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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48,373 | Facilitators and barriers to postnatal care guideline implementation: A systematic scoping review | 1 | dx.doi.org/10.17504/protocols.io.btgvnjw6 | https://www.protocols.io/view/facilitators-and-barriers-to-postnatal-care-guidel-btgvnjw6 | Lenka Benova, Aline Semaan | TITLE: Facilitators and barriers to postnatal care guideline implementation: A systematic scoping review
AUTHORS: Lenka Benova, Aline Semaan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This review seeks to understand and synthesise the available evidence about the extent of implementation of ro... | ["[Research team]\nLead researchers: Lenka BenovaAline SemaanContributors:Mercedes BonetAllisyn MoranAnayda PortelaThomas van den AkkerAndrea B Pembe", "[Objectives]\nThe scoping review aims to identify themes in the literature related to the implementation of routine postnatal guidelines globally.\n\t\t\t\t\t\t\t .ju... |
59,342 | Sample Cutting/Processing Protocol | 4 | dx.doi.org/10.17504/protocols.io.36wgq7nryvk5/v1 | https://www.protocols.io/view/sample-cutting-processing-protocol-b57nq9me | Khai-Minh H Nguyen, Katarina A Cohen, Abraham Palmer, Oksana Polesskaya | TITLE: Sample Cutting/Processing Protocol
AUTHORS: Khai-Minh H Nguyen, Katarina A Cohen, Abraham Palmer, Oksana Polesskaya
[DESCRIPTION]
Procedure for preparing a 96 sample plate for extraction on the EPmotion 5075 (can also do by hand). This protocol is created for Agencourt's DNAdvance extraction Kit.
[BEFORE_STA... | ["[Preparing Workstation] 1. Fill insulated foam box with dry ice and place empty tube rack to chill.", "[Logging New Samples in Excel] 1. Place 16 samples on tube rack in two rows of 8.\nLeave them to thaw for 15 min \nWhile you allow them to thaw, proceed to the next steps", "[Processing Samples] Cut a small section ... |
99,251 | Fluorescence size exclusion chromatography (FSEC) of native nanodiscs | 0 | dx.doi.org/10.17504/protocols.io.14egn676ml5d/v1 | https://www.protocols.io/view/fluorescence-size-exclusion-chromatography-fsec-of-dc6t2zen | Caroline Brown, Snehasish Ghosh, Kallol Gupta | TITLE: Fluorescence size exclusion chromatography (FSEC) of native nanodiscs
AUTHORS: Caroline Brown, Snehasish Ghosh, Kallol Gupta
[DESCRIPTION]
This is a protocol describing how to conduct Fluorescence size exclusion chromatography of native nanodiscs.
[STEPS]
1. Conduct extraction into native nanodiscs following ... | ["Conduct extraction into native nanodiscs following established protocols.", "Inject 200uL native nanodiscs onto a Superose6 (10/300GL) column which is pre-equilibrated with TBS.", "Perform separation at a flow rate of 0.5 mL/min and detect eluent with a Shimadzu fluorometer with excitation set to 488 nm and emission ... |
70,656 | Do differences exist in the hamstring muscles architectural characteristics of elite-level male and female rugby players | 1 | dx.doi.org/10.17504/protocols.io.kxygx9e4kg8j/v1 | https://www.protocols.io/view/do-differences-exist-in-the-hamstring-muscles-arch-cg88tzzw | Kevin Cronin, Shane Foley, Sean Cournane, Eamonn Delahunt | TITLE: Do differences exist in the hamstring muscles architectural characteristics of elite-level male and female rugby players
AUTHORS: Kevin Cronin, Shane Foley, Sean Cournane, Eamonn Delahunt
[DESCRIPTION]
Hamstring injuries carry a high injury burden and are more prevalent in males than females. This study is desi... | [] |
109,513 | GEARBOCS protocols | 0 | dx.doi.org/10.17504/protocols.io.36wgqnq15gk5/v3 | https://www.protocols.io/view/gearbocs-protocols-dn7h5hj6 | Justin T Savage, Luke Bradley, Nicholas Brose | TITLE: GEARBOCS protocols
AUTHORS: Justin T Savage, Luke Bradley, Nicholas Brose
[DESCRIPTION]
Protocols for AAV production and use of the GEARBOCS system.
[STEPS] | [] |
78,362 | Statistical Analysis Plan (Part 8 of "Effects of Online Exercise Intervention on Physical and Mental Conditions in Young Adults with Chronic Neck Pain") | 1 | dx.doi.org/10.17504/protocols.io.e6nvwj469lmk/v1 | https://www.protocols.io/view/statistical-analysis-plan-part-8-of-34-effects-of-cqr2vv8e | Yiting Lin | TITLE: Statistical Analysis Plan (Part 8 of "Effects of Online Exercise Intervention on Physical and Mental Conditions in Young Adults with Chronic Neck Pain")
AUTHORS: Yiting Lin
[DESCRIPTION]
This is Part 8 of "Effects of Online Exercise Intervention on Physical and Mental Conditions in Young Adults with Chr... | [] |
43,077 | Multitissue transcriptome profiling during onset of salmon maturation | 5 | dx.doi.org/10.17504/protocols.io.bnbdmai6 | https://www.protocols.io/view/multitissue-transcriptome-profiling-during-onset-o-bnbdmai6 | Amin Mohamed, Bradley Evans, Antonio Reverter, James Kijas | TITLE: Multitissue transcriptome profiling during onset of salmon maturation
AUTHORS: Amin Mohamed, Bradley Evans, Antonio Reverter, James Kijas
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Despite the importance of sexual maturation as a trait of interest it can be difficult to study, as t... | ["[Induction of maturation through photoperiod manipulation]\nAnimals were managed using photoperiod manipulation to synchronise the timing of commitment into maturation. A population of female brood stock were used that were ∼ 36 months post fertilization in April 2017. In order to measure and control for variation be... |
null | null | null | dx.doi.org/10.17504/protocols.io.ewrbfd6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Assembling <em>actual</em> reads from the <a href="https://github.com/MicroB3-IS/osd-analysis" target="_blank">Ocean Sampling Day (2014)</a> using SPAdes, an assembler implemented in <a href="cyverse.org" target="_blank">Cyverse</a>.
[BEFORE_START]
To run this protocol, users m... | [] |
34,195 | Transformation of heterolous DNA in Bacillus subtilis | 1 | dx.doi.org/10.17504/protocols.io.bdmti46n | https://www.protocols.io/view/transformation-of-heterolous-dna-in-bacillus-subti-bdmti46n | Kristoffer Bach Falkenberg, Cristina Hernandez Rollan, Maja Rennig, Andreas Birk Bertelsen, Morten Norholm | TITLE: Transformation of heterolous DNA in Bacillus subtilis
AUTHORS: Kristoffer Bach Falkenberg, Cristina Hernandez Rollan, Maja Rennig, Andreas Birk Bertelsen, Morten Norholm
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-style:italic;">B. subtilis </span><span>is a gram-posit... | ["[Preparation of stock solutions]\nMix 10xSM1 stock", "[Preparation of stock solutions]\nMix 1xSM2 stock\nSM2 is made as a 1x stock since it otherwise precipitates", "[Preparation of stock solutions]\nWeigh the following in a 100mL blue cap bottle:2 g ammonium sulphate14 g dipotassium hydrogen phosphate6 g potassium d... |
81,345 | Research on ERIH PLUS approved SSH journals present in OpenCitations Meta database | 5 | dx.doi.org/10.17504/protocols.io.5jyl8jo1rg2w/v2 | https://www.protocols.io/view/research-on-erih-plus-approved-ssh-journals-prese-ctn9wmh6 | Ali Ghasempouri, maddalena.ghiotto, sebastiano.giacomini | TITLE: Research on ERIH PLUS approved SSH journals present in OpenCitations Meta database
AUTHORS: Ali Ghasempouri, maddalena.ghiotto, sebastiano.giacomini
[DESCRIPTION]
In this study, we present a comprehensive workflow to assess the coverage of publications in Social Science and Humanities (SSH) journals indexed i... | ["[Retrieve OpenCitation Meta publication and Journals that are registered in ERIH-PLUS index] Starting from the ERIH-PLUS index of Social Science and Humanities approved journals dataset \n (downloaded 27/04/2023) we want to retrieve all the publications belonging to one of those journals, included in OpenCitations M... |
104,300 | Detection of central and obstructive sleep apneas in mice: a new surgical and recording protocol | 0 | dx.doi.org/10.17504/protocols.io.yxmvme54og3p/v2 | https://www.protocols.io/view/detection-of-central-and-obstructive-sleep-apneas-dh4k38uw | Gabriele Matteoli, Sara Alvente, Chiara Berteotti, Dario Coraci, Viviana Lo Martire, Martina Lops, Elena Miglioranza, Alessandro Silvani, Emilia Volino, Giovanna Zoccoli, Stefano Bastianini* | TITLE: Detection of central and obstructive sleep apneas in mice: a new surgical and recording protocol
AUTHORS: Gabriele Matteoli, Sara Alvente, Chiara Berteotti, Dario Coraci, Viviana Lo Martire, Martina Lops, Elena Miglioranza, Alessandro Silvani, Emilia Volino, Giovanna Zoccoli, Stefano Bastianini*
[DESCRIPTION]
S... | ["[Overview] Figure 1 summarizes the chronological steps of the protocol.\n\nFigure 1. Overview of the protocol\n\nThe experimental protocol involves the crafting (Day -1) and the surgical implantation (Day 0) of the electrodes for the recording of electroencephalogram (EEG), nuchal muscle electromyogram (nEMG), and di... |
96,380 | Prevalence of psychoactive substance use and changes in consumption during the COVID-19 Pandemic in people with substance use disorders: systematic review and meta-analysis | 0 | dx.doi.org/10.17504/protocols.io.kxygx3rydg8j/v1 | https://www.protocols.io/view/prevalence-of-psychoactive-substance-use-and-chang-dac42ayw | Sara Ribeiro Carvalho, Clarissa de Paula Andrade, Laisa Marcorela Andreoli Sartes, Layane Aparecida ferraz de Azevedo, Pedro Matheus Lopes Peralta Abranches, Ken Youens-Clark | TITLE: Prevalence of psychoactive substance use and changes in consumption during the COVID-19 Pandemic in people with substance use disorders: systematic review and meta-analysis
AUTHORS: Sara Ribeiro Carvalho, Clarissa de Paula Andrade, Laisa Marcorela Andreoli Sartes, Layane Aparecida ferraz de Azevedo, Pedro Mathe... | ["[PREVALENCE OF PSYCHOACTIVE SUBSTANCE USE AND CONSUMPTION PATTERN DURING THE COVID-19 PANDEMIC IN PEOPLE WITH SUBSTANCE USE DISORDERS: SYSTEMATIC REVIEW AND META-ANALYSIS] Background\n\nThe COVID-19 pandemic, a recent public health emergency of international interest, represents a major challenge for mental health, g... |
20,061 | U Mass - C-reactive Peptide | null | dx.doi.org/10.17504/protocols.io.xt5fnq6 | null | Jason Kim | TITLE: U Mass - C-reactive Peptide
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. Serum levels... | ["Perform daily quality control assessment of instrumentation before analysis.", "Load each sample into a specialized micro-sample cup for the clinical chemistry analyzer.", "Select C-reactive Peptide test on display and run the analysis.", "Collect and analyze the data."] |
73,974 | Use of systemic antibiotics in patients with COVID-19 in Colombia. A cross-sectional study | 1 | dx.doi.org/10.17504/protocols.io.rm7vzbk5xvx1/v1 | https://www.protocols.io/view/use-of-systemic-antibiotics-in-patients-with-covid-ckgwutxe | Jorge Machado Alba | TITLE: Use of systemic antibiotics in patients with COVID-19 in Colombia. A cross-sectional study
AUTHORS: Jorge Machado Alba
[DESCRIPTION]
Abstract
Antibiotics are frequently prescribed to patients with COVID-19. The aim was to determine the pattern of use of systemic antibiotics in a group of patients diagn... | [] |
90,323 | Evercode WT v2.2.1 | 4 | null | https://www.protocols.io/view/evercode-wt-v2-2-1-c4ftytnn | Parse Biosciences, Elisabeth Rebboah | TITLE: Evercode WT v2.2.1
AUTHORS: Parse Biosciences, Elisabeth Rebboah
[DESCRIPTION]
This protocol describes the original Parse Biosciences Evercode WT v2 protocol for single-nucleus or single-cell RNA-seq of 100,000 nominal nuclei or cells. Unlike other scRNA-seq methods that physically separate individual cells int... | ["[Section 1: Barcoding Single Cells] 1.1: Experimental Setup", "[Section 1: Barcoding Single Cells] Prepare for the first round of barcoding with the following checklist:\nEach sample should have been counted after nuclei fixation and recorded on the spreadsheet in order to calculate volumes to normalize concentration... |
null | null | null | dx.doi.org/10.17504/protocols.io.u3jeykn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
How to run uproc v1.2.0 (Meinicke, 2014) through the iMicrobe plaform.
The ultrafast protein classification (UProC) toolbox implements a mosaic matching algorithm for large-scale protein annotation analysis. UProC is up to three orders of magnitude faster than profile-based me... | ["[Run uproc on metagenomic reads] {\"blocks\":[{\"key\":\"4he0p\",\"text\":\"This protocol section uses SRS01342, a metagenomic sample from the HMP project. This sample is a posterior formix sample. The app was run on the read pair 1.\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[{\"offset\":0,\"length\":... |
11,464 | Preparation of libraries (Metabarcoding) for Illumina sequencing - Genomer Platform | 1 | dx.doi.org/10.17504/protocols.io.5qpvo6mdv4o1/v1 | https://www.protocols.io/view/preparation-of-libraries-metabarcoding-for-illumin-pfgdjjw | Estelle Bigeard, Adriana Lopes Dos Santos, Catherine Ribeiro | TITLE: Preparation of libraries (Metabarcoding) for Illumina sequencing - Genomer Platform
AUTHORS: Estelle Bigeard, Adriana Lopes Dos Santos, Catherine Ribeiro
[DESCRIPTION]
The following detailed protocol is for the generation of paired-end sequencing reads of 16S or 18S (or any other marker) PCR amplicons with ... | ["[General workflow] The general workflow is composed by 5 different parts:\n\n1. DNA/RNA extraction protocols. \n\n2. PCR amplification protocols. \nSeveral genes amplification protocols are available on protocols.io for 18S rRNA, plastid 16S, bacterial 16s, nifH etc\n\n3. Library preparation protocols. \nThis protoco... |
54,188 | Gradient PCR with DMSO | 4 | dx.doi.org/10.17504/protocols.io.by6kpzcw | https://www.protocols.io/view/gradient-pcr-with-dmso-by6kpzcw | Ashwinuday | TITLE: Gradient PCR with DMSO
AUTHORS: Ashwinuday
[DESCRIPTION]
This protocol can be used to confirm genes or DNA of interest from a template using PCR. Also to amplify required amount of genes to larger amounts.
Gradient is used to find out the best annealing temperature.
DMSO is required for the Pfu polymerase... | ["Prepare the working stock solution of all the reagents required. If already prepared and stored, takeout from the refrigerator and thaw on ice.", "Prepare the following mixes each of total 50 µL and 5 test samples were made for the 5 different annealing temperatures to be varied at each of the following percentages o... |
36,021 | Preparation of 5M Guanidine thiocyanate L6 Inactivation Buffer | null | dx.doi.org/10.17504/protocols.io.bfevjje6 | https://www.protocols.io/view/preparation-of-5m-guanidine-thiocyanate-l6-inactiv-bfevjje6 | Nicola O'Reilly, Svend Kjaer | TITLE: Preparation of 5M Guanidine thiocyanate L6 Inactivation Buffer
AUTHORS: Nicola O'Reilly, Svend Kjaer
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Purpose of examination / Clinical relevance</span></div><div class = "text-block">At the end of 2019, several ... | ["[Preparation of L6 Lysis Buffer]\nPlease select between the recipes for 1 L, 2 L, 4.3 L and 5.4 L L6 5 M Guanidine thiocyanate Inactivation buffer.\nUpon contact with acids, GuSCN can produce a toxic gas (HCN). As a precaution, GuSCN-containing buffers are prepared in a fume hood.", "[Preparation of L6 Lysis Buffer]\... |
68,275 | Post-Surgical Dissection of Fallopian Tubes | 4 | dx.doi.org/10.17504/protocols.io.14egn75eqv5d/v1 | https://www.protocols.io/view/post-surgical-dissection-of-fallopian-tubes-cewttfen | Stephen Fisher, Marielena Grijalva, Rong Guo, sarahjoh, Hieu Nguyen, John Renz, Jean G Rosario, Steven Rudich, Brian Gregory, Junhyong Kim, Kate O'Neill | TITLE: Post-Surgical Dissection of Fallopian Tubes
AUTHORS: Stephen Fisher, Marielena Grijalva, Rong Guo, sarahjoh, Hieu Nguyen, John Renz, Jean G Rosario, Steven Rudich, Brian Gregory, Junhyong Kim, Kate O'Neill
[DESCRIPTION]
This protocol describes dissection of the Fallopian tubes in preparation for 10X Visium, 10X... | ["After removing uterus and Fallopian tubes from ice, dry each Fallopian tube and use marking dye to label the superior edge (12 o’clock), inferior edge (6 o’clock), anterior surface (3 o’clock) and posterior surface (9 o’clock).", "Measure the Fallopian tube from cornua to fimbriated end.", "Using a disposable scalpel... |
52,950 | ChIP-seq in human cells with mouse cells spike-in | 4 | null | https://www.protocols.io/view/chip-seq-in-human-cells-with-mouse-cells-spike-in-bxxwpppe | Michael Tellier | TITLE: ChIP-seq in human cells with mouse cells spike-in
AUTHORS: Michael Tellier
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol to perform ChIP-seq in human cells with spike-in. </div></div>
[STEPS]
?. [Day 1]
Split the human cells in a 150 mm dish for a ~80% confluence on Day 2. Do the ... | ["[Day 1]\nSplit the human cells in a 150 mm dish for a ~80% confluence on Day 2. Do the same for the mouse cells.", "[Day 2]\nChromatin preparationAdd 1% formaldehyde to the cells and mix 10 minutes on a shaker at 20-25 rpm at room temperature (540.5 μl 37% formaldehyde for 20 ml of medium).Add 125 mM Glycine and mix ... |
69,270 | Simultaneous detection of miRNA and mRNA at the single-cell level in plant tissues | 4 | dx.doi.org/10.17504/protocols.io.x54v9deppg3e/v1 | https://www.protocols.io/view/simultaneous-detection-of-mirna-and-mrna-at-the-si-cfvwtn7e | Chi-Chih Wu | TITLE: Simultaneous detection of miRNA and mRNA at the single-cell level in plant tissues
AUTHORS: Chi-Chih Wu
[DESCRIPTION]
Detecting the simultaneous presence of a microRNA (miRNA) and a mRNA in a specific tissue can provide support for the prediction that the miRNA regulates the mRNA. Ｗe develop a method that uses ... | ["miRNA hybridization\n \n 1. The slides with sections are taken out the freezer and equilibrated to RT for 40 mins. 2. Permeabilized in 20 ug/ml proteinase k for proper duration 3. Quickly wash in DEPC-PBS 4. Quickly dehydrate the slides in EtOH (50, 70, 99 %) and then air dry 5. Mount the s... |
11,348 | Plate assay for quantification of Root System Architecture of Arabidopsis seedlings | null | dx.doi.org/10.17504/protocols.io.pbudinw | null | Magdalena Julkowska | TITLE: Plate assay for quantification of Root System Architecture of Arabidopsis seedlings
AUTHORS: Magdalena Julkowska
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a standard assay for examining Root System Architecture of Arabidopsis seedling in response to hormone treatment or any othe... | ["[Sterilize the seeds of Arabidopsis lines that you wish to use for the RSA assay and keep them for at least 48 h at 4°C to ensure higher germination rates]\nSterilize the seeds by putting them first in 50% household bleach (the one you can buy at the supermarket - but no \"extra strenght\") for 10 minutes, then wash ... |
41,051 | Managements for brain tumours cases during the COVID-19 pandemic. A protocol for systematic review and meta-analysis. | 3 | dx.doi.org/10.17504/protocols.io.bkb3ksqn | https://www.protocols.io/view/managements-for-brain-tumours-cases-during-the-cov-bkb3ksqn | Mohammed A Azab, Sherief Ghozy, Abdulraheem Alomari, Ahmed Y Azzam | TITLE: Managements for brain tumours cases during the COVID-19 pandemic. A protocol for systematic review and meta-analysis.
AUTHORS: Mohammed A Azab, Sherief Ghozy, Abdulraheem Alomari, Ahmed Y Azzam
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Background and O... | [] |
108,592 | Longitudinal evaluation of whole blood viscosity for evidence-based pathology in cardiovascular medicine: Study protocol | 0 | dx.doi.org/10.17504/protocols.io.kqdg32z71v25/v1 | https://www.protocols.io/view/longitudinal-evaluation-of-whole-blood-viscosity-f-dnaq5adw | Bupe Amon Kyelu, Phillip Taderera Bwititi, Ezekiel Uba Nwose | TITLE: Longitudinal evaluation of whole blood viscosity for evidence-based pathology in cardiovascular medicine: Study protocol
AUTHORS: Bupe Amon Kyelu, Phillip Taderera Bwititi, Ezekiel Uba Nwose
[DESCRIPTION]
Background: Mental and work-related stress is a significant global concern with huge social and economic im... | ["[Introduction] Whole blood viscosity (WBV) is a laboratory test in medical practice. Currently WBV testing for stasis (how the thinness or thickness of the blood may be affecting its flow or pooling) is mainly restricted to the management of diseases associated with too much protein (hyperproteinaemia), too many red ... |
50,264 | Bacterial transformation | 1 | null | https://www.protocols.io/view/bacterial-transformation-bvbyn2pw | Joris Van Asselberghs, Addgene The Nonprofit Plasmid Repository | TITLE: Bacterial transformation
AUTHORS: Joris Van Asselberghs, Addgene The Nonprofit Plasmid Repository
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The following protocol is for bacterial transformation. To see the full abstract and additional resources, visit the </span><a href="https://... | ["Take competent cells out of and thaw on ice (approximately - ).\n-80 °C", "Remove agar plates (containing the appropriate antibiotic) from storage at and let warm up to room temperature and then (optional) incubate in incubator.\n4 °C\n37 °C", "Mix - of plasmid DNA (usually - ) of competent cells in a microc... |
71,932 | Proteomics -Cell Lysis and Protein Digestion/Proteomics -Tandem Mass Tag Labeling | 1 | null | https://www.protocols.io/view/proteomics-cell-lysis-and-protein-digestion-proteo-cig4ubyw | gustavo.parfitt | TITLE: Proteomics -Cell Lysis and Protein Digestion/Proteomics -Tandem Mass Tag Labeling
AUTHORS: gustavo.parfitt
[DESCRIPTION]
Proteomics -Cell Lysis and Protein Digestion/Proteomics -Tandem Mass Tag Labeling
[STEPS]
1. For the proteomics your protocols were based on publish protocols with no modifications dx.doi.o... | ["For the proteomics your protocols were based on publish protocols with no modifications dx.doi.org/10.17504/protocols.io.bxa4pigw"] |
66,113 | Agarose gel electrophoresis | 4 | null | https://www.protocols.io/view/agarose-gel-electrophoresis-ccs9swh6 | Brian P Teague | TITLE: Agarose gel electrophoresis
AUTHORS: Brian P Teague
[DESCRIPTION]
We use agarose gel electrophoresis to analyze DNA samples -- is there DNA present? What size is it?
[BEFORE_START]
Before starting, make sure you have the DNA samples you'll be analyzing (either PCR or restriction digest) thawed on ice.
[GUIDEL... | ["[Cast the gel] Using a balance, weigh out 0.5 g in a weigh boat.", "[Cast the gel] In a 250 Erlenmeyer flask, mix 50 mL, 0.5 g , and 2 µL DNA stain. Swirl to mix.", "[Cast the gel] Microwave on HIGH for 30 s; the solution should begin to boil. Remove from the microwave and swirl.", "[Cast the gel] Look carefully a... |
28,985 | Low-Dose Streptozotocin Induction Protocol (mouse) | null | dx.doi.org/10.17504/protocols.io.8izhuf6 | null | Frank Brosius | TITLE: Low-Dose Streptozotocin Induction Protocol (mouse)
AUTHORS: Frank Brosius
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block"><span>This protocol is used by DiaComp members to induce diabetes in a number of the anim... | ["Prepare the buffers and solutions as described below. Please note that the STZNa-Citrate solution should be prepared immediately prior to injection so as to avoid degradation of the STZ.", "Mice should be fasted prior to injection; four hours is usually sufficient.", "Place one mouse in the Isoflurane drop jar, accor... |
47,696 | Efficacy, safety and complications of autologous fat grafting to the eyelids and periorbital area: A systematic review and meta-analysis | 4 | dx.doi.org/10.17504/protocols.io.bstqnemw | https://www.protocols.io/view/efficacy-safety-and-complications-of-autologous-fa-bstqnemw | Fan Yang | TITLE: Efficacy, safety and complications of autologous fat grafting to the eyelids and periorbital area: A systematic review and meta-analysis
AUTHORS: Fan Yang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Background: In recent years, autologous fat grafting (AFG), also known as fat transfer or ... | ["We will search the PubMed, Cochrane library, and Embase databases for articles published prior to November 11, 2020.", "We will scrutinize the titles, abstracts, and full text of the retrieved articles and screen out articles that do not meet the inclusion and exclusion criteria.", "We will perform meta-analysis by... |
104,816 | Tooth Clearing with KneeEZ | 0 | null | https://www.protocols.io/view/tooth-clearing-with-kneeez-dikq4cvw | Akash Gandhi | TITLE: Tooth Clearing with KneeEZ
AUTHORS: Akash Gandhi
[DESCRIPTION]
KneeEZ is a robust method for clearing highly calcified tooth structures. In the Emrick Lab, it can be used to clear extracted tooth samples. In this application, the #D visualization of neuronal endings can be achieved via immunolabeling. Additiona... | ["[Retro-orbital Injection (Day 1)] Anesthetize the mouse via induction at 5%", "[Retro-orbital Injection (Day 1)] Toe pinch to ensure that the mouse is unresponsive", "[Retro-orbital Injection (Day 1)] Take the mouse out of the induction chamber and immediately inject 100 uL of Lectin DyLight 647 into both the left an... |
94,347 | DNA damage assessment in the adult Drosophila brain via comet assay | 1 | dx.doi.org/10.17504/protocols.io.eq2lyjrrplx9/v1 | https://www.protocols.io/view/dna-damage-assessment-in-the-adult-drosophila-brai-c8djzs4n | Mel Feany | TITLE: DNA damage assessment in the adult Drosophila brain via comet assay
AUTHORS: Mel Feany
[DESCRIPTION]
This protocol describes how to determine DNA damage in the adult drosophila brain using the comet assay
[STEPS]
1. Prepare a Lysis solution for one slide by mixing 20 mL of lysis buffer (Trevigen Comet Assay Re... | ["Prepare a Lysis solution for one slide by mixing 20 mL of lysis buffer (Trevigen Comet Assay Reagent Kit) and 2 mL of DMSO", "Melt LMAgarose in a boiling water bath, aliquot to 1.5ml tubes, and place at 37 °Cuntil use", "Place comet slide at 37 °Cuntil use", "Dissect 2 adult fly brains per the desired genotype in ice... |
43,188 | Protocol: Know Your BentoLab | 3 | null | https://www.protocols.io/view/protocol-know-your-bentolab-bneumbew | TITLE: Protocol: Know Your BentoLab
AUTHORS:
[STEPS] | [] | |
29,590 | Cultivation protocol for anaerobic ciliates | null | dx.doi.org/10.17504/protocols.io.85why7e | null | Johana Rotterova, Ivan Čepička | TITLE: Cultivation protocol for anaerobic ciliates
AUTHORS: Johana Rotterova, Ivan Čepička
[STEPS]
?. [Sample isolation]
Cultivation protocol is followed by methods described in Rotterová et al. 2018 and Bourland et al. 2017.Isolate 10 ml of targeted sample from environments of interest (e.g., freshwater sulphidic sed... | ["[Sample isolation]\nCultivation protocol is followed by methods described in Rotterová et al. 2018 and Bourland et al. 2017.Isolate 10 ml of targeted sample from environments of interest (e.g., freshwater sulphidic sediment).", "[Media preparation]\nPrepare ATCC medium: 802 (Sonneborn's Paramecium medium) for freshwa... |
83,350 | Confirmation of axenic seedlings | 4 | dx.doi.org/10.17504/protocols.io.rm7vzxm94gx1/v1 | https://www.protocols.click/view/confirmation-of-axenic-seedlings-cvmww47e | Elena L. Peredo, Suzanne M Thomas, Zoe Cardon | TITLE: Confirmation of axenic seedlings
AUTHORS: Elena L. Peredo, Suzanne M Thomas, Zoe Cardon
[DESCRIPTION]
Sporobolus alterniflorus plants are known to be rich in endophytes. In order to ensure the success of an in vitro culturing approach, it is crucial to remove any potential contaminants. Here, we present a proto... | ["[Culture-dependent methods] We use here two different culture media to detect the presence of possible contaminants. One of the media is the same medium the plants are growing in. The second is a rich, general-purpose medium broadly used in microbiology.", "[Culture-dependent methods] Prepare culture media.\n\nLysoge... |
95,660 | Single-molecule Immunofluorescence Tissue Staining Protocol for Oligomer Imaging | 4 | dx.doi.org/10.17504/protocols.io.5qpvorp6bv4o/v3 | https://www.protocols.io/view/single-molecule-immunofluorescence-tissue-staining-c9nkz5cw | Rebecca Andrews, Joanne Lachica, Steven F. Lee, Sonia Ghandi | TITLE: Single-molecule Immunofluorescence Tissue Staining Protocol for Oligomer Imaging
AUTHORS: Rebecca Andrews, Joanne Lachica, Steven F. Lee, Sonia Ghandi
[DESCRIPTION]
This protocol details background fluorescence quenching and immunofluorescence staining of human brain tissue for oligomer imaging.
[GUIDELINES]
U... | ["[Immunofluorescences staining protocol for oligomer imaging] Cut tissue sections on a microtome and load onto glass slides.", "[Immunofluorescences staining protocol for oligomer imaging] Dry slides 10 min at 37 °C – cover over the top.", "[Immunofluorescences staining protocol for oligomer imaging] Before staining... |
51,732 | Isolation of Nucleated Cells from Bone Marrow Aspirate | 1 | dx.doi.org/10.17504/protocols.io.bwrupd6w | https://www.protocols.io/view/isolation-of-nucleated-cells-from-bone-marrow-aspi-bwrupd6w | Steven B. Wells, Peter A. Szabo, Nora Lam | TITLE: Isolation of Nucleated Cells from Bone Marrow Aspirate
AUTHORS: Steven B. Wells, Peter A. Szabo, Nora Lam
[DESCRIPTION]
This protocol describes a method for the isolation of pan-lymphocytes, pan-myeloid cells, and progenitors from human bone marrow aspirate. By providing defined media formulations, volumes at e... | ["[Preparing Mediums and Buffers] Create the following IMDM-FBS-PSQ Media in a 500 mL bottle of IMDM by using the table below:\n \n Component Volume (mL) Starting Conc. Final Conc.* IMDM 500 - - Penicillin-Streptomycin-Glutamine 5 100X 1X FBS 50 100% 10%", "[Preparing Mediums and Buffers] Cre... |
30,498 | Marchantia agrobacterium transformation of sporelings in multi-well plates (plus materials info) | null | dx.doi.org/10.17504/protocols.io.92ah8ae | null | Linda Silvestri, Eftychis Frangedakis, Susana Sauret-Gueto, Marius Rebmann, Marta Tomaselli | TITLE: Marchantia agrobacterium transformation of sporelings in multi-well plates (plus materials info)
AUTHORS: Linda Silvestri, Eftychis Frangedakis, Susana Sauret-Gueto, Marius Rebmann, Marta Tomaselli
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>A modification of the </span><a href="htt... | ["[Spores sterilisation and plating]\nDay 0Transfer sporangia to a 1.5 mL Eppendorf tube. Use 2 sporangia per construct, e.g. for 6 transformations, use 12 sporangia.", "[Agrobacterium preparation]\nDay 0/1Transform Agrobacterium with your plasmid of interest. On ice, add 50 ng of the plasmid to 50 μL of thawed electro... |
28,369 | Determining Chlorophyll Concentration using CuSO4 Magnesium-Copper Exchange Titration | null | dx.doi.org/10.17504/protocols.io.7xrhpm6 | null | Victor Rodriguez | TITLE: Determining Chlorophyll Concentration using CuSO4 Magnesium-Copper Exchange Titration
AUTHORS: Victor Rodriguez
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is designed to be able to extract and analyze the concentration of chlorophyll within a sample on a molecular level. ... | ["[Preparation of Sample and Extraction]\nAdd of sample plant matter or other test article to a mortar.\n2 g", "[Preparation of Sample and Extraction]\nAdd of crystals to the mortar.\n1 g", "[Preparation of Sample and Extraction]\nGrind the sample item and together until the leaves are ground up, the magnesium sulfa... |
57,040 | Growing overnight culture of OP50 as worm food | 1 | dx.doi.org/10.17504/protocols.io.b3xqqpmw | https://www.protocols.io/view/growing-overnight-culture-of-op50-as-worm-food-b3xqqpmw | Bonnie Evans | TITLE: Growing overnight culture of OP50 as worm food
AUTHORS: Bonnie Evans
[DESCRIPTION]
Luria broth (LB) is a nutrient-rich media commonly used to culture bacteria in the lab. LB agar plates are frequently used to isolate individual (clonal) colonies of bacteria carrying a specific plasmid. However, a liquid cultur... | ["Obtain 1L LB Broth from the media kitchen\n\nLB Broth contents: \n4gNaCl\n4 g Tryptone\n2 g Yeast Extract dH2O to 400 mL", "Obtain 2 x 2L sterile Erlenmeyer flask from the glassware room", "In the microbial hood, add 500mL liquid LB to each flask", "Using a sterile pipette tip, select a single colony from your plate.... |
9,148 | NEBNext End Repair Module E6050 | 1 | dx.doi.org/10.17504/protocols.io.k64czgw | https://www.protocols.io/view/nebnext-end-repair-module-e6050-k64czgw | Isabel Gautreau | TITLE: NEBNext End Repair Module E6050
AUTHORS: Isabel Gautreau
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Mix the following components in a sterile microfuge tube:]
Fragmented DNA: variableNEBNext End Repair Reaction Buffer (10X): 10 μlNEBNext End Repair Enzyme Mix: 5 μlSterile H20 for a final volum... | ["[Mix the following components in a sterile microfuge tube:]\nFragmented DNA: variableNEBNext End Repair Reaction Buffer (10X): 10 μlNEBNext End Repair Enzyme Mix: 5 μlSterile H20 for a final volume of 100 μl: variableTotal volume: 100 μl", "Incubate in a thermal cycler for 30 minutes at 20°C.", "Purify DNA sample on ... |
69,481 | Cas9 RNP electroporation (suspension and adherent cells) | 1 | dx.doi.org/10.17504/protocols.io.e6nvw98wgmkj/v4 | https://www.protocols.io/view/cas9-rnp-electroporation-suspension-and-adherent-c-cf4htqt6 | Lena Kobel, Eric Aird, Mark Dewitt & Julia Wong | TITLE: Cas9 RNP electroporation (suspension and adherent cells)
AUTHORS: Lena Kobel, Eric Aird, Mark Dewitt & Julia Wong
[DESCRIPTION]
This protocol, based on published work, demonstrates how to delivery Cas9 RNP-based gene editing reagents to cultured mamallian cells by electroporation with a Lonza 4d Nucleofector in... | ["[Prepare RNP Mix] For a standard reaction, we use 100 pmol Cas9 and 120 pmol sgRNA to form the RNP in a ≤ 5 ul volume. You will need a minimum sgRNA concentration of 48 uM. Mix the following in this order, add Cas9 to the sgRNA slowly while swirling the pipette tip:", "[Prepare RNP Mix] Allow RNP to form for 10-20 mi... |
94,277 | SOP for cDNA synthesis by RT (Reverse Transcription) Promega kit | 4 | dx.doi.org/10.17504/protocols.io.8epv5xqkjg1b/v1 | https://www.protocols.io/view/sop-for-cdna-synthesis-by-rt-reverse-transcription-c8bdzsi6 | Malu G Tansey | TITLE: SOP for cDNA synthesis by RT (Reverse Transcription) Promega kit
AUTHORS: Malu G Tansey
[DESCRIPTION]
SOP for cDNA synthesis by RT (Reverse Transcription) Promega kit
[STEPS]
SECTION: Protocol:
2. Prepare per sample:
SECTION: Protocol:
3. Heat samples at 70°C for 5 min (prepare mix for step 4).
SECTION:... | ["[Protocol:] Prepare per sample:", "[Protocol:] Heat samples at 70°C for 5 min (prepare mix for step 4).", "[Protocol:] Snap freeze samples at +4°C or on ice for a minimum of 5 min.", "[Protocol:] Prepare RT mix (vol per samples, calculate for all your samples + 1):", "[Protocol:] Brief centrifugation.", "[Protocol:] ... |
79,036 | QIAamp DNA Extraction Protocol | 1 | dx.doi.org/10.17504/protocols.io.yxmvm212ng3p/v1 | https://www.protocols.io/view/qiaamp-dna-extraction-protocol-cre4v3gw | Vicky Ooi, Lee McMichael, Margaret E. Hunter, Aristide Takoukam Kamla, Janet M. Lanyon | TITLE: QIAamp DNA Extraction Protocol
AUTHORS: Vicky Ooi, Lee McMichael, Margaret E. Hunter, Aristide Takoukam Kamla, Janet M. Lanyon
[DESCRIPTION]
Non-invasively collected faecal samples are an alternative source of DNA to tissue samples, that may be used in genetic studies of wildlife when direct sampling of animals... | ["[Faecal Sampling and Processing] Use a sterile blade to scrape off 220 mg of faecal material from the outside surface of a stool and then transfer it into a 2 mL microcentrifuge tube.\n\n220 mg", "[Faecal Sampling and Processing] Transfer the faecal material into a mortar and grind the faeces into powder with liquid ... |
75,372 | (official) Extraction of Herbarium material for chemical profiling - Protocol #1 | 1 | dx.doi.org/10.17504/protocols.io.dm6gpjwkdgzp/v2 | https://www.protocols.io/view/official-extraction-of-herbarium-material-for-che-cmuku6uw | Ricardo M. Borges | TITLE: (official) Extraction of Herbarium material for chemical profiling - Protocol #1
AUTHORS: Ricardo M. Borges
[DESCRIPTION]
From the perspective of the documentation of plant biological diversity, herbaria are the repository of intraspecific and interspecific variability. The rich assortments contained in these c... | ["[Sample preparation] Organize every sample that will be used in each study into an EXCEL Sheet;\ninclude information and comments on every sample\nhave information about classification grouping on every sample\neach sample should also have the filename for their analytical data indexed (these can be added afterward)\... |
40,923 | ELISA for quantification of human C2 in serum or plasma. | 6 | dx.doi.org/10.17504/protocols.io.bj73krqn | https://www.protocols.io/view/elisa-for-quantification-of-human-c2-in-serum-or-bj73krqn | Angel Justiz-Vaillant, Belkis Ferrer-Cosme | TITLE: ELISA for quantification of human C2 in serum or plasma.
AUTHORS: Angel Justiz-Vaillant, Belkis Ferrer-Cosme
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. An anti-human C2 coating antibody is adsorbed onto the microwells by incubation overnight at 4°C with carbonate-bicarbonate buffer.
?.... | ["An anti-human C2 coating antibody is adsorbed onto the microwells by incubation overnight at 4°C with carbonate-bicarbonate buffer.", "Add 50 µl of human serum or plasma. Human C2 present in the serum or plasma binds to antibodies adsorbed into the microwells.", "The microplate is blocked with 3% non-fat milk-PBS buf... |
null | null | null | dx.doi.org/10.17504/protocols.io.fixbkfn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Quality impact results is the universal first step for all sequencing methods. This protocol is for sequencing results in FASTQ format. FastQC allows for visualization of quality scores. Sequence trimming allows for removal of residual primer sequences and increases overall q... | [] |
95,382 | Free floating immunofluorescence protocol on mouse brain sections for tau pathology | 1 | dx.doi.org/10.17504/protocols.io.6qpvr3j23vmk/v1 | https://www.protocols.io/view/free-floating-immunofluorescence-protocol-on-mouse-c9dwz27e | Felicia Suteja, Hongyun Li, YuHong Fu | TITLE: Free floating immunofluorescence protocol on mouse brain sections for tau pathology
AUTHORS: Felicia Suteja, Hongyun Li, YuHong Fu
[DESCRIPTION]
This protocol describes our free-floating multiplexed immunofluorescent staining protocol to ascertain levels of tau and phospho- tau in mouse tissue from transplante... | ["[Experimental outline] Briefly, the mouse brain tissue sections are prepared by washing off the cryoprotectant medium and then antigen retrieval is performed followed by quenching, blocking and primary antibody incubation. Sections are then washed and incubated in the appropriate secondary antibody solution and are t... |
90,528 | LIFEPLAN soil sampling | 1 | null | https://www.protocols.io/view/lifeplan-soil-sampling-c4m8yu9w | Gaia Giedre Banelyte, Arielle M Farrell, Hanna M.K. Rogers, Deirdre Kerdraon | TITLE: LIFEPLAN soil sampling
AUTHORS: Gaia Giedre Banelyte, Arielle M Farrell, Hanna M.K. Rogers, Deirdre Kerdraon
[DESCRIPTION]
Lifeplan is a global biodiversity monitoring project with the aim of assessing the current state of biodiversity worldwide, and using this knowledge to generate predictions of how biodivers... | ["[Soil sampling] Remove any layer of live cryptogams (including moss, lichen or algae) and loose debris from the sampling area (such as dry or uncompacted leaves, branches, twigs, loose needles, etc.). Keep the litter layer, i.e. any layers which remain stuck to the ground. In habitats that have a lot of litter (such ... |
95,163 | Flowcytometry analysis of lysosomal pulldown with anti-TMEM192 magnetic beads from PBMCs | 4 | dx.doi.org/10.17504/protocols.io.n2bvj378xlk5/v1 | https://www.protocols.io/view/flowcytometry-analysis-of-lysosomal-pulldown-with-c863zzgn | Enrico Bagnoli, Karolina Zeneviciute, Esther Sammler, Dario R Alessi | TITLE: Flowcytometry analysis of lysosomal pulldown with anti-TMEM192 magnetic beads from PBMCs
AUTHORS: Enrico Bagnoli, Karolina Zeneviciute, Esther Sammler, Dario R Alessi
[DESCRIPTION]
We describe a method that allows the staining of intact lysosomes using lysotracker for flow cytometry analysis. The analysis can p... | ["[Materials and reagents] PBMCs (or other cells)\nBafilomycin A1 (Enzo LifeScience, BML-CM110-0100)\nDeep Red Lysotracker (Thermo, L12492)\nDMSO\nanti-TMEM192 magnetic beads\nBSA magnetic beads\nKPBS\nFlow cytometry tubes\nFlow cytometer with APC lasers and filters\nWater bath", "[Intro] The following protocol allows ... |
16,159 | DNA extraction, amplification, and sequencing of Ophiothrix (Echinodermata: Ophiuroidea) | null | dx.doi.org/10.17504/protocols.io.tz7ep9n | null | Renata Alitto, Michela Borges, Letícia Dias de Oliveira, Karin Regina Seger | TITLE: DNA extraction, amplification, and sequencing of Ophiothrix (Echinodermata: Ophiuroidea)
AUTHORS: Renata Alitto, Michela Borges, Letícia Dias de Oliveira, Karin Regina Seger
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>DNA extraction, amplification, and sequencing, particularly for t... | ["[DNA extraction]\nSamples of tube feet from the arms or gonads were soaked in two changes of Tris-EDTA (TE) buffer for 30 minutes each. The samples were then macerated in 500 μl of TE buffer with a pestle. A volume of 300 μl of a 10 % Chelex 100 solution (BioRad) was added. The samples were then incubated at 55°C for... |
90,072 | Performance comparison of stress hyperglycemia ratio for predicting fatal outcomes in patients with thrombolyzed acute ischemic stroke | 1 | dx.doi.org/10.17504/protocols.io.bp2l6xr8klqe/v1 | https://www.protocols.io/view/performance-comparison-of-stress-hyperglycemia-rat-c37yyrpw | Sarawut Krongsut, Chatchon Kaewkrasaesin | TITLE: Performance comparison of stress hyperglycemia ratio for predicting fatal outcomes in patients with thrombolyzed acute ischemic stroke
AUTHORS: Sarawut Krongsut, Chatchon Kaewkrasaesin
[DESCRIPTION]
Stroke is a prevalent neurological condition and a primary global cause of death, resulting in
approximately 6 mi... | ["Performance comparison of stress hyperglycemia ratio for predicting fatal outcomes in patients with thrombolyzed acute ischemic stroke"] |
93,855 | Sticker Removal | 4 | dx.doi.org/10.17504/protocols.io.q26g7pjo9gwz/v1 | https://www.protocols.io/view/sticker-removal-c7v7zn9n | Ian N Krout, Tim Sampson | TITLE: Sticker Removal
AUTHORS: Ian N Krout, Tim Sampson
[DESCRIPTION]
The sticker removal test is a form of adhesive removal task assessment that is used by our lab to asses sensory stimuli and motor tasks in mice. Simply, an adhesive substance is placed on the nose of the mouse which is sensed, then removed by the m... | ["[Acclimation] Bring mice up from vivarium in their home cage to acclimate for at least 1h prior to sticker removal assessment.", "[Assessment] With one hand use the tweezers to pick up one sticker, allowing it to sit on a single prong with the\nadhesive side freely visible.", "[Assessment] With the free hand grab one... |
69,582 | Lentivirus production | 4 | dx.doi.org/10.17504/protocols.io.6qpvr4xn3gmk/v1 | https://www.protocols.io/view/lentivirus-production-cf7ntrme | Itika Saha, F. Ulrich Hartl, Mark S. Hipp | TITLE: Lentivirus production
AUTHORS: Itika Saha, F. Ulrich Hartl, Mark S. Hipp
[DESCRIPTION]
This protocol describes the production of lentiviruses to transduce HEK293T cells and has to be performed in a biosafety level 2 laboratory
[STEPS]
SECTION: Lentivirus production
1. Plate ~3.6x106 Lenti-X HEK293T cells (Taka... | ["[Lentivirus production] Plate ~3.6x106 Lenti-X HEK293T cells (Takara) in 10 cm dish in 10 mL standard DMEM. Cells should be ~80% confluent at the time of transfection.", "[Lentivirus production] Next day, remove 5 mL medium and replenish with fresh medium.", "[Lentivirus production] Warm up reduced serum medium e.g. ... |
34,634 | IPMC SARS-CoV-2 Two-Step qPCR Protocol on BIOMARK | 1 | dx.doi.org/10.17504/protocols.io.bd3ii8ke | https://www.protocols.io/view/ipmc-sars-cov-2-two-step-qpcr-protocol-on-biomark-bd3ii8ke | Julien Fassy, Caroline Lacoux, David Rouquié, Jean Louis Nahon, Pascal Barbry, Laure-Emmanuelle Zaragosi, Bernard Mari | TITLE: IPMC SARS-CoV-2 Two-Step qPCR Protocol on BIOMARK
AUTHORS: Julien Fassy, Caroline Lacoux, David Rouquié, Jean Louis Nahon, Pascal Barbry, Laure-Emmanuelle Zaragosi, Bernard Mari
[DESCRIPTION]
<div class = "text-blocks"><div style = "text-align :; float : ;"><img style = "" src = "https://s3.amazonaws.com/protoc... | ["[RNA Extraction with QIAamp Viral RNA Mini Kit Qiagen]\nTo be performed in the appropriate biosafety conditions (BSL2 laboratory)Transfer the totality of the transport medium into a 2 mL cryotube. OPTIONAL: in the case of a non-virucide transport medium, heat the sample for 10 min at 65°C. This step should strongly d... |
26,789 | Preparation of s/o/w emulsion using SPG membrane | 1 | dx.doi.org/10.17504/protocols.io.6edhba6 | https://www.protocols.io/view/preparation-of-s-o-w-emulsion-using-spg-membrane-6edhba6 | Daisuke Yasui | TITLE: Preparation of s/o/w emulsion using SPG membrane
AUTHORS: Daisuke Yasui
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Solid-in-oil-in-water emulsion of miriplatin is prepared by pushing miriplatin suspension through 20 μm SPG membrane (SPG technology) using a syringe pump.</div><div class =... | ["Prepare half-saline and add of Polyoxyethylene hydrogenated castor oil 60 (HCO 60).Use a starler to make the solution.\n10 mL\n0.08 mg", "Aspirate the solution to 10mL syringe and connect it to a filter kit with 20μm hydrophilic-coated SPG membrage(SPG Technology Co.,Ltd).Push the whole solution into the filter ki... |
28,904 | Bradford Assay with RotiQuant (ROTH) | null | dx.doi.org/10.17504/protocols.io.8gghttw | null | iGEM Dusseldorf | TITLE: Bradford Assay with RotiQuant (ROTH)
AUTHORS: iGEM Dusseldorf
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Assay for quantification of protein by comparing measured Absorbance at 595 nm to bovine serum albumine standard</div></div>
[STEPS]
?. [Standard measurements]
Dilute your BSA stock ... | ["[Standard measurements]\nDilute your BSA stock solution to 200µg/ml in the same buffer used for your solution of interest.", "[Standard measurements]\nDilute the Roti-Quant 5x reagent at a rate of 2:7,5. For 15 ml solution, this means 4 ml Roti-Quant added to 11 ml of Water.", "[Standard measurements]\nCreate 200 µl ... |
22,263 | Samuel Lab Media and Buffers | 2 | null | https://www.protocols.io/view/samuel-lab-media-and-buffers-zyxf7xn | Adrien Assie, Buck Samuel | TITLE: Samuel Lab Media and Buffers
AUTHORS: Adrien Assie, Buck Samuel
[DESCRIPTION]
This is a collection of protocol for the preparation of standard media used in the Samuel Lab
[STEPS] | [] |
53,078 | CHOP TMC Single Cell Multiome ATAC + Gene Expression | 4 | dx.doi.org/10.17504/protocols.io.bx3wpqpe | https://www.protocols.io/view/chop-tmc-single-cell-multiome-atac-gene-expression-bx3wpqpe | Po Hu, Liming Pei | TITLE: CHOP TMC Single Cell Multiome ATAC + Gene Expression
AUTHORS: Po Hu, Liming Pei
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The human heart is vital for our survival and health, and it presents remarkable anatomical, cellular and functional heterogeneity. The four chambers of the heart, t... | ["[Nuclei Isolation ]\nBring the -80 frozen transmural human heart sample on dry ice, trim off the fat covering the samples as much as possible", "[Nuclei Isolation ]\nHomogenize the trimmed frozen ventricle or atrium in 0.5-1ml 0.1x lysis buffer using a 2ml Dounce homogenizer(A-loose :25 strokes; B-tight: 30-50 stroke... |
16,959 | Steps of Clinical Reasoning Process and Variables of Quality Indicators for Physiotherapy Care Process of Patients with WAD for Analysis | 1 | dx.doi.org/10.17504/protocols.io.us7ewhn | https://www.protocols.io/view/steps-of-clinical-reasoning-process-and-variables-us7ewhn | Rob A B Oostendorp | TITLE: Steps of Clinical Reasoning Process and Variables of Quality Indicators for Physiotherapy Care Process of Patients with WAD for Analysis
AUTHORS: Rob A B Oostendorp
[DESCRIPTION]
Appendix 2.
Overview of 9 Steps of Clinical Reasoning Process including the Variables of Quality Indicators for Physiotherapy Care Pr... | [] |
74,016 | Schistosome DNA Isolation and Colorimetric LAMP protocol for the detection of Schistosomiasis | 1 | dx.doi.org/10.17504/protocols.io.5qpvor97xv4o/v1 | https://www.protocols.io/view/schistosome-dna-isolation-and-colorimetric-lamp-pr-ckh8ut9w | Isaac Owusu-Frimpong, Linda B. Debrah, samuel.k.armoo, Edward J. Tettevi, Yvonne A. Ashong, Naa A. Kuma, Frank Twum FTA Aboagye, Bright K. Idun, Mike Y. Osei-Atweneboana | TITLE: Schistosome DNA Isolation and Colorimetric LAMP protocol for the detection of Schistosomiasis
AUTHORS: Isaac Owusu-Frimpong, Linda B. Debrah, samuel.k.armoo, Edward J. Tettevi, Yvonne A. Ashong, Naa A. Kuma, Frank Twum FTA Aboagye, Bright K. Idun, Mike Y. Osei-Atweneboana
[DESCRIPTION]
Schistosomiasis keeps dev... | ["[Schistosoma-DNA Extraction from Stool (Zymo Kits) Protocol] 0.12-gram stool is suspended in 300µL of PBS (1X phosphate-buffered saline) with 2% PVPP (polyvinylpolypyrrolidone) in a 2ml microcentrifuge tube containing glass beads and vortex.", "[Schistosoma-DNA Extraction from Stool (Zymo Kits) Protocol] Freeze the s... |
27,618 | UC Davis - Gross Body Composition (DEXA) | null | dx.doi.org/10.17504/protocols.io.68ahhse | null | Trina Knotts | TITLE: UC Davis - Gross Body Composition (DEXA)
AUTHORS: Trina Knotts
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span><span style = "font-weight:bold;"> </span></div><div class = "text-block">Rapid and accurate measures of fat and lean mass will be ca... | ["Setup:1. Turn on Piximus at least 2 hours prior to start of 1st scan.2. Open Piximus software and initiate calibration using “phantom” (an object with defined bone mineral density and fat content for unit calibration).NOTE: This step requires approximately 1 hr to complete.", "Prepare animal1. Anesthetize animal usin... |
20,149 | Single cell rDNA amplification of Spumellaria (Radiolaria) | 3 | dx.doi.org/10.17504/protocols.io.xwvfpe6 | https://www.protocols.io/view/single-cell-rdna-amplification-of-spumellaria-radi-xwvfpe6 | Miguel Mendez Sandin | TITLE: Single cell rDNA amplification of Spumellaria (Radiolaria)
AUTHORS: Miguel Mendez Sandin
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. | [] |
81,026 | Donor Selection Criteria for Adipose Procurement -- University of Minnesota Human TMC | 1 | dx.doi.org/10.17504/protocols.io.rm7vzbp98vx1/v1 | https://www.protocols.io/view/donor-selection-criteria-for-adipose-procurement-u-ctdawi2e | Sayeed Ikramuddin, Laura Niedernhofer | TITLE: Donor Selection Criteria for Adipose Procurement -- University of Minnesota Human TMC
AUTHORS: Sayeed Ikramuddin, Laura Niedernhofer
[DESCRIPTION]
This document outlines the inclusion and exclusion criteria for donors of adipose (visceral, subcutenous) and blood for the SenNet Consortium program from the Univer... | ["[Inclusion Criteria] Age 18 years old or older", "[Exclusion Criteria] Pregnancy or nursing -- Pregnancy is routinely an exclusion for surgery. If patients are scheduled for surgery, they receive a pregnancy test per clinical care. The study team will utilize the results available in the medical record to determine e... |
43,633 | Testing For Cellulose Degradation | 3 | dx.doi.org/10.17504/protocols.io.bnurmev6 | https://www.protocols.io/view/testing-for-cellulose-degradation-bnurmev6 | Jiri Hulcr | TITLE: Testing For Cellulose Degradation
AUTHORS: Jiri Hulcr
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes how to test for cellulose degradation using the congo red method.</div><div class = "text-block"><span>This protocol is part of the Bark Beetle Mycobiome (BBM) Researc... | [] |
13,525 | 18S V4 tag sequencing PCR amplification and library prep (Illumina) | null | dx.doi.org/10.17504/protocols.io.rfvd3n6 | null | Lisa Mesrop, Sarah Hu | TITLE: 18S V4 tag sequencing PCR amplification and library prep (Illumina)
AUTHORS: Lisa Mesrop, Sarah Hu
[DESCRIPTION]
<p> </p>
<p>Protocol for PCR amplification of extracted cDNA or DNA and downstream library preparation for MiSeq sequencing.</p>
<p> </p>
<p>See other related protocols for extraction of RNA and/or ... | ["[Amplification step with V4 primers (optional Illumina Adaptors for in house barcoding)]\nWe use Q5 High-Fidelity 2x Master Mix for our PCR reactions. The convenient 2x master mix formulation is easy to use and is suitable for PCR applications requiring greater accuracy and amplification of difficult or low genomic D... |
103,469 | Nuclei Isolation from Human Synovium and Infrapatellar Fat Pad for 10x Multiome | 0 | dx.doi.org/10.17504/protocols.io.ewov193molr2/v1 | https://www.protocols.io/view/nuclei-isolation-from-human-synovium-and-infrapate-dham32c6 | Irene Lorenzo Gomez, Erpei Wang, Merissa Olmer, Martin Lotz | TITLE: Nuclei Isolation from Human Synovium and Infrapatellar Fat Pad for 10x Multiome
AUTHORS: Irene Lorenzo Gomez, Erpei Wang, Merissa Olmer, Martin Lotz
[DESCRIPTION]
This protocol describes isolation of nuclei from fresh-frozen human knee synovium and fat pad for use in Omics analyses, including RNA-sequencing of ... | [] |
44,352 | Apple Cider Mimosa Recipe | 1 | null | https://www.protocols.io/view/apple-cider-mimosa-recipe-bpi8mkhw | Diana Curcio | TITLE: Apple Cider Mimosa Recipe
AUTHORS: Diana Curcio
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">protocols.io Team Friendsgiving 2020</div><div class = "text-block">This protocol is a quick recipe for how to make an apple cider mimosa. </div></div>
[STEPS]
?. [Prep]
Ingredients:• Zeigler's Ap... | ["[Prep]\nIngredients:• Zeigler's Apple Cider 64 oz – also works with any apple cider brand • 1 bottle of champagne, La Marca Prosecco is what I use, but also works with your preferred champagne • Optional add ons – Marzetti Caramel Dip, Classic 13.05 oz\nTo prep, keep all ingredients refrigerated until chilled.", "[Mi... |
57,704 | HuBMAP | GE/URMC/SCH Cell DIVE™ Modality Overview | 1 | dx.doi.org/10.17504/protocols.io.b4kgqutw | https://www.protocols.io/view/hubmap-ge-urmc-sch-cell-dive-modality-overview-b4kgqutw | Gloria S Pryhuber, gail.deutsch , Christine Surrette, Lisa Lowery, heidie_huyck , Cory Poole | TITLE: HuBMAP | GE/URMC/SCH Cell DIVE™ Modality Overview
AUTHORS: Gloria S Pryhuber, gail.deutsch , Christine Surrette, Lisa Lowery, heidie_huyck , Cory Poole
[DESCRIPTION]
This is an overview of all protocols currently in use for the GE/URMC/SCH Cell DIVE collaboration for the Human BioMolecular Atlas Program (H... | ["Confirm donor acceptance criteria for inclusion.\n\nURMC | Donor Acceptance Criteria for GE/URMC HuBMAP Inclusion\nURMC | COVID+ Donor Acceptance Criteria for GE/URMC HuBMAP Inclusion", "Prepare paraffin blocks and FFPE sections from tissue samples.\n\nURMC | Whole Lung and Lobe Processing - Formalin Fixation and Gro... |
92,559 | Double digestion RADseq library | 4 | dx.doi.org/10.17504/protocols.io.n92ldm66nl5b/v1 | https://www.protocols.io/view/double-digestion-radseq-library-c6mpzc5n | David Macaya-Sanz | TITLE: Double digestion RADseq library
AUTHORS: David Macaya-Sanz
[DESCRIPTION]
A protocol to create libraries for Illumina to genotype through double digestion sequencing. The goal is to create a protocol that reduces costs and dedicated time at the expense of a slight reduction of quality, meaning that some of your ... | ["[DNA dilution] Measure your DNA stock concentration. Recommended Nanodrop One.", "[DNA dilution] Dilute DNA stock to 20 ng/µl at minimum volume of 7.5 µL", "[Annealing of adapters] Dilute oligos EcoRI_P1.1, EcoRI_P1.2, MseI_P2.1_2N, and MseI_P2.2_2N to 100 micromolar (µM) \nIn case you have Tris EDTA (TE) ready, you ... |
90,491 | DNA extraction of water sample from sylphium filters | 4 | dx.doi.org/10.17504/protocols.io.4r3l22y83l1y/v1 | https://www.protocols.io/view/dna-extraction-of-water-sample-from-sylphium-filte-c4k3yuyn | Omneya Osman | TITLE: DNA extraction of water sample from sylphium filters
AUTHORS: Omneya Osman
[DESCRIPTION]
https://www.qiagen.com/se/products/discovery-and-translational-research/dna-rna-purification/dna-purification/genomic-dna/dneasy-blood-and-tissue-kit
[BEFORE_START]
The workspace should be cleaned with bleach solu... | ["[Prepare lysate] Prepare sampling kit (sylphium filter, gloves, ATL buffer, syringe)\nFind an interesting of environmental site.\nInject 1-3 L of environmental water into sylphium filter using a clean sterile beaker and 50 ml syringe.\nInject a volume of 3 ml ATL buffer (Qiagen) in the sylphium filter to be stored a... |
83,946 | Neural differentiation of AAVS1-TRE3G-NGN2 pluripotent stem cells | 1 | dx.doi.org/10.17504/protocols.io.x54v9p8b4g3e/v1 | https://www.protocols.io/view/neural-differentiation-of-aavs1-tre3g-ngn2-pluripo-cv8iw9ue | Jiuchun Zhang, Harper JW | TITLE: Neural differentiation of AAVS1-TRE3G-NGN2 pluripotent stem cells
AUTHORS: Jiuchun Zhang, Harper JW
[DESCRIPTION]
This protocol is about neural differentiation of AAVS1-TRE3G-NGN2 pluripotent stem cells.
[BEFORE_START]
Prepare ND1 Medium and ND2 Medium:
ND1 Medium
DMEM/F12
N2 (100x) 1x
BDNF ... | ["[Day 0:] Treat H9 AAVS1-TRE3G-NGN2 cells with Accutase and plate the dissociated cells in matrigel-coated 6-well plates (2x105 cells/well) in ND1 Medium supplemented with Y27632 (10 micromolar (µM)).", "[Day 1:] Replace the medium with ND1 Medium.", "[Day 2:] Replace the medium with ND2 Medium.", "[Day 4:] Exchange 5... |
59,375 | Imaging of Calcium Dynamics in Vasoactive Intestinal Peptide-expressing Neurons of Enteric Nervous System | 1 | dx.doi.org/10.17504/protocols.io.14egn76xpv5d/v1 | https://www.protocols.io/view/imaging-of-calcium-dynamics-in-vasoactive-intestin-b58pq9vn | Joseph Margiotta, Marthe Howard | TITLE: Imaging of Calcium Dynamics in Vasoactive Intestinal Peptide-expressing Neurons of Enteric Nervous System
AUTHORS: Joseph Margiotta, Marthe Howard
[DESCRIPTION]
The protocol was published on behalf of the investigators by the SPARC project team.
The University of Toledo Health Science Campus animal care an... | ["Remove the colon.", "Pinn the colon segment mucosal side down onto a Sylgard surface lining a glass coverslip attached to the bottom of a plastic imaging chamber containing artificial CSF perfused and bubbled with Carbogen (95% O2/5% CO2) to oxygenate and achieve pH 7.4.", "On the day of the experiment prepare soluti... |
76,314 | Chronic Recoverable Neuropixels in Mice | 2 | dx.doi.org/10.17504/protocols.io.e6nvwjo87lmk/v1 | https://www.protocols.io/view/chronic-recoverable-neuropixels-in-mice-cnr2vd8e | Emily A Aery Jones | TITLE: 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 1 Neuropixels 1.0 probe or 2 Neuropixels 2.0 probes into mice, record during freely moving behavior, then recover the probes for future use. ... | [] |
98,874 | A protocol for computerized quantitative analysis of nerve fibers, mast cells, enteric glial cells and the proximity of mast cells to the nerve fibers in 3D Images of human sigmoid mucosal biopsies | 0 | dx.doi.org/10.17504/protocols.io.rm7vzj3qrlx1/v1 | https://www.protocols.io/view/a-protocol-for-computerized-quantitative-analysis-dcs22wge | Tao Li, Pu-Qing Yuan, Yvette Taché | TITLE: A protocol for computerized quantitative analysis of nerve fibers, mast cells, enteric glial cells and the proximity of mast cells to the nerve fibers in 3D Images of human sigmoid mucosal biopsies
AUTHORS: Tao Li, Pu-Qing Yuan, Yvette Taché
[DESCRIPTION]
This protocol describes a step-by-step computational wor... | [] |
98,853 | Fluorescence assay for MERS-CoV Mpro activity measurement | 1 | dx.doi.org/10.17504/protocols.io.8epv5rzm4g1b/v1 | https://www.protocols.io/view/fluorescence-assay-for-mers-cov-mpro-activity-meas-dcsd2wa6 | Charline Giroud, oleg.fedorov | TITLE: Fluorescence assay for MERS-CoV Mpro activity measurement
AUTHORS: Charline Giroud, oleg.fedorov
[DESCRIPTION]
This protocol details the fluorescence assay for MERS-CoV Mpro protease activity measurement. This method is intended to measure the activity of viral proteases by using a specific labelled peptide tha... | ["[MERS-MPro IC50 Measurement] Add 50 µLof 2x protein 1.2 micromolar (µM) solution to each well containing the compounds to be tested previously dispensed onto the plate.", "[MERS-MPro IC50 Measurement] Incubate the mix for 60 min at Room temperature to initiate the enzymatic reaction by the addition of 50 µL of 2x (20... |
21,735 | PHYTOHORMONE PROFILING BY LIQUID CHROMATOGRAPHY COUPLED TO MASS SPECTROMETRY (LC/MS) | null | dx.doi.org/10.17504/protocols.io.zgff3tn | null | Camilo E. Vital, Jenny D. Gómez, Pedro M. Vidigal, Edvaldo Barros, Claudia S.L. Pontes, Nívea M. Vieira, Humberto Ramos | TITLE: PHYTOHORMONE PROFILING BY LIQUID CHROMATOGRAPHY COUPLED TO MASS SPECTROMETRY (LC/MS)
AUTHORS: Camilo E. Vital, Jenny D. Gómez, Pedro M. Vidigal, Edvaldo Barros, Claudia S.L. Pontes, Nívea M. Vieira, Humberto Ramos
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Phytohormones play a key role i... | ["[PHYTOHORMONES EXTRACTION]\n1) Collect samples of plant tissues, immediately freeze in liquid nitrogen and store them in freezer -80°C until use.2) Macerate the samples in liquid nitrogen using mortar and pestle. Do not allow to thaw. Weigh approximately 110mg of each sample into microtubes (2ml) and annotate the wei... |
null | null | null | dx.doi.org/10.17504/protocols.io.pxbdpin | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>For isolate the desired product or reoptimize the PCR to obtain a single product.</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
65,256 | Assessment of cognition as a predictor of prognosis in inpatients with brain damage: A Scoping Review Protocol | 1 | dx.doi.org/10.17504/protocols.io.kxygxz8ykv8j/v1 | https://www.protocols.io/view/assessment-of-cognition-as-a-predictor-of-prognosi-cbygsptw | Michihito Mitsuyasu, Yuro Yamauchi, Daichi Ando, Takashi Kitagawa | TITLE: Assessment of cognition as a predictor of prognosis in inpatients with brain damage: A Scoping Review Protocol
AUTHORS: Michihito Mitsuyasu, Yuro Yamauchi, Daichi Ando, Takashi Kitagawa
[DESCRIPTION]
Objective:
The purpose of this study is to determine what cognitive assessments are used to predict or determ... | [] |
47,598 | Assay for dual cargo sorting into endoplasmic reticulum exit sites imaged by super-resolution confocal live imaging microscopy (SCLIM) | 4 | dx.doi.org/10.17504/protocols.io.bsqnndve | https://www.protocols.io/view/assay-for-dual-cargo-sorting-into-endoplasmic-reti-bsqnndve | Sofia Rodriguez-Gallardo †, Kazuo Kurokawa †*, Susana Sabido-Bozo, Alejandro Cortes-Gomez, Ana Maria Perez-Linero, Auxiliadora Aguilera-Romero, Sergio Lopez, Miho Waga, Akihiko Nakano, Manuel Muñiz | TITLE: Assay for dual cargo sorting into endoplasmic reticulum exit sites imaged by super-resolution confocal live imaging microscopy (SCLIM)
AUTHORS: Sofia Rodriguez-Gallardo †, Kazuo Kurokawa †*, Susana Sabido-Bozo, Alejandro Cortes-Gomez, Ana Maria Perez-Linero, Auxiliadora Aguilera-Romero, Sergio Lopez, Miho Waga, ... | ["Pick up sec31-1 temperature-sensitive mutant yeast cells expressing two galactose-inducible secretory cargos (i.e. the GPI-AP cargo Gas1-GFP and the transmembrane plasma membrane protein Mid2-iRFP) and the constitutive COPII outer coat protein Sec13-mCherry as ERES marker from a frozen stock using a sterile toothpick... |
67,573 | CFE Expression and Lyophilization of β-Galactosidase (LacZ) | 4 | null | https://www.protocols.io/view/cfe-expression-and-lyophilization-of-galactosidase-cd8vs9w6 | Felipe Navarro Martínez, Anibal Arce Medina, Fernan Federici | TITLE: CFE Expression and Lyophilization of β-Galactosidase (LacZ)
AUTHORS: Felipe Navarro Martínez, Anibal Arce Medina, Fernan Federici
[DESCRIPTION]
This protocol includes the expression and lyophilization of the β-Galactosidase enzyme (from the LacZ gene) in a cell-free system. We used it to prepare and conduct exp... | ["[CFE Expression and Lyophilization of β-Galactosidase] For the cell-free expression of β-Galactosidase, we prepare the following reaction according to the guidelines of this article:", "[CFE Expression and Lyophilization of β-Galactosidase] Vortex the tubes. Incubate at in an orbital shaker.", "[CFE Expression an... |
78,253 | Efficient third generation lentiviral particle production | 4 | dx.doi.org/10.17504/protocols.io.261ge42pyv47/v4 | https://www.protocols.io/view/efficient-third-generation-lentiviral-particle-pro-cqnmvvc6 | Michelle Newbery, Simon Maksour, Amy Hulme, Neville S Ng, Mirella Dottori, Lezanne Ooi | TITLE: Efficient third generation lentiviral particle production
AUTHORS: Michelle Newbery, Simon Maksour, Amy Hulme, Neville S Ng, Mirella Dottori, Lezanne Ooi
[DESCRIPTION]
The overexpression of a gene of interest by third generation lentiviral particle generation systems is a critical ... | ["[Lentiviral transfection] Maintain HEK293T cells in animal product free FreeStyle 293 Expression Medium or DMEM/F12 + GlutaMAX + HEPES + 5% FBS or 5% KSR. Include 50 U/mL Penicillin and Streptomycin to reduce risk of bacterial contamination if necessary.\n\nDissociate and subculture HEK293T at a density of >50000 cel... |
94,683 | Cloning, Protein Expression, and Purification of 20S CPs and Assembly Intermediates | 4 | dx.doi.org/10.17504/protocols.io.n92ldmd59l5b/v1 | https://www.protocols.io/view/cloning-protein-expression-and-purification-of-20s-c8p3zvqn | Frank Adolf | TITLE: Cloning, Protein Expression, and Purification of 20S CPs and Assembly Intermediates
AUTHORS: Frank Adolf
[DESCRIPTION]
This protocol details methods for cloning, expression, and purification of 20S CPs and assembly intermediates for biochemical and structural analysis.
[GUIDELINES]
Please familiarise yourself... | ["[Purification of 20S CPs and 20S CP assembly intermediates] Purification of mature 20S CPs together with their assembly intermediates", "[Baculo virus amplification and insect cell expression] Culture Sf9 insect cells (Thermo Fisher Scientific) for virus amplification in serum-free Ex-cell 420 medium (Sigma-Aldrich)\... |
62,631 | DNA extraction from dermatophytes using the Qiagen DNEasy™ UltraClean Microbial kit (REF: 12224-50) | 4 | dx.doi.org/10.17504/protocols.io.q26g74d79gwz/v1 | https://www.protocols.io/view/dna-extraction-from-dermatophytes-using-the-qiagen-b9efr3bn | Khalid El Moussaoui | TITLE: DNA extraction from dermatophytes using the Qiagen DNEasy™ UltraClean Microbial kit (REF: 12224-50)
AUTHORS: Khalid El Moussaoui
[DESCRIPTION]
This protocol describes the steps necessary to extract and purify genomic DNA from dermatophytes (and more specifically from dermatophytes of the genus Trichophyton).
... | ["[Medium preparation] Dissolve 30 g of in 1 L \nof and let mix on the heated magnetic stirrer for 5 min(temperature and mixing speed knob at mid-step).", "[Medium preparation] Cover the flask with glass wool and aluminium foil. Autoclave it at 121 °C 121 °C for 30 min.", "[Cultivation of the strains] After allowin... |
97,952 | S-Trap™ plate digestion protocol (Protifi) of proteins for LC-MS / proteomics | 1 | null | https://www.protocols.io/view/s-trap-plate-digestion-protocol-protifi-of-protein-dbv82n9w | ronan o'cualain, David Knight, Stacey Warwood, James Allsey, Emmakeevill | TITLE: S-Trap™ plate digestion protocol (Protifi) of proteins for LC-MS / proteomics
AUTHORS: ronan o'cualain, David Knight, Stacey Warwood, James Allsey, Emmakeevill
[DESCRIPTION]
This protocol details the in-house BioMS procedure of S-Trap™ 96-well plate protein clean-up and digestion.
It is adapted from the long p... | ["[Sample preparation] To the 50 µLvolume of sample in S-trap lysis buffer, add 5 µL of 12 % (v/v) aqueous phosphoric acid at 1:10 for a final concentration of 1.2 % (v/v) phosphoric acid and vortex mix.", "[Sample preparation] Add 350 µL of S-Trap binding buffer to the acidified lysis buffer and mix.", "[Sample prepar... |
null | null | null | dx.doi.org/10.17504/protocols.io.cr3v8m | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.crhv35 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is the protocol for the removal of single-stranded extension using Mung Bean Nuclease (M0250).
[STEPS]
?.
?.
?.
?.
?. | [] |
57,147 | RasberryPi-computer based phenotyping for side view image process | 4 | dx.doi.org/10.17504/protocols.io.eq2lynp7pvx9/v1 | https://www.protocols.io/view/rasberrypi-computer-based-phenotyping-for-side-vie-b323qqgn | Li'ang Yu, Magdalena M Julkowska | TITLE: RasberryPi-computer based phenotyping for side view image process
AUTHORS: Li'ang Yu, Magdalena M Julkowska
[DESCRIPTION]
Imaging of plants can be done in an inexpensive way, using Raspberry Pi based setup. Here - we describe how we are processing the side-view images taken from 7 different sides - using the ... | ["[Data preparation] Download the data from RaspberryPi computer, where the images are being saved into one folder. If you have multiple stands for side-view image collection - download all the images into one folder entitled as your experiment. \n\nNOTE - please make sure that the RapberryPi's were recording the times... |
59,034 | Rab8a expression and purification | 4 | dx.doi.org/10.17504/protocols.io.6qpvr63mzvmk/v1 | https://www.protocols.io/view/rab8a-expression-and-purification-b5v2q68e | David M. Snead, Mariusz Matyszewski | TITLE: Rab8a expression and purification
AUTHORS: David M. Snead, Mariusz Matyszewski
[DESCRIPTION]
Recombinant Rab8a expression and purification protocol as used by the Leschziner and Reck-Peterson Labs.
Original protocol by David Snead. Adapted for protocols.io by Mariusz Matyszewski.
Current version as used in S... | ["[Expression] Transform n-terminally His6-ZZ tagged Rab8a (pET28a backbone) into BL21(DE3) E. coli cells.", "[Expression] Grow an overnight culture in LB media with 50 µg/mL \nMake 50 mL . This is enough for the main 4L growth.", "[Expression] Add the overnight culture into main LB flasks with antibiotic present (50 µ... |
100,763 | Bacteria Transformation | 0 | dx.doi.org/10.17504/protocols.io.n2bvjn3kpgk5/v1 | https://www.protocols.io/view/bacteria-transformation-dem33c8n | Carolina Lopez | TITLE: Bacteria Transformation
AUTHORS: Carolina Lopez
[DESCRIPTION]
General protocol for bacteria transformation
[STEPS]
SECTION: Bacteria Transformation:
1. 1. Pipette 2 µL of product to 50 µL of E. coli competent cells and pipette slowly up and down 5 times to mix. For plasmids, use 2 µL ul of 0.005 µg/µLplasmid... | ["[Bacteria Transformation:] 1. Pipette 2 µL of product to 50 µL of E. coli competent cells and pipette slowly up and down 5 times to mix. For plasmids, use 2 µL ul of 0.005 µg/µLplasmid solution. For ligation reactions, DNA concentrations will vary so use 2 µL ul of reaction. \n2. Incubate for 20 min on ice.\n3. Hea... |
42,387 | Colloidal Coomassie Blue Stain: Recipe and Protocol | 4 | dx.doi.org/10.17504/protocols.io.bmmtk46n | https://www.protocols.io/view/colloidal-coomassie-blue-stain-recipe-and-protocol-bmmtk46n | Jeremy Kamil | TITLE: Colloidal Coomassie Blue Stain: Recipe and Protocol
AUTHORS: Jeremy Kamil
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">I learned this Colloidal Coomassie Blue staining recipe and protocol when I was a postdoc at Harvard Medical School.. Rumor has it, a postdoc reverse engineered a “safe st... | ["Dissolve 0.5 grams Coomassie Brilliant Blue G powder in 250 mL ethanol (200 proof), mix very well on stir bar until it seems fully or very nearly fully dissolved.", "Filter the Coomassie Blue G in ethanol solution through 0.2 or 0.45 um membrane, like a bottle top vaccum filter, to produce a solution that is free of ... |
92,636 | CRISPRi screen, MYH9 locus | 4 | dx.doi.org/10.17504/protocols.io.yxmvm3b46l3p/v1 | https://www.protocols.io/view/crispri-screen-myh9-locus-c6p4zdqw | Brian D. Cosgrove, Lexi Bounds, Carson Key Taylor, Alan L. Su, Anthony J. Rizzo, Alejandro Barrera, Andrea R Daniel, Gregory E. Crawford, Brenton D. Hoffman, Charles A. Gersbach | TITLE: CRISPRi screen, MYH9 locus
AUTHORS: Brian D. Cosgrove, Lexi Bounds, Carson Key Taylor, Alan L. Su, Anthony J. Rizzo, Alejandro Barrera, Andrea R Daniel, Gregory E. Crawford, Brenton D. Hoffman, Charles A. Gersbach
[DESCRIPTION]
This protocol describes methods for a CRISPR interference screen to identify open ch... | ["[Library design and cloning] Open chromatin regions within 440 kb of the MYH9 TSS are used to generate the oligo pool (identified from ATAC-seq of primary human fibroblasts cultured on soft and stiff ECM). For each ATAC-seq peak, any gRNA with a GuideScan specificity score of > 0.2 is included [which has previously b... |
70,908 | Laboratory risk factors for mortality in severe and critical COVID-19 patients admitted to the ICU | 1 | dx.doi.org/10.17504/protocols.io.kxygx9peog8j/v1 | https://www.protocols.io/view/laboratory-risk-factors-for-mortality-in-severe-an-chg4t3yw | Garidya Bestari, Tommy Suharjo, Lulu Ayu Nuari, Faujan Abdul Hadi, Lucas Welfried Panjaitan, Muhammad Begawan Bestari | TITLE: Laboratory risk factors for mortality in severe and critical COVID-19 patients admitted to the ICU
AUTHORS: Garidya Bestari, Tommy Suharjo, Lulu Ayu Nuari, Faujan Abdul Hadi, Lucas Welfried Panjaitan, Muhammad Begawan Bestari
[DESCRIPTION]
Background :Several studies have reported clinical characteristics and r... | ["All demographic, clinical, laboratory, and outcome data were extracted from the electronic medical record. Demographic characteristics of patients (age and sex), comorbidities (hypertension, diabetes, chronic obstructive pulmonary disease, coronary artery disease, heart failure, stroke history, chronic kidney disease... |
100,235 | Simple protocol for combined extraction of exocrine secretion and RNA in small arthropods | 0 | dx.doi.org/10.17504/protocols.io.n92ld8mb7v5b/v1 | https://www.protocols.io/view/simple-protocol-for-combined-extraction-of-exocrin-dd5j284n | David Fröhlich, Bodner Michaela, Dr. Guenther Raspotnig, Christoph Hahn | TITLE: Simple protocol for combined extraction of exocrine secretion and RNA in small arthropods
AUTHORS: David Fröhlich, Bodner Michaela, Dr. Guenther Raspotnig, Christoph Hahn
[DESCRIPTION]
We here introduce a novel combination of different methods, namely gas chromatography-mass spectrometry and RNAseq. The descri... | ["[Preparation] Chemical extraction.", "[Preparation] Put some crushed ice into a box and place it at your fume cupboard for chemical extraction.", "[Preparation] For each sample, label two GC-MS vials with glass inlets and put them for cooling into the crushed ice.", "[Preparation] Take some methylene chloride as sol... |
33,460 | Acropra DNA extraction with Qiagen DNAease tissue kit | null | dx.doi.org/10.17504/protocols.io.bcwuixew | null | Iliana Baums | TITLE: Acropra DNA extraction with Qiagen DNAease tissue kit
AUTHORS: Iliana Baums
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">DNA extraction protocol for Acropora tissue based on Qiagen DNAeasy kit</div></div>
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.eh6bb9e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol outlines the analysis used to plot contig coverage stats, as well as sequence count and length stats. We begin with visualizing contig length vs coverage. We then visualize the distributions of sequence counts per sample as a probability density plot (similar idea ... | [] |
44,328 | Activation of Human T cells with Phytohaemagglutinin (PHA) | 4 | dx.doi.org/10.17504/protocols.io.bpigmkbw | https://www.protocols.io/view/activation-of-human-t-cells-with-phytohaemagglutin-bpigmkbw | Zaki Molvi | TITLE: Activation of Human T cells with Phytohaemagglutinin (PHA)
AUTHORS: Zaki Molvi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Activating T cells with Phytohaemagglutinin (PHA) is a cheap and easy way to initiate a culture of rapidly growing T cells from human samples. PHA-activated T cells,... | ["Resuspend PBMCs at 2e6 cells/mL in complete medium (e.g. IMDM + 2mM L-Glutamine + 10% FBS). Add PHA to a final concentration of 5-10ug/mL (PHA-L or PHA-P both work in my experience). Incubate for 5 days in an appropriate vessel for your culture size (both flasks and plates will work, even if the latter is not TC coat... |
null | null | null | dx.doi.org/10.17504/protocols.io.d7t9nm | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
The Gibson Assembly <sup>®</sup> HiFi 1 Step method utilizes a blend of enzymes to assemble the DNA quickly and efficiently. The use of a High-Fidelity DNA polymerase enzyme allowsfor error free cloning resulting in a seamless construct ready for multiple downstream applications... | [] |
104,325 | Nielsen and Ford (2024) - Reduced striatal M4-cholinergic signaling following dopamine loss differentially contributes to parkinsonian and L-DOPA-induced dyskinetic behaviors | 2 | dx.doi.org/10.17504/protocols.io.dm6gp336jvzp/v2 | https://www.protocols.io/view/nielsen-and-ford-2024-reduced-striatal-m4-choliner-dh5d3826 | Beatriz E Nielsen, Christopher P Ford | TITLE: Nielsen and Ford (2024) - Reduced striatal M4-cholinergic signaling following dopamine loss differentially contributes to parkinsonian and L-DOPA-induced dyskinetic behaviors
AUTHORS: Beatriz E Nielsen, Christopher P Ford
[DESCRIPTION]
This collection contains protocols detailing methods used in Nielsen and For... | [] |
76,332 | Comprehensive analysis methods for developmental GC exposed zebrafish | 3 | dx.doi.org/10.17504/protocols.io.kxygx9ooog8j/v1 | https://www.protocols.io/view/comprehensive-analysis-methods-for-developmental-g-cnskvecw | Min-Kyeung Choi, Alex Cook, Helen Eachus, Anna Tochwin, Sara Kuntz, Soojin Ryu | TITLE: Comprehensive analysis methods for developmental GC exposed zebrafish
AUTHORS: Min-Kyeung Choi, Alex Cook, Helen Eachus, Anna Tochwin, Sara Kuntz, Soojin Ryu
[DESCRIPTION]
This protocol describes methods for the molecular, behavioral, and bioinformatic analyses of GC-exposed zebrafish. All procedures were used ... | [] |
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