 | dx.doi.org/10.17504/protocols.io.b4miqu4e | https://www.protocols.io/view/seeding-nucleofected-hpscs-in-96-well-plates-using-b4miqu4e | Hanqin Li, Yogendra Verma, Dirk Hockemeyer, Frank Soldner | TITLE: Seeding nucleofected hPSCs in 96-well plates using limited dilution
AUTHORS: Hanqin Li, Yogendra Verma, Dirk Hockemeyer, Frank Soldner
[DESCRIPTION]
This protocol describes a standard procedure for seeding nucleofected human pluripotent stem cells in 96-well plates using limited dilution. This protocol follows... | ["For an editing with 10% efficiency, prepare two 96-well MEFs plates with a density at 2 million cells/plate at least 1 day ahead. Do not shake the plate after seeding MEFs. It generates swirls and causes cells to accumulate at the center. If editing efficiency is expected to be low, prepare more 96-well plates.", "Ca... |
49,085 | Investigating DOIs' classes of errors | 5 | dx.doi.org/10.17504/protocols.io.bt65nrg6 | https://www.protocols.io/view/investigating-dois-39-classes-of-errors-bt65nrg6 | Ricarda Boente, Deniz Tural, Cristian Santini, Arcangelo Massari | TITLE: Investigating DOIs' classes of errors
AUTHORS: Ricarda Boente, Deniz Tural, Cristian Santini, Arcangelo Massari
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The purpose of this protocol is to describe an automated process to repair invalid DOIs. In particular, four classes of errors ar... | ["[Checking the DOI names' invalidity]\nWe import a CSV containing invalid DOI-to-DOI citations organized as follow: the first column contains valid citing DOIs and the second contains invalid cited DOIs", "[Checking the DOI names' invalidity]\nFirst, we check for each cited DOI if it is factually invalid. For this p... |
27,980 | Yeast transformation | null | dx.doi.org/10.17504/protocols.io.7jkhkkw | null | Marijn Ceelen | TITLE: Yeast transformation
AUTHORS: Marijn Ceelen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a protocol for the transformation of yeast cells with linear or circular DNA.</div></div>
[STEPS]
?. Make a transformation mix consisting of: AB1DNA34 µL (0.5-4 µg per fragment)2Salmon sperm ... | ["Make a transformation mix consisting of: AB1DNA34 µL (0.5-4 µg per fragment)2Salmon sperm DNA 2 mg/mL50 µL3PEG-3350240 µL41M LiOAc36 µL5MQ waterup to a final volume of 360 µL\nAB1DNA34 µL (0.5-4 µg per fragment)2Salmon sperm DNA 2 mg/mL50 µL3PEG-3350240 µL41M LiOAc36 µL5MQ waterup to a final volume of 360 µL", "Cent... |
null | null | null | dx.doi.org/10.17504/protocols.io.fcrbiv6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p> </p>
<p><strong>Lysogeny <a href="https://en.wikipedia.org/wiki/Broth" target="_blank">broth</a></strong> (<strong>LB</strong>), a <a href="https://en.wikipedia.org/wiki/Nutrient" target="_blank">nutritionally</a> rich <a href="https://en.wikipedia.org/wiki/Growth_medium" ta... | [] |
85,798 | Gene editing of YIPF4 in hESCs V3 | 4 | dx.doi.org/10.17504/protocols.io.rm7vzxy44gx1/v1 | https://www.protocols.io/view/gene-editing-of-yipf4-in-hescs-v3-cx2exqbe | Harper JW, Kelsey Hickey, sharan_swarup | TITLE: Gene editing of YIPF4 in hESCs V3
AUTHORS: Harper JW, Kelsey Hickey, sharan_swarup
[DESCRIPTION]
This protocol describes the creation of YIPF4 knockout hESCs.
[STEPS]
SECTION: Cell line maintenance
1. Maintain H9 human embryonic stem cells (AAVS1-TRE3G-NGN2 hESCs) in complete (E8 media).
SECTION: Targeted knoc... | ["[Cell line maintenance] Maintain H9 human embryonic stem cells (AAVS1-TRE3G-NGN2 hESCs) in complete (E8 media).", "[Targeted knock-out of YIPF4] For YIPF4 knock-out, the following sgRNA sequences was designed and ordered from Synthego (5’ AAGAGGTTATGGCTGGCTTC 3').", "[Targeted knock-out of YIPF4] 0.6 μg sgRNA was in... |
102,378 | Behavioral Consequences of Dopaminergic Dysregulation Resulting from Violence-Induced Brain Trauma | 0 | dx.doi.org/10.17504/protocols.io.261ge5e17g47/v1 | https://www.protocols.io/view/behavioral-consequences-of-dopaminergic-dysregulat-df8i3rue | Spencer Lee | TITLE: Behavioral Consequences of Dopaminergic Dysregulation Resulting from Violence-Induced Brain Trauma
AUTHORS: Spencer Lee
[DESCRIPTION]
This study protocol outlines the experimental procedures designed to assess the influence of trauma resulting from violence on dopamine activation and subsequent behavior. The ex... | ["[This study aimed to investigate dopaminergic dysregulation caused by trauma induced by violence, and its subsequent behaviors. This study will conduct a systematic review and meta-analysis and incorporate correlation statistical analysis.] The relationship between dopamine activation and subsequent dopamine release ... |
22,996 | Biolistic transformation of Isochrysis galbana | null | dx.doi.org/10.17504/protocols.io.2pugdnw | null | Glen Wheeler, Rowena Stern | TITLE: Biolistic transformation of Isochrysis galbana
AUTHORS: Glen Wheeler, Rowena Stern
[STEPS]
?. [Preparing tungsten beads]
Weigh out 60 mg tungsten into a microfuge tube
?. [Preparing tungsten beads]
Wash in 1 mL 100% ethanol. Vortex. Centrifugation at 13000rpm for 1 minute then remove ethanol
?. [Preparing tungs... | ["[Preparing tungsten beads]\nWeigh out 60 mg tungsten into a microfuge tube", "[Preparing tungsten beads]\nWash in 1 mL 100% ethanol. Vortex. Centrifugation at 13000rpm for 1 minute then remove ethanol", "[Preparing tungsten beads]\nWash four times in 1 mL molecular grade water. Centrifugation at 13000rpm for 1 minute... |
60,337 | RT-qPCR Detection of Process Controls (Murine noroviurs and crAssphage) from Wastewater using AB 7500 | 4 | dx.doi.org/10.17504/protocols.io.kqdg36j9pg25/v2 | https://www.protocols.io/view/rt-qpcr-detection-of-process-controls-murine-norov-b66rrhd6 | Jacquelina.Woods , rachel.rodriguez | TITLE: RT-qPCR Detection of Process Controls (Murine noroviurs and crAssphage) from Wastewater using AB 7500
AUTHORS: Jacquelina.Woods , rachel.rodriguez
[DESCRIPTION]
This method was developed at the FDA’s Center for Food Safety and Applied Nutrition for GenomeTrakr’s pandemic response project, monitoring SARS-CoV... | ["[Master Mix Preparation] Prepare Master Mix for all sample and control reactions based on the volumes per 25 µl reaction in this table. Composition of mixes are listed here: Reagent Mixes for RT-qPCR Detection of Process Controls from Wastewater Samples (protocols.io) and should be prepared in advance and stored appr... |
87,732 | Fluorescent Western Protocol | 4 | null | https://www.protocols.io/view/fluorescent-western-protocol-czwux7ew | Lynn Doran, Steven J Burgess | TITLE: Fluorescent Western Protocol
AUTHORS: Lynn Doran, Steven J Burgess
[DESCRIPTION]
Analysis of proteins using fluorescent immunoblot with optional total protein stain.
Note:
- The choice of secondary antibody depends on the choice of primary antibody, whether it is derived from a mouse (monoclonal) or a rabbit... | ["Keep membranes in the black Western Blot incubation box for all steps, this is important after adding the secondary antibody because the signal is light-sensitive and will become bleached if exposed to light for a long enough period.", "[Fluorescent Western Protocol] Wet with 1x PBS for 2 min min", "[Fluorescent West... |
20,446 | Serial Dilution of Nucleofected iPSC Pools | null | dx.doi.org/10.17504/protocols.io.x76frre | null | Celeste Karch, Rita Martinez, Jacob Marsh | TITLE: Serial Dilution of Nucleofected iPSC Pools
AUTHORS: Celeste Karch, Rita Martinez, Jacob Marsh
[STEPS]
?. Coat 3 wells of a 6 well plate with Matrigel (supplemented with RGD fragment)
1 ml
?. Aspirate media from cells in culture.
?. Wash with - PBS per well.
1 ml
2 ml
?. Add Accutase per well.
1 ml
?. Incubate... | ["Coat 3 wells of a 6 well plate with Matrigel (supplemented with RGD fragment)\n1 ml", "Aspirate media from cells in culture.", "Wash with - PBS per well.\n1 ml\n2 ml", "Add Accutase per well.\n1 ml", "Incubate at for to achieve single cells.\nIndividual donor lines exhibit variable sensitivity to accutase-mediated... |
98,507 | Multiple Myeloma Immune Atlas Consortium: Gene Expression Profiling of the Bone Marrow Microenvironment | 0 | dx.doi.org/10.17504/protocols.io.q26g718z3gwz/v1 | https://www.protocols.io/view/multiple-myeloma-immune-atlas-consortium-gene-expr-dcfj2tkn | Manoj Bhasin | TITLE: Multiple Myeloma Immune Atlas Consortium: Gene Expression Profiling of the Bone Marrow Microenvironment
AUTHORS: Manoj Bhasin
[DESCRIPTION]
A comprehensive gene expression (GEX) profiling protocol that assists in
generating the most granular map of single cell landscape from clinical trials
supported by Multip... | ["[Thawing & Washing bone marrow (BM) derived cells] Preparation", "[GEM Generation and Barcoding] Prepare Master Mix on ice according to the standard 10X protocol and dispense 31.8 µL per sample into a 8 strip tube kept on ice.", "[Sample Index PCR] Choose the appropriate sample index sets to ensure that no sample... |
28,004 | HiFi Gibson Assembly (Protocol for the NEBuilder® HiFi DNA Assembly Master Mix) | null | dx.doi.org/10.17504/protocols.io.7kchksw | null | Alba Balletbó | TITLE: HiFi Gibson Assembly (Protocol for the NEBuilder® HiFi DNA Assembly Master Mix)
AUTHORS: Alba Balletbó
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is the protocol for DNA Assembly using the NEBuilder® HiFi DNA Assembly Master Mix.</div></div>
[STEPS]
?. Set up the following reaction... | ["Set up the following reaction on ice (to 20μl total volume): ABC12-3 Fragment Assembly4-6 Fragment Assembly2DNA RatioVector:Insert = 1:2Vector:Insert = 1:13Total amount of Fragments0.03-0.2 pmols0.2-0.5 pmols4NEBuilder HiFi DNA Assembly Master Mix10 μL10 μL5Deionized H2O10 - X μL10 - X μL6Total Volume20 μL20 μL\nABC... |
82,017 | 10x Protocols: Visium v2 CytAssist FFPE Library Construction -- University of Minnesota TMCs (CG000495 Rev D) | 1 | dx.doi.org/10.17504/protocols.io.3byl4jpzzlo5/v1 | https://www.protocols.io/view/10x-protocols-visium-v2-cytassist-ffpe-library-con-cub9wsr6 | IOx Genomics, Laura J Niedernhofer, David A Bernlohr | TITLE: 10x Protocols: Visium v2 CytAssist FFPE Library Construction -- University of Minnesota TMCs (CG000495 Rev D)
AUTHORS: IOx Genomics, Laura J Niedernhofer, David A Bernlohr
[DESCRIPTION]
Protocols from 10x Genomics for Visium Spatial Gene Expression v2 chemistry on FPPE samples with the CytAssist component.
Pro... | ["10x protocol CG000 495, Revision D (Library construction with CytAssist)", "Additional Protocols/Resources\nhttps://www.10xgenomics.com/support/spatial-gene-expression-ffpe"] |
19,342 | High-Density Penetrating Microelectrode Recordings from Anesthetized Feline Dorsal Root Ganglia | 1 | dx.doi.org/10.17504/protocols.io.w5nfg5e | https://www.protocols.io/view/high-density-penetrating-microelectrode-recordings-w5nfg5e | Zachariah Sperry, Kyounghwan Na, Mihaly Vöröslakos, Saman Parizi, James Jun, Tim M. Bruns, Euisik Yoon, John P. Seymour | TITLE: High-Density Penetrating Microelectrode Recordings from Anesthetized Feline Dorsal Root Ganglia
AUTHORS: Zachariah Sperry, Kyounghwan Na, Mihaly Vöröslakos, Saman Parizi, James Jun, Tim M. Bruns, Euisik Yoon, John P. Seymour
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Dorsal root ganglia ... | ["[Diamond Shuttle Fabrication]\nPattern tapered trenches onto silicon wafer.", "[Recording Apparatus Assembly]\nBond array interconnects to circuit board for connection to Omnetics adaptor.", "[Insertion and Stabilization Apparatus Assembly]\nMove subject to support stand with overhead rack and ability to lower legs b... |
81,504 | Preparação para ir ao campo | 1 | dx.doi.org/10.17504/protocols.io.dm6gpjz31gzp/v2 | https://www.protocols.io/view/prepara-o-para-ir-ao-campo-ctt8wnrw | Alicia Rafaelly Vilefort Sales, Daniel Vartanian, Maria Augusta Medeiros Andrade | TITLE: Preparação para ir ao campo
AUTHORS: Alicia Rafaelly Vilefort Sales, Daniel Vartanian, Maria Augusta Medeiros Andrade
[DESCRIPTION]
Este protocolo foi desenhado para o processo de coleta de dados do projeto de pesquisa Associações entre a duração e a qualidade do sono de gestantes no terceiro trimestre com a du... | ["[Agenda] Consulte a agenda do projeto e verifique a quantidade de gestantes a serem recrutadas no seu turno.", "[Agenda] Verifique os horários e o trajeto que você terá que fazer para que você chegue com ao menos 30 minutos de antecedência na Casa de Parto.", "[Actígrafos] Separe um actígrafo para cada gestante a ser... |
92,647 | Use of the waxworm Galleria mellonella larvae as an infection model to study Acinetobacter baumannii | 4 | dx.doi.org/10.17504/protocols.io.n92ldpr38l5b/v2 | https://www.protocols.io/view/use-of-the-waxworm-galleria-mellonella-larvae-as-a-c6qfzdtn | Kah Ern Ten, Nazmul Hasan Muzahid, Sadequr Rahman, tan.hocksiew | TITLE: Use of the waxworm Galleria mellonella larvae as an infection model to study Acinetobacter baumannii
AUTHORS: Kah Ern Ten, Nazmul Hasan Muzahid, Sadequr Rahman, tan.hocksiew
[DESCRIPTION]
Galleria mellonella larvae have been increasingly used in various scientific research, including microbial infection studie... | ["[Galleria mellonella rearing and maintenance] Research-grade Galleria mellonella larvae were ordered in bulk from Carolina Biological (US).", "[Galleria mellonella rearing and maintenance] Set up Galleria mellonella housing according to Figure 2.", "[Galleria mellonella rearing and maintenance] Fill 2/3 of the larvae... |
102,535 | Platelet purification and coating of plates for adhesion assays | 0 | dx.doi.org/10.17504/protocols.io.n92ld8wb8v5b/v1 | https://www.protocols.io/view/platelet-purification-and-coating-of-plates-for-ad-dgdf3s3n | Samantha King | TITLE: Platelet purification and coating of plates for adhesion assays
AUTHORS: Samantha King
[DESCRIPTION]
This is the protocol we use to prepare fixed platelets from human blood and coat wells ready for adhesion assays.
[GUIDELINES]
We typically have greater success when using at least 180 mls of blood. When usi... | ["Blood from healthy donors was collected in 1/6th volume of acid citrate dextrose solution (ACD). Mix gently.", "Blood was spun down for 20 min at 200 x g, deaccelerating step without brake.", "Platelet rich plasma was collected (top yellow layer) and mixed (inverting the tube) 1:1 with HEP buffer.", "Platelets were c... |
52,645 | NCBI submission protocol for SARS-CoV-2 wastewater data: SRA, BioSample, and BioProject | 1 | dx.doi.org/10.17504/protocols.io.bxndpma6 | https://www.protocols.io/view/ncbi-submission-protocol-for-sars-cov-2-wastewater-bxndpma6 | Ruth Timme, Maria Balkey | TITLE: NCBI submission protocol for SARS-CoV-2 wastewater data: SRA, BioSample, and BioProject
AUTHORS: Ruth Timme, Maria Balkey
[DESCRIPTION]
PURPOSE:
This method was developed at the FDA’s Center for Food Safety and Applied Nutrition for GenomeTrakr’s pandemic response project, monitoring SARS-CoV-2 variants in ... | ["["Ingredients" to have in place before starting your submissions] Set up a new NCBI submission environment for your lab\n1.1: Create an NCBI user account\n1.2: Set up an NCBI submission user group for your lab\n1.4: Bookmark the link to your Submission Portal\n1.5. Identify or establish new BioProjects (det... |
54,237 | Titan Clear Labs SARS-CoV-2 Strain Characterization Workflow for the Terra Platform | 5 | null | https://www.protocols.io/view/titan-clear-labs-sars-cov-2-strain-characterizatio-by75pzq6 | Frank J Ambrosio, Jill V Hagey, Kevin Libuit, Technical Outreach and Assistance for States Team | TITLE: Titan Clear Labs SARS-CoV-2 Strain Characterization Workflow for the Terra Platform
AUTHORS: Frank J Ambrosio, Jill V Hagey, Kevin Libuit, Technical Outreach and Assistance for States Team
[DESCRIPTION]
The Titan_ClearLabs workflow is a part of the Public Health Viral Genomics Titan series for SARS-CoV-2 geno... | ["[Setup Terra and Google Cloud Accounts]", "[Import Titan Clear Labs workflow from Dockstore] Importing the Titan Workflow from Dockstore to the User Workspace\n\nThe Titan Clear Labs workflow is hosted in the Theiagen Dockstore (https://dockstore.org/) repository and has to be imported into the user's Terra Workspace... |
79,371 | DNA extraction (BOMB) | 4 | dx.doi.org/10.17504/protocols.io.n2bvj6mdnlk5/v3 | https://www.protocols.io/view/dna-extraction-bomb-crrjv54n | Tsu-Chun Hung, Yin-Tse Huang | TITLE: DNA extraction (BOMB)
AUTHORS: Tsu-Chun Hung, Yin-Tse Huang
[DESCRIPTION]
DNA extraction (BOMB)
[STEPS]
SECTION: Sample Collection
1. Add 200 µL of 1mm beads to 2ml eppendorf tube
SECTION: Sample Collection
2. Add200 µL of 0.5mm beads to 2ml eppendorf tube
SECTION: Sample Collection
3. Add867 µL Lysis mast... | ["[Sample Collection] Add 200 µL of 1mm beads to 2ml eppendorf tube", "[Sample Collection] Add200 µL of 0.5mm beads to 2ml eppendorf tube", "[Sample Collection] Add867 µL Lysis master mix to 2ml eppendorf tube", "[Sample Collection] Collect 10-20 mg of sample to 2ml eppendorf tube", "[Sample crush] Put 2ml eppendorf tu... |
19,963 | U Mass - Ammonia | null | dx.doi.org/10.17504/protocols.io.xq3fmyn | null | Jason Kim | TITLE: U Mass - Ammonia
AUTHORS: Jason Kim
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">This experiment involves a spectrophotometric measurement using Roche Cobas Clinical Chemistry Analyzer.</div></div>
[STEPS]
?.... | ["Perform daily quality control assessment of instrumentation before analysis.", "Load each sample into a specialized micro-sample cup for the clinical chemistry analyzer.", "Select Ammonia test on display and run the analysis.", "Collect and analyze the data."] |
81,675 | Individual AAV production and purification | 4 | dx.doi.org/10.17504/protocols.io.14egn2dqzg5d/v1 | https://www.protocols.io/view/individual-aav-production-and-purification-ctzjwp4n | Miguel Chuapoco | TITLE: Individual AAV production and purification
AUTHORS: Miguel Chuapoco
[DESCRIPTION]
We recently developed adeno-associated virus (AAV) capsids to facilitate efficient and noninvasive gene transfer to the central and peripheral nervous systems. However, a detailed protocol for generating and systemically deliverin... | ["[Reagent setup: Plasmid DNA] Grow bacterial stocks in LB or Plasmid+ media containing the appropriate selective antibiotic; refer\nto the Addgene catalog for suggested growth conditions. Use a large-scale endotoxin-free plasmid purification kit to isolate plasmids; elute plasmid DNA with the supplied Tris-EDTA (TE) b... |
97,520 | Tissue H&E Staining | HuBMAP | JHU-TMC | 0 | dx.doi.org/10.17504/protocols.io.kqdg3242qv25/v1 | https://www.protocols.io/view/tissue-h-amp-e-staining-hubmap-jhu-tmc-dbgq2jvw | Kyu Sang Han, Pei-Hsun Wu, Joel Sunshine, Ashley Kiemen, Miklhail James, Sashank Reddy, Denis Wirtz | TITLE: Tissue H&E Staining | HuBMAP | JHU-TMC
AUTHORS: Kyu Sang Han, Pei-Hsun Wu, Joel Sunshine, Ashley Kiemen, Miklhail James, Sashank Reddy, Denis Wirtz
[DESCRIPTION]
The following are guidelines that will have an effective staining window of 2 to 5 minutes. Developed as progressive stains, the intensity of nucl... | ["[H&E staining] Final Step: Mount and Coverslip with Covermount", "Set 2 stations with 100% ethanol. Submerge the slide for a minute in each station.", "[H&E staining] Wash the slide in running warm water for a minute", "[H&E staining] Submerge the slide in Optik Hematoxylin for 3 minutes", "[H&E stain... |
64,423 | Ocuprime Scam Or Legit Updated 2022 Must See before buy | 3 | dx.doi.org/10.17504/protocols.io.eq2lynqywvx9/v1 | https://www.protocols.io/view/ocuprime-scam-or-legit-updated-2022-must-see-befor-ca6fshbn | fluxactive | TITLE: Ocuprime Scam Or Legit Updated 2022 Must See before buy
AUTHORS: fluxactive
[DESCRIPTION]
(LOWEST PRICE GUARANTEED) Click Here to Buy Ocuprime For The Lowest Price Today
[STEPS] | [] |
64,722 | Beneficial Bio Products: Quality control tests | 4 | null | https://www.protocols.io/view/beneficial-bio-products-quality-control-tests-cbfssjne | Nadine Mowoh, Stephane Fadanka | TITLE: Beneficial Bio Products: Quality control tests
AUTHORS: Nadine Mowoh, Stephane Fadanka
[DESCRIPTION]
After production, we typically subject our products to a batch of quality control assays to ascertain their functionality, efficacy and ability to meet their intended purpose.
Strict quality control is nec... | ["[Functionality tests] Pipetting:\n \n\nDNA polymerase and Master mix enzyme\n\nThaw all reagents on ice in a bowl\nLabel reaction tubes (PCR tubes) according to the number of samples, and including controls in each run (negative and positive controls) as needed.\n\nPolymerase enzyme type:\nIf using a 10x cellular rea... |
81,449 | Surgical decision-making in the management of knee cartilage injuries in football players: Development of patient-specific recommendations using the RAND/UCLA appropriateness method | 1 | null | https://www.protocols.io/view/surgical-decision-making-in-the-management-of-knee-ctshwnb6 | Giuseppe Filardo, Andreas Serner, Luca Andriolo, Andrew Massey, Emmanuel Papakostas, Peter Verdonk, Elizaveta Kon | TITLE: Surgical decision-making in the management of knee cartilage injuries in football players: Development of patient-specific recommendations using the RAND/UCLA appropriateness method
AUTHORS: Giuseppe Filardo, Andreas Serner, Luca Andriolo, Andrew Massey, Emmanuel Papakostas, Peter Verdonk, Elizaveta Kon
[DESCRI... | [] |
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