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 |
|---|---|---|---|---|---|---|---|
46,109 | led protocol | 1 | dx.doi.org/10.17504/protocols.io.bq95mz86 | https://www.protocols.io/view/led-protocol-bq95mz86 | Mohammad Tahan | TITLE: led protocol
AUTHORS: Mohammad Tahan
[STEPS]
?. | [] |
58,785 | General predation trial protocol | 3 | null | https://www.protocols.io/view/general-predation-trial-protocol-b5m9q496 | Laura Lopez, Meghan Duffy | TITLE: General predation trial protocol
AUTHORS: Laura Lopez, Meghan Duffy
[DESCRIPTION]
This is a protocol to quantify number of Daphnia that a Chaoborus will predate upon within a given time frame.
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.trdem26 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Zonulin is a protein, synthesized in intestinal and liver cells, that reversibly regulates intestinal permeability. Zonulin modulates the permeability of tight junctions between cells of the wall of the digestive tract. It was discovered in 2000 by Alessio Fasano and his team at... | [] |
54,708 | Querying the NCBI database for GenomeTrakr data | 1 | dx.doi.org/10.17504/protocols.io.bznup5ew | https://www.protocols.io/view/querying-the-ncbi-database-for-genometrakr-data-bznup5ew | Maria Balkey, Julie Haendiges, Ruth Timme, Candace.Bias | TITLE: Querying the NCBI database for GenomeTrakr data
AUTHORS: Maria Balkey, Julie Haendiges, Ruth Timme, Candace.Bias
[DESCRIPTION]
This protocol describes methods to query GenomeTrakr sequencing records and metadata across multiple NCBI resources: BioSample, BioProject, Sequencing Read Archive, Pathogen Detec... | ["[Pathogen Detection] Visit the Pathogen Detection (https://www.ncbi.nlm.nih.gov/pathogens/) to access real-time analyses of isolates obtained from ongoing pathogen surveillance activities.\n\nMore details on how to navigate the Pathogen Detection can be found at: https://www.ncbi.nlm.nih.gov/pathogens/pathogens_help/... |
null | null | null | dx.doi.org/10.17504/protocols.io.jn4cmgw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>ELISPOT allows detection of single IFN-γ-secreting cell, but the use of unseparated spleen cells removes the advantages of the method due to a high back ground of IFN-γ-production and uncertainty of the phenotype of secreting cells (CD4, CD8 or NK).</p>
<p>We used high purity... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.es3begn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
For use in <a href="https://www.protocols.io/view/CviRI-Purification-From-XZ-6E-Virus-Infected-NC64A-er4bd8w" target="_blank">CviRI Purification From XZ-6E Virus Infected NC64A Chlorella</a>.
[STEPS]
?.
?.
?. | [] |
79,805 | Ex vivo culture of SPMs | 1 | dx.doi.org/10.17504/protocols.io.8epv5jpdjl1b/v1 | https://www.protocols.click/view/ex-vivo-culture-of-spms-cr65v9g6 | michela.deleidi, Bianca Marchetti, Federico Bertoli, Carmela Giachino | TITLE: Ex vivo culture of SPMs
AUTHORS: michela.deleidi, Bianca Marchetti, Federico Bertoli, Carmela Giachino
[DESCRIPTION]
Ex vivo culture of spleen derived macrophages.
[STEPS]
SECTION: Ex vivo culture of spleen derived macrophages
1. Dissect spleens from abdominal cavity and filter it through a 40-μm nylon strain... | ["[Ex vivo culture of spleen derived macrophages] Dissect spleens from abdominal cavity and filter it through a 40-μm nylon strainer.", "[Ex vivo culture of spleen derived macrophages] Then, obtain a single splenic cell suspension. Culture cells in Roswell Park Memorial Institute (RPMI) medium 1640 RPMI 1640 (BioConcep... |
86,538 | Targeted analysis of Short Chain Fatty Acids (SCFAs) in human serum using derivatization and LC-HRMS analysis | 1 | dx.doi.org/10.17504/protocols.io.e6nvwddj7lmk/v1 | https://www.protocols.io/view/targeted-analysis-of-short-chain-fatty-acids-scfas-cyrixv4e | Margaux Billen, Scott G Denham, Joanna P Simpson, Natalie ZM Homer | TITLE: Targeted analysis of Short Chain Fatty Acids (SCFAs) in human serum using derivatization and LC-HRMS analysis
AUTHORS: Margaux Billen, Scott G Denham, Joanna P Simpson, Natalie ZM Homer
[DESCRIPTION]
This protocol describes the sample preparation and analysis of short chain fatty acids in human serum samples. S... | ["[Solvent preparation] Prepare Mobile Phase A: water + 0.1% Formic Acid\nAdd 1 L of LC-MS grade water to a 1L glass bottle.\nAdd 1 mL of LC-MS grade Formic Acid to the water.\nMix thoroughly.", "[Solvent preparation] Prepare Mobile Phase B: Acetonitrile\nAdd 1 L of LC-MS grade Acetonitrile to a 1L glass bottle.", "[So... |
103,428 | In situ Hybridization for Tyrosinase | 0 | dx.doi.org/10.17504/protocols.io.5jyl821w6l2w/v1 | https://www.protocols.io/view/in-situ-hybridization-for-tyrosinase-dg9c3z2w | Ariadna Laguna, Miquel Vila | TITLE: In situ Hybridization for Tyrosinase
AUTHORS: Ariadna Laguna, Miquel Vila
[DESCRIPTION]
In situ hybridization protocol with DIG-labelled riboprobes
[STEPS]
SECTION: Brain sectioning
1. Paraformaldehide perfused brains are cryoprotected in 30% sucrose and frozen with cold isopentane.
SECTION: Brain sectioning... | ["[Brain sectioning] Paraformaldehide perfused brains are cryoprotected in 30% sucrose and frozen with cold isopentane.", "[Brain sectioning] Frozen brains are cryosectioned at 30 microns in a cryostat", "[Brain sectioning] Cryosections are mounted on superfrost slides and dried over-night at room temperature before st... |
53,319 | Salmonella serotype prediction using the GalaxyTrakr SeqSero2 workflow | 5 | dx.doi.org/10.17504/protocols.io.bybfpsjn | https://www.protocols.io/view/salmonella-serotype-prediction-using-the-galaxytra-bybfpsjn | Paul Morin, Ruth Timme, Michelle Moore, Shauna Madson, Evelyn Ladines, Julia Manetas, Karen Jinneman | TITLE: Salmonella serotype prediction using the GalaxyTrakr SeqSero2 workflow
AUTHORS: Paul Morin, Ruth Timme, Michelle Moore, Shauna Madson, Evelyn Ladines, Julia Manetas, Karen Jinneman
[DESCRIPTION]
Salmonella serotypes are defined by two surface structures, O antigen and two H antigens. Traditional serotype d... | ["[GalaxyTrakr Account set up] Login to GalaxyTrakr: https://galaxytrakr.org/root/login\n\nOtherwise, create a GalaxyTrakr account here: https://account.galaxytrakr.org/Account/Register", "[Login and import workflow] Log into GalaxyTrakr 1909 (https://galaxytrakr.org/root/login)\n\n \n\nLink to create a new GalaxyTra... |
74,006 | Determining biofilm growth amount (absorbance) | 4 | dx.doi.org/10.17504/protocols.io.n2bvj8x95gk5/v2 | https://www.protocols.io/view/determining-biofilm-growth-amount-absorbance-ckhwut7e | An.Huang | TITLE: Determining biofilm growth amount (absorbance)
AUTHORS: An.Huang
[DESCRIPTION]
This protocol describes a method to determine the growth amount of biofilm at the early stage of biofilm formation by measuring absorbance. Here we use our own engineered bacteria, and it requires induction of IPTG and cultured with... | ["[IPTG induction] Escherichia coli grown overnight was diluted by LB to OD600=0.4-0.6.", "[IPTG induction] IPTG was added to cell culture to 1mM IPTG finally, and incubated 3h at 171 rpm, 37℃ in orbital shaking incubator.", "[Sample preparation] Preparing several 100mL flasks by filling the flasks with MBBR carrier K1... |
37,749 | Digoxigenin Labeled In Vitro Transcription and Ribogreen Quantification | 1 | dx.doi.org/10.17504/protocols.io.bg4vjyw6 | https://www.protocols.io/view/digoxigenin-labeled-in-vitro-transcription-and-rib-bg4vjyw6 | Allen Institute for Brain Science | TITLE: Digoxigenin Labeled In Vitro Transcription and Ribogreen Quantification
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used for in vitro transcription (IVT) reaction generating DIG-labeled anti-sense (AS) RNA from polymerase chain r... | [] |
29,838 | Field Genomics Protocols | null | dx.doi.org/10.17504/protocols.io.9dnh25e | https://www.protocols.io/view/field-genomics-protocols-9dnh25e | Mrinalini Watsa, Gideon Erkenswick, Stefan Prost, Aaron Pomerantz | TITLE: Field Genomics Protocols
AUTHORS: Mrinalini Watsa, Gideon Erkenswick, Stefan Prost, Aaron Pomerantz
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This collection of protocols are examples of protocols used for education in high throughput sequencing with Oxford Nanopore Technology's MinION ... | [] |
79,939 | Most Probable Number Relative Fluorescence Units Microplate Assay | 4 | null | https://www.protocols.click/view/most-probable-number-relative-fluorescence-units-csbbwain | Karla Franco Melendez, Layla Schuster, Melinda Chue Donahey, Emily Kairalla, Christopher Reisch, Adam R Rivers, Michael Andrew Jansen | TITLE: Most Probable Number Relative Fluorescence Units Microplate Assay
AUTHORS: Karla Franco Melendez, Layla Schuster, Melinda Chue Donahey, Emily Kairalla, Christopher Reisch, Adam R Rivers, Michael Andrew Jansen
[DESCRIPTION]
The most probable number (MPN) assay is a culture-dependent method of quantification mo... | ["[Inoculating soil microcosms with rfp-tagged Ralstonia] Transfer overnight culture to a 50 mL polypropylene centrifuge conical tube. Pellet sample 4000 rpm, 23 °C for 30 min.", "[Preparing cultures of rfp-tagged Ralstonia] Sreak Ralstonia from a glycerol stock on casamino acid-peptone-glucose (CPG)9 agar supplemente... |
null | null | null | dx.doi.org/10.17504/protocols.io.mmrc456 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Male adult Sprague–Dawley rats, weighing 270–300 g, obtained from the Animal Center of the Fujian Medical University, were anesthetized with intraperitoneal sodium pentobarbital (50 mg/kg). After intravenous injection of heparinized (50 IU) the hearts were quickly excised and... | [] |
53,364 | VigorNow Male Enhancement Reviews | 1 | dx.doi.org/10.17504/protocols.io.bycupsww | https://www.protocols.io/view/vigornow-male-enhancement-reviews-bycupsww | Tahir Qasim | TITLE: VigorNow Male Enhancement Reviews
AUTHORS: Tahir Qasim
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">VigorNow is a must to ensure that each person is able to sleep and perform at all times he wants to.</div></div>
[STEPS]
?. https://www.healthpills24x7.com/order-vigornow-meVigorNow is a mu... | ["https://www.healthpills24x7.com/order-vigornow-meVigorNow is a must to ensure that each person is able to sleep and perform at all times he wants to. No matter if you’ve been experiencing the consequences of maturing due to sexual rot, or if you’re able to ensure that the effects don’t occur for you, this enhancement... |
99,876 | Identifying Analytic Moves | 0 | dx.doi.org/10.17504/protocols.io.5jyl82je6l2w/v1 | https://www.protocols.io/view/identifying-analytic-moves-ddsc26aw | Andrea Ballestero, Katie Ulrich | TITLE: Identifying Analytic Moves
AUTHORS: Andrea Ballestero, Katie Ulrich
[DESCRIPTION]
When we are working through existing literature, the data/materials we collect or produce, and our own writing within the interpretive social sciences or humanities, there is a tendency to privilege two things: overall argument an... | ["When encountering a text or other form of knowledge, experiment with distinguishing argument, evidence, and analytic moves.", "Compare the analytic moves you have identified. What do they share? Are they geared primarily to empirics (i.e., as forms of organizing evidence) or are they geared towards associating argume... |
29,142 | Electrode cleaning solution | null | dx.doi.org/10.17504/protocols.io.8pwhvpe | null | Michael Economo | TITLE: Electrode cleaning solution
AUTHORS: Michael Economo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">How to make a cleaning solution for cleaning silicon probes</div></div>
[STEPS]
?. Make 1.2X strength cleaning solution (167.67 mL)First, measure H2O in beakerAdd: NaCl 10% SDS 0.2 M Tris Bu... | ["Make 1.2X strength cleaning solution (167.67 mL)First, measure H2O in beakerAdd: NaCl 10% SDS 0.2 M Tris Buffer, pH 8.5\n116.67 ml\n0.117 g\n10 ml\n50 ml", "[On day of use] Add 10X trypsin to 1.2X cleaning solution to make 12 mL 1x cleaning solution\n2 ml\n10 ml"] |
22,144 | Single-nucleus isolation from frozen human lung tissue for single-nucleus RNA-seq | null | dx.doi.org/10.17504/protocols.io.zu8f6zw | null | Nikita Joshi, Alexander Misharin | TITLE: Single-nucleus isolation from frozen human lung tissue for single-nucleus RNA-seq
AUTHORS: Nikita Joshi, Alexander Misharin
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">We aimed to develop a protocol for isolation of the single nuclei from the archival frozen human lung tissue suitable for... | ["[General Protocol]\nPrepare cOmplete stock, 10x, keep on ice. Prepare Lysis buffer, 2 ml per sample, keep on ice.Prepare Wash buffer, 4 ml per sample, keep on ice.Prepare Resuspension buffer, 0.3 ml per sample, keep on ice.", "[General Protocol]\nTake human lung sample from -80C or LN2 storage, cut ~5-73 mm piece, ke... |
62,256 | Kelly Clarkson CBD Gummies Reviews - What are the variants of Kelly Clarkson CBD Gummies? | 3 | dx.doi.org/10.17504/protocols.io.kxygxzoekv8j/v1 | https://www.protocols.io/view/kelly-clarkson-cbd-gummies-reviews-what-are-the-va-b82qrydw | Natures cbd Gummies | TITLE: Kelly Clarkson CBD Gummies Reviews - What are the variants of Kelly Clarkson CBD Gummies?
AUTHORS: Natures cbd Gummies
[DESCRIPTION]
Kelly Clarkson CBD Gummies
[STEPS] | [] |
66,456 | Functionality test (Borax Buffer) | 4 | null | https://www.protocols.io/view/functionality-test-borax-buffer-cc5ysy7w | Nadine Mowoh, Shalo Minette, Stephane Fadanka | TITLE: Functionality test (Borax Buffer)
AUTHORS: Nadine Mowoh, Shalo Minette, Stephane Fadanka
[DESCRIPTION]
This protocol describes the comparative analysis of visual and band patterns after electrophoresis with the BenBio Borax buffer as compared with a commercial TBE buffer. We use 0.5 kb and 1kb PCR amplicons... | ["[PCR amplification] Preparing PCR amplicons\n\nIn order to have the PCR amplicons to use for this experiment we typically amplify the 0.5 and/or 1kb regions of the Lambda DNA in a PCR reaction as follows:\n\nCrush some ice and put in a clean bowl\nRemove and thaw all PCR reagents on ice (dNTP mix, 10x PCR buffers, pr... |
96,355 | DOH Workshop Protocol Parts 1, 2 and 3 | 0 | dx.doi.org/10.17504/protocols.io.q26g7pqpkgwz/v1 | https://www.protocols.io/view/doh-workshop-protocol-parts-1-2-and-3-dacb2asn | Vesa Qarkaxhija, Bryan Wee, Natalie Ring | TITLE: DOH Workshop Protocol Parts 1, 2 and 3
AUTHORS: Vesa Qarkaxhija, Bryan Wee, Natalie Ring
[DESCRIPTION]
This collection of protocols details the extraction of high-molecular-weight DNA from Gram-negative bacterial culture, purification of dsDNA, removing contaminants and low molecular weight DNA, and creation of... | [] |
88,974 | Error-prone PCR (Random Mutagenesis) | 4 | dx.doi.org/10.17504/protocols.io.rm7vzx57xgx1/v1 | https://www.protocols.io/view/error-prone-pcr-random-mutagenesis-c25nyg5e | NUS iGEM | TITLE: Error-prone PCR (Random Mutagenesis)
AUTHORS: NUS iGEM
[DESCRIPTION]
2023 NUS-Singapore iGEM Team followed this protocol to introduce random mutation in DNA fragments.
[STEPS]
SECTION: Error-prone PCR (Mutagenesis)
1. Add the primers, the DNA template, and the following reagents from the into a PCR tube to m... | ["[Error-prone PCR (Mutagenesis)] Add the primers, the DNA template, and the following reagents from the into a PCR tube to make a 50 µL PCR sample:\n DI\n water 41.5μL 10x Mutazyme II (10x Reaction Buffer) 5μL 40mM\n dNTP Mix 1μL Each Primer (both forward & reverse) 0.5μ... |
40,280 | Focus group methodology for Doctor Who viewing behaviors | 1 | dx.doi.org/10.17504/protocols.io.bjjykkpw | https://www.protocols.io/view/focus-group-methodology-for-doctor-who-viewing-beh-bjjykkpw | Hannah Gunderman | TITLE: Focus group methodology for Doctor Who viewing behaviors
AUTHORS: Hannah Gunderman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is a description of how Hannah Gunderman facilitates her focus groups around </span><span style = "font-style:italic;">Doctor Who</span><spa... | ["[Introduction]\nProject Abstract: Focus group methodology has been extensively used by researchers in communications, media studies, and media geographies to gauge how viewers interact with and learn from a television show. When studying concepts of empathy, landscape interpretation, and science fiction fandom, focus... |
null | null | null | dx.doi.org/10.17504/protocols.io.dai2cd | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<p style="text-align: left;">Modified from Marcia Osburne<br /><br />F1 = 5’-CTTCCTCGTGAAGGTGGAA-3’ (“published”)</p>
<p>R1 = 5’-CAGCGAAGTAATTGTCTGCAATATAATC-3’ (“published”)</p>
<p>F2 = 5’-GTTGCCTAGAAGAGAAGGTGGTCG-3’ (&... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.grpbv5n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Denville LE Agarose is an all purpose agarose for routine nucleic acid electrophoresis of fragments between 500bp-23,000 bp.</p>
<p> </p>
<p>Denville LE Agarose has no detectable DNase or RNase activity.</p>
[GUIDELINES]
<p><strong>Introduction</strong></p>
<p>Denville LE Ag... | [] |
69,633 | OMS Atlas FFPE Spatial Mapping | 1 | dx.doi.org/10.17504/protocols.io.8epv56ppjg1b/v5 | https://www.protocols.io/view/oms-atlas-ffpe-spatial-mapping-cf89trz6 | Brett Johnson, Danielle Galipeau, George Thomas | TITLE: OMS Atlas FFPE Spatial Mapping
AUTHORS: Brett Johnson, Danielle Galipeau, George Thomas
[DESCRIPTION]
This protocol describes the procedure by which the OMS Atlas serially sections a FFPE block, prepares the resulting slides, and then distributes the specimens for downstream analysis.
[BEFORE_START]
Transfer... | ["[Preparation] Verify the identity of the FFPE block to be cut against written request for sectioning.", "[Preparation] Label all slides with a unique BEMS ID and slide number, corresponding to the written request and FFPE spatial map (below).", "[Sectioning] Align block on microtome to minimize tissue loss.", "[Secti... |
null | null | null | dx.doi.org/10.17504/protocols.io.c9mz45 | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<strong>Turk's Island Salt Mix</strong><br />
<table>
<tbody>
<tr>
<td style="text-align: center;">Chemical</td>
<td style="text-align: center;">g/2 L</td>
<td style="text-align: center;">Final Conc.</td>
<td style="text-align: center;">Mfc.-PN</td>
<td style="text-align: center;... | [] |
66,007 | DNA Gel Electrophoresis | 4 | dx.doi.org/10.17504/protocols.io.q26g74j61gwz/v1 | https://www.protocols.io/view/dna-gel-electrophoresis-ccpxsvpn | An.Huang | TITLE: DNA Gel Electrophoresis
AUTHORS: An.Huang
[DESCRIPTION]
Agarose gel electrophoresis can help determine the mass of a certain DNA fragment. This protocol will help user conduct gel electrophoresis appropriately.
[STEPS]
1. Mix 1 g agarose with 100 mL electrophoresis buffer (1X TAE) in a flask, then heat and sti... | ["Mix 1 g agarose with 100 mL electrophoresis buffer (1X TAE) in a flask, then heat and stir until agarose is completely dissolved.", "Add 10 µL 10000X GelRed nucleic acid stain into molten agarose and mix well.", "Wait until the molten agarose cools down to around 40 °C .", "While waiting for the cool down of molten a... |
75,680 | Expression and purification of recombinant gp32 protein | 1 | dx.doi.org/10.17504/protocols.io.kxygx957wg8j/v1 | https://www.protocols.io/view/expression-and-purification-of-recombinant-gp32-pr-cm58u89w | lucero.mascaro.r, lucero.merino.c, Pajuelo, Monica, Arias, Nicolas, Guerra, Daniel | TITLE: Expression and purification of recombinant gp32 protein
AUTHORS: lucero.mascaro.r, lucero.merino.c, Pajuelo, Monica, Arias, Nicolas, Guerra, Daniel
[DESCRIPTION]
The gp32 is a single strand binding protein (SSB) that plays a role in genetic recombination, replication and repair from the bacteriophage T4. The gp... | ["[DAY1: Transformation of competent cells] Quantify the plasmid containing the LbCas12a gene and determine the volume that contains 100 ng of the plasmid", "[DAY1: Transformation of competent cells] Defrost the aliquot of BL21(DE3) chemically competent cells on ice. Softly pipette 100 ng of the plasmid in the aliquot... |
74,740 | Plasma protein expression pattern in congenital analbuminemia – systematic review protocol | 1 | dx.doi.org/10.17504/protocols.io.5qpvoro4bv4o/v1 | https://www.protocols.io/view/plasma-protein-expression-pattern-in-congenital-an-ck8uuzww | Bailey M. Foster, Afsoun Abdollahi, Gregory C. Henderson | TITLE: Plasma protein expression pattern in congenital analbuminemia – systematic review protocol
AUTHORS: Bailey M. Foster, Afsoun Abdollahi, Gregory C. Henderson
[DESCRIPTION]
Congenital analbuminemia patients do not express albumin due to genetic mutation. Here a protocol is described for carrying out a systematic... | ["[Article selection] Literature search is carried out using multiple databases for case reports on congenital analbuminemia patients that were written in the English language.", "[Article selection] Case reports on congenital analbuminemia patients are included in the systematic review when the genetic condition was c... |
16,173 | Integrative taxonomy of Ophiothrix (Echinodermata: Ophiuroidea) | null | dx.doi.org/10.17504/protocols.io.t2meqc6 | null | Renata Alitto, Michela Borges, Letícia Dias de Oliveira, Helena Serrano | TITLE: Integrative taxonomy of Ophiothrix (Echinodermata: Ophiuroidea)
AUTHORS: Renata Alitto, Michela Borges, Letícia Dias de Oliveira, Helena Serrano
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">In this protocol, we highlight that molecular data did not have preference over morphological featur... | ["[Character sets]\nSpecies boundaries among populations of Ophiothrix were evaluated using four independent character sets in order to test: i) external morphology, ii) arm microstructures morphology, iii) morphometry, and iv) molecular data (16S and COI fragments).", "[Congruence framework]\nThe CS were classified ac... |
null | null | null | dx.doi.org/10.17504/protocols.io.c2pydm | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?. | [] |
28,485 | RNA Extraction from Cryptococcal Cells. | 1 | null | https://www.protocols.io/view/rna-extraction-from-cryptococcal-cells-73dhqi6 | Liz Hughes, Edward Wallace, Elizabeth Ballou | TITLE: RNA Extraction from Cryptococcal Cells.
AUTHORS: Liz Hughes, Edward Wallace, Elizabeth Ballou
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is for extracting RNA from Cryptococcal cell cultures.</div><div class = "text-block">Cell pellets are fixed in methanol, lyophilised ove... | ["Prepare Cryptococcal cells for RNA extraction.", "Streak out appropriate glycerol stock on YPD plate. Incubate @ 30ºC for 2 days.", "Lyophilise cell pellets overnight.", "Pick a single colony from the freshly streaked plate and put in required volume of appropriate media. Incubate in appropriate conditions depending ... |
20,016 | U Mass - Body composition (whole body) | null | dx.doi.org/10.17504/protocols.io.xsqfndw | null | Jason Kim | TITLE: U Mass - Body composition (whole body)
AUTHORS: Jason Kim
[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">
The EchoMRI 3-in-1 uses ¹H- magnetic resonance spectroscopy to ... | ["Place awake mice into an instrument column.", "Measure whole body fat mass, lean mass, and water mass using instrument standard operating procedure."] |
85,647 | SNARE-seq2 with Nuclei Hashing | 1 | dx.doi.org/10.17504/protocols.io.eq2lyjn4qlx9/v1 | https://www.protocols.click/view/snare-seq2-with-nuclei-hashing-cxvpxn5n | Nongluk Plongthongkum, Dinh H Diep, Song Chen, Blue Lake, Kun Zhang | TITLE: SNARE-seq2 with Nuclei Hashing
AUTHORS: Nongluk Plongthongkum, Dinh H Diep, Song Chen, Blue Lake, Kun Zhang
[DESCRIPTION]
To study the heterogeneity of complex tissues by joint profiling of gene expression and its regulation, we require an accurate and high-throughput method. Here we described improved high-th... | ["[Reagent setup] 40% (wt/vol) PEG 6000. Weigh 16.0 g of PEG 6000 in 50 mL tube. Add nuclease-free water and bring the total volume to 40 mL. Rotate the tube at room temperature until PEG 6000 completely dissolved. Spin down the tube at 200 g for 2 min, at room temperature to remove the tiny bubble. CRITICAL: 40% (wt/v... |
27,389 | Make serotonin and naloxone drug plates | null | dx.doi.org/10.17504/protocols.io.6y5hfy6 | null | Serena Ding | TITLE: Make serotonin and naloxone drug plates
AUTHORS: Serena Ding
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for making a set of three serotonin drug plates and a set of three naloxone drug plates. Serotonin (20 mM) is added to molten agar, whereas naloxone (10 mM) is made into a 10X... | ["First identify the drugs (serotonin and naloxone) to be used in the study and ensure that they are correctly labelled and handled.", "Since these are powered compounds, calculate the desired weight required for 10 mL of serotonin agar (at 20 mM final concentration), and for 1 mL of 10X naloxone stock solution (10X is... |
100,828 | DESS (DMSO/EDTA/NACL) Protocol | 0 | dx.doi.org/10.17504/protocols.io.5jyl822n9l2w/v1 | https://www.protocols.io/view/dess-dmso-edta-nacl-protocol-dep43dqw | Mirayana Marcelino Barros, Tiago Pereira, Alejandro De Santiago Perez, Hunter Powell, Jenna Brown | TITLE: DESS (DMSO/EDTA/NACL) Protocol
AUTHORS: Mirayana Marcelino Barros, Tiago Pereira, Alejandro De Santiago Perez, Hunter Powell, Jenna Brown
[DESCRIPTION]
DESS (DMSO/EDTA/NACL) protocol instructing how to make the solution for the preservation of samples.
[STEPS]
SECTION: Make 2L stock solution of 0.5M EDTA; if ... | ["[Make 2L stock solution of 0.5M EDTA; if stock is already made, proceed to step 4.] Combine 372.24 g disodium EDTA and 500 mLdeionized water.\nTip: Disodium EDTA is labeled PINK in the Bik Lab.", "[Make 2L stock solution of 0.5M EDTA; if stock is already made, proceed to step 4.] Add enough 5M NaOH to the solution to... |
26,521 | Make LB agar medium | null | dx.doi.org/10.17504/protocols.io.55zg876 | null | Gurdon Institute mediak | TITLE: Make LB agar medium
AUTHORS: Gurdon Institute mediak
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Make LB agar medium.</div></div>
[STEPS]
?.
?. ABCDEF1Solution LB (ready mix) + Agar 2Strength pH: 7.0Batch size5L3 45Ingredients Quantity 6LB mix 125g 7NaOH 10Mfew drops ... | ["ABCDEF1Solution LB (ready mix) + Agar 2Strength pH: 7.0Batch size5L3 45Ingredients Quantity 6LB mix 125g 7NaOH 10Mfew drops 8Distilled H2Oup to 5L 9Agarper 1L bottle14g 10 per 500ml bottle7g 11 1213Method 141In the fume cupboard, add the LB mix to 2L \n distilled H2O\n in a be... |
34,629 | Fitting PDB files to SAXS data using FOXS web server | 1 | null | https://www.protocols.io/view/fitting-pdb-files-to-saxs-data-using-foxs-web-serv-bd3di8i6 | Chris Berndsen | TITLE: Fitting PDB files to SAXS data using FOXS web server
AUTHORS: Chris Berndsen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">FOXS is a server for fitting models to SAXS data. It can also predict the SAXS data for protein models in the absence of SAXS data. </div><div class = "text-block">Schn... | ["[.dat file]\nTo perform this analysis you will need subtracted SAXS data in a .dat file that has the structure shown below:", "[.dat file]\nIf you do not have subtracted SAXS data see the protocol on SCATTER or ATSAS to generate this file.", "[Loading the data into webserver]\nNavigate to the FOXS webserver", "[Loadi... |
61,631 | Lipid droplet visualisation in cultured cells using BODIPY 493/503 stain | 4 | dx.doi.org/10.17504/protocols.io.q26g74xqqgwz/v1 | https://www.protocols.io/view/lipid-droplet-visualisation-in-cultured-cells-usin-b8e7rthn | Laura Smith | TITLE: Lipid droplet visualisation in cultured cells using BODIPY 493/503 stain
AUTHORS: Laura Smith
[DESCRIPTION]
Lipid droplets are organelles involved in intracellular lipid homeostasis, as well as playing key roles in a variety of cellular functions including cellular signalling, metabolic disease and inflammatio... | ["[Basal conditions] Plate cells onto coverslips in 6 wells plate – want cells to be 60-80% confluent for analysis.", "[Basal conditions] Remove media and wash 2x in PBS", "[Basal conditions] Fix cells in 4% PFA at RT for 20 minutes.", "[Basal conditions] Wash 1x in PBS", "[Basal conditions] Make up BODIPY 493/503:\nSt... |
24,971 | iconHi-C Protocol (ver. 1.0) | null | dx.doi.org/10.17504/protocols.io.4mjgu4n | null | Mitsutaka Kadota, Osamu Nishimura, Hisashi Miura, Kaori Tanaka, Ichiro Hiratani, Shigehiro Kuraku | TITLE: iconHi-C Protocol (ver. 1.0)
AUTHORS: Mitsutaka Kadota, Osamu Nishimura, Hisashi Miura, Kaori Tanaka, Ichiro Hiratani, Shigehiro Kuraku
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Hi-C, a derivative of chromosome conformation capture (3C) targeting the whole genome, was originally d... | ["[Section 1. (DAY 0) Preparation of cells/tissue]\nDissociate cells, count cell number, and collect 1 ×107 cells in a microtube (1.5 or 2.0 ml).", "[Section 1. (DAY 0) Preparation of cells/tissue]\nCentrifuge the cells.Centrifugation speed: Centrifugation time: Centifugation temperature:\n4 °C", "[Section 1. (DAY 0) P... |
101,575 | Collection of PROTOCOLS for Standardised Feed Formulation, Time-to-event Y-maze, and Length and Weight Measurement in P. hawaiensis | 0 | dx.doi.org/10.17504/protocols.io.14egn6996l5d/v1 | https://www.protocols.io/view/collection-of-protocols-for-standardised-feed-form-dfff3jjn | Ibrahim Lawan | TITLE: Collection of PROTOCOLS for Standardised Feed Formulation, Time-to-event Y-maze, and Length and Weight Measurement in P. hawaiensis
AUTHORS: Ibrahim Lawan
[DESCRIPTION]
This collection of protocols detailed the methods for preparing the standardised feed tabs, Y-maze for time-to-event analysis of chemosensory r... | [] |
94,804 | Differential gene expression analysis | 4 | dx.doi.org/10.17504/protocols.io.5jyl8p7k9g2w/v1 | https://www.protocols.io/view/differential-gene-expression-analysis-c8tuzwnw | Peter Kilfeather | TITLE: Differential gene expression analysis
AUTHORS: Peter Kilfeather
[DESCRIPTION]
Differential gene expression analysis from Kilfeather, Khoo et al., 2024
[STEPS]
SECTION: Protocol
1. Differential gene expression analysis in TRAP samples (including calculation of gene enrichment and depletion, relative to tissue h... | ["[Protocol] Differential gene expression analysis in TRAP samples (including calculation of gene enrichment and depletion, relative to tissue homogenate RNA) was performed using DESeq2 (v1.36.0, RRID:SCR_015687) in R (v4.2.1, RRID:SCR_001905) with Bioconductor (v3.15, RRID:SCR_006442). Adaptive shrinkage of log fold c... |
null | null | null | dx.doi.org/10.17504/protocols.io.sqcedsw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Cell type distribution and axon projection mapping - data acquisition and processing</p>
[STEPS] | [] |
46,304 | 3DRAM-seq enables joint epigenome profiling of spatial genome organization, chromatin accessibility and DNA methylation at high resolution | 1 | null | https://www.protocols.io/view/3dram-seq-enables-joint-epigenome-profiling-of-spa-brf8m3rw | Florian Noack, Boyan Bonev | TITLE: 3DRAM-seq enables joint epigenome profiling of spatial genome organization, chromatin accessibility and DNA methylation at high resolution
AUTHORS: Florian Noack, Boyan Bonev
[DESCRIPTION]
3DRAM-seq (3D genome, RNA, Accessibility and Methylation sequencing) is a novel multiomic method that simultaneously interr... | ["[3DRAM-seq: Methylation controls] NOTE: Control DNA has to prepared only once and can be reused. \n\nTo prepare GpC methylated control DNA, mix 10µl of CpG methylated pUC19 DNA (Zymo Research, Cat. N.: D5017) with 10µl of unmethylated lambda DNA (Promega, Cat. N: D1521).", "[3DRAM-seq: Methylation controls] Shear the... |
40,250 | FFPE Tissue Pre-treatment Before t-CyCIF on Leica Bond RX | 1 | dx.doi.org/10.17504/protocols.io.bji2kkge | https://www.protocols.io/view/ffpe-tissue-pre-treatment-before-t-cycif-on-leica-bji2kkge | Jia Ren Lin, Benjamin Izar, Zoltan Maliga, Yu-An Chen, Giorgio Gaglia, Ziming Du, Clarence Yapp, Shaolin Mei, Sandro Santagata, Peter Sorger | TITLE: FFPE Tissue Pre-treatment Before t-CyCIF on Leica Bond RX
AUTHORS: Jia Ren Lin, Benjamin Izar, Zoltan Maliga, Yu-An Chen, Giorgio Gaglia, Ziming Du, Clarence Yapp, Shaolin Mei, Sandro Santagata, Peter Sorger
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Tissue-based cyclic immunofluorescenc... | ["Create a protocol file named \"t-CyCIF\" on the Leica Bond RX (see user manual for instrument-specific details):", "Bake FFPE slides at for .\n60 °C", "Dewax by rinsing three times with preheated () Bond dewax solution, following by 3 rinses of , 200 proof ethanol.\n150 µl\n60 °C\n150 µl", "Remove the Bond dewax so... |
41,457 | Golden Gate Assembly (Esp31 or Bsa1 v2 HF) | 4 | dx.doi.org/10.17504/protocols.io.bkqrkvv6 | https://www.protocols.io/view/golden-gate-assembly-esp31-or-bsa1-v2-hf-bkqrkvv6 | Jamie Auxillos, Edward Wallace | TITLE: Golden Gate Assembly (Esp31 or Bsa1 v2 HF)
AUTHORS: Jamie Auxillos, Edward Wallace
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is for the assembly of DNA parts using Golden Gate assembly (Engler et al. 2008) with modifications from on publication by Garcia-Ruiz et al. ... | ["Note - This master mix needs to be prepared on ice and kept on ice!Taking into consideration the volume for the insert and vector DNA, prepare the following Golden Gate master mix for a final reaction volume of . Prepare the master mix according to the table below in a 1.5 ml eppendorf tube.Scale up the mix below bas... |
91,338 | FAVIS: Fast and Versatile protocol for metabarcoding of bulk Insect Samples from large-scale diversity monitoring projects | 4 | dx.doi.org/10.17504/protocols.io.kqdg36261g25/v2 | https://www.protocols.io/view/favis-fast-and-versatile-protocol-for-metabarcodin-c5fiy3ke | Elżbieta Iwaszkiewicz-Eggebrecht, Piotr Łukasik, Mateusz Buczek, Junchen Deng, Emily Hartop, Harald Havnås, Monika Prus-Frankowska, Carina R. Ugarph, Paulina Viteri, Anders F. Andresson, Tomas Roslin, Ayco J. M. Tack, Fredrik Ronquist, Andreia Miraldo | TITLE: FAVIS: Fast and Versatile protocol for metabarcoding of bulk Insect Samples from large-scale diversity monitoring projects
AUTHORS: Elżbieta Iwaszkiewicz-Eggebrecht, Piotr Łukasik, Mateusz Buczek, Junchen Deng, Emily Hartop, Harald Havnås, Monika Prus-Frankowska, Carina R. Ugarph, Paulina Viteri, Anders F. Andre... | ["[SECTION 1: Preparation] Set up washing stations", "[SECTION 1: Preparation] Set up a 80 L plastic container with washing liquid and water.", "[SECTION 1: Preparation] Set up a 80 L plastic container with 10% bleach solution by adding nine parts water to one part laboratory bleach (NaOCl - sodium hypochlorite soluti... |
89,091 | Archived Human Tissue Collection 1999-Aug 2015 -- University of Minnesota TMCs | 1 | dx.doi.org/10.17504/protocols.io.4r3l22n14l1y/v1 | https://www.protocols.io/view/archived-human-tissue-collection-1999-aug-2015-uni-c29byh2n | Laura J Niedernhofer, David A Bernlohr | TITLE: Archived Human Tissue Collection 1999-Aug 2015 -- University of Minnesota TMCs
AUTHORS: Laura J Niedernhofer, David A Bernlohr
[DESCRIPTION]
Liver and adipose tissue samples obtained from the UMN Biospecimen Repository that were collected and stored between 1999 and August 2015 not have documented collection pr... | ["Adipose and liver samples collected and stored between 1999 - Aug. 2015 do not have a record of tissue collection. \n\nThe following information was documented and is available for each tissue: \n- Date and time of collection\n- Processed time \n- Age\n- Ethnicity \n- Race\n- Gender \n- Material group and type\n- Vol... |
21,271 | Vandy – Energy Balance with Promethion | null | dx.doi.org/10.17504/protocols.io.yzxfx7n | null | Louise Lantier | TITLE: Vandy – Energy Balance with Promethion
AUTHORS: Louise Lantier
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block"><span>The Promethion from Sable Systems (Las Vegas, NV) assesses several key metabolic characteristi... | ["One week prior to the experiment start date, mice are singly housed for acclimation.", "On the day of the experiment start date, mice are weighed and body composition is assessed.", "The mice are placed in the cages of the Promethion system, one mouse per cage. The cages are housedin a light and temperature controlle... |
32,254 | Multi-Seq: my notes from the lab v2 | null | dx.doi.org/10.17504/protocols.io.bbq6imze | null | Luciano Martelotto | TITLE: Multi-Seq: my notes from the lab v2
AUTHORS: Luciano Martelotto
[DESCRIPTION]
<div class = "text-blocks"><table border><tr style = "text-align:center;"><td> </td><td>A</td></tr><tr><td style = "text-align:center;">1</td><td rowspan = "" colspan = "" style ="display : table-cell;">Please note these are just my ... | ["First thing to do is to get very clean nuclei preps. You may start with less clean nuclei if you like but it is likely that CMO will bind to the debris, and that is not good (just a thought). So, if you work with cell lines, iPSCs, PBMCs or some of the ‘liquid’ cancers then nuclei will be pretty clean, but depending ... |
83,959 | Instructions for CytoFLEX “Ready to Use” (RTU) QC Calibration Fluorospheres | 1 | dx.doi.org/10.17504/protocols.io.n92ldm3e8l5b/v1 | https://www.protocols.click/view/instructions-for-cytoflex-ready-to-use-rtu-qc-cali-cv8xw9xn | Jamie C Tijerina | TITLE: Instructions for CytoFLEX “Ready to Use” (RTU) QC Calibration Fluorospheres
AUTHORS: Jamie C Tijerina
[DESCRIPTION]
The CytoFLEX "Ready To Use" (RTU) QC Calibration Fluorospheres do not need to be diluted which reduces QC failures that are related to bead preparation errors. This protocol has been tested in the... | ["[To Run QC in Plate Mode] Remove the RTU QC Calibration fluorospheres box from the refrigerator.", "[To Run QC in Plate Mode] Check the bead lot number on the bottle or on the side of the box. Under the drop-down menu for the “bead lot,” ensure that the bead lot on the box matches your selection.", "[To Run QC in Pla... |
31,158 | SPARC - Attune NxT Set-up for Milli-metabolic bead assay Acquisition | 1 | dx.doi.org/10.17504/protocols.io.6qpvro3o3vmk/v1 | https://www.protocols.io/view/sparc-attune-nxt-set-up-for-milli-metabolic-bead-a-banwidfe | J Paul Robinson | TITLE: SPARC - Attune NxT Set-up for Milli-metabolic bead assay Acquisition
AUTHORS: J Paul Robinson
[DESCRIPTION]
This protocol is to demonstrate how to run a standard plate-based assay on the flow cytometer to produced appropiate concentations of the various analytes to be measured.
[BEFORE_START]
Setting up instru... | ["Check the waste and \n\nIf the waste is full, disconnect the tank and dispose of the waste down the sink with running water. Add 200 mL of 5% bleach to the tank and reconnect to the Attune NxT. Fill the Focusing Fluid tank from the focusing fluid cube.", "Check and fill as needed the shutdown solution reservoir and t... |
24,650 | Sample fixation of biopsy tissue for Electron Microscopy (EM) | null | dx.doi.org/10.17504/protocols.io.4bigske | https://www.protocols.io/view/sample-fixation-of-biopsy-tissue-for-electron-micr-4bigske | Jessica Riesterer, Erin Stempinski, Claudia Lopez | TITLE: Sample fixation of biopsy tissue for Electron Microscopy (EM)
AUTHORS: Jessica Riesterer, Erin Stempinski, Claudia Lopez
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The most crucial step in the entire electron microscopy workflow is sample fixation. Tissue needs to be preserved in strong ... | ["In order to facilitate quick fixation, the team of clinical coordinators should be provided with Eppendorf tubes containing 1.5 mL of fixative solution to have on-hand in the operating room during biopsies using 18-gauge core needles where 3-4mm of core is preserved. Larger volumes may be required for resections.", "... |
98,582 | Vasopressin Use During Liver Transplantation Is Not Associated with Severe Acute Kidney Injury: A Propensity Score Adjusted Regression Analysis | 0 | dx.doi.org/10.17504/protocols.io.6qpvr8dd2lmk/v1 | https://www.protocols.io/view/vasopressin-use-during-liver-transplantation-is-no-dchw2t7e | Edoardo Antonucci, Michael Bokoch, Rishi Kothari | TITLE: Vasopressin Use During Liver Transplantation Is Not Associated with Severe Acute Kidney Injury: A Propensity Score Adjusted Regression Analysis
AUTHORS: Edoardo Antonucci, Michael Bokoch, Rishi Kothari
[DESCRIPTION]
Acute kidney injury is a common complication after liver transplantation. Acute kidney injury oc... | ["[Vasopressin Use During Liver Transplantation Is Not Associated with Severe Acute Kidney Injury: A Propensity Score Adjusted Regression Analysis - Clinical Research Study Protocol] Research Hypothesis\nVasopressin use during liver transplantation reduces postoperative acute kidney injury\n(AKI).", "[Vasopressin Use D... |
28,889 | Extracellular vesicle isolation from bacterial cultures | null | dx.doi.org/10.17504/protocols.io.8fzhtp6 | null | Steven Biller | TITLE: Extracellular vesicle isolation from bacterial cultures
AUTHORS: Steven Biller
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Steps for isolating extracellular vesicles and other small particles from a bacterial culture</div></div>
[STEPS]
?. [Culturing]
Grow bacterial culture to mid/late e... | ["[Culturing]\nGrow bacterial culture to mid/late exponential phase", "[Vesicle+Particle Isolation]\nRemove cells by filtration through a 0.2µm filter and collect the filtrate (", "[Vesicle+Particle Isolation]\nConcentrate", "[Vesicle+Particle Isolation]\nRe-filter concentrated material through a 0.2 µm syringe filter.... |
58,592 | SARS-CoV-2 Omicron detection RT-qPCR assay with BA.1 and BA.2/BA.3 differentitation | 1 | dx.doi.org/10.17504/protocols.io.b5f8q3rw | https://www.protocols.io/view/sars-cov-2-omicron-detection-rt-qpcr-assay-with-b-b5f8q3rw | Nikita Yolshin , Kirill Varchenko, Andrey Komissarov | TITLE: SARS-CoV-2 Omicron detection RT-qPCR assay with BA.1 and BA.2/BA.3 differentitation
AUTHORS: Nikita Yolshin , Kirill Varchenko, Andrey Komissarov
[DESCRIPTION]
Omicron lineage (B.1.1.529) – SARS-CoV-2 variant of concern designated on 26 November 2021 by WHO. This variant has a large number of mutations, som... | ["Order oligonucleotides with following sequences 5'->3':\n target name sequence ORF1 2-SARS-CoV-2-ORF-1-F AGAGCTATGAATTGCAGAC ORF1 2-SARS-CoV-2-ORF-1-R GGGAAATACAAAATTTGGACA ORF1 2-SARS-CoV-2-ORF-1-P FAM-AATTGGCAAAGAAATTTGACACCTTCA-BHQ1 ESR31del N31-33del F GTTTGGTGGACCCTCAGATT ... |
91,882 | RNA/DNA extraction from plankton natural samples using NucleoSpin RNA + RNA/DNA Buffer kits (Macherey Nagel) | 4 | dx.doi.org/10.17504/protocols.io.eq2lynz2qvx9/v2 | https://www.protocols.io/view/rna-dna-extraction-from-plankton-natural-samples-u-c5yiy7ue | Sarah Romac, Morgane Ratin | TITLE: RNA/DNA extraction from plankton natural samples using NucleoSpin RNA + RNA/DNA Buffer kits (Macherey Nagel)
AUTHORS: Sarah Romac, Morgane Ratin
[DESCRIPTION]
This protocol has been developped for simultaneous nucleic acid (RNA and DNA) extraction from environmental water samples collected by filtration on poly... | ["[Lysis] Lyse your plankton filter samples following the protocol :\n\nhttps://www.protocols.io/edit/cryogrinding-protocol-mecanic-lysis-of-142mm-filte-beqpjdvn", "[Lysis] Depending of the plankton size fraction samples you have, select :\n\n1 - RNA/DNA extraction using NucleoSpin RNA MIDI kit regarding [>20µ] size fr... |
62,261 | https://thefeedfeed.com/cassava2871/articles/keto-start-acv-gummies-reviews-facts-2022-keto-start-acv-work-scam-or-legit-1 | 1 | dx.doi.org/10.17504/protocols.io.dm6gpbxrjlzp/v1 | https://www.protocols.io/view/https-thefeedfeed-com-cassava2871-articles-keto-st-b82vrye6 | habenjosh | TITLE: https://thefeedfeed.com/cassava2871/articles/keto-start-acv-gummies-reviews-facts-2022-keto-start-acv-work-scam-or-legit-1
AUTHORS: habenjosh
[DESCRIPTION]
https://www.facebook.com/Keto.Start.ACV.Gummies.Official
https://www.facebook.com/Keto-Start-ACV-Gummies-108483741663388/
[STEPS]
1. Shop Now:- https://... | ["Shop Now:- https://supplement24hours.com/keto-start-acv-gummies/\n\nKeto Start ACV Gummies:When under pressure, the typical individual worries over their weight and has a wide range of dreams about how they can thin down. In any case, it's pivotal to understand that uneasiness and greasy food utilization are similarl... |
85,121 | 20 minute PCR Enzymatic Cleanup | 4 | dx.doi.org/10.17504/protocols.io.ewov1q4bkgr2/v1 | https://www.protocols.click/view/20-minute-pcr-enzymatic-cleanup-cxc9xiz6 | Julian Liber | TITLE: 20 minute PCR Enzymatic Cleanup
AUTHORS: Julian Liber
[DESCRIPTION]
A rapid microplate-compatible protocol for cleanup of PCR products prior to Sanger sequencing. Verify that the PCR produces a single band, and retain some PCR product for cleanup and sequencing. Set up at room temperature, and react on the ther... | ["[Making the enzyme master mix] Add to a 1.5 mL sterile conical tube\n760 uL water\n94 uL 10x rCutSmart buffer\n96 uL 10x Exonuclease I buffer (NEBuffer r3.1)\n4 uL Quick CIP (5U/uL) NEB #M0525\n10 uL Thermolabile Exonuclease I (20U/uL) NEB #M0568", "[Making the enzyme master mix] Mix, then aliquot 200 uL into separat... |
96,649 | Prospective Human Liver, Adipose and Blood Collection -- University of Minnesota TMC | 0 | dx.doi.org/10.17504/protocols.io.j8nlko7j5v5r/v1 | https://www.protocols.io/view/prospective-human-liver-adipose-and-blood-collecti-damh2c36 | Laura J Niedernhofer, David A Bernlohr | TITLE: Prospective Human Liver, Adipose and Blood Collection -- University of Minnesota TMC
AUTHORS: Laura J Niedernhofer, David A Bernlohr
[DESCRIPTION]
Collection protocol obtained from the attached BioNet Specimen Procurement Agreement provided by the UMN CTSI Biorepository and Laboratory Services (BLS).
[ST... | [] |
23,190 | Collection and RNA Isolation from stabilized Whole Blood using TempusTM Blood RNA Tube and Spin RNA Isolation Reagent Kit | null | dx.doi.org/10.17504/protocols.io.2vwge7e | null | Lisa-Maria Rosenthal, Giang Tong, Katharina Schmitt | TITLE: Collection and RNA Isolation from stabilized Whole Blood using TempusTM Blood RNA Tube and Spin RNA Isolation Reagent Kit
AUTHORS: Lisa-Maria Rosenthal, Giang Tong, Katharina Schmitt
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol was used to isolate RNA from whole blood samples... | ["•\tDraw 3 mL of blood directly into the Tempus Blood RNA Tube, following clinic’s standard procedures for drawing blood from individuals into blood collection tubes containing liquid reagents.", "•\tImmediately after the Tempus tube is filled, stabilize the blood by shaking the tube vigorously or vortexing the conten... |
29,346 | Immunohistochemistry Protocol for Frozen Sections | null | dx.doi.org/10.17504/protocols.io.8wahxae | null | Kelsey Knight | TITLE: Immunohistochemistry Protocol for Frozen Sections
AUTHORS: Kelsey Knight
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The following is a general procedure guide for preparation and staining of acetone-fixed frozen tissues using a purified, unconjugated primary antibody, biotinylated ... | ["[Prepare frozen tissue sections:]\nPlace a freshly dissected tissue block (", "[Prepare frozen tissue sections:]\nCover the entire tissue block with cryo-embedding media (e.g. OCT).", "[Prepare frozen tissue sections:]\nSlowly place the base mold containing the tissue block into liquid nitrogen till the entire tissue... |
76,114 | Resource 7: rEV immunophenotyping | 4 | dx.doi.org/10.17504/protocols.io.e6nvwjo5zlmk/v1 | https://www.protocols.io/view/resource-7-rev-immunophenotyping-cnjsvcne | Vera A. Tang, Sean M Cook, Joanne Lannigan, Jennifer Jones, Joshua A Welsh | TITLE: Resource 7: rEV immunophenotyping
AUTHORS: Vera A. Tang, Sean M Cook, Joanne Lannigan, Jennifer Jones, Joshua A Welsh
[DESCRIPTION]
Flow cytometry (FCM) is a common extracellular particles (EPs), including viruses and extracellular vesicles (EVs), characterization method. Frameworks such as MIFlowCyt-EV exist t... | ["[Sample Preparation] Briefly centrifuge the rEVs 100 x g, 5 min, 4 °C before opening", "[Sample Preparation] In the same 96-well V-bottom plate from , add 10 µL 1:5 rEV solution to wells B1-G3. Add 10 µL DPBS to wells A1-G1. Add 10 µL from the PE working solution tubes to wells B1-G1, add 10 µL from the APC working ... |
null | null | null | dx.doi.org/10.17504/protocols.io.ejwbcpe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is the quick version of the Monarch® DNA Gel Extraction Kit Protocol (NEB #T1020). For the full protocol, please click <a href="https://www.neb.com/protocols/2015/11/23/monarch-dna-gel-extraction-kit-protocol-t1020" target="_blank">here</a>.
[BEFORE_START]
Add 4 volumes of... | [] |
42,303 | Chapter 2: Stabilizing the bird, conducting an initial clinical exam | 4 | null | https://www.protocols.io/view/chapter-2-stabilizing-the-bird-conducting-an-initi-bmi7k4hn | Kerri Wolter | TITLE: Chapter 2: Stabilizing the bird, conducting an initial clinical exam
AUTHORS: Kerri Wolter
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines steps to stabilize a bird after intake and conduction of an initial clinical exam.</div></div>
[STEPS]
?. [Assessing dehydration]
... | ["[Assessing dehydration]\nObserve the bird to assess the state of dehydration.\nIn the long-necked Gyps species, necks are useful in determining the state of dehydration as they have large patches of bare skin which can be used to determine the level of dehydration. Wrinkled skin indicates dehydration, while smooth, p... |
75,854 | A simple and efficient protocol for generating transgenic hairy roots using Agrobacterium rhizogenes | 4 | dx.doi.org/10.17504/protocols.io.261ge3xkjl47/v1 | https://www.protocols.io/view/a-simple-and-efficient-protocol-for-generating-tra-cnbnvame | Shaun Ferguson, Nikolaj B. Abel, Dugald Reid, Lene H. Madsen, Thi-Bich Luu, Kasper R. Andersen, Jens Stougaard, Simona Radutoiu | TITLE: A simple and efficient protocol for generating transgenic hairy roots using Agrobacterium rhizogenes
AUTHORS: Shaun Ferguson, Nikolaj B. Abel, Dugald Reid, Lene H. Madsen, Thi-Bich Luu, Kasper R. Andersen, Jens Stougaard, Simona Radutoiu
[DESCRIPTION]
For decades, Agrobacterium rhizogenes (now Rhizobium rhizoge... | ["[Transformation of chemical competent E. coli ST18] Mix in a 1.5 ml tube:\n 20 µL 5X KCM buffer\n 5 µL Golden Gate cloning mix (from step 1.1 following completion of the program)\n 75 µL ddH2O", "[Transformation of chemical competent E. coli ST18] Incubate for 2 min on ice", "[Transformation of chemical competent E. ... |
53,512 | Optimized protocol for the RNA isolation of laser microdissected formalin-fixed paraffin-embedded uterine scar tissues for RNA expression analyses | 1 | dx.doi.org/10.17504/protocols.io.byhgpt3w | https://www.protocols.io/view/optimized-protocol-for-the-rna-isolation-of-laser-byhgpt3w | Alexander Paping, Clara Basler , Rebecca C. Rancourt, Loreen Ehrlich, Kerstin Melchior, Wolfgang Henrich, Thorsten Braun | TITLE: Optimized protocol for the RNA isolation of laser microdissected formalin-fixed paraffin-embedded uterine scar tissues for RNA expression analyses
AUTHORS: Alexander Paping, Clara Basler , Rebecca C. Rancourt, Loreen Ehrlich, Kerstin Melchior, Wolfgang Henrich, Thorsten Braun
[DESCRIPTION]
Samples for histo... | ["[Step 2: Tissue Processing] Treat surfaces and eqipment with RNase Away to prevent RNA degradation by RNases during tissue preparation.", "[Step 4: Sectioning of Tissue Blocks with Microtome] Before cutting, cool tissue blocks at 4°C for 1 hour to harden the wax and thus allow easier cutting.", "[Step 7: Laser Microd... |
54,936 | Native Protein Analysis on TIMSTOF Pro mass spectrometer | 1 | null | https://www.protocols.io/view/native-protein-analysis-on-timstof-pro-mass-spectr-bzvyp67w | David Roberts | TITLE: Native Protein Analysis on TIMSTOF Pro mass spectrometer
AUTHORS: David Roberts
[DESCRIPTION]
Method described in David Robert et al., https://pubs.acs.org/doi/10.1021/jacs.1c02713
[STEPS]
1. Method for native protein analysis on a TIMSTOF Pro mass spectrometOriginal study by David Robert et al., | ["Method for native protein analysis on a TIMSTOF Pro mass spectrometOriginal study by David Robert et al.,"] |
34,766 | Dissolved silica colorimetric assay using a plate reader (96-well plate) | null | dx.doi.org/10.17504/protocols.io.bd7ni9me | null | Jian Gong | TITLE: Dissolved silica colorimetric assay using a plate reader (96-well plate)
AUTHORS: Jian Gong
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describes the adaption of a silica colorimetric assay originally described in </span><a href="https://epic.awi.de/id/eprint/39262/1/S... | ["At room temperature, in 2 mL microcentrifuge tubes, add rapidly reagent A (molybdate solution) to of sample/standard/blank solutions while using the pipet (dispensing up and down a few times) to help mix the mixture. Let the mixture stand for (to allow silicomolybdate complex to form). At this point, if there is en... |
52,309 | Protocol for sgRNA in vitro transcription and screening for effective SaCas9 RNP complex cleavage assay | 1 | dx.doi.org/10.17504/protocols.io.bxbvpin6 | https://www.protocols.io/view/protocol-for-sgrna-in-vitro-transcription-and-scre-bxbvpin6 | Fatma Gomaa, Zhu-Hong Li, Roberto Docampo, Virginia Edgcomb | TITLE: Protocol for sgRNA in vitro transcription and screening for effective SaCas9 RNP complex cleavage assay
AUTHORS: Fatma Gomaa, Zhu-Hong Li, Roberto Docampo, Virginia Edgcomb
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify"><span>Developing tra... | ["Step 1: PCR amplification of the targeted gene-The targeted gene in our study is the 69 KDa paraflagellar rod protein 2C (PFR-2) from extracted DNA of wild Bodo saltans. The PCR amplification reaction consists of Onetaq® 2x master mix with standard buffer (New England BioLabs) and specific primers that we designed: P... |
61,962 | Titan XL Male Enhancement Achieve Bigger & Harder Erections With This Supplement(Work Or Hoax) | 3 | dx.doi.org/10.17504/protocols.io.e6nvwk8m7vmk/v1 | https://www.protocols.io/view/titan-xl-male-enhancement-achieve-bigger-amp-harde-b8rirv4e | Titan XL Male Enhancement | TITLE: Titan XL Male Enhancement Achieve Bigger & Harder Erections With This Supplement(Work Or Hoax)
AUTHORS: Titan XL Male Enhancement
[DESCRIPTION]
READ ALSO: Does the Titan XL Male Enhancement Work For Everyone? Before you buy, read real customer reviews and testimonials!
[STEPS] | [] |
101,683 | Genome assembly (Nanopore and Illumina reads) | 0 | dx.doi.org/10.17504/protocols.io.kxygxywyol8j/v2 | https://www.protocols.io/view/genome-assembly-nanopore-and-illumina-reads-dfit3ken | Rafael Rodrigues Ferrari, Thiago Mafra Batista | TITLE: Genome assembly (Nanopore and Illumina reads)
AUTHORS: Rafael Rodrigues Ferrari, Thiago Mafra Batista
[DESCRIPTION]
This protocol offers detailed, step-by-step instructions for students and researchers to assemble nuclear genomes using long reads generated by Nanopore technology. Before assembling the genome, w... | ["[SEQUENCING QUALITY CHECK] ****LongQC (https://github.com/yfukasawa/LongQC)****\n\n***Prepare a .pbs file to run the analysis remotely on Sagarana***", "[CROSS-SPECIES CONTAMINATION FILTERIN] ****Magic-BLAST (https://ncbi.github.io/magicblast/)****\n\n***Index the database***\n \n***ONT whole-genome sequencing***\n\n... |
22,370 | BDA Histology | null | dx.doi.org/10.17504/protocols.io.z4af8se | null | Blake Butler | TITLE: BDA Histology
AUTHORS: Blake Butler
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Staining protocol for visualization of BDA 3K.</div><div class = "text-block">Species - Feline</div><div class = "text-block">Tissue Preparation - Perfusion of 4% PAF; Cryoprotected 30% Sucrose; Section thickn... | ["[Preparatory Steps]\nReconstitute the Vectastain ABC solution Prepare 80 mL solution: Physiological Buffer Solution A Solution BThaw 6 x 1mL vials of NGS for later use\n79 ml\n480 µl\n480 µl", "[Histological Reaction]", "[Histological Reaction]\nRinse sections in 0.1 M Physiological Buffer (4x5min)", "[Histological R... |
100,348 | Transfection of HT22 cells with Lipofectamine LTX | 0 | null | https://www.protocols.io/view/transfection-of-ht22-cells-with-lipofectamine-ltx-dd8429yw | Signe Goeke | TITLE: Transfection of HT22 cells with Lipofectamine LTX
AUTHORS: Signe Goeke
[DESCRIPTION]
Transfection of HT22 cells
[STEPS]
SECTION: Day 0
1. Plate HT22 cells in 6 well plate: 250K per well
If you want to perform transfection next day plate 500K.
SECTION: Day 1
2. Check cells --> less than ~60-70% confluent wait... | ["[Day 0] Plate HT22 cells in 6 well plate: 250K per well\nIf you want to perform transfection next day plate 500K.", "[Day 1] Check cells --> less than ~60-70% confluent wait another day", "[Day 3] Dilute the optimized amount of plasmid DNA in 500 μl Opti-MEMI Reduced Serum Medium (no A/A, no FCS). Mix thoroughly.", "... |
null | null | null | dx.doi.org/10.17504/protocols.io.ssqeedw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is a protocol for <em>in vitro</em> transcription of DNA oligos by T7 polymerase from the <a href="http://doudnalab.org/" target="_blank" rel="noopener noreferrer">Doudna Lab</a>. </p>
[BEFORE_START]
<p><strong>Stock solutions: </strong></p>
<p> </p>
<table style="heigh... | [] |
55,006 | Diagnosis of Taenia solium infections based on “mail order” RNA-sequencing of single tapeworm egg isolates from stool samples | 1 | dx.doi.org/10.17504/protocols.io.bzx6p7re | https://www.protocols.io/view/diagnosis-of-taenia-solium-infections-based-on-mai-bzx6p7re | Henrik Sadlowski, Veronika Schmidt, Jonathan Hiss, Christian G. Schneider, Gideon Zulu, Alex Hachangu, Chummy S. Sikasunge, Kabemba E. Mwape, Andrea S. Winkler, Markus Schuelke | TITLE: Diagnosis of Taenia solium infections based on “mail order” RNA-sequencing of single tapeworm egg isolates from stool samples
AUTHORS: Henrik Sadlowski, Veronika Schmidt, Jonathan Hiss, Christian G. Schneider, Gideon Zulu, Alex Hachangu, Chummy S. Sikasunge, Kabemba E. Mwape, Andrea S. Winkler, Markus Schuelke
... | ["[Clinical sample stability, transportation and storage] Store both, the Eppendorf tube with the matrix from the microscope slide and the stool sample at 4°C", "[Routine Diagnostic Workflow] Place 1 gram of a fresh native stool sample into a 15 mL Falcon tube and resuspend it in 10 mL PBS.", "[Routine Diagnostic Workf... |
82,110 | Nuclei Isolation and Immunoprecipitation for 10X Sequencing | 4 | null | https://www.protocols.click/view/nuclei-isolation-and-immunoprecipitation-for-10x-s-cue6wthe | Lakme Caceres | TITLE: Nuclei Isolation and Immunoprecipitation for 10X Sequencing
AUTHORS: Lakme Caceres
[DESCRIPTION]
This protocol is for assessing the MIT AAVs from pooled injections.
[GUIDELINES]
Keep tissue/nuclei on ice as much as possible.
[STEPS]
SECTION: Prepare Fresh Solutions
5. Make 3 mL Homogenization Buffer per samp... | ["[Prepare Fresh Solutions] Make 3 mL Homogenization Buffer per sample by adding 2.895 mL Nuclear Isolation Media (filtered via syringe) to a 5 mL eppendorf. Then add 3 μL 100 mM DTT and 30 μL 10% Triton X-100. Add 15 uL RNAsin and invert to mix. Store on ice.", "[Prepare Stock Solutions] Make 20 mL 10% BSA by combinin... |
30,707 | LEGEND MAX™ Human α-Synuclein ELISA Kit Protocol | null | dx.doi.org/10.17504/protocols.io.98th9wn | null | Sam Li | TITLE: LEGEND MAX™ Human α-Synuclein ELISA Kit Protocol
AUTHORS: Sam Li
[STEPS]
?. [I. Preparation of 1X Wash Buffer]
Label a 1L bottle as “1X Wash Buffer”.
?. [I. Preparation of 1X Wash Buffer]
Dilute 5X Wash Buffer 1:5 using lab grade water* and mix well.*Note: Lab grade filtered water such as injection grade, cell ... | ["[I. Preparation of 1X Wash Buffer]\nLabel a 1L bottle as “1X Wash Buffer”.", "[I. Preparation of 1X Wash Buffer]\nDilute 5X Wash Buffer 1:5 using lab grade water* and mix well.*Note: Lab grade filtered water such as injection grade, cell culture grade, Reverse Osmosis De-Ionization (RODI).", "[II. Preparation of 1X R... |
19,153 | Staining and imaging of mouse submandibular ganglion by α-bungarotoxin and nanosensor | 1 | dx.doi.org/10.17504/protocols.io.wxrffm6 | https://www.protocols.io/view/staining-and-imaging-of-mouse-submandibular-gangli-wxrffm6 | Hongrong Yang, Junfei Xia, James Monaghan, Heather A Clark | TITLE: Staining and imaging of mouse submandibular ganglion by α-bungarotoxin and nanosensor
AUTHORS: Hongrong Yang, Junfei Xia, James Monaghan, Heather A Clark
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes how to label acetylcholine receptors in isolated submandibular gang... | ["[Staining of submandibular ganglion by α-bungarotoxin and nanosensor (formulated by Clark Lab)]\n1. Rinse submandibular ganglion with PBS for 2. Soak submandibular ganglion in for .Alternatively, soak submandibular ganglion in nanosensor solution formulated by Clark Lab for 3. Rinse submandibular ganglion with PBS fo... |
80,656 | SARS-COV-2 Main Protease (Mpro) Fluorescence Dose Response | 1 | null | https://www.protocols.io/view/sars-cov-2-main-protease-mpro-fluorescence-dose-re-cszqwf5w | Haim Barr, Noa Lahav | TITLE: SARS-COV-2 Main Protease (Mpro) Fluorescence Dose Response
AUTHORS: Haim Barr, Noa Lahav
[DESCRIPTION]
This is a functional, biochemical assay used to identify treatments for viral infectious disease that target SARS-COV-2 Main Protease (MPro).
Utilizing a direct enzyme activity measurement method, the experi... | ["[Prepare 384 Well Plate] PRIME Multi-Drop Combi Tube Dispensing Cassette with Assay Buffer by selecting the PRIME button on the Combi Dispenser until the tubes are filled completely.", "[Prepare 384 Well Plate] DISPENSE 10 µL to Columns 1 and 23 of assay plate\nNote: These will represent the inhibitor control column... |
86,193 | Reverse-phase high pH fractionation, using the Pierce kit | 4 | null | https://www.protocols.io/view/reverse-phase-high-ph-fractionation-using-the-pier-cyerxtd6 | Louise Uoselis | TITLE: Reverse-phase high pH fractionation, using the Pierce kit
AUTHORS: Louise Uoselis
[DESCRIPTION]
This protocol uses the Pierce™ High pH Reversed-Phase Peptide Fractionation Kit (Thermo Fisher, Cat# 84868)
[STEPS]
SECTION: Conditioning the columns
1. Remove the white cap on the end of the column and place t... | ["[Conditioning the columns] Remove the white cap on the end of the column and place the column in a 2 mL collection tube", "[Conditioning the columns] Centrifuge at 5000 rcf, 2 min at Room temperature, discard the liquid", "[Conditioning the columns] Remove the screw cap and add 300 µL ACN to the column (replacing the... |
36,762 | Storage and Processing of Tissue for bulk RNA Isolation | null | dx.doi.org/10.17504/protocols.io.bf52jq8e | https://www.protocols.io/view/storage-and-processing-of-tissue-for-bulk-rna-isol-bf52jq8e | Aaron Horning | TITLE: Storage and Processing of Tissue for bulk RNA Isolation
AUTHORS: Aaron Horning
[STEPS]
?. [Storing Tissue for RNA Isolation]
After resection, tissue is immediately flash frozen in 50 ml Falcon tube or 2 ml cryovial tubes by placing tissue into tube then simply dropping filled tube into liquid nitrogen.
?. [Stor... | ["[Storing Tissue for RNA Isolation]\nAfter resection, tissue is immediately flash frozen in 50 ml Falcon tube or 2 ml cryovial tubes by placing tissue into tube then simply dropping filled tube into liquid nitrogen.", "[Storing Tissue for RNA Isolation]\nThe tubes are stored on dry ice or -80C until they can be stored... |
51,779 | Phenol first aid and personal protective equipment | 1 | dx.doi.org/10.17504/protocols.io.bwtbpein | https://www.protocols.io/view/phenol-first-aid-and-personal-protective-equipment-bwtbpein | Roey Angel, Eva Petrova | TITLE: Phenol first aid and personal protective equipment
AUTHORS: Roey Angel, Eva Petrova
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left"><span>Phenol is a common chemical used for nucleic acid extraction. Phenol can be a component in a commercial re... | ["[Instructions Phenol Skin (Dermal) Exposure First Aid]\nRemove all contaminated clothes, including jewelry or any leather items such as watch bands or belts.", "[Instructions Phenol Skin (Dermal) Exposure First Aid]\nPut on safety glasses and Silver Shield® gloves (but don’t put on the gloves if you are treating your... |
21,777 | Microorganisms and culture conditions - Comparative genomics of Staphylococcus aureus associated with subclinical and clinical bovine mastitis (Rocha et al., 2019) | null | dx.doi.org/10.17504/protocols.io.zhrf356 | null | Lis Rocha | TITLE: Microorganisms and culture conditions - Comparative genomics of Staphylococcus aureus associated with subclinical and clinical bovine mastitis (Rocha et al., 2019)
AUTHORS: Lis Rocha
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Many efforts have been made to understand the pathogenes... | ["[Growing and storing conditions]\nThe bacteria used in this study were maintained on BHI agar (Brain Heart Infusion, BHI HiMedia, Mumbai, India) at 37 °C", "[Growing and storing conditions]\nand stored in the long term in BHI containing 20% glycerol."] |
26,481 | Transcription Factor-Mediated Differentiation of Human iPSCs into Neurons | null | dx.doi.org/10.17504/protocols.io.54rg8v6 | null | Michael S. Fernandopulle, Ryan Prestil, Christopher Grunseich, Chao Wang, Li Gan, Michael E. Ward | TITLE: Transcription Factor-Mediated Differentiation of Human iPSCs into Neurons
AUTHORS: Michael S. Fernandopulle, Ryan Prestil, Christopher Grunseich, Chao Wang, Li Gan, Michael E. Ward
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Accurate modeling of human neuronal cell biology has been ... | [] |
55,152 | Multi tissue processing for single cell sequencing of human immune cells | 4 | dx.doi.org/10.17504/protocols.io.bz4qp8vw | https://www.protocols.io/view/multi-tissue-processing-for-single-cell-sequencing-bz4qp8vw | Daniel Rainbow, Sarah Howlett, Lorna Jarvis, Joanne Jones | TITLE: Multi tissue processing for single cell sequencing of human immune cells
AUTHORS: Daniel Rainbow, Sarah Howlett, Lorna Jarvis, Joanne Jones
[DESCRIPTION]
This protocol has been developed for the simultaneous processing of multiple human tissues to extract immune cells for single cell RNA sequencing using the 1... | ["[Tissue to cell suspension - Bone Marrow and Blood] No processing, go straight to ficoll layering.", "[Tissue to cell suspension - Bone Marrow and Blood] Placeon iceuntil other tissues have caught up.", "[Tissue to cell suspension - Lymphoid Tissues (Spleen, Lymph node)] Mash the lymphoid tissue through a filter pl... |
43,325 | Single digested | 1 | dx.doi.org/10.17504/protocols.io.bni5mcg6 | https://www.protocols.io/view/single-digested-bni5mcg6 | Jiaxin Li | TITLE: Single digested
AUTHORS: Jiaxin Li
[STEPS]
?. Add the following reagents to a tube. AB1Total10ul210 x Buffer1ul3Template（500ng）According to different template4Enzyme0.5ul5ddWaterAdd to 10ul
AB1Total10ul210 x Buffer1ul3Template（500ng）According to different template4Enzyme0.5ul5ddWaterAdd to ... | ["Add the following reagents to a tube. AB1Total10ul210 x Buffer1ul3Template（500ng）According to different template4Enzyme0.5ul5ddWaterAdd to 10ul\nAB1Total10ul210 x Buffer1ul3Template（500ng）According to different template4Enzyme0.5ul5ddWaterAdd to 10ul", "Pipette up and down thoroughly.", "Put at 3... |
79,201 | Immunofluorescence microscopy of R1441C or VPS35 D620N MEF cells | 4 | dx.doi.org/10.17504/protocols.io.j8nlkw1n5l5r/v1 | https://www.protocols.io/view/immunofluorescence-microscopy-of-r1441c-or-vps35-d-crj9v4r6 | Chloe A Hecht, Herschel Dhekne, Wondwossen Yeshaw, Suzanne Pfeffer | TITLE: Immunofluorescence microscopy of R1441C or VPS35 D620N MEF cells
AUTHORS: Chloe A Hecht, Herschel Dhekne, Wondwossen Yeshaw, Suzanne Pfeffer
[DESCRIPTION]
We present here a method to culture, fix, permeabilize, and stain R1441C or VPS35 D620N MEF cells to visualize transfected Myc-RILPL1 and endogenous TMEM55... | ["[Culturing, plating, and treating cells] Seed R1441C MEF cells or VPS35 D620N MEF cells at 50-60% confluency in a six well plate in 2 mL of complete DMEM (DMEM containing 10% FBS and 1% penicillin-streptomycin) 24 hours before transfection.", "[Culturing, plating, and treating cells] Transfect with Myc-RILPL1 plasmid... |
47,353 | Staging colonial ascidians | 4 | dx.doi.org/10.17504/protocols.io.bsgznbx6 | https://www.protocols.io/view/staging-colonial-ascidians-bsgznbx6 | Simon Blanchoud, Marta Wawrzyniak | TITLE: Staging colonial ascidians
AUTHORS: Simon Blanchoud, Marta Wawrzyniak
[DESCRIPTION]
This protocol has been successfully used to stage Botrylloides diegensis in our laboratory and was based on the following publication:
Ontology for the Asexual Development and Anatomy of the Colonial Chordate Botryllus schlos... | ["[Staging] Select the slides to be staged.", "[Staging] Clean the colony. See Cleaning colonial ascidians V.2", "[Staging] Observe the organization of the zooids and the systems. Check for signs of takeover:", "[Staging] No signs of active filter-feeding.", "[Staging] Zooids within systems are not properly fused yet."... |
24,408 | Monosynaptic circuit mapping | 1 | dx.doi.org/10.17504/protocols.io.33ygqpw | https://www.protocols.io/view/monosynaptic-circuit-mapping-33ygqpw | Rui Zhang, Heike Muenzberg | TITLE: Monosynaptic circuit mapping
AUTHORS: Rui Zhang, Heike Muenzberg
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Investigate the preganglionic neurons in the intermediolaterol nucleus (IML) that innervate the postganglionic neurons innervating interscapular brown adipose tissue (iBAT) and in... | ["[2nd virus injection]\n2nd virus injection.- After sufficient viral expression (4 weeks) mice received another iBAT injection with the modified rabies virus G-Deleted Rabies-mCherry that lacks glycoprotein gene (commercially available from Salk Institute GT3 Core) and thus cannot be further propagated into upstream n... |
53,824 | Proteomics workflow for APP/Aβ TOMAHAQ analysis in endosomal and lysosomal fractions | 4 | dx.doi.org/10.17504/protocols.io.bys8pwhw | https://www.protocols.io/view/proteomics-workflow-for-app-a-tomahaq-analysis-in-bys8pwhw | Hankum Park, Frances V Hundley, J. Wade Harper | TITLE: Proteomics workflow for APP/Aβ TOMAHAQ analysis in endosomal and lysosomal fractions
AUTHORS: Hankum Park, Frances V Hundley, J. Wade Harper
[DESCRIPTION]
The ability to detect processing of APP to the Ab amyloid peptide is challenging. This protocols describes methods for analysis of Ab "half-tryptic" peptides... | ["[Sample preraration] Prepare all samples (unfiltered PNS, Lyso, and Endo; Amicon-filtered PNS_LMW, Lyso_LMW, and Endo_LMW) as described (dx.doi.org/10.17504/protocols.io.byjfpujn). For full peptide sequences and associated proteomic parameters, see the attached document.", "[Sample preraration] Reduce all samples by... |
null | null | null | dx.doi.org/10.17504/protocols.io.cgutwv | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?. | [] |
35,289 | Pulling Pipettes using the DMZ-Zeitz Universal | null | dx.doi.org/10.17504/protocols.io.bepzjdp6 | null | Allen Institute for Brain Science | TITLE: Pulling Pipettes using the DMZ-Zeitz Universal
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol is used for the manufacture of glass pipettes for patch clamp electrophysiology using the DMZ-Zeitz Universal puller.</div><div class = "text-bloc... | [] |
19,355 | Sectioning Rat Heart | null | dx.doi.org/10.17504/protocols.io.w53fg8n | null | Shaina Robbins, Sean Nieves | TITLE: Sectioning Rat Heart
AUTHORS: Shaina Robbins, Sean Nieves
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is the straightforward procedure we follow when sectioning rat heart.</div></div>
[STEPS]
?. [Sectioning]
1. Take rat heart our of freezer and place into cryostat.2. Set the cryost... | ["[Sectioning]\n1. Take rat heart our of freezer and place into cryostat.2. Set the cryostat to desired tissue thickness and begin the tissue sectioning process3. Collect the tissue section gently onto the slide4. Immediately after tissue sections are collected, place slides into a box containing dry ice until slides ... |
46,725 | Solanum pimpinellifolium seed propagation protocol | 1 | dx.doi.org/10.17504/protocols.io.j8nlk4dexg5r/v1 | https://www.protocols.io/view/solanum-pimpinellifolium-seed-propagation-protocol-brvdm626 | Hayley Sussman, Magdalena M Julkowska | TITLE: Solanum pimpinellifolium seed propagation protocol
AUTHORS: Hayley Sussman, Magdalena M Julkowska
[DESCRIPTION]
This protocol describes S. pimpinellifolium propagation from seed to seed. It describes seed germination, plant care and growth. It also covers pollination, fruit harvesting, seed cleaning and seed... | ["Place 2-4 seeds (more if you know the seeds are old) per genotype in a 1.5 ml tube filled with tap water and stratify at 4C overnight", "If the accession has difficulty germinating, nick the seed coat by lightly slicing the seed coat along its margin with a razor blade, being careful not to cut the embryo.", "Pre-moi... |
84,687 | Single-fill cystometry at varying bladder infusion rates in urethane anesthetized rats | 1 | dx.doi.org/10.17504/protocols.io.n2bvj3xoblk5/v1 | https://www.protocols.io/view/single-fill-cystometry-at-varying-bladder-infusion-cwxpxfmn | Daniel J Jaskowak, Zachary C Danziger | TITLE: Single-fill cystometry at varying bladder infusion rates in urethane anesthetized rats
AUTHORS: Daniel J Jaskowak, Zachary C Danziger
[DESCRIPTION]
Cystometry is a common method to observe the function of the lower urinary tract (LUT) in in vivo animal models where an infusion pump fills the bladder at a set ra... | ["[Animal Preparation] Urethane Anesthesia Protocol", "[Animal Preparation] Suprapubic bladder catheterization", "[Animal Preparation] Anesthetize rat via inhalation of isoflurane", "[Animal Preparation] Weigh Animal", "[Animal Preparation] Use animal weight to determine urethane dosage (1.2 g of Urethane per kg of bod... |
72,002 | Single Cell Isolation from Human Skin Biopsies | 4 | dx.doi.org/10.17504/protocols.io.rm7vzbbm8vx1/v1 | https://www.protocols.io/view/single-cell-isolation-from-human-skin-biopsies-cijaucie | johanng, Maksim Plikus | TITLE: Single Cell Isolation from Human Skin Biopsies
AUTHORS: johanng, Maksim Plikus
[DESCRIPTION]
This protocol describes necessary reagents and step-by-step procedures for processing normal human skin (from skin punch biopsy) for single-cell isolation to be used for scRNA-seq experiments.
[STEPS]
SECTION: Samples
... | ["[Samples] Determine beforehand whether skin epidermis and dermis will be sent for sequencing separately or batched (and if so at what proportion; e.g. all:all or 1:1)\n\nDetermine number of cells targeted (1,000 to 10,000)\nWe generally target 10,000 to increase diversity at the expense of depth\nFor skin samples, ac... |
65,885 | Diaetoxil Germany: Pills Price 2022 | 1 | dx.doi.org/10.17504/protocols.io.dm6gpb6djlzp/v1 | https://www.protocols.io/view/diaetoxil-germany-pills-price-2022-ccj5suq6 | kankcfz | TITLE: Diaetoxil Germany: Pills Price 2022
AUTHORS: kankcfz
[DESCRIPTION]
Diatoxil Reviews: Many people try to lose weight Diaetoxil by following strict diets. You won't see any benefits from strict diets or rigorous exercise plans. To lose fat and get in shape, you will need to work harder. Detoxil, an advanced... | [] |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.