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 |
|---|---|---|---|---|---|---|---|
null | null | null | dx.doi.org/10.17504/protocols.io.j9wcr7e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>ADAMTS5, the main aggrecanase, is a protein that seems to play a functional role in the development of brown and white adipose tissue (WAT) and browning of WAT. These observations were made using the <span lang="EN-US" style="margin: 0px; line-height: 200%; font-family: 'Aria... | [] |
103,905 | RSV Illumina Whole Genome Sequencing | 0 | null | https://www.protocols.io/view/rsv-illumina-whole-genome-sequencing-dhp935r6 | Katharine Mathers, Madhuri Barge, Seema Jasim, Kerry Falconer, Goncalo Fernandes, Daniel Maloney, Kate Templeton | TITLE: RSV Illumina Whole Genome Sequencing
AUTHORS: Katharine Mathers, Madhuri Barge, Seema Jasim, Kerry Falconer, Goncalo Fernandes, Daniel Maloney, Kate Templeton
[DESCRIPTION]
This is the Illumina sequencing protocol used with ARTIC RSV primers to sequence RSV samples in the Royal Infirmary of Edinburgh, which has... | ["[Reverse Transcription (RT) using LunaScript RT SuperMix] Invert extract tubes and pulse spin to 3000 rpm to remove drops from lids.", "[Reverse Transcription (RT) using LunaScript RT SuperMix] In clean area, label a PCR plate with RSV, date, run number, and “RT”.", "[Reverse Transcription (RT) using LunaScript RT Su... |
40,407 | Universal sandwich enzyme linked immunosorbent assay for investigating protein-AG (SpAG) interactions with immunoglobulins using a SpL-HRP conjugate. | 6 | dx.doi.org/10.17504/protocols.io.bjpxkmpn | https://www.protocols.io/view/universal-sandwich-enzyme-linked-immunosorbent-ass-bjpxkmpn | Angel Justiz-Vaillant, Norma McFarlane-Anderson | TITLE: Universal sandwich enzyme linked immunosorbent assay for investigating protein-AG (SpAG) interactions with immunoglobulins using a SpL-HRP conjugate.
AUTHORS: Angel Justiz-Vaillant, Norma McFarlane-Anderson
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. This ELISA is used to study the interacti... | ["This ELISA is used to study the interaction of a protein-AG (SpAG) with different immunoglobulin preparations from mammalian species.", "The 96 well microtitre plate is coated overnight at 4°C with 2 µg/µl per well of a mixture of protein-A and protein-G in carbonate-bicarbonate buffer pH 9.6.", "Then plate is treate... |
27,681 | MojoSort™ Mouse anti-APC Nanobeads Column Protocol | null | dx.doi.org/10.17504/protocols.io.699hh96 | null | Sam Li | TITLE: MojoSort™ Mouse anti-APC Nanobeads Column Protocol
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>BioLegend MojoSort™ nanobeads work in commonly used separation columns, based on our internal research as well as validation by external testing by academic labs. This simp... | ["Prepare cells from your tissue of interest or blood without lysing erythrocytes.", "In the final wash of your sample preparation, resuspend the cells in MojoSort™ Buffer by adding up to 4 mL in a 5 mL (12 x 75 mm) polypropylene tube.Note: Keep MojoSort™ Buffer on ice throughout the procedure.", "Filter the cells with... |
77,136 | NCBI data curation protocol - SOP for editing GenomeTrakr submissions | 1 | dx.doi.org/10.17504/protocols.io.36wgq5jb5gk5/v4 | https://www.protocols.io/view/ncbi-data-curation-protocol-sop-for-editing-genome-cpjqvkmw | Ruth Timme, Candace.Bias, Errol Strain, Tina.Pfefer, Maria Balkey | TITLE: NCBI data curation protocol - SOP for editing GenomeTrakr submissions
AUTHORS: Ruth Timme, Candace.Bias, Errol Strain, Tina.Pfefer, Maria Balkey
[DESCRIPTION]
PURPOSE: After data are submitted to NCBI submitters often encounter the need to update, retract, or replace these records. This is called data curation... | ["[BioProject Curation] How to edit a BioProject", "[BioProject Curation] 1. Click on the \"Manage Data\" tab within the submission portal, or navigate directly to \"Manage Data\": https://dataview.ncbi.nlm.nih.gov to edit Title, Organism, Description, URL, or publications for your BioProject.\n\n \n\n \n2. In the men... |
98,144 | U2OS Nucleofection & Analysis Protocol for MSPH Validation | 0 | dx.doi.org/10.17504/protocols.io.kqdg325kqv25/v1 | https://www.protocols.io/view/u2os-nucleofection-amp-analysis-protocol-for-msph-db382qrw | Jason Waligorski, Colin Kremitzki, Graham Bachman, Mallory Wright, William J Buchser | TITLE: U2OS Nucleofection & Analysis Protocol for MSPH Validation
AUTHORS: Jason Waligorski, Colin Kremitzki, Graham Bachman, Mallory Wright, William J Buchser
[DESCRIPTION]
Validation steps.
[STEPS]
SECTION: Design
1. Choosing synGRNA sequence
This is the method utilized in 2023 for the MSPH library in U2OS ce... | ["[Design] Choosing synGRNA sequence\n\nThis is the method utilized in 2023 for the MSPH library in U2OS cells for validating Raft-Seq hits. This is NOT the tandem gRNA method.\n\nChoose one gRNA that was a hit from the primary screen, usually from a published library (Brunello)\nDesign a 2nd 'backup' gRNA sequenced wh... |
53,477 | RNA-Stable Isotope Probing | 1 | dx.doi.org/10.17504/protocols.io.bygdpts6 | https://www.protocols.io/view/rna-stable-isotope-probing-bygdpts6 | Roey Angel, Eva Petrova, Ana Lara | TITLE: RNA-Stable Isotope Probing
AUTHORS: Roey Angel, Eva Petrova, Ana Lara
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The following protocol describes how to perform an RNA-Stable Isotope Probing experiment. The scope of this protocol only covers the parts involving separating labelled ... | ["[Solutions for SIP]\nPrepare the following solutions:\nAll glassware and plasticware must be clean and free of RNA and RNAse. Glassware can be baked at for", "[Solutions for SIP]\nGradient buffer (0.1 M Tris-HCl, 0.1 M KCl, 1 mM EDTA) :Dissolve the salts in RNase-free water and fill up to. Filter sterilise (0.1-0.... |
107,459 | GCase activity in mouse brain samples | 0 | dx.doi.org/10.17504/protocols.io.n92ld8eq7v5b/v1 | https://www.protocols.io/view/gcase-activity-in-mouse-brain-samples-dk7b4zin | Pietro La Vitola | TITLE: GCase activity in mouse brain samples
AUTHORS: Pietro La Vitola
[DESCRIPTION]
This protocol is designed for assessing the beta-glucocerebrosidase activity in fresh collected mouse brain samples
[STEPS]
SECTION: Samples homogenization
1. Homogenize fresh collected mouse brain samples in lysis buffer (50 mM Tri... | ["[Samples homogenization] Homogenize fresh collected mouse brain samples in lysis buffer (50 mM Tris-HCl, pH 7.4 and 750 mM NaCl, 5 mM EDTA and 10%Triton X-100).", "[Samples homogenization] Centrifuge samples at 5000 g (10 min at 4 °C )", "[Samples homogenization] Collect the supernatant", "[Samples homogenization] M... |
33,946 | Non-radioactive phosphorylation with T4 PNK (M0201) | 1 | dx.doi.org/10.17504/protocols.io.bdd2i28e | https://www.protocols.io/view/non-radioactive-phosphorylation-with-t4-pnk-m0201-bdd2i28e | New England Biolabs | TITLE: Non-radioactive phosphorylation with T4 PNK (M0201)
AUTHORS: New England Biolabs
[DESCRIPTION]
Protocol for non-radioactive phosphorylation with T4 PNK.
[STEPS]
1. Set up the following reaction in a microcentrifuge tube on ice:
2. Incubate at 37 °C for 30 min.
3. Heat inactivate by incubating at 65 °C... | ["Set up the following reaction in a microcentrifuge tube on ice:", "Incubate at 37 °C for 30 min.", "Heat inactivate by incubating at 65 °C for 20 min."] |
61,826 | DIMPLE library generation and assembly protocol | 4 | dx.doi.org/10.17504/protocols.io.rm7vzy7k8lx1/v1 | https://www.protocols.io/view/dimple-library-generation-and-assembly-protocol-b8maru2e | Christian Macdonald, David Nedrud, Patrick Rockefeller Grimes, Donovan Trinidad, James Fraser, Willow Coyote-Maestas | TITLE: DIMPLE library generation and assembly protocol
AUTHORS: Christian Macdonald, David Nedrud, Patrick Rockefeller Grimes, Donovan Trinidad, James Fraser, Willow Coyote-Maestas
[DESCRIPTION]
This is a protocol for generating and QCing mutagenic libraries using the DIMPLE protocol.
[STEPS]
SECTION: Preparation
1... | ["[Preparation] Use DIMPLE to generate mutagenic oligos and primers.", "[Preparation] Important note: DIMPLE breaks a gene up into sub-library fragments and generates mutagenic insert oligo pools, where each oligo contains barcodes, Type IIS restriction cutsites, and a sub-region of the gene. Be sure to review your lib... |
87,937 | Differentiation of WTC11 and KOLF2.1 iPSCs to dopaminergic neurons | 1 | dx.doi.org/10.17504/protocols.io.dm6gp39m8vzp/v1 | https://www.protocols.io/view/differentiation-of-wtc11-and-kolf2-1-ipscs-to-dopa-cz49x8z6 | Nisha Mohd Rafiq, Pietro De Camilli | TITLE: Differentiation of WTC11 and KOLF2.1 iPSCs to dopaminergic neurons
AUTHORS: Nisha Mohd Rafiq, Pietro De Camilli
[DESCRIPTION]
This protocol describes the differentiation of iPSCs (WTC11 and KOLF2.1) to dopaminergic neurons according to Bressan et al 2021. ... | ["[Differentiation of iPSCs into midbrain dopaminergic (mDA) neurons] Note: This protocol is optimized for mDA neuron differentiation in 6-well plate format.\n\nMedium change schema:\nDay 0-20:4 mL\nDay 21-65:3 mL \nDay 0-15: daily media changes\nDay 16-20: media changes every 2 days\nDay 21-65: media changes every 2-3... |
47,760 | Patient Satisfaction Survey of the Knee Surgery Project | 1 | dx.doi.org/10.17504/protocols.io.bsvqne5w | https://www.protocols.io/view/patient-satisfaction-survey-of-the-knee-surgery-pr-bsvqne5w | Maressa Lima, Fabricio Loures, Guilherme Runco, José Maurício Moraes do Carmo | TITLE: Patient Satisfaction Survey of the Knee Surgery Project
AUTHORS: Maressa Lima, Fabricio Loures, Guilherme Runco, José Maurício Moraes do Carmo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">To evaluate the satisfaction rate of patients who underwent surgical treatment of total knee arthro... | ["To raise the files of all patients who underwent total knee arthroplasty at the Pedro Ernesto University Hospital in 2020.", "Make telephone contact and explain the content and importance of the research to improve the quality of assistance", "Conduct the interview with nine questions for patients who agree to partic... |
106,122 | Brain Data Alchemy Project: Meta-Analysis of Preprocessed Public Transcriptional Profiling Data in the Gemma Database (v.2023) | 0 | dx.doi.org/10.17504/protocols.io.x54v925d4l3e/v1 | https://www.protocols.io/view/brain-data-alchemy-project-meta-analysis-of-prepro-djvi4n4e | Megan Hagenauer, Elizabeth Flandreau, Toni Duan, Anne Bader, Christabel Mclain, Trevonn Gyles, Ashlee Lewis, Duy Manh Nguyen | TITLE: Brain Data Alchemy Project: Meta-Analysis of Preprocessed Public Transcriptional Profiling Data in the Gemma Database (v.2023)
AUTHORS: Megan Hagenauer, Elizabeth Flandreau, Toni Duan, Anne Bader, Christabel Mclain, Trevonn Gyles, Ashlee Lewis, Duy Manh Nguyen
[DESCRIPTION]
Background: Over the past two decades... | ["[Project Preparation: Environment Set-Up] Install R and RStudio", "[Project Preparation: Environment Set-Up] Install R", "[Project Preparation: Environment Set-Up] Install R Studio", "[Project Preparation: Environment Set-Up] Follow the Brain Data Alchemy code repository on Github", "[Project Preparation: Environment... |
34,684 | Phylogenetic analysis | null | dx.doi.org/10.17504/protocols.io.bd44i8yw | https://www.protocols.io/view/phylogenetic-analysis-bd44i8yw | Joachim Nwezeobi, Onyeyirichi Onyegbule, Chukwuemeka Nkere, Joseph Onyeka, Sharon van Brunschot, Susan Seal, John Colvin | TITLE: Phylogenetic analysis
AUTHORS: Joachim Nwezeobi, Onyeyirichi Onyegbule, Chukwuemeka Nkere, Joseph Onyeka, Sharon van Brunschot, Susan Seal, John Colvin
[STEPS]
?. The partial mtCO1 sequences obtained from sequencing two randomly selected whiteflies from each of the 119 locations were first screened using qualit... | ["The partial mtCO1 sequences obtained from sequencing two randomly selected whiteflies from each of the 119 locations were first screened using quality checks in Geneious (v10.2.6) and those failing to meet the following criteria were discarded", "First, the sequence chromatograms were manually checked and translated ... |
52,110 | Genotyping Arabidopsis T-DNA lines | 1 | dx.doi.org/10.17504/protocols.io.bw5npg5e | https://www.protocols.io/view/genotyping-arabidopsis-t-dna-lines-bw5npg5e | Steven J Burgess | TITLE: Genotyping Arabidopsis T-DNA lines
AUTHORS: Steven J Burgess
[DESCRIPTION]
This protocol is used for genotyping Arabidopsis seedlings to test for the presence of a transfer DNA (T-DNA) insertion. By using two primer sets it is possible to determine whether a seedling is homozygous, heterozygous or azygous for a... | ["[Prepare primer working solution] Re-suspend lyophilized primers in dH2O to a stock concentration of 100 mM. Note: primer sequences can be obtained from SALK T-DNA express if you have the T-DNA accession number (http://signal.salk.edu/tdnaprimers.2.html)", "[Prepare primer working solution] Create a 10 mM working sol... |
86,216 | Measuring mitophagy via FACS with mtKeima reporter | 1 | dx.doi.org/10.17504/protocols.io.5qpvo3rd9v4o/v1 | https://www.protocols.io/view/measuring-mitophagy-via-facs-with-mtkeima-reporter-cyfgxtjw | Louise Uoselis | TITLE: Measuring mitophagy via FACS with mtKeima reporter
AUTHORS: Louise Uoselis
[DESCRIPTION]
Preparation of samples for measuring mitophagy levels using mtKeima reporter by fluorescence activated cell sorting (FACS).
[STEPS]
SECTION: Day 1
1. Seed cells in a 24 well plate, aiming for a confluency of ~80-90% at the... | ["[Day 1] Seed cells in a 24 well plate, aiming for a confluency of ~80-90% at the time of treatment. Seed additional wells of cells not expressing any fluorescent proteins, cells expressing only mtKeima, and cells expressing only YFP-Parkin (to be used as gating controls).", "[Day 2] Feed all cells with standard growt... |
null | null | null | dx.doi.org/10.17504/protocols.io.e6kbhcw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is a protocol for the Isolation of Genomic DNA from Fresh Blood, Bone Marrow & Buffy Coat (5ml blood). </p>
<p>If the buffy coat preparation was processed from 5ml whole blood then follow the Protocol for 5ml Blood.</p>
<p> </p>
<p>(Cat. # <a href="http://www.gbiosci... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.kcicsue | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>A bone marrow aspirate was obtained from equine ilium, and mesenchymal stem cells (MSCs) were separated from the aspirate by density-gradient centrifugation (Ficoll-Hypaque gradient centrifugation) (GE Healthcare, Pittsburgh, PA, USA) and further cultured.</p>
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.mtdc6i6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol has been very widely used in our laboratory. The local lab labeling is called « amplification of the <em>R0</em> region », However it is clearer to say that the amplicon corresponds to position 912 to 1264 of reference sequence from Kuo et al 1988, excluding the... | [] |
106,027 | Environmental DNA (eDNA) Extraction at OSU using the KingFisher Flex with the Omega Bio-Tek Mag-Bind® Blood & Tissue DNA HDQ 96 Kit | 1 | dx.doi.org/10.17504/protocols.io.14egn6rxql5d/v1 | https://www.protocols.io/view/environmental-dna-edna-extraction-at-osu-using-the-djsj4ncn | Jacoby Baker, Kathleen Pitz, Katie Carter | TITLE: Environmental DNA (eDNA) Extraction at OSU using the KingFisher Flex with the Omega Bio-Tek Mag-Bind® Blood & Tissue DNA HDQ 96 Kit
AUTHORS: Jacoby Baker, Kathleen Pitz, Katie Carter
[DESCRIPTION]
This protocol describes the DNA extraction process at Oregon State University (OSU) using the KingFisher Flex ... | ["[MIOP: Minimum Information about an Omics Protocol] MIOP Term\nValue\n \nmethodology category\n\n \nproject\n\n \npurpose\n\n \nanalyses\n\n \ngeographic location\n\n \nbroad-scale environmental context\n\n \nlocal environmental context\n\n \nenvironmental medium\n\n \ntarget\n\n \ncreator\n\n \nmaterials required\... |
94,138 | Immunofluorescence free-floating rat brain cryosections | 4 | dx.doi.org/10.17504/protocols.io.e6nvwdyzzlmk/v1 | https://www.protocols.io/view/immunofluorescence-free-floating-rat-brain-cryosec-c762zrge | mariangela.massarocenere | TITLE: Immunofluorescence free-floating rat brain cryosections
AUTHORS: mariangela.massarocenere
[DESCRIPTION]
Protocol for immunofluorescence on rat brain cryosections
[STEPS]
SECTION: 1. Sections selection
1. Collect the cryosections needed for a caudo-rostral representation of each brain region (every fifth or si... | ["[1. Sections selection] Collect the cryosections needed for a caudo-rostral representation of each brain region (every fifth or sixth section depending on the section's thickness, brain region, and animal species) into a 24-well-plate (3-4 sections per well)", "[1. Sections selection] Wash in PB1X 3 times x 5 min (5... |
42,583 | Protocol for IGV | 3 | null | https://www.protocols.io/view/protocol-for-igv-bmtxk6pn | TITLE: Protocol for IGV
AUTHORS:
[STEPS] | [] | |
89,038 | ICGRC Portal Tripal Data Generation and Setup | 5 | null | https://www.protocols.io/view/icgrc-portal-tripal-data-generation-and-setup-c27nyhme | Locedie Mansueto, ramil.mauleon, Tobias Kretzschmar, Graham King | TITLE: ICGRC Portal Tripal Data Generation and Setup
AUTHORS: Locedie Mansueto, ramil.mauleon, Tobias Kretzschmar, Graham King
[DESCRIPTION]
The data provided by the International Cannabis Genomics Research Consortium (ICGRC, https://icgrc.info) web portal consists of published results from past analyses, and resu... | ["[Prepare RNA-Seq Sequences] Next Generation Sequencing (NGS) RNA-Seq sequences are downloaded from NCBI SRA, and trimmed to remove adapters. Three sets of RNA-Seqs are prepared for: 1) Purple Kush gene prediction, 2) Finola gene prediction, 3) transcript assembly, expression level, and variant discovery for trichomes... |
null | null | null | dx.doi.org/10.17504/protocols.io.k8kczuw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div title="Page 4">
<div>
<div><strong>PROTOCOL SUMMARY</strong></div>
<div>
<p><strong>Title:</strong></p>
<p>The DHA(docosahexaenoic acid) Oxford Learning and Behaviour (DOLAB) II Study.</p>
<p> </p>
<p><strong>Type of Study: </strong></p>
<p>The study is a randomized, placeb... | [] |
34,728 | Protocol for whitefly genetic analysis | null | dx.doi.org/10.17504/protocols.io.bd6gi9bw | https://www.protocols.io/view/protocol-for-whitefly-genetic-analysis-bd6gi9bw | Joachim Nwezeobi, Onyeyirichi Onyegbule, Chukwuemeka Nkere, Joseph Onyeka, Sharon van Brunschot, Susan Seal, John Colvin | TITLE: Protocol for whitefly genetic analysis
AUTHORS: Joachim Nwezeobi, Onyeyirichi Onyegbule, Chukwuemeka Nkere, Joseph Onyeka, Sharon van Brunschot, Susan Seal, John Colvin
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-style:italic;">Bemisia tabaci</span><span style = "font-... | [] |
18,363 | Measurement of insulin concentration | null | dx.doi.org/10.17504/protocols.io.v63e9gn | null | Kiichi Hirota, Yoshiyuki Matsuo | TITLE: Measurement of insulin concentration
AUTHORS: Kiichi Hirota, Yoshiyuki Matsuo
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. MIN6 cells were cultured for 30 min in Krebs-Ringer bicarbonate HEPES (KRBH) buffer (140 mM NaCl, 3.6 mM KCl, 0.5 mM NaH2PO4, 0.5 mM MgSO4, 1.5 mM CaCl2, 2 mM NaHCO3, 10 mM H... | ["MIN6 cells were cultured for 30 min in Krebs-Ringer bicarbonate HEPES (KRBH) buffer (140 mM NaCl, 3.6 mM KCl, 0.5 mM NaH2PO4, 0.5 mM MgSO4, 1.5 mM CaCl2, 2 mM NaHCO3, 10 mM HEPES, and 0.1% bovine serum albumin) containing 2 mM glucose.", "The buffer was then changed to another KRBH buffer solution containing the rele... |
69,806 | ONT DNA Barcoding Fungal Amplicons w/ MinION & Flongle | 2 | null | https://www.protocols.io/view/ont-dna-barcoding-fungal-amplicons-w-minion-amp-fl-cgenttde | Stephen Douglas Russell | TITLE: ONT DNA Barcoding Fungal Amplicons w/ MinION & Flongle
AUTHORS: Stephen Douglas Russell
[DESCRIPTION]
This collection of protocols outline a working methodology to DNA barcode fungal specimens. This process will work for dried tissue, fresh tissue, or with DNA template that has already gone through an... | [] |
29,100 | MINUTE ChIP | null | dx.doi.org/10.17504/protocols.io.8nkhvcw | null | Banushree Kumar, Simon Elsässer | TITLE: MINUTE ChIP
AUTHORS: Banushree Kumar, Simon Elsässer
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left">The need for quantitative ChIP-seq has been widely appreciated, and a number of quantitative methods have been proposed. Mint-ChIP, developed b... | ["[LYSIS AND DIGESTION]\nHarvest 10^6 cells, spin, flash freeze the pellet.\nMake sure cell pellet is frozen with as little excess liquid as possible", "[LYSIS AND DIGESTION]\nOn the day of experiment resuspend in of ice cold PBS.\n50 µl", "[LYSIS AND DIGESTION]\nAdd of MNase mix (final 2U/ul in 2xLyB for mouse embryo... |
31,582 | Protocol for manual von Frey | 1 | null | https://www.protocols.io/view/protocol-for-manual-von-frey-ba36igre | Nathan Rizo, Lauren Smith, Olivier George | TITLE: Protocol for manual von Frey
AUTHORS: Nathan Rizo, Lauren Smith, Olivier George
[STEPS]
?. [Procecdure]
Place netting on surface set: (x2)
?. [Procecdure]
Place clear boxes on top of netting (4 boxes x2 = 8)
?. [Procecdure]
Place one animal per box, leave animals in box for 10 minutes to stabilize to the enviro... | ["[Procecdure]\nPlace netting on surface set: (x2)", "[Procecdure]\nPlace clear boxes on top of netting (4 boxes x2 = 8)", "[Procecdure]\nPlace one animal per box, leave animals in box for 10 minutes to stabilize to the environment", "[Procecdure]\nLabel your experimental sheet (L/R, X/), Name/Date/Experiment/Rats)", "... |
48,539 | Preparation of ink for electrode deposition via paint brushing using oxide powder | 6 | dx.doi.org/10.17504/protocols.io.btm3nk8n | https://www.protocols.io/view/preparation-of-ink-for-electrode-deposition-via-pa-btm3nk8n | Giulio Cordaro | TITLE: Preparation of ink for electrode deposition via paint brushing using oxide powder
AUTHORS: Giulio Cordaro
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A simple and efficient procedure to produce a viscous ink for brush painting of porous electrodes on top of electrolyte pellets for Sol... | ["[1.\tPreparation of organic viscous paste ]\nWeigh terpineol directly inside the bottle CompoundsCAS NumberPercentage [wt./wt.]Amount [g]Ethyl-cellulose9004-57-3 4%0.0800Terpineol95-55-5 76%1.5200Iso-propanol67-63-0 20%0.4000\n[or rescale all ingredients if need different amount ]\nCompoundsCAS NumberPercentage [wt./... |
52,207 | Cyanobacterial OD based Growth Assay - iGEM IISER Pune 2021 | 4 | null | https://www.protocols.io/view/cyanobacterial-od-based-growth-assay-igem-iiser-pu-bw8pphvn | misaal.bedi | TITLE: Cyanobacterial OD based Growth Assay - iGEM IISER Pune 2021
AUTHORS: misaal.bedi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol can be used to measure the optical density (OD) based growth of Cyanobacteria to obtain a growth curve.</div></div>
[STEPS]
?. [Sample Preparation]
... | ["[Sample Preparation]\nStart with a single colony of Synechococcus elongatus UTEX 2973 and inoculate it in of liquid BG-11 media containing of NaCl.\n10 mL", "[Sample Preparation]\nAllow the colony to grow to a dark green color for 1-2 days in a shaker incubator at 150 rpm, at the temperature for which you want a gr... |
91,589 | RNAseq of primary human T cells overexpressing BATF3 | 4 | null | https://www.protocols.io/view/rnaseq-of-primary-human-t-cells-overexpressing-bat-c5pdy5i6 | Andrea R Daniel | TITLE: RNAseq of primary human T cells overexpressing BATF3
AUTHORS: Andrea R Daniel
[DESCRIPTION]
This is a protocol describes methods for performing RNAseq using human CD8+ T cells overexpressing BATF3 or a GFP control.
[STEPS]
SECTION: Transfections for high-titer lentiviral production
1. Plate 1.2 x 106 or 7 x 10... | ["[Transfections for high-titer lentiviral production] Plate 1.2 x 106 or 7 x 106 HEK293T cells in a 6 well plate or 10 cm dish in the afternoon with 2 mL or 12 mL of complete opti-MEM (Opti-MEM‱ I Reduced Serum Medium supplemented with 1x Glutamax, 5% FBS, 1 mM Sodium Pyruvate, and 1x MEM Non-Essential Amino Acids)."... |
36,861 | Ampure Bead Cleanup | 1 | null | https://www.protocols.io/view/ampure-bead-cleanup-bf85jry6 | Alex Shaw, Manasi Majumdar, Catherine Troman, Javier Martin, Nick Grassly | TITLE: Ampure Bead Cleanup
AUTHORS: Alex Shaw, Manasi Majumdar, Catherine Troman, Javier Martin, Nick Grassly
[STEPS]
?. Prepare the AMPure XP beads for use; resuspend by vortexing.
?. Add required volume of resuspended AMPure XP beads to the reaction and mix by pipetting.
?. Incubate on a rotator for 5 minutes at roo... | ["Prepare the AMPure XP beads for use; resuspend by vortexing.", "Add required volume of resuspended AMPure XP beads to the reaction and mix by pipetting.", "Incubate on a rotator for 5 minutes at room temperature.", "Spin down the sample and pellet on a magnet. Keep the tube on the magnet, and pipette off the supernat... |
null | null | null | dx.doi.org/10.17504/protocols.io.piadkae | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is an example of a simple read mapping workflow. It is designed to be performed via the command line on an Ubuntu 16.06 OS. </p>
<p> </p>
<p>After completing this tutorial you should:</p>
<p>1) Have a practical understanding of how read mapping analyses are performed in ... | [] |
24,600 | Human adult generic tissue dissociation *in development* | null | dx.doi.org/10.17504/protocols.io.39ygr7w | null | Anna Wilbrey-Clark, Adam Hunter | TITLE: Human adult generic tissue dissociation *in development*
AUTHORS: Anna Wilbrey-Clark, Adam Hunter
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The aim with this protocol is to pull together what we have learnt from dissociating other tissues, to generate a 'generic' protocol that can be us... | ["Tissue Dissociation Part 1Place tissue piece on a 10cm petri dish and weigh and record tissue weight and size.", "Wash sample with cold DPBS(-/-) to remove most of the debris.", "Cover sample with 250µl ice cold DPBS(-/-).", "Using two scalpels, chop the piece as finely as possible.", "Transfer minced sample into a 1... |
84,851 | Plasma procurement and processing | 1 | dx.doi.org/10.17504/protocols.io.14egn3z6ml5d/v1 | https://www.protocols.click/view/plasma-procurement-and-processing-cw4txgwn | hannah.anvari, asma.giornazi, shriya.shah, maryellen.pavone, francesca.e.duncan francesca.duncan | TITLE: Plasma procurement and processing
AUTHORS: hannah.anvari, asma.giornazi, shriya.shah, maryellen.pavone, francesca.e.duncan francesca.duncan
[DESCRIPTION]
Purpose: This protocol is intended for use in the collection and storage of human plasma in a research setting. The protocol details the collection, processi... | ["Blood samples in BD Vacutainer™ Plastic Blood Collection Tubes with K2EDTA with Tube Stopper (Fisher Scientific, 23-021-013) are collected in pre-op from nurses. Samples are kept upright and placed on ice immediately following collection. Research coordinator will bring both specimens to the lab on ice (2-4 °C). Samp... |
null | null | null | dx.doi.org/10.17504/protocols.io.uvdew26 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Adapted from https://www.protocols.io/view/Gibson-Assembly-Protocol-E5510-imss45
[GUIDELINES]
To perform this protocol you need Gibson Assembly Master Mix 2X
[STEPS]
?.
?.
?.
?.
?.
?.
?. | ["{\"blocks\":[{\"key\":\"dcu9g\",\"text\":\"Add 100ng of vector \",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[{\"offset\":19,\"length\":1,\"key\":0}],\"data\":[]},{\"key\":\"96tsg\",\"text\":\"\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[... |
106,781 | R2C2 protocol using 10x Single-Cell RNA-seq Assay cDNA | 0 | dx.doi.org/10.17504/protocols.io.81wgbzonygpk/v1 | https://www.protocols.io/view/r2c2-protocol-using-10x-single-cell-rna-seq-assay-dkh54t86 | Xian Adiconis, Joshua Z Levin | TITLE: R2C2 protocol using 10x Single-Cell RNA-seq Assay cDNA
AUTHORS: Xian Adiconis, Joshua Z Levin
[DESCRIPTION]
This protocol is based on the published Rolling Circle to Concatemeric Consensus (R2C2) method (1). The aim is to make elongated cDNA via rolling circle amplification using cDNA generated from the 10x Chr... | ["[Splint generation] Prepare the following on ice", "[Splint generation] Run the following program\nThermocycler Conditions: (Lid@105 °C, 50 µl)\n \n 95 °C, 3 min\nfollowed by 1 cycle of:\n98 °C, 1 min\n62 °C, 1 min\n72 °C, 6 min\nthen\n4 °C,", "[Splint generation] Cleanup with Select-a-Size columns (Zymo) and a size ... |
34,255 | 3D Reconstruction of Neurons in Vaa3D | null | dx.doi.org/10.17504/protocols.io.bdppi5mn | null | Allen Institute for Brain Science | TITLE: 3D Reconstruction of Neurons in Vaa3D
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used to generate accurate digital representations of neuron morphologies from a variety of brain regions and species. Each reconstruction captures ... | [] |
63,423 | Natures One CBD Gummies: Is It 100% Effective and Proven Formula? | 3 | dx.doi.org/10.17504/protocols.io.eq2lyn23qvx9/v1 | https://www.protocols.io/view/natures-one-cbd-gummies-is-it-100-effective-and-pr-b967r9hn | H H | TITLE: Natures One CBD Gummies: Is It 100% Effective and Proven Formula?
AUTHORS: H H
[DESCRIPTION]
There are so many products available in the market that will help the person to remove all the problems from his body with ease. Here is our product that will help you from inside out. Do check out the product details ... | [] |
49,593 | Hybridization Chain Reaction (HCR) In Situ Protocol | 1 | dx.doi.org/10.17504/protocols.io.bunznvf6 | https://www.protocols.io/view/hybridization-chain-reaction-hcr-in-situ-protocol-bunznvf6 | Heather Bruce, Gabby Jerz, Sophia Kelly, Jenny McCarthy, Aaron Pomerantz, Gayani Senevirathne, Alice Sherrard, Dennis Sun, Carsten Wolff, Nipam Patel | TITLE: Hybridization Chain Reaction (HCR) In Situ Protocol
AUTHORS: Heather Bruce, Gabby Jerz, Sophia Kelly, Jenny McCarthy, Aaron Pomerantz, Gayani Senevirathne, Alice Sherrard, Dennis Sun, Carsten Wolff, Nipam Patel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "... | ["[Day 1 ]\nPerform PTw Washes:Note: If your embryos/tissue are stored in methanol, first rehydrate into PTw. For larger embryos, we recommend rehydrating step-wise 75/50/25% methanol in PTw). 1 × 10min PTw wash 1 × 5min PTw wash (Sonicate here if necessary due to cuticle, see St... |
88,499 | A live-cell platform to isolate phenotypically defined subpopulations for spatial multi-omic profiling | 4 | dx.doi.org/10.17504/protocols.io.14egn34yml5d/v1 | https://www.protocols.io/view/a-live-cell-platform-to-isolate-phenotypically-def-c2ntyden | Tala O. Khatib, Angelica M. Amanso, Christina M. Knippler, Brian Pedro, Emily R. Summerbell, Najdat M. Zohbi, Jessica M. Konen, Janna K. Mouw, Adam I. Marcus | TITLE: A live-cell platform to isolate phenotypically defined subpopulations for spatial multi-omic profiling
AUTHORS: Tala O. Khatib, Angelica M. Amanso, Christina M. Knippler, Brian Pedro, Emily R. Summerbell, Najdat M. Zohbi, Jessica M. Konen, Janna K. Mouw, Adam I. Marcus
[DESCRIPTION]
Numerous techniques have b... | ["[Thawing and maintenance of cells] Prepare cell culture media as described in reagent set up.", "[Thawing and maintenance of cells] Warm desired volume of culture media in 50 mL conical tubes at 37 °C in bead or water bath.", "[Thawing and maintenance of cells] Prepare tissue culture appropriate laminar flow hood usi... |
51,741 | Amplicon sequencing on the MinION platform | 4 | dx.doi.org/10.17504/protocols.io.bwr5pd86 | https://www.protocols.io/view/amplicon-sequencing-on-the-minion-platform-bwr5pd86 | Yoshiyuki Matsuo | TITLE: Amplicon sequencing on the MinION platform
AUTHORS: Yoshiyuki Matsuo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Amplicon sequencing on the MinION platform</div></div>
[STEPS]
?. [Materials]
KAPA2G Robust HotStart ReadyMix (2X) (KAPA BIOSYSTEMS, KK5701)Inner primer (forward): 5'-TTTCTGTT... | ["[Materials]\nKAPA2G Robust HotStart ReadyMix (2X) (KAPA BIOSYSTEMS, KK5701)Inner primer (forward): 5'-TTTCTGTTGGTGCTGATATTGC - target-specific sequence -3' (User-supplied)Inner primer (reverse): 5'-ACTTGCCTGTCGCTCTATCTTC - target-specific sequence -3' (User-supplied)PCR Barcoding Kit (Oxford Nanopore Technologies, SQ... |
35,572 | Blood collection for BALs | 1 | null | https://www.protocols.io/view/blood-collection-for-bals-beyujfww | Brent Boomhower, Olivier George | TITLE: Blood collection for BALs
AUTHORS: Brent Boomhower, Olivier George
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol specifically outlines the blood collection procedure for gas chromatography BAL analysis by Dr. Amanda Robert's Lab at TSRI's Alcohol Research Center.</div></div>
... | ["Submit a BAL request a day before collecting blood on https://www.oliviergeorge.com/balIACUC Protocol : S19016Funding Source : ARCMethod : GCComments : State the time & date the samples will be delivered to TSRI\nAsk mentor for directions to the specific drop-off site for blood samples.", "Label 1.5 mL microcentrifu... |
40,663 | Copy of Direct ELISA for investigating the binding of chemically-made Protein-LAG to immunoglobulins. | 6 | dx.doi.org/10.17504/protocols.io.bjxxkppn | https://www.protocols.io/view/copy-of-direct-elisa-for-investigating-the-binding-bjxxkppn | Angel Justiz-Vaillant | TITLE: Copy of Direct ELISA for investigating the binding of chemically-made Protein-LAG to immunoglobulins.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protein LAG (SpLAG) is an immunoglobulin-binding protein that interacts with the Fc and Fab regions of ma... | ["This ELISA is used to study the interaction of protein-LAG (SpLAG) with diverse immunoglobulins.", "The 96 well microtitre plate is coated overnight at 4°C with 1 µg/µl per well of purified immunoglobulins or 50 µl of any animal sera in carbonate-bicarbonate buffer pH 9.6.", "Then plate is treated with bovine serum a... |
42,219 | Isolation of mouse islet cells, culture with heparan sulfate mimetics and flow cytometry analysis of beta cell viability | 1 | dx.doi.org/10.17504/protocols.io.bmgjk3un | https://www.protocols.io/view/isolation-of-mouse-islet-cells-culture-with-hepara-bmgjk3un | Sarah Popp, Sarita Dhounchak, Charmaine Simeonovic | TITLE: Isolation of mouse islet cells, culture with heparan sulfate mimetics and flow cytometry analysis of beta cell viability
AUTHORS: Sarah Popp, Sarita Dhounchak, Charmaine Simeonovic
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Isolated mouse islets were dispersed into single cells usi... | ["See Guidelines, “Before starting”", "Isolated mouse islets were transferred to a 15 ml tube and excess medium was removed using a pipette. Resuspend in ~10-15 ml PBS/3mM EDTA. Centrifuge at 249g.", "Resuspend the islets in PBS/3mM EDTA. Centrifuge at 249g then carefully remove the supernatant.", "Gently resuspend eac... |
72,966 | Golgi immunopurification (Golgi-IP) for subcellular metabolite profiling | 1 | dx.doi.org/10.17504/protocols.io.36wgqj3p3vk5/v1 | https://www.protocols.io/view/golgi-immunopurification-golgi-ip-for-subcellular-cjheuj3e | Wentao Dong, Eshaan S Rawat, Monther Abu-Remaileh | TITLE: Golgi immunopurification (Golgi-IP) for subcellular metabolite profiling
AUTHORS: Wentao Dong, Eshaan S Rawat, Monther Abu-Remaileh
[DESCRIPTION]
The Golgi is a membrane-bound organelle that is central to protein and lipid processing, sorting and secretion in the cell. Despite its critical cellular function, th... | ["[Preparation of homogenizers and sample tubes] Wash the glass vessel homogenizer with MilliQ Water, 10 times each. wash the tissue grinder homogenizer thoroughly with DI Water and MilliQ Water, especially the gap between the white parts, don’t touch the part that goes into the glass vessel. Then dry upside-down using... |
29,635 | AccuBlue®Broad Range RNA Quantitation | null | dx.doi.org/10.17504/protocols.io.87bhzin | null | Ajit N Shah | TITLE: AccuBlue®Broad Range RNA Quantitation
AUTHORS: Ajit N Shah
[STEPS]
?. Warm all components to room temperature before use.RNA Broad Range Dyeis provided in DMSO, which may freeze during storage at 4°C.
?. Prepare 200 uL of working solution for each sample to be tested. Dilute the RNA Broad Range Dye in RNA Broad... | ["Warm all components to room temperature before use.RNA Broad Range Dyeis provided in DMSO, which may freeze during storage at 4°C.", "Prepare 200 uL of working solution for each sample to be tested. Dilute the RNA Broad Range Dye in RNA Broad Range Buffer at a ratio of 1:200 in a plastic container and mix well by vor... |
14,725 | DNA Methylation Signatures Predict HIV Prognosis and Mortality | null | dx.doi.org/10.17504/protocols.io.smdec26 | null | Xinyu Zhang, Ying Hu, Ke Xu | TITLE: DNA Methylation Signatures Predict HIV Prognosis and Mortality
AUTHORS: Xinyu Zhang, Ying Hu, Ke Xu
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Background</span><span> The effects of tobacco smoking upon epigenome-wide methylation signatures in white bl... | ["[Epigenome-wide Association Analysis]\nFollowing protocols of https://www.nature.com/protocolexchange/protocols/6335", "[Meta-analysis]\nWe conducted an EWAS meta-analysis by combining the data from the discovery and replication samples. Effect size and p-values for each probe were obtained from analyses in cohort 1 ... |
41,133 | ELISA for quantification of IL-31 in human serum. | 6 | dx.doi.org/10.17504/protocols.io.bkemktc6 | https://www.protocols.io/view/elisa-for-quantification-of-il-31-in-human-serum-bkemktc6 | Angel Justiz-Vaillant | TITLE: ELISA for quantification of IL-31 in human serum.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Interleukins (IL) are a type of cytokine first thought to be expressed by leukocytes alone but have later been found to be produced by many other body cells.... | ["An anti-human IL-31 coating antibody is adsorbed onto the microwells by incubation overnight at 4°C with carbonate-bicarbonate buffer.", "Add 50 µl of human serum. Human IL-31 present in the serum sample binds to antibodies adsorbed into the microwells.", "The microplate is blocked with 3% non-fat milk-PBS buffer and... |
43,587 | Stripping Membranes | 4 | dx.doi.org/10.17504/protocols.io.bntbmein | https://www.protocols.io/view/stripping-membranes-bntbmein | Jonathan Houseley, Cristina Cruz | TITLE: Stripping Membranes
AUTHORS: Jonathan Houseley, Cristina Cruz
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Over the past decade a plethora of noncoding RNAs (ncRNAs) have been identified, initiating an explosion in RNA research. Although RNA sequencing methods provide unsurpassed insights ... | ["[Stripping Membranes]\nWash with boiling 0.1× SSC 0.1% SDS in a plastic box on a rocker, check residual signal with a Geiger counter and repeat if necessary."] |
25,462 | UP: IO: Small protocol with all content PikaPoka 3983 9898 two step | null | dx.doi.org/10.17504/protocols.io.44wgyxe | null | Darja Darja | TITLE: UP: IO: Small protocol with all content PikaPoka 3983 9898 two step
AUTHORS: Darja Darja
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol Repository and Exporting</div><div class = "text-block">Once protocols are created, they can be exported for use in other sciNote projects and/or c... | ["[1. step ball]\nProtocol Repository and ExportingOnce protocols are created, they can be exported for use in other sciNote projects and/or copied directly to the sciNote Protocol Repository, where they are versioned and accessible to designated users.Exporting a ProtocolExporting a protocol saves it in a place of you... |
43,582 | Hybridization of DNA Oligonucleotide Probes | 4 | dx.doi.org/10.17504/protocols.io.bns6mehe | https://www.protocols.io/view/hybridization-of-dna-oligonucleotide-probes-bns6mehe | Jonathan Houseley, Cristina Cruz | TITLE: Hybridization of DNA Oligonucleotide Probes
AUTHORS: Jonathan Houseley, Cristina Cruz
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Over the past decade a plethora of noncoding RNAs (ncRNAs) have been identified, initiating an explosion in RNA research. Although RNA sequencing methods provi... | ["[Hybridization of DNA Oligonucleotide Probes]\nOligonucleotide probes are normally 20–45 nt, 40% GC, this protocol is designed for 30–45 nt DNA probes. They are very good for detecting abundant targets by northern blot and allow precise dissection of processing intermediates, but not all probes label or hybridize wel... |
42,392 | Concentrate viruses from sewage using HA filters | 4 | null | https://www.protocols.io/view/concentrate-viruses-from-sewage-using-ha-filters-bmmyk47w | Adélaïde Roguet | TITLE: Concentrate viruses from sewage using HA filters
AUTHORS: Adélaïde Roguet
[STEPS]
?. [Filtration of the sewage samples (in the biosafety cabinet)]
Take the sample out from the refrigerator.
?. [Filtration of the sewage samples (in the biosafety cabinet)]
Homogenize the sample thoroughly, avoiding foaming.
?. [F... | ["[Filtration of the sewage samples (in the biosafety cabinet)]\nTake the sample out from the refrigerator.", "[Filtration of the sewage samples (in the biosafety cabinet)]\nHomogenize the sample thoroughly, avoiding foaming.", "[Filtration of the sewage samples (in the biosafety cabinet)]\nUse a pipette controller, tr... |
46,197 | Semi-Automated Extraction of Viral RNA using the MagMax Viral Pathogen (MVPII) 96 Kit for SARS-CoV-2 Detection | 4 | dx.doi.org/10.17504/protocols.io.brcvm2w6 | https://www.protocols.io/view/semi-automated-extraction-of-viral-rna-using-the-m-brcvm2w6 | Pedro Belda-Ferre, Lisa Marotz, Greg Humphrey, Sydney Morgan, Rob Knight | TITLE: Semi-Automated Extraction of Viral RNA using the MagMax Viral Pathogen (MVPII) 96 Kit for SARS-CoV-2 Detection
AUTHORS: Pedro Belda-Ferre, Lisa Marotz, Greg Humphrey, Sydney Morgan, Rob Knight
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The purpose of this protocol is to describe a semi-a... | ["[Sample Extraction Plate (SEP) Preparation]\nTransfer proteinase K into KingFisher deep-well 96-well plates using the epMotion 5075: Turn on the epMotion 5075.Open the epBlue software (version 40.7) on the associated laptop, enter username and password.Within the epBlue program, double click to open the 'Application... |
77,126 | Apparent Diffusion Coefficient Measurement of Myelofibrosis in Mouse Tibia | 1 | dx.doi.org/10.17504/protocols.io.rm7vzb1z2vx1/v1 | https://www.protocols.io/view/apparent-diffusion-coefficient-measurement-of-myel-cpjevkje | Thomas L Chenevert | TITLE: Apparent Diffusion Coefficient Measurement of Myelofibrosis in Mouse Tibia
AUTHORS: Thomas L Chenevert
[DESCRIPTION]
The goal of this Co-Clinical Imaging Research Program (CIRP) pre-clinical imaging protocol (PIP) is to provide detailed description of key steps used to achieve a stated level of technical repeat... | [] |
101,410 | Systematic literature review on PAI and needle positioning errors | 0 | dx.doi.org/10.17504/protocols.io.6qpvr89eplmk/v1 | https://www.protocols.io/view/systematic-literature-review-on-pai-and-needle-po-dfaa3iae | Jette Bloemberg | TITLE: Systematic literature review on PAI and needle positioning errors
AUTHORS: Jette Bloemberg
[DESCRIPTION]
This protocol aims to ensure the reproducibility of the systematic literature review carried out on the quantification of and current guidelines on the hazards related to needle positioning in prostate canc... | ["[Literature search method] Databases: Embase, Medline ALL, Web of Science Core Collection*, and Cochrane Central Register of Controlled Trials databases\nThe search keywords: (a) therapy (e.g., brachytherapy, ablation therapy, laser ablation), (b) target (e.g., prostate, prostate tumor), and (c) needles and challenge... |
78,943 | CARD COUNT AND VIAL DEPLOYMENT/RETRIEVAL PROTOCOL | 4 | dx.doi.org/10.17504/protocols.io.4r3l27z5qg1y/v1 | https://www.protocols.io/view/card-count-and-vial-deployment-retrieval-protocol-crb7v2rn | Grace Sandel, Laura Barragan, Erica Garibay, Kiran Bengard, Ellis Gelt, Sage Moloney | TITLE: CARD COUNT AND VIAL DEPLOYMENT/RETRIEVAL PROTOCOL
AUTHORS: Grace Sandel, Laura Barragan, Erica Garibay, Kiran Bengard, Ellis Gelt, Sage Moloney
[DESCRIPTION]
Procedure to conduct "Crazy Yellow Ant Sampling on Tetiaroa"
This protocol provides instructions for performing card counts and deploying/retrieving vials... | ["[Card Count Protocol] If needed, scrape the ground (at least a 10x10cm area) at the site so the card sits flat on the ground (i.e. if there are branches or leaf litter, scrape them away).", "[Card Count Protocol] Place the card down on the ground.", "[Card Count Protocol] For 30 seconds, count the number of yellow cr... |
33,458 | HuBMAP: Embedding Fresh Frozen OCT Samples | null | dx.doi.org/10.17504/protocols.io.bcwsixee | null | Marda Jorgensen, Jerelyn Nick | TITLE: HuBMAP: Embedding Fresh Frozen OCT Samples
AUTHORS: Marda Jorgensen, Jerelyn Nick
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The purpose of this Standard Operating Procedure (SOP) is to outline procedures for the OCT embedding of HuBMAP fresh frozen specimens.</div></div>
[STEPS]
?. Col... | ["Collect tissue specimen from the designated common coordinate framework sites. (See case processing SOP diagrams)\n{\"blocks\":[{\"data\":[],\"depth\":0,\"entityRanges\":[],\"inlineStyleRanges\":[],\"key\":\"bi6am\",\"text\":\"This is an appendix diagram for spleen tissue cutting. \",\"type\":\"unstyled\"}],\"entityM... |
105,963 | Poly(A)-ClickSeq: Poly(A)-Primed Protocol with Single Indexing using Poly(A)-ClickSeq Kit | 0 | dx.doi.org/10.17504/protocols.io.n2bvjnb5xgk5/v1 | https://www.protocols.io/view/poly-a-clickseq-poly-a-primed-protocol-with-single-djqj4mun | Andrew Routh, Elizabeth Jaworski | TITLE: Poly(A)-ClickSeq: Poly(A)-Primed Protocol with Single Indexing using Poly(A)-ClickSeq Kit
AUTHORS: Andrew Routh, Elizabeth Jaworski
[DESCRIPTION]
Poly(A)-ClickSeq is a library preparation method used to target the 3’ ends of polyadenylated RNA, such as eukaryotic mRNAs. This technique offers an alternative to c... | ["[Reverse Transcription and RNA Removal] In a 0.2ml tube, dilute 100 ng-2 µg of input RNA to 10 µL using nuclease free water.", "[Reverse Transcription and RNA Removal] Add 3 µL of PAC Primer Mix (PPM) to the diluted RNA. Mix well.", "[Reverse Transcription and RNA Removal] Incubate the mixture at 65 °C for 5 min to m... |
47,381 | High-throughput Wastewater SARS-CoV-2 Detection Pipeline | 1 | dx.doi.org/10.17504/protocols.io.bshvnb66 | https://www.protocols.io/view/high-throughput-wastewater-sars-cov-2-detection-pi-bshvnb66 | Caroline Sheikhzadeh, Luis Gonzalez-barranca, Anna Adams, Olivia Ott, Smruthi Karthikeyan, Lisa Marotz, Greg Humphrey | TITLE: High-throughput Wastewater SARS-CoV-2 Detection Pipeline
AUTHORS: Caroline Sheikhzadeh, Luis Gonzalez-barranca, Anna Adams, Olivia Ott, Smruthi Karthikeyan, Lisa Marotz, Greg Humphrey
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Large-scale wastewater surveillance offers a great tool for ... | ["[Concentration]\nRaw sewage samples should only be handled/plated inside a certified Biosafety Cabinet (BSL 2+). Prepare three 24-well plates under a biosafety cabinet (BSL 2+), two of which are used as identical Sample Plates and one which serves as the Elution Plate. Sanitize the work area by wiping down all surfac... |
null | null | null | dx.doi.org/10.17504/protocols.io.gsvbwe6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div class="page" title="Page 2">
<div class="layoutArea">
<div class="column">
<p>This protocol describes a cell viability assay that uses near-infrared fluorescent detection. Sapphire700 Stain is used to determine cell viability by assessing cell membrane integrity, and the as... | ["[Cell Preparation] Grow RAW264.7 cells in a 100-mm tissue culture dish with growth medium (DMEM supplemented with 10% FBS) using standard cell culture practices. Always make sure that cells are healthy before using them for the experiment.", "[Camptothecin Treatment] {\"blocks\":[{\"key\":\"6lnio\",\"text\":\" ... |
null | null | null | dx.doi.org/10.17504/protocols.io.e3mbgk6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>BioLegend MojoSort™ nanobeads work in commonly used separation columns, based on our internal research as well as validation by external testing by academic labs. This simple protocol consists of following the MojoSort™ protocol to label the cells with pre-diluted MojoSort™ r... | [] |
22,571 | Quick staining procedure of nuclei in Euplotes using DAPI | null | dx.doi.org/10.17504/protocols.io.2ajgacn | null | Rachele Cesaroni | TITLE: Quick staining procedure of nuclei in Euplotes using DAPI
AUTHORS: Rachele Cesaroni
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. Mix concentrated Euplotes cells together with Ethanol 70% in a ratio of 1:1.
Better to have a completely starved Euplotes culture to avoid autofuorescence from bacteria... | ["Mix concentrated Euplotes cells together with Ethanol 70% in a ratio of 1:1.\nBetter to have a completely starved Euplotes culture to avoid autofuorescence from bacteria/algae.", "Add DAPI (0.01 mg/ml) to the mix in a ratio of 1:10, and stain for 15 minutes at room temperature.", "Observe cells by fluorescence micros... |
12,420 | Barcoding PCR for MiSeq sequencing | 1 | dx.doi.org/10.17504/protocols.io.kqdg3jb7l25z/v1 | https://www.protocols.io/view/barcoding-pcr-for-miseq-sequencing-qdcds2w | Eva Petrova, Roey Angel | TITLE: Barcoding PCR for MiSeq sequencing
AUTHORS: Eva Petrova, Roey Angel
[DESCRIPTION]
Barcoding PCR for MiSeq sequencing
Barcode head 8mer-GCT ATG CGC GAG CTG C Modified from Rudi et al. (2003)
[STEPS]
SECTION: PCR mixture
1.
* Buffer already contains MgCl2 at a final conc. of 2.0 mM.
SECTION: PCR progr... | ["[PCR mixture] * Buffer already contains MgCl2 at a final conc. of 2.0 mM.", "[PCR program] 1. 94◦C – 4′\n2. x 4 – 9 {\n a. 52◦C – 30′′\n b. 72◦C – 45′′\n c. 94◦C – 30′′\n }\n3. 52◦C – 30′′\n4. 72◦C – 10'"] |
51,519 | Digitalization of home-based records for maternal, newborn and child health (MNCH): a scoping review protocol | 1 | dx.doi.org/10.17504/protocols.io.bwi7pchn | https://www.protocols.io/view/digitalization-of-home-based-records-for-maternal-bwi7pchn | Marije Geldof, Anayda Gerarda Portela, Nina Gerlach, Caroline Sauvé | TITLE: Digitalization of home-based records for maternal, newborn and child health (MNCH): a scoping review protocol
AUTHORS: Marije Geldof, Anayda Gerarda Portela, Nina Gerlach, Caroline Sauvé
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Background: </span></d... | [] |
50,606 | Cas9-targeted Nanopore sequencing (CANS) | 1 | dx.doi.org/10.17504/protocols.io.261ge48mjv47/v1 | https://www.protocols.io/view/cas9-targeted-nanopore-sequencing-cans-bvnnn5de | Pavel Merkulov, Ilya Kirov | TITLE: Cas9-targeted Nanopore sequencing (CANS)
AUTHORS: Pavel Merkulov, Ilya Kirov
[DESCRIPTION]
Here we provide a protocol for Cas9-targeted Nanopore sequencing.
We successfully applied this method for targeted sequencing and DNA methylation profiling of genes in cereal genomes, as well as for insertions of transpo... | ["[Preparing the Cas9 ribonucleoprotein complexes (RNPs)] Add water to get 11 µL", "[Preparing the Cas9 ribonucleoprotein complexes (RNPs)] Heat and cool each sgRNAs to obtain pure monomers: 95 °C for 3 min , then cool to 95 Room temperature for 2 min", "[Preparing the Cas9 ribonucleoprotein complexes (RNPs)] To form C... |
74,698 | TAP 0.5%-0.75% impranil agarose plates | 4 | dx.doi.org/10.17504/protocols.io.rm7vzb695vx1/v1 | https://www.protocols.io/view/tap-0-5-0-75-impranil-agarose-plates-ck7iuzke | Joao Vitor Molino, Barbara Saucedo | TITLE: TAP 0.5%-0.75% impranil agarose plates
AUTHORS: Joao Vitor Molino, Barbara Saucedo
[DESCRIPTION]
The protocol describes the preparation of TAP media plates containing 0.5% to 0.75% Impranil, with the inclusion of antifungal and ampicillin. Notably, agarose was employed instead of agar to achieve a lighter gel c... | ["[TAP media] Take a stir rod and place into a 1 L erlenmeyer flask then fill with 900 mL of Milli-Q water. Place flask on stir plate and stir gently.", "[TAP media] Add 20 mL of 1M Tris Base\nAdd 1 mL of Phosphate Buffer II\nAdd 10 mL of Solution A\nAdd 1 mL of Trace Elements\nLet it stir.", "[TAP media] Place a pH pr... |
null | null | null | dx.doi.org/10.17504/protocols.io.ibscane | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The Microbial mutagenicty Ames bioassay is a short term microbial assay performed in<em> vitro.</em> It consisting of several <em>Salmonella typhimurium/E.coli </em>different strains, which are used to evaluate the mutagenicity of different environmental carcinogens and mutag... | [] |
29,499 | Neurosphere Protocol - A rapid and detailed method for the isolation of spheres in-vitro | null | dx.doi.org/10.17504/protocols.io.823hygn | null | Christopher Blackwood | TITLE: Neurosphere Protocol - A rapid and detailed method for the isolation of spheres in-vitro
AUTHORS: Christopher Blackwood
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The neurosphere assay is a powerful </span><span style = "font-style:italic;">in-vitro </span><span>tool that has been ... | ["[Before you begin dissections]\n1.\tSet-up prior to embryo dissection", "[Before you begin dissections]\n1.1)\tEstablish breeding pairs of mice to obtain embryonic day 17 (E17) embryos. Day 0 is defined as the day a vaginal plug is detected.", "[Before you begin dissections]\n1.2)\tPrepare sterile surgical tools (sc... |
70,220 | High-throughput workflow for the genotypic characterization of transposon library variants | 4 | dx.doi.org/10.17504/protocols.io.kqdg394jzg25/v1 | https://www.protocols.io/view/high-throughput-workflow-for-the-genotypic-charact-cgtktwkw | Lorea Alejaldre, Ana Mariya Anhel, Ángel Goñi-Moreno | TITLE: High-throughput workflow for the genotypic characterization of transposon library variants
AUTHORS: Lorea Alejaldre, Ana Mariya Anhel, Ángel Goñi-Moreno
[DESCRIPTION]
This is a workflow for the genotypic characterization of transposon library variants. It has been developed using an open-source Opentrons OT-2 r... | ["[Colony picking in selective media] Dispense 100 µL of selective media (M9-citrate for P. putida or Luria-Bertani plus 20 ng/µL nalidixic acid for DH5α E. coli) plus transposon cassette antiobiotic in a 96-well plate", "[Counter-selection and glycerol stocks pre-cultures] Inoculation of counter-selection plate in sel... |
null | null | null | dx.doi.org/10.17504/protocols.io.dph5j5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is a protocol from: <br /><br />Stedman, K. M., K. Porter, and M. L. Dyall-Smith. 2010. Chapter 6: The isolation of viruses infecting Archaea. Manual of Aquatic Viral Ecology. Waco, TX:American Society of Limnology and Oceanography. doi:10.4319/mave.2010.978-0-9845591-0-7<b... | [] |
75,396 | DNA Barcoding Standard Operating Protocol, Plants and Lichens at RBGE, Lab methods: PCR and Sequencing | 1 | null | https://www.protocols.io/view/dna-barcoding-standard-operating-protocol-plants-a-cmvcu62w | Laura L Forrest, Michelle Hart | TITLE: DNA Barcoding Standard Operating Protocol, Plants and Lichens at RBGE, Lab methods: PCR and Sequencing
AUTHORS: Laura L Forrest, Michelle Hart
[DESCRIPTION]
This is part of the collection DToL Taxon-specific Standard Operating Procedures for the Plant Working Group (protocols.io). The SOP collection contains gu... | ["[PCR mix] Create a Master Mix for each locus. Per reaction, add:\n\nFOR LAND PLANTS (20 μl total volume reactions):\n\n2 µL PCR buffer (at 10x), 2 µL dNTPs (each at 2 mM), 0.6 µL MgCl2 (at 50 mM), 4 µL TBT-PAR or CES additive (both at 5x), 2 µL forward primer,2 µL reverse primer (each at 10 μM), 0.25 µL BIOTAQ (at 5 ... |
21,276 | Yale - Alanine Aminotransferase | null | dx.doi.org/10.17504/protocols.io.yz4fx8w | null | Gary Cline, John Stack | TITLE: Yale - Alanine Aminotransferase
AUTHORS: Gary Cline, John Stack
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Procedure used to measure the Alanine Amino activity in blood, plasma, and serum. Alanine Amino (AL... | ["Calibrate Cobas for Alanine Transaminase Activity analysis by running two assayed control serum.", "Sample handling as performed by the Cobas Mira Plus. a) Pipette 16 µL of sample into a cuvette slot. b) Add 145 µL of Alanine Transaminase Reagent. c) Mixture is incubated at 37˚C and spun for 10 minutes. ... |
69,982 | Accurate profiling of diazotrophic communities using unique molecular identifiers with Nanopore sequencing | 1 | dx.doi.org/10.17504/protocols.io.6qpvr4embgmk/v1 | https://www.protocols.io/view/accurate-profiling-of-diazotrophic-communities-usi-cgj6ture | Nobuhiko Shigyo | TITLE: Accurate profiling of diazotrophic communities using unique molecular identifiers with Nanopore sequencing
AUTHORS: Nobuhiko Shigyo
[DESCRIPTION]
This protocol applies the method by Karst et al. (2021), who used UMI-tagged primers to perform highly accurate long-read amplicon analysis on the full-length ribosom... | ["[DNA extraction] Extract total genomic DNA (gDNA) from 500 mgof fresh soil and 100 mg of air-dried litter using the ISOIL for Beads Beating kit (Nippon Gene Corporation, Tokyo, Japan), a CTAB-based DNA extraction kit.", "[DNA extraction] Measure the extracted gDNA concentration using a Qubit fluorometer with the Qubi... |
26,991 | Ampure bead clean up for high molecular weight DNA | 1 | null | https://www.protocols.io/view/ampure-bead-clean-up-for-high-molecular-weight-dna-6kphcvn | Natalie Solonenko | TITLE: Ampure bead clean up for high molecular weight DNA
AUTHORS: Natalie Solonenko
[STEPS]
?. [Add beads ]
Make sure beads are completely resuspended before use by vortexing vigorously.
?. [Add beads ]
Add ratio of resuspended beads specified in your main protocol.
This ratio is dependent on the length of DNA you w... | ["[Add beads ]\nMake sure beads are completely resuspended before use by vortexing vigorously.", "[Add beads ]\nAdd ratio of resuspended beads specified in your main protocol.\nThis ratio is dependent on the length of DNA you want to recover.", "[Add beads ]\nFlick tube gently to mix beads and sample.", "[Incubate ]\nI... |
null | null | null | dx.doi.org/10.17504/protocols.io.qqkdvuw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Functional SMN protein of peripheral blood-derived mononuclear cells was detected with an anti-SMN antibody labeled with a fluorescent dye and analyzed semiquantitatively using intracellular expression intensity and SMN spot formed in cell nucleus as an index, Consider the re... | [] |
30,441 | Human Spinal Cord Nuclei Isolation | null | dx.doi.org/10.17504/protocols.io.9yhh7t6 | null | Abbas Rizvi, Elena Kandror, Tom Maniatis | TITLE: Human Spinal Cord Nuclei Isolation
AUTHORS: Abbas Rizvi, Elena Kandror, Tom Maniatis
[STEPS]
?. [Buffer Prep]
10x Stock Salt Solution: (raise to 50mL in water)note: can be stored at for up to 2 weeks Final Concentration CaCl2 (1M) ... | ["[Buffer Prep]\n10x Stock Salt Solution: (raise to 50mL in water)note: can be stored at for up to 2 weeks Final Concentration CaCl2 (1M) 50mM Magnesium Acetate (1M) 30mM Tris pH7.8 (1M) ... |
87,920 | JHM-MSMP Muscle Flow Cytometry | 1 | null | https://www.protocols.io/view/jhm-msmp-muscle-flow-cytometry-cz4qx8vw | ccherry | TITLE: JHM-MSMP Muscle Flow Cytometry
AUTHORS: ccherry
[DESCRIPTION]
Muscle flow cytometry
[STEPS]
SECTION: Protocol
1. Prepare viability dye solution for 100 μL / well to be stained. Dilute stock dyes in PBS.
SECTION: Protocol
2. Spin down plate at 400g for 5 min at 4°C or room temp.
SECTION: Protocol
3. Resuspend c... | ["[Protocol] Prepare viability dye solution for 100 μL / well to be stained. Dilute stock dyes in PBS.", "[Protocol] Spin down plate at 400g for 5 min at 4°C or room temp.", "[Protocol] Resuspend cells in 100μL of appropriate viability dye solution or 100μL of PBS for Unstained samples, all non-viability single-color c... |
null | null | null | dx.doi.org/10.17504/protocols.io.mzkc74w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The NEBNext rRNA Depletion Kit (Human/Mouse/Rat) depletes both cytoplasmic (5S rRNA, 5.8S rRNA, 18S rRNA and 28S rRNA) and mitochodrial ribosomal RNA (12S rRNA and 16S rRNA) from human, mouse and rat total RNA preparations. This product is suitable for both intact and degrade... | [] |
66,892 | Arctos Portable AC Reviews- Scam or Legit? REad Canada Price Before Buy | 1 | dx.doi.org/10.17504/protocols.io.kqdg3pz6pl25/v1 | https://www.protocols.io/view/arctos-portable-ac-reviews-scam-or-legit-read-cana-cdjks4kw | health | TITLE: Arctos Portable AC Reviews- Scam or Legit? REad Canada Price Before Buy
AUTHORS: health
[DESCRIPTION]
Arctos Portable Air Cooler runs very successfully, including humidity to the air the usage of evaporation generation. Simply plug it in to start using your private cooler as a humidifier.
[STEPS]
1. Arctos P... | ["Arctos Portable AC Fresh water filters are absolutely to be had on the reputable Arctos website and may be changed right now. Adjustable vents: The vents on the Arctos Portable Air Cooler are conveniently adjustable. The chilly air emitted from the air cooler spreads for your environment via these vents, which creat... |
null | null | null | dx.doi.org/10.17504/protocols.io.rusd6we | null | null | TITLE: No Title
AUTHORS:
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ecpbavn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<strong>Viral Bioinformatic Resource Centre</strong>
<ul>
<li><strong>Provide databases of viral genomic information.</strong>
<ul>
<li>Please check the <strong><em>Organisms</em></strong> menu to see which viruses we support: we’re now focusing on large DNA viruses</li>
<li>The... | [] |
41,789 | SPOT1 assay | 4 | dx.doi.org/10.17504/protocols.io.bk25kyg6 | https://www.protocols.io/view/spot1-assay-bk25kyg6 | Guanhua Xun, Huimin Zhao, stlane2 | TITLE: SPOT1 assay
AUTHORS: Guanhua Xun, Huimin Zhao, stlane2
[STEPS]
?. Using the first provided microcap, a sample is collected into capillary A, containing QuickExtract DNA Extraction Solution (Lucigen). Insert the capillary into the SPOT1 device and press the "Start" button to run the 5-minute pretreatment.
95 °... | ["Using the first provided microcap, a sample is collected into capillary A, containing QuickExtract DNA Extraction Solution (Lucigen). Insert the capillary into the SPOT1 device and press the \"Start\" button to run the 5-minute pretreatment.\n95 °C", "After pretreatment, remove capillary A from the SPOT1 device and ... |
null | null | null | dx.doi.org/10.17504/protocols.io.r8hd9t6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The second half of the workshop was an exercise that I copied from Professor Elizabeth Sargent.</p>
<p>https://twitter.com/esargent184/status/1009430882413883394</p>
<p><img id="s-mce-img" class="s-mce-img" src="https://s3.amazonaws.com/pr-journal/4tacz36.png" data-src="https... | [] |
60,193 | F0 knockout—single gene | 1 | dx.doi.org/10.17504/protocols.io.5qpvo52wdl4o/v3 | https://www.protocols.io/view/f0-knockout-single-gene-b6z9rf96 | Francois Kroll, J Rihel | TITLE: F0 knockout—single gene
AUTHORS: Francois Kroll, J Rihel
[DESCRIPTION]
Please cite 10.7554/eLife.59683 if you use this protocol.
Note; our eLife publication used Version 2 of this protocol. Later version are subsequent improvements/simplifications.
Get in touch for questions/suggestions
twitter – @francois_... | ["crRNA selection\n\nThis protocol is to disrupt one gene at three target sites.\n\nTo select your gRNAs, please refer to protocol \n\nHow to select the best gRNA(s) for frameshift knockouts in zebrafish\ndx.doi.org/10.17504/protocols.io.81wgb6r5qlpk/v1", "Re-suspend\n\nDo everything on ice \n\nFirst, spin down the via... |
79,004 | Fecobionics Test in Subjects with Fecal Incontinence | 1 | dx.doi.org/10.17504/protocols.io.5jyl8jx57g2w/v1 | https://www.protocols.io/view/fecobionics-test-in-subjects-with-fecal-incontinen-crd4v28w | Yanmin Wang, Hans Gregersen | TITLE: Fecobionics Test in Subjects with Fecal Incontinence
AUTHORS: Yanmin Wang, Hans Gregersen
[DESCRIPTION]
It is the protocol of Fecobionics test in normal subjects. Briefly, the device will be inserted into participants' rectum and several motions (cough, squeeze, straining) will be done. After the motions, the b... | ["Make sure the participant is diagnosed as fecal incontinence and eligible to do the study. Make sure he/she understands the study and has signed the informed consent form.", "Ask the subject to empty bladder and rectum before the test.", "Participant changes clothes and lies on left side.", "Calibrate the Fecobionics... |
63,331 | ViaKeto BHB Apple Gummies Reviews! | 3 | dx.doi.org/10.17504/protocols.io.q26g74wokgwz/v1 | https://www.protocols.io/view/viaketo-bhb-apple-gummies-reviews-b94br8sn | ViaKeto BHB Apple Gummies | TITLE: ViaKeto BHB Apple Gummies Reviews!
AUTHORS: ViaKeto BHB Apple Gummies
[DESCRIPTION]
CHOOSE YOUR COUNTRY FOR ORDER VIAKETO GUMMIES!
| ORDER VIAKETO APPLE GUMMIES IN UNITED KINGDOM |
| ORDER VIAKETO APPLE GUMMIES IN UNITED STATE |
| ORDER VIAKETO APPLE GUMMIES IN FRANCE |
| ORDER VIAKETO APPLE GUMMIES IN CAN... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.egibbue | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
49,885 | Single coacervate sequencing | 4 | dx.doi.org/10.17504/protocols.io.bux5nxq6 | https://www.protocols.io/view/single-coacervate-sequencing-bux5nxq6 | Franziska Aron, Damian Wollny | TITLE: Single coacervate sequencing
AUTHORS: Franziska Aron, Damian Wollny
[DESCRIPTION]
Here, we present a protocol which enables the comprehensive characterization of the RNA content of single phase-separated coacervates. We adapted single-cell RNA sequencing technology in combination with fluorescence activ... | ["[Droplet production] Calculate the droplet production according to your experiment. \n\nThe example is made for CM-Dextran:PDDA coacervates (molar ratio: 6:1)", "[Droplet production] Mix the droplet buffer with the CM-Dextran Sodium Salt", "[Droplet production] Add the RNA and mix briefly", "[Droplet production] Fina... |
45,103 | test rating 2 | 1 | null | https://www.protocols.io/view/test-rating-2-bqapmsdn | asfasasasdasd | TITLE: test rating 2
AUTHORS: asfasasasdasd
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.g5aby2e | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.fwvbpe6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?. | [] |
21,342 | Preparing water samples for analysis using ultrahigh resolution mass spectrometry | null | dx.doi.org/10.17504/protocols.io.y36fyre | null | Krista Longnecker | TITLE: Preparing water samples for analysis using ultrahigh resolution mass spectrometry
AUTHORS: Krista Longnecker
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Solid phase extraction using PPL modified from Dittmar et al. (2008): Dittmar, T.; Koch, B.; Hertkorn, N.; Kattner, G., A simple a... | ["[Extraction of organic compounds using the Bond Elut PPL solid phase extraction resin]\nRemove biotic and abiotic particulate matter with filtration method of choice. We generally use 0.2 um Omnipore (PTFE, hydrophilic) filters from Millipore in Teflon filter holders with a peristaltic pump. At the pump head, we use ... |
null | null | null | dx.doi.org/10.17504/protocols.io.iyxcfxn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p> After total genomic DNA was extracted, complete cytochrome <em>b</em> (cyt <em>b</em>) gene and 11 microsatellite loci were examined for all sampled individuals. Based on the cyt <em>b </em>sequences, phylogenetic analyses with maximum likelihood and Bayesian inference metho... | [] |
90,195 | PCR protocol for gene COXI neo-caledonian freshwater micro-crustaceans | 4 | dx.doi.org/10.17504/protocols.io.261ge4y4jv47/v3 | https://www.protocols.io/view/pcr-protocol-for-gene-coxi-neo-caledonian-freshwat-c4btysnn | Coline Royaux, Nicolas Rabet, Céline Bonillo | TITLE: PCR protocol for gene COXI neo-caledonian freshwater micro-crustaceans
AUTHORS: Coline Royaux, Nicolas Rabet, Céline Bonillo
[DESCRIPTION]
This PCR protocol has been used to amplify the Cytochrome Oxydase I gene of neo-caledonian genera Boeckella, Lynceus, Eulimnadia and Streptocephalus with several primers.
[... | ["Prepare the mix for the PCR depending on the quantity of DNA samples you want to amplify", "For each well, mix 12.44 µL, 2 µL, 1 µL, 1 µL, 0.8 µL and 0.12 µL. This mix is hereafter named \"intermediary mix\".", "Add your primers to the mix, 0.32 µL 10 picomolar (pM) and 0.32 µL 10 picomolar (pM) for each well. This ... |
85,015 | Updating or using the microgAMBI database to assess the ecological status of marine sediments and water | 5 | dx.doi.org/10.17504/protocols.io.n2bvj3xjnlk5/v1 | https://www.protocols.io/view/updating-or-using-the-microgambi-database-to-asses-cw9xxh7n | ángel borja | TITLE: Updating or using the microgAMBI database to assess the ecological status of marine sediments and water
AUTHORS: ángel borja
[DESCRIPTION]
Microbes have usually been neglected as indicators to assess the ecological status, under multiple human pressures. Some years ago, a biotic index (microgAMBI) was proposed ... | ["[Steps of updating or using the microgAMBI database] Collect bacterial abundance data (either total, as number of reads, or relative) for each sample or replicate, based on metabarcoding.", "[Steps of updating or using the microgAMBI database] Download the latest microgAMBI taxa list (which should be updated regularl... |
86,340 | Reverse transcription, primer pools preparation and multiplex PCR steps for CHIKV serotype genomic sequencing | 4 | dx.doi.org/10.17504/protocols.io.5qpvo3rm7v4o/v1 | https://www.protocols.io/view/reverse-transcription-primer-pools-preparation-and-cyjcxuiw | Laís Ceschini, Luisa Maria Inácio da Silva, Gabriel Luz Wallau | TITLE: Reverse transcription, primer pools preparation and multiplex PCR steps for CHIKV serotype genomic sequencing
AUTHORS: Laís Ceschini, Luisa Maria Inácio da Silva, Gabriel Luz Wallau
[DESCRIPTION]
This step-by-step protocol describes the cDNA synthesis, primer pools preparation and multiplex PCR conditions wit... | ["[Reverse transcription] Using a 2mL tube prepare the Mix 1 described below for 96 samples:", "[Reverse transcription] Using 0,2mL PCR tubes or 96 wells plates add 11-16µL of extracted RNA from\nRT-PCR positive samples. Add 2µL of Mix 1 to the tube/well and take it to the\nthermocycler with the following set up:\n\n65... |
87,498 | Estimation uncertainty in calculations of apparent iron solubility in seawater | 1 | null | https://www.protocols.io/view/estimation-uncertainty-in-calculations-of-apparent-czpix5ke | Kechen Zhu, Mark James Hopwood, Martha Gledhill | TITLE: Estimation uncertainty in calculations of apparent iron solubility in seawater
AUTHORS: Kechen Zhu, Mark James Hopwood, Martha Gledhill
[DESCRIPTION]
The apparent iron (Fe) solubility (SFe(III)app) was calculated via an ion paring-organic matter (NICA-Donnan) model at ambient pH, temperature and dissolved organ... | ["[Run the speciation code ORCHESTRA in parallel with code PEST++] Set up calculations of iron speciation and solubility in seawater via the speciation code ORCHESTRA.", "[Run the speciation code ORCHESTRA in parallel with code PEST++] In the same sub-folder of ORCHESTRA, write the code for combining PEST++ to ORCHESTR... |
65,031 | Live imaging to investigate mitophagy kinetics and NEMO recruitment in HeLa-M cells (Provisional unformatted) | 1 | null | https://www.protocols.io/view/live-imaging-to-investigate-mitophagy-kinetics-and-cbrfsm3n | OLIVIA HARDING, holzbaur | TITLE: Live imaging to investigate mitophagy kinetics and NEMO recruitment in HeLa-M cells (Provisional unformatted)
AUTHORS: OLIVIA HARDING, holzbaur
[DESCRIPTION]
There is no substitute for live cell imaging in the investigation of the kinetics of subcellular biology. Here, we enumerate a protocol to visualize f... | ["- This protocol was developed with the HeLa subtype, HeLa-M. HeLa-M cells are flatter than standard HeLa cells, making them easier to image. They also uptake siRNA better than standard HeLa. Regardless, the protocol would be easily adaptable to standard HeLa cells or other cell culture lines.", "- This pr... |
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