id float64 1.55k 110k ⌀ | title stringlengths 1 256 ⌀ | template_id float64 0 6 ⌀ | doi stringlengths 39 49 ⌀ | url stringlengths 40 92 ⌀ | authors stringlengths 1 933 ⌀ | protocol_text stringlengths 34 1.08M | steps_list stringlengths 2 269k |
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29,674 | Lysozyme-based removal of bacteria from cultures of the marine heterotrophic flagellate Cafeteria roenbergensis | null | dx.doi.org/10.17504/protocols.io.88ihzue | null | Monica Berjon-Otero, Sarah Duponchel, Matthias Fischer | TITLE: Lysozyme-based removal of bacteria from cultures of the marine heterotrophic flagellate Cafeteria roenbergensis
AUTHORS: Monica Berjon-Otero, Sarah Duponchel, Matthias Fischer
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol allows to remove bacteria from cultures of the marine h... | ["[Preparation of Cafeteria roenbergensis culture]\nDetermine the cell density of Cafeteria roenbergensis : stain 10 µL of a Cafeteria culture with 1 µL of Lugol’s acid iodine solution and count the cells on a haemocytometer (Neubauer Chamber)", "[Preparation of Cafeteria roenbergensis culture]\nDilute the Cafeteria cu... |
40,602 | Vezina Lab RNA in situ hybridization on vibratome sections | 1 | null | https://www.protocols.io/view/vezina-lab-rna-in-situ-hybridization-on-vibratome-bjv2kn8e | Chad Vezina | TITLE: Vezina Lab RNA in situ hybridization on vibratome sections
AUTHORS: Chad Vezina
[STEPS]
?. [Prior to starting]
Prep stock solutions, make baskets, make probes, section samples.
?. [Day 1]
Prep baskets: a. close cap of tube, affix sticker to cap and label with probe nameb. to facilitate air movement, heat large ... | ["[Prior to starting]\nPrep stock solutions, make baskets, make probes, section samples.", "[Day 1]\nPrep baskets: a. close cap of tube, affix sticker to cap and label with probe nameb. to facilitate air movement, heat large gauge needle in flame & push through plastic cap to puncture two holes in each basketc. partial... |
99,317 | DNA imaging with CRISPRdelight labeling system | 0 | dx.doi.org/10.17504/protocols.io.3byl49b5jgo5/v1 | https://www.protocols.io/view/dna-imaging-with-crisprdelight-labeling-system-dc8v2zw6 | Liang-Zhong Yang, Ling-Ling Chen | TITLE: DNA imaging with CRISPRdelight labeling system
AUTHORS: Liang-Zhong Yang, Ling-Ling Chen
[DESCRIPTION]
Tracking the dynamics of genomic loci is very important to know genome organization and gene function regulation. However, tools for imaging genomes, especially non-repetitive locus have still been limited. Th... | ["[crRNA designing] Find ATAC-seq data for targeted cell lines, like the ATAC-seq data for HeLa (GEO Accession viewer (nih.gov)). Download the .bw file", "[crRNA designing] Open IGV application, choose the associated genome (GRCh38/hg38), load ATAC-seq .bw file to get the accessibility of each gene or locus.", "[crRNA ... |
101,648 | Post GEM–RT Cleanup and cDNA Amplification | 0 | dx.doi.org/10.17504/protocols.io.bp2l62d3dgqe/v1 | https://www.protocols.io/view/post-gem-rt-cleanup-and-cdna-amplification-dfhq3j5w | Heidi Monroe, Nayra Cardenes, Melanie Königshoff, koenigshoffm, Robert Lafyatis | TITLE: Post GEM–RT Cleanup and cDNA Amplification
AUTHORS: Heidi Monroe, Nayra Cardenes, Melanie Königshoff, koenigshoffm, Robert Lafyatis
[DESCRIPTION]
The Chromium Single Cell Gene Expression Solution upgrades short read sequencers to deliver a scalable microfluidic platform for 3’ digital gene expression by profili... | ["[Dynabeads] Add 125 µL Recovery Agent to each sample at Room temperature. \n\n \n\nThe resulting biphasic mixture contains Recovery Agent/Partitioning Oil (pink) and aqueous phase (clear), with no persisting emulsion (opaque).", "[Dynabeads] Slowly remove and discard 125 µLRecovery Agent/Partitioning Oil (pink) from ... |
28,837 | Golden Gate lvl 0 | null | dx.doi.org/10.17504/protocols.io.8edhta6 | null | Vinca Seiler, René Inckemann | TITLE: Golden Gate lvl 0
AUTHORS: Vinca Seiler, René Inckemann
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Golden Gate reaction protocol for lvl 0</div></div>
[STEPS]
?. [Pipetting scheme for assembly reaction]
of DNA insert ( )
0.5 µl
?. [Pipetting scheme for assembly reaction]
of entry Vector... | ["[Pipetting scheme for assembly reaction]\nof DNA insert ( )\n0.5 µl", "[Pipetting scheme for assembly reaction]\nof entry Vector (15 ng/ μL)\n0.5 µl", "[Pipetting scheme for assembly reaction]\nT4 DNA Ligase buffer (NEB)\n1 µl", "[Pipetting scheme for assembly reaction]\nT4 DNA Ligase (NEB)\n0.5 µl", "[Pipetting sche... |
61,864 | Protein extraction, quantification, and western blot for Bodo saltans | 4 | dx.doi.org/10.17504/protocols.io.5qpvobqodl4o/v1 | https://www.protocols.io/view/protein-extraction-quantification-and-western-blot-b8ngrvbw | Ewa Chrostek, Mastaneh Ahrar, Gregory Dd Hurst | TITLE: Protein extraction, quantification, and western blot for Bodo saltans
AUTHORS: Ewa Chrostek, Mastaneh Ahrar, Gregory Dd Hurst
[DESCRIPTION]
This protocol is used in our Laboratory in Liverpool to work with proteins from Bodo saltans and other kinetoplastids (eg. trypanosomes).
[STEPS]
SECTION: Culture co... | ["[Culture conditions] Bodo saltans was cultured in a cerophyl-based medium enriched with 3.5 mM sodium phosphate dibasic (Na2HPO4)1. Cultures were incubated at 22 °C in T25 tissue culture flasks containing 20 ml of media bacterized with Klebsiella pneumoniae subsp. Pneumoniae (ATCC® 700831).", "[Protein extraction and... |
null | null | null | dx.doi.org/10.17504/protocols.io.mpec5je | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?. | [] |
98,674 | Fecal Output Protocol | 0 | dx.doi.org/10.17504/protocols.io.rm7vzj3j5lx1/v1 | https://www.protocols.io/view/fecal-output-protocol-dcks2uwe | Adam Hamilton, Ian N Krout, Tim Sampson | TITLE: Fecal Output Protocol
AUTHORS: Adam Hamilton, Ian N Krout, Tim Sampson
[DESCRIPTION]
This assay is used to quantify the number of fecal pellets produced over a short period of time, which serves as a measure of colonic motility. Mice are placed into individual clear plastic beakers and the number of fecal pelle... | ["[Prior to Assay] Prepare clean 1 liter (~12cm x 25cm) translucent beakers- sterilize if necessary, with\naluminum foil covers. These should be autoclaved before use if collection of fecal pellets for microbiome analysis is required.", "[Day of Set-up] Bring mice to testing room for at least 60 min prior to assay, to ... |
43,635 | Fungal Extraction from Beetle Galleries | 3 | dx.doi.org/10.17504/protocols.io.bnutmewn | https://www.protocols.io/view/fungal-extraction-from-beetle-galleries-bnutmewn | You Li, Jiri Hulcr | TITLE: Fungal Extraction from Beetle Galleries
AUTHORS: You Li, Jiri Hulcr
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes how to extract fungi from beetle galleries. </div><div class = "text-block"><span>This protocol is part of the Bark Beetle Mycobiome (BBM) Research Coord... | [] |
99,664 | Yeast protoplast fusion | 0 | dx.doi.org/10.17504/protocols.io.5qpvokrxdl4o/v1 | https://www.protocols.io/view/yeast-protoplast-fusion-ddjq24mw | is Sparrow, Ulschan Bathe, Kristen Van Gelder | TITLE: Yeast protoplast fusion
AUTHORS: is Sparrow, Ulschan Bathe, Kristen Van Gelder
[DESCRIPTION]
This protocol was based on the original protocol by Ulschan Bathe and Kristen Van Gelder from the Hanson Lab at UF in 2023.
It details how to fuse 2 yeast protoplasts. It is focused on obtaining an evolution strain wit... | ["[Media and buffers] Make the following solutions ahead of time. They do not need to be sterilized.\n\nUnless specified, all solutions are made in water", "[Media and buffers] CPB (Citrate Phosphate Buffer) solution\n\nSolution A\n0.1 Molarity (M) Citric Acid (dihydrate)\n\nSolution B\n0.2 Molarity (M)Na2HPO4 \n\nComb... |
98,845 | Crystallization of MERS-CoV Mpro | 1 | dx.doi.org/10.17504/protocols.io.ewov194x7lr2/v1 | https://www.protocols.io/view/crystallization-of-mers-cov-mpro-dcr52v86 | blake.h.balcomb, Peter Marples, Lizbé Koekemoer, Daren Fearon, Charlie Tomlinson | TITLE: Crystallization of MERS-CoV Mpro
AUTHORS: blake.h.balcomb, Peter Marples, Lizbé Koekemoer, Daren Fearon, Charlie Tomlinson
[DESCRIPTION]
The COVID-19 pandemic has highlighted the need to identify novel therapeutic interventions and strategies for pandemic preparedness. Other than Severe Acute Respiratory Syndr... | ["[Crystallization experiment] Protein and buffer requirements:\n32 µL17 mg/mL \n3.36 mL \n14.4 µL seeds, dilution 1:1000", "[Crystallization experiment] Dispense 35 µL into SwissCI 3 lens plate reservoir wells using a 100 µl multi-channel pipette.\nDispense 150 nL17 mg/mL to each lens using the SPT mosquito.\nDi... |
null | null | null | dx.doi.org/10.17504/protocols.io.iepcbdn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Melting and alloying operations were performed in a low carbon steel crucible in an inert ultra-high purity argon environment, preventing the oxidation reactions of molten Mg. High purity Mg (99.97%) was heated to 710°C for 10 minutes until the slug was completely melted. Eac... | [] |
94,643 | The Burden of Unlawful Use of Opioid and Epidemiological Characteristics in Africa: A Scoping Review protocol | 1 | dx.doi.org/10.17504/protocols.io.4r3l22kq3l1y/v1 | https://www.protocols.io/view/the-burden-of-unlawful-use-of-opioid-and-epidemiol-c8ntzven | Hope onohuean, Frasia OOSTHUIZEN | TITLE: The Burden of Unlawful Use of Opioid and Epidemiological Characteristics in Africa: A Scoping Review protocol
AUTHORS: Hope onohuean, Frasia OOSTHUIZEN
[DESCRIPTION]
Abstract
Introduction:
There is an ongoing global upsurge of opioid misuse/ abuse, fatal overdose and other related disorders and may be heating ... | ["The Burden of Unlawful Use of Opioid and Epidemiological Characteristics in Africa: A Scoping Review protocol", "Materials and Method\n\nThe procedure suggested by the Joanna Briggs Institute (JBI) [51,57] and the step outline in Fig. 1 will be used for this scoping review.", "Search strategy\nThe keyword relevant to... |
68,282 | Experimental protocol for data collection of Datura spp. | 1 | dx.doi.org/10.17504/protocols.io.6qpvr6b7ovmk/v1 | https://www.protocols.io/view/experimental-protocol-for-data-collection-of-datur-cew2tfge | Eunice Kariñho-Betancourt | TITLE: Experimental protocol for data collection of Datura spp.
AUTHORS: Eunice Kariñho-Betancourt
[DESCRIPTION]
Experimental design employed to obtain biological materials for RNA seq analysis. We collected leaf tissue to examine gene family evolution of four Datura species.
[STEPS]
SECTION: Germination
1. Plants... | ["[Germination] Plants were started from seed between March-April, growing under 16:8, L:D cycle with 25:20°C (L:D) in the glasshouse of the Institute of Ecology, National Autonomous University of Mexico. Experimental plants were obtained by sowing seeds of maternal families (natural progenies). Once the true leaves ap... |
4,711 | Isolation of total DNA from Synechocystis sp. PCC 6803 | null | dx.doi.org/10.17504/protocols.io.gufbwtn | null | Anna Behle | TITLE: Isolation of total DNA from Synechocystis sp. PCC 6803
AUTHORS: Anna Behle
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol can be used for extraction of total genomic DNA from </span><span style = "font-style:italic;">Synechocystis</span><span> sp. PCC 6803.</span></div></... | ["[Culturing]\nGrow 50 mL Synechocystis culture to the end of the logarithmic phase (OD750 ≈ 1.0).Centrifuge at 4800 rpm and 4°C for 7 minutes. Remove supernatant.", "[Wash steps:]\nResuspend cells in 10 mL TE-buffer, centrifuge at 4800 rpm and 4°C for 7 minutes. Remove supernatant.", "Repeat washing step. Resuspend pe... |
48,761 | Contractile response to chemogenetic activation or inhibition of cholinergic or nitrergic myenteric neurons of the mouse colon | 4 | dx.doi.org/10.17504/protocols.io.btuznnx6 | https://www.protocols.io/view/contractile-response-to-chemogenetic-activation-or-btuznnx6 | Thomas Gould, Dante Heredia | TITLE: Contractile response to chemogenetic activation or inhibition of cholinergic or nitrergic myenteric neurons of the mouse colon
AUTHORS: Thomas Gould, Dante Heredia
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for measuring colonic migrating motor complexes in response to chemogene... | ["A ventral midline incision is made and the whole colon is carefully excised into a Sylgard-lined dissection dish containing oxygenated Krebs-ringer solution.", "The colon is then drawn over a 1.5-mm diameter fire-polished capillary tube, whose length exceeds that of the colon.", "An artificial pellet is mounted to th... |
null | null | null | dx.doi.org/10.17504/protocols.io.hrmb546 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is used to clarify the process of total DNA extration for our R. crenulata genome.</p>
[STEPS]
?.
?.
?.
?.
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?.
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?.
?.
?.
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?.
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?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
57,655 | iNDI PiggyBac-TO-hNGN2 transfection protocol Version 1 | 4 | dx.doi.org/10.17504/protocols.io.q26g744b1gwz/v1 | https://www.protocols.io/view/indi-piggybac-to-hngn2-transfection-protocol-versi-b4ixqufn | Mark Cookson, michael.ward , Erika Lara Flores | TITLE: iNDI PiggyBac-TO-hNGN2 transfection protocol Version 1
AUTHORS: Mark Cookson, michael.ward , Erika Lara Flores
[DESCRIPTION]
PiggyBac Method for hNGN2 transfection
Transfection protocol
Use of CEPT: Nature Methods 18, 528-541, 2021
[STEPS]
SECTION: Transfection protocol
1. Observe KOLF2.1 iPSCs under a phas... | ["[Transfection protocol] Observe KOLF2.1 iPSCs under a phase contrast microscope to assess confluency and presence of cells debris. Dish should be dissociated at ~70% to 90% confluency.\n\nCoat a well of 6 well plate to be used for transfection with 1 mL of Matrigel solution, tilting to ensure coverage of entire surfa... |
91,547 | Top agar: 0.7% w/v LB(Miller) agar | 4 | dx.doi.org/10.17504/protocols.io.eq2lyj2oelx9/v1 | https://www.protocols.io/view/top-agar-0-7-w-v-lb-miller-agar-c5m3y48n | HANNAH ZHU | TITLE: Top agar: 0.7% w/v LB(Miller) agar
AUTHORS: HANNAH ZHU
[DESCRIPTION]
how to make Top agar for plaque assay experiment
[STEPS]
SECTION: Top agar: 0.7% w/v LB(Miller) agar
1. Dissolve following components in 200 mL MilliQ water
SECTION: Top agar: 0.7% w/v LB(Miller) agar
2. Autoclave at 121 °C for 15 min
S... | ["[Top agar: 0.7% w/v LB(Miller) agar] Dissolve following components in 200 mL MilliQ water", "[Top agar: 0.7% w/v LB(Miller) agar] Autoclave at 121 °C for 15 min", "[Top agar: 0.7% w/v LB(Miller) agar] Store in oven (> 50 °C)"] |
101,685 | SARS-CoV-2 nsp3 macrodomain expression and purification protocol for crystallization | 1 | dx.doi.org/10.17504/protocols.io.dm6gpz9xplzp/v1 | https://www.protocols.io/view/sars-cov-2-nsp3-macrodomain-expression-and-purific-dfiv3ke6 | Korvus Wang, michael fairhead, Eleanor Williams | TITLE: SARS-CoV-2 nsp3 macrodomain expression and purification protocol for crystallization
AUTHORS: Korvus Wang, michael fairhead, Eleanor Williams
[DESCRIPTION]
This protocol details the expression and purification of SARS-CoV-2 nsp3 macrodomain crystallization construct bearing a N-terminal His-tag at small scale (... | ["[Plasmid Transformation] CVNSP3mac1 N-terminal His-tagged construct was inoculated from its BL21(DE3)-RR glycerol stock.", "[Protein expression] When the OD600 reaches approximately 1.4, reduce temperature to 18 °C and incubate for an additional hour. Add 0.4 millimolar (mM) IPTG. Lower shaker speed to . Incubate ... |
82,315 | Primary cortical neuron isolation and culture | 3 | dx.doi.org/10.17504/protocols.io.n2bvj8k7wgk5/v1 | https://www.protocols.io/view/primary-cortical-neuron-isolation-and-culture-cumjwu4n | Shiyi Wang | TITLE: Primary cortical neuron isolation and culture
AUTHORS: Shiyi Wang
[DESCRIPTION]
Primary cortical neuron isolation and culture
[STEPS] | [] |
29,013 | Spectral Recording of Gene Expression History by Fluorescent Timer Protein | null | dx.doi.org/10.17504/protocols.io.8jvhun6 | null | Anna R. Tröscher, Barbara Werner, Nadia Kaouane, Wulf Haubensak | TITLE: Spectral Recording of Gene Expression History by Fluorescent Timer Protein
AUTHORS: Anna R. Tröscher, Barbara Werner, Nadia Kaouane, Wulf Haubensak
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Monitoring spatio-temporal patterns of gene expression by fluorescent proteins requires lon... | ["[Cell Culture and Transfection]\nGrow HeLa cells overnight in standard incubator conditions (, 5 % CO2) on 6-well plate in standard medium (DMEM + 10 % FCS + 1 % Pen/Strep + 1 % L-Glutamine) to a confluency of about 80 %.\n37.5 °C", "[Cell Culture and Transfection]\nTransfection with the TransIT-LT1 transfection reag... |
86,203 | Mitophagy induction using Oligomycin/Antimycin A | 1 | dx.doi.org/10.17504/protocols.io.14egn32yql5d/v1 | https://www.protocols.io/view/mitophagy-induction-using-oligomycin-antimycin-a-cye3xtgn | Louise Uoselis | TITLE: Mitophagy induction using Oligomycin/Antimycin A
AUTHORS: Louise Uoselis
[DESCRIPTION]
Mitophagy induction in HeLa cells using Oligomycin/Antimycin A.
[STEPS]
SECTION: Day 1
1. Seed cells, aiming for a confluency of 80-90% at the time of treatment the next day.
SECTION: Day 2
2. Feed cells for 60 min in an ap... | ["[Day 1] Seed cells, aiming for a confluency of 80-90% at the time of treatment the next day.", "[Day 2] Feed cells for 60 min in an appropriate volume of standard growth media.", "[Day 2] To start the treatment, replace the media in each well with standard growth media that contains 10 micromolar (µM) Oligomycin, 4 m... |
103,024 | vGlutI-pH imaging experiment analysis | 0 | dx.doi.org/10.17504/protocols.io.bp2l6275zgqe/v1 | https://www.protocols.io/view/vgluti-ph-imaging-experiment-analysis-dguq3wvw | Alexandros C Kokotos, Tim Ryan | TITLE: vGlutI-pH imaging experiment analysis
AUTHORS: Alexandros C Kokotos, Tim Ryan
[DESCRIPTION]
This protocol describes how to analyze imaging experiments using vGlutI-pH from primary neurons.
[STEPS]
SECTION: vGlutI-pH image analysis
1. Open the image stacks to by analyzed with ImageJ by drag and drop.
SECTION: v... | ["[vGlutI-pH image analysis] Open the image stacks to by analyzed with ImageJ by drag and drop.", "[vGlutI-pH image analysis] Identify nerve terminals that responded to electrical stimulation, by observing their fluorescence increasing in sync with the timing of the action potential train.", "[vGlutI-pH image analysis]... |
48,691 | U-251MG Spheroid Generation Using Hanging Drop Method Protocol | 1 | dx.doi.org/10.17504/protocols.io.btstnnen | https://www.protocols.io/view/u-251mg-spheroid-generation-using-hanging-drop-met-btstnnen | Lara Carroll, Brijesh Tiwari, James Curtin, Janith Wanigasekara | TITLE: U-251MG Spheroid Generation Using Hanging Drop Method Protocol
AUTHORS: Lara Carroll, Brijesh Tiwari, James Curtin, Janith Wanigasekara
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The use of 3D cell culture has been a major step in developing cellular models that can mimic physiological t... | ["U-251 MG cells are cultured in 100mm or 150mm dishes until reaching approximately 80-90% confluency and washed with 1X PBS solution.", "Dissociate U-251 MG cells by incubating for 4 minutes at 37°C with Trypsin-EDTA solution (0.25%w/v) and inactivate the trypsin by re-suspending in the full growth medium pre-warmed i... |
43,740 | IPMC SARS-CoV-2 One-Step qPCR Protocol on BIOMARK | 1 | dx.doi.org/10.17504/protocols.io.bnx4mfqw | https://www.protocols.io/view/ipmc-sars-cov-2-one-step-qpcr-protocol-on-biomark-bnx4mfqw | Julien Fassy, Caroline Lacoux, David Rouquié, Jean Louis Nahon, Pascal Barbry, Laure-Emmanuelle Zaragosi, Bernard Mari | TITLE: IPMC SARS-CoV-2 One-Step qPCR Protocol on BIOMARK
AUTHORS: Julien Fassy, Caroline Lacoux, David Rouquié, Jean Louis Nahon, Pascal Barbry, Laure-Emmanuelle Zaragosi, Bernard Mari
[DESCRIPTION]
<div class = "text-blocks"><div style = "text-align :; float : ;"><img style = "" src = "https://s3.amazonaws.com/protoc... | ["[Sample processing upon arrival]\nTo be performed in the appropriate biosafety conditions (BSL2 laboratory)Transfer the totality of the transport medium into a 2 mL cryotube and stored at -80°C in a hermetically sealed body bag.If performing RNA extraction prior to RT-PCR, proceed to steps 2 to 8.If performing RT-PCR... |
45,829 | C-SOP-901: Preparation of DNA Isolates for Domestic and Overseas Transport | 4 | null | https://www.protocols.io/view/c-sop-901-preparation-of-dna-isolates-for-domestic-bqzdmx26 | Mihir Kekre | TITLE: C-SOP-901: Preparation of DNA Isolates for Domestic and Overseas Transport
AUTHORS: Mihir Kekre
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify">DNA eluted in nuclease-free water or low-TE solution is stable enough to be shipped at ambient te... | ["[Before Starting]\nEnsure that all of the materials listed are available before you begin aliquoting and packaging DNA samples for transport. Contact your local courier provider to obtain consignment containers.\nOptional project (or site) specific items include sample manifests and unique plate IDs (barcodes) that e... |
34,124 | SSLib v2.0 (Gansauge et al. 2017) | 1 | dx.doi.org/10.17504/protocols.io.bp2l6n395gqe/v1 | https://www.protocols.io/view/sslib-v2-0-gansauge-et-al-2017-bdjki4kw | Alicia Grealy | TITLE: SSLib v2.0 (Gansauge et al. 2017)
AUTHORS: Alicia Grealy
[DESCRIPTION]
This bench protocol is based on the work of Gansauge and Meyer (2013) and Gansauge et al (2017), for preparing shotgun libraries from single-stranded DNA, typically for ancient and degraded DNA.
[BEFORE_START]
Note that you will need to a... | ["[Preparation] \"Suit up\" in this order: hair net, nitrile gloves, facemask, coveralls, gumboots, booties, second pair of gloves.", "[Preparation] Ensure ice is available. Thaw reagents on ice as needed. Keep enzymes on ice at all times. Do not vortex enzymes to mix but mix by flicking the tube gently. Pulse centrifu... |
80,506 | Transformation of Arabidopsis Thaliana Protocol | 4 | dx.doi.org/10.17504/protocols.io.261ge3b7wl47/v1 | https://www.protocols.io/view/transformation-of-arabidopsis-thaliana-protocol-csu2weye | creative-biogene | TITLE: Transformation of Arabidopsis Thaliana Protocol
AUTHORS: creative-biogene
[DESCRIPTION]
In this experiment, the flower immersion method was used to transfer the target gene into Arabidopsis thaliana using Agrobacterium mediated.
[STEPS]
SECTION: Experiment Summary
1. In this experiment, the flower immersion me... | ["[Experiment Summary] In this experiment, the flower immersion method was used to transfer the target gene into Arabidopsis thaliana using Agrobacterium mediated.", "[Main Reagents] YEB liquid medium, LB medium, 0.1 M CaCl2, 0.05 M MgSO4, flower immersion buffer (0.5XMS, 5% sucrose, 0. 03% Silwet L-77), Rif, Kan.", "[... |
11,509 | EVALUATION OF TWO COMMUNITY-BASED MENTAL HEALTH INTERVENTIONS FOR AFRO-COLOMBIANS VICTIMS OF VIOLENCE | null | dx.doi.org/10.17504/protocols.io.pgvdjw6 | null | Francisco J. Bonilla-Escobar, Andrés Fandiño-Losada, Diana M. Martínez-Buitrago, Julián Santaella-Tenorio, Daniel Tobón-García, Edgar J. Muñoz-Morales, María I. Gutiérrez-Martínez., Judith K. Bass, Laura K. Murray, Paul Bolton, Shannon Dorsey | TITLE: EVALUATION OF TWO COMMUNITY-BASED MENTAL HEALTH INTERVENTIONS FOR AFRO-COLOMBIANS VICTIMS OF VIOLENCE
AUTHORS: Francisco J. Bonilla-Escobar, Andrés Fandiño-Losada, Diana M. Martínez-Buitrago, Julián Santaella-Tenorio, Daniel Tobón-García, Edgar J. Muñoz-Morales, María I. Gutiérrez-Martínez., Judith K. Bass, Laur... | ["[Phase 1: Qualitative study of the effects of violence.]\nCISALVA Institute staff conducted a pre-intervention qualitative research on the effects of violence on individuals and communities, which included a structured process to identify problems affecting the survivors of violence and their families; JHU staff acco... |
87,167 | Hemlock Sample Analysis for Headspace Terpenes, Liquid Analysis, and Sugars | 1 | dx.doi.org/10.17504/protocols.io.4r3l22qqxl1y/v1 | https://www.protocols.io/view/hemlock-sample-analysis-for-headspace-terpenes-liq-czc7x2zn | Hamid Rashidi Nodeh, Roland Kersten, Timothy Cernak, Niharica Suri Kannan | TITLE: Hemlock Sample Analysis for Headspace Terpenes, Liquid Analysis, and Sugars
AUTHORS: Hamid Rashidi Nodeh, Roland Kersten, Timothy Cernak, Niharica Suri Kannan
[DESCRIPTION]
This protocol was developed by the Cernak Lab at the University of Michigan to analyze the terpene concentration and content of various spe... | ["[Sample Preparation] Pick off the leaves of the hemlock stem using your fingers and gloved hands.", "[Sample Preparation] Weigh approximately 0.1 g of each sample of hemlock leaves and put the sample into a headspace vial compatible with the autosampler of your GC-MS.", "[Sample Preparation] Add 1000 microliters (1mL... |
53,323 | Lysosome immunopurification (LysoIP) protocol for subcellular metabolite profiling | 1 | dx.doi.org/10.17504/protocols.io.bybjpskn | https://www.protocols.io/view/lysosome-immunopurification-lysoip-protocol-for-su-bybjpskn | Wentao Dong, Nouf Laqtom, Monther Abu-Remaileh | TITLE: Lysosome immunopurification (LysoIP) protocol for subcellular metabolite profiling
AUTHORS: Wentao Dong, Nouf Laqtom, Monther Abu-Remaileh
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Lysosomes function as metabolic hub in the cell by degrading and recycling biomolecules. Despite its criti... | ["[Preparation of homogenizers and sample tubes]\nWash 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 usin... |
104,423 | DAB Immunohistochemistry (IHC) Staining for Stereological Analysis | 0 | dx.doi.org/10.17504/protocols.io.eq2lyw1jmvx9/v1 | https://www.protocols.io/view/dab-immunohistochemistry-ihc-staining-for-stereolo-dh8f39tn | Nicolas Giguère, louis-eric.trudeau Trudeau | TITLE: DAB Immunohistochemistry (IHC) Staining for Stereological Analysis
AUTHORS: Nicolas Giguère, louis-eric.trudeau Trudeau
[DESCRIPTION]
DAB (3,3'-diaminobenzidine) is oxidized in the presence of peroxidase and hydrogen peroxide resulting in the deposition of a brown, alcohol-insoluble precipitate at the site of e... | ["[Procedures] Basic protocol for a peroxidase reaction using free floating sections. \n\n \n\nWash in 0.01 Molarity (M) PBS for 10 min (use cell strainers for all washing steps).", "[Procedures] Wash in 0.01 Molarity (M) PBS containing 0.9% H202 for 10 min (90 µL in 10 mL PBS 0.01M) (Blocking of endogenous peroxidase)... |
30,259 | Single Nuclei RNA Sequencing of Tendon Tissue - small tissue biopsies | null | dx.doi.org/10.17504/protocols.io.9sth6en | null | Adam Cribbs, Jolet Mimpen | TITLE: Single Nuclei RNA Sequencing of Tendon Tissue - small tissue biopsies
AUTHORS: Adam Cribbs, Jolet Mimpen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used the the Tendon Seed Network to extract nuclei from small tissue biopsies of Tendon tissue. For larger pieces opf tissu... | ["[Preparation]\nPre-cool all solutions and equipment (including centrifuge (+4oC), homogeniser (+4oC), dissection Tray (-20oC), scissors (-20oC) and scalpel/razor blade (-20oC)`).\nAll steps in the protocol should be performed on ice or in a cold room (4oC) to minimise RNA degradation", "[Large tissue digestion]\nChop... |
85,739 | Image analysis of plasma membrane contacts | 1 | dx.doi.org/10.17504/protocols.io.n2bvj364plk5/v1 | https://www.protocols.io/view/image-analysis-of-plasma-membrane-contacts-cxyjxpun | Chase Amos, Pietro De Camilli | TITLE: Image analysis of plasma membrane contacts
AUTHORS: Chase Amos, Pietro De Camilli
[DESCRIPTION]
This protocol details the image analysis of overexpressed VPS13A^Halo at plasma membrane contact sites in K562 cells.
[STEPS]
SECTION: Image analysis of plasma membrane contacts
1. Using the image analysis program F... | ["[Image analysis of plasma membrane contacts] Using the image analysis program FIJI, split the channels of the image containing the mitochondria (TMRE stain or overexpressed mito-BFP) and overexpressed VPS13A^Halo.", "[Image analysis of plasma membrane contacts] Threshold the mitochondria channel to include the mitoch... |
38,310 | Exiting the Lab (Covid-19 Shutdown Re-Entry, Srivastava Lab) | 1 | dx.doi.org/10.17504/protocols.io.bhnej5be | https://www.protocols.io/view/exiting-the-lab-covid-19-shutdown-re-entry-srivast-bhnej5be | Srivastava Lab | TITLE: Exiting the Lab (Covid-19 Shutdown Re-Entry, Srivastava Lab)
AUTHORS: Srivastava Lab
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Disclaimer: </span><span>The SOP presented here has been designed by the Srivastava Lab at Harvard University and is being sha... | ["If it is your “high touch” day, wipe all handles (incubator, freezer, door, etc) with 70% ethanol", "Wipe bench piettes, etc with 70% ethanol", "Wipe phone/other objects in workspace (laptops, etc) with 70% ethanol", "Wash hands at the sink", "Turn on water", "Wash hands", "Dry hands with paper towel", "Turn off fauc... |
46,325 | Punch incision versus elliptical excision for epidermal inclusion cysts Systematic review and meta-analysis_protocol | 1 | dx.doi.org/10.17504/protocols.io.brgvm3w6 | https://www.protocols.io/view/punch-incision-versus-elliptical-excision-for-epid-brgvm3w6 | Kengo Mukuda, Jun Watanabe | TITLE: Punch incision versus elliptical excision for epidermal inclusion cysts Systematic review and meta-analysis_protocol
AUTHORS: Kengo Mukuda, Jun Watanabe
[STEPS] | [] |
71,641 | Family Quality of Life during Covid-19 Pandemic | 1 | dx.doi.org/10.17504/protocols.io.3byl4jbz2lo5/v1 | https://www.protocols.io/view/family-quality-of-life-during-covid-19-pandemic-ch7zt9p6 | Tery Setiawan, Ria Wardani, ellen.theresia | TITLE: Family Quality of Life during Covid-19 Pandemic
AUTHORS: Tery Setiawan, Ria Wardani, ellen.theresia
[DESCRIPTION]
This protocol describes survey procedures taken in our investigation on the relation between Covid-19 economic impact and parental stress on one hand, and the family quality of life on the other. We... | ["[Research objective] Research objective and purpose\n\nThis study was conducted to investigate the relation between Covid-19 economic impact and parental stress during the pandemic on one hand, and family quality of life (FQOL) in Indonesia on the other. Specifically, we aimed to answer to what extent Covid-19 econom... |
59,030 | NCBI submission protocol for SARS-CoV-2 wastewater data: SRA, BioSample, and BioProject | 1 | dx.doi.org/10.17504/protocols.io.b5vwq67e | https://www.protocols.io/view/ncbi-submission-protocol-for-sars-cov-2-wastewater-b5vwq67e | Ruth Timme, Maria Balkey | TITLE: NCBI submission protocol for SARS-CoV-2 wastewater data: SRA, BioSample, and BioProject
AUTHORS: Ruth Timme, Maria Balkey
[DESCRIPTION]
PURPOSE:
This method was developed at the FDA’s Center for Food Safety and Applied Nutrition for GenomeTrakr’s pandemic response project, monitoring SARS-CoV-2 variants in ... | ["["Ingredients" to have in place before starting your submissions] Set up a new NCBI submission environment for your lab\n1.1: Create an NCBI user account\n1.2: Set up an NCBI submission user group for your lab\n1.3: Bookmark the link to your Submission Portal\n1.4. Identify or establish new BioProjects (det... |
45,900 | Protocol: A Scoping Review of the Biomechanics of the Autogenous Bone Graft Harvest from Proximal Tibia | 3 | dx.doi.org/10.17504/protocols.io.bq3kmykw | https://www.protocols.io/view/protocol-a-scoping-review-of-the-biomechanics-of-t-bq3kmykw | pooyan.eshkevari , riley.sumner , Robert Leon Flint, David Seligson | TITLE: Protocol: A Scoping Review of the Biomechanics of the Autogenous Bone Graft Harvest from Proximal Tibia
AUTHORS: pooyan.eshkevari , riley.sumner , Robert Leon Flint, David Seligson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Background:</span><span> The m... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.qrfdv3n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>RNA from matched FFPE, PFPE and cryo preserved rat tissues, stored for up to nine years at 22°C, 4°C, -20°C or -80°C, examined for integrity and usability in quantitative RT-PCR</p>
[STEPS]
?. | [] |
78,313 | Coleta de dados actigráficos - ActTrust | 2 | dx.doi.org/10.17504/protocols.io.4r3l241x4g1y/v4 | https://www.protocols.io/view/coleta-de-dados-actigr-ficos-acttrust-cqqhvvt6 | Daniel Vartanian | TITLE: Coleta de dados actigráficos - ActTrust
AUTHORS: Daniel Vartanian
[DESCRIPTION]
Esta coleção reúne os protocolos do processo de coleta de dados actigráficos do Grupo Interdisciplinar de Pesquisa em Ritmos Biológicos (GIPERBIO). Esses protocolos foram desenhados para os actígrafos provenientes da companhia Condo... | [] |
39,074 | Parallel Selection Protocol for the Maize ATLAS Project | 1 | dx.doi.org/10.17504/protocols.io.bieakbae | https://www.protocols.io/view/parallel-selection-protocol-for-the-maize-atlas-pr-bieakbae | The Maize ATLAS Project | TITLE: Parallel Selection Protocol for the Maize ATLAS Project
AUTHORS: The Maize ATLAS Project
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">As part of the Maize ATLAS project on adaptation and diversification along a latitudinal axis of the USA, this protocol describes procedures used for a par... | ["[Selection Procedure]\nMetadata: If a seed treatment is applied, record the product and dosage used.", "[Selection Procedure]\nSeed: Use a balanced bulk of 15,000 kernels for the experimental plot. The unbalanced bulk of ~3,000 kernels can be used for border rows, if needed (step 3).", "[Selection Procedure]\nPlantin... |
40,609 | Vezina Lab RT-PCR Protocol | 1 | null | https://www.protocols.io/view/vezina-lab-rt-pcr-protocol-bjv9kn96 | Chad Vezina | TITLE: Vezina Lab RT-PCR Protocol
AUTHORS: Chad Vezina
[STEPS]
?. [RNA Isolation]
Obtain Supplies:TinfoilMicrofuge-sized Pestles and Molecular Grinding Resin (G-Biosciences, Cat. No. 786-138PR).The Pestles can be washed, autoclaved, and reused.RNase-Free microfuge tubesBeta-mercaptoethanol70% Ethanol55C incubatorLiqui... | ["[RNA Isolation]\nObtain Supplies:TinfoilMicrofuge-sized Pestles and Molecular Grinding Resin (G-Biosciences, Cat. No. 786-138PR).The Pestles can be washed, autoclaved, and reused.RNase-Free microfuge tubesBeta-mercaptoethanol70% Ethanol55C incubatorLiquid NitrogenTube decapperIllustra RNAspin Mini kit (GE Healthcare ... |
78,064 | Iso-Seq mapping to L1HS/PA2 consensus sequence | 5 | dx.doi.org/10.17504/protocols.io.5qpvorw7dv4o/v1 | https://www.protocols.io/view/iso-seq-mapping-to-l1hs-pa2-consensus-sequence-cqgqvtvw | Raquel Garza | TITLE: Iso-Seq mapping to L1HS/PA2 consensus sequence
AUTHORS: Raquel Garza
[DESCRIPTION]
The protocol describes the steps to map HiFi reads to a consensus sequence and retrieve density plots
[STEPS]
SECTION: Mapping to L1HS/PA2 consensus sequence
1. A L1HS and L1PA2 consensus sequence was used to create a minimap2 (... | ["[Mapping to L1HS/PA2 consensus sequence] A L1HS and L1PA2 consensus sequence was used to create a minimap2 (version 2.24; RRID:SCR_018550) index\n \nto map FLNC reads (HiFi reads).", "[Mapping to L1HS/PA2 consensus sequence] The density of mapped reads was visualized in the Integrative Genomics Viewer (IgV) (version ... |
72,238 | Protocol 7: Picking colonies of transformed Spizellomyces punctatus (Sp) | 4 | dx.doi.org/10.17504/protocols.io.e6nvwjjewlmk/v1 | https://www.protocols.io/view/protocol-7-picking-colonies-of-transformed-spizell-cisnuede | Sarah M Prostak, Edgar M Medina, Erik Kalinka, Lillian Fritz-Laylin | TITLE: Protocol 7: Picking colonies of transformed Spizellomyces punctatus (Sp)
AUTHORS: Sarah M Prostak, Edgar M Medina, Erik Kalinka, Lillian Fritz-Laylin
[DESCRIPTION]
If transformation was successful, antibiotic-resistant Spizellomyces colonies should appear after 4-6 days of growth on selection media. These colon... | ["[Steps] Divide one K1 plate with selection antimicrobials into four sections using a marker on the bottom of the plate.", "[Steps] Aliquot 50 µL of DS into one microcentrifuge tube per colony to be picked.", "[Steps] Using an 18G needle, gently lift the colony of interest from the agar.", "[Steps] Resuspend the colon... |
89,562 | extract dropped plasmid DNA from filter paper | 4 | dx.doi.org/10.17504/protocols.io.e6nvwd887lmk/v1 | https://www.protocols.io/view/extract-dropped-plasmid-dna-from-filter-paper-c3p2ymqe | Joseph Shenekji | TITLE: extract dropped plasmid DNA from filter paper
AUTHORS: Joseph Shenekji
[DESCRIPTION]
this is a short yet effective protocol to extract plasmid DNA on filter paper, this protocol could benefit plasmid production labs and companies and also receiving researchers or universities from underdeveloped countries.
[B... | ["[extraction of DNA from filter paper] locate the dropped plasmid on filter paper, it is usually circled with a marker or a pencil, it is preferable to take a photo and look at the texture if it looks \"powdery\" then you have a high concentration, if it looks flat then you have a low concentration and need additional... |
62,991 | Liberty CBD Gummies | 3 | dx.doi.org/10.17504/protocols.io.4r3l2oy9pv1y/v1 | https://www.protocols.io/view/liberty-cbd-gummies-b9rpr55n | H Douglas Morris | TITLE: Liberty CBD Gummies
AUTHORS: H Douglas Morris
[DESCRIPTION]
Thus, prepare to carry on with your life liberated from that multitude of inconveniences! Now is the ideal time to break free the normal way, so go attempt CBD!
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ki9cuh6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div title="Page 55">
<div>
<div>
<p>Thrombus formation was measured by the viscoelastic test: ROTEM (Tem International GmbH c/o Dutch Affiliate, Tilburg, The Netherlands). Standard assays were used according to the manufac- turer’s recommendations: EXTEM (ref.: 503-05, Tem Inte... | [] |
40,751 | transmissive blood test | 4 | dx.doi.org/10.17504/protocols.io.bj2pkqdn | https://www.protocols.io/view/transmissive-blood-test-bj2pkqdn | mbloore , marcello.manfredi | TITLE: transmissive blood test
AUTHORS: mbloore , marcello.manfredi
[STEPS]
?. Collect blood with finger prick.
[2 drops]
0 Room temperature
?. Place blood in cuvette well, either directly or from a micro pipette. This image shows the same protocol being followed using human milk.
?. Slide cuvette window over well. T... | ["Collect blood with finger prick.\n[2 drops]\n0 Room temperature", "Place blood in cuvette well, either directly or from a micro pipette. This image shows the same protocol being followed using human milk.", "Slide cuvette window over well. This image shows the same protocol being followed using human milk.", "Place c... |
77,877 | How to make Tol2 mRNA | 4 | dx.doi.org/10.17504/protocols.io.8epv5jo94l1b/v1 | https://www.protocols.io/view/how-to-make-tol2-mrna-cqavvse6 | FishFloorUCL | TITLE: How to make Tol2 mRNA
AUTHORS: FishFloorUCL
[DESCRIPTION]
These are instructions to make highly concentrated (> 1000 ng/µL) Tol2 mRNA. Note, the in-vitro transcription kit (mMESSAGE mMACHINE) is not cheap. 5–6 reactions like the protocol suggests come to ~ 100–120£, so please be thrifty with it.
[STEPS]
SECTIO... | ["[Linearise the Tol2 plasmid] Find the Tol2 plasmid from the Wilson lab freezer. It is #1151 and is labelled Tol2.\n\nThe concentration (measured on Qubit) is ~ 690 ng/µL (as of the Eppendorf in 2022).\n\nThaw it.", "[Linearise the Tol2 plasmid] We linearise the plasmid using the restriction enzyme NotI HiFi.\n\nOn ic... |
null | null | null | dx.doi.org/10.17504/protocols.io.cp6vrd | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.rf3d3qn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The understanding of genome characteristics for a given new species, i.e., genome size and heterozygosity, facilitates customizing a specific sequencing and assembling strategy. Thus, the genome size was estimated using four independence methods, i.e., a script of KmerSpectru... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.p5sdq6e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is a multiplex PCR-SSP for amplification of the follow SNPs of CR1 gene:</p>
<p>rs3849266;</p>
<p>rs2274567;</p>
<p>rs4844610;</p>
<p>rs12034383.</p>
[BEFORE_START]
<p>1- Wear clean gloves;<br />2- Clean pipettes and stand with hypochlorite and 70% alcohol;<br />3- Defr... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.h43b8yn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?. | [] |
80,662 | Recording Whale Watching Boat and Humpback Whale Collisions | 4 | dx.doi.org/10.17504/protocols.io.e6nvwjrpwlmk/v1 | https://www.protocols.io/view/recording-whale-watching-boat-and-humpback-whale-c-cszwwf7e | Laura Barragan | TITLE: Recording Whale Watching Boat and Humpback Whale Collisions
AUTHORS: Laura Barragan
[DESCRIPTION]
The purpose of this research protocol is to record collisions caused by whale watching boat tours. We make use of remotely operated water vehicles to collect video footage of whale watching tours and analyze the fo... | ["[Remotely Operated Underwater Vehicle Set Up and Deployment] Drive ship to 300 feet distance from whale watching tour site", "[Observation Methods] For 14 hours that ROV is underwater, monitor video footage carefully", "[Closing Steps]", "[Remotely Operated Underwater Vehicle Set Up and Deployment] Equip the ROV with... |
45,593 | Microbiome and eDNA sampling of water using Sterivex filters | 1 | dx.doi.org/10.17504/protocols.io.ewov1494kvr2/v1 | https://www.protocols.io/view/microbiome-and-edna-sampling-of-water-using-steriv-bqrzmv76 | Daniel S Read | TITLE: Microbiome and eDNA sampling of water using Sterivex filters
AUTHORS: Daniel S Read
[DESCRIPTION]
Protocol for field based sampling of bacterial biomass or environmental DNA (eDNA) using Sterivex filters and syringes.
[STEPS]
1. Open sampling pack and put gloves on.
2. Take the 60 mL syringe and Sterivex ... | ["Open sampling pack and put gloves on.", "Take the 60 mL syringe and Sterivex filter out of the packaging.", "Fill the syringe with 60 mL of water to be sampled (either directly from the water source or collected in a clean sampling container that has been thoroughly rinsed with water from the sampling site).", "Conne... |
17,632 | Online microscopy and histology resources | null | dx.doi.org/10.17504/protocols.io.vf8e3rw | null | Zbigniew Mikulski | TITLE: Online microscopy and histology resources
AUTHORS: Zbigniew Mikulski
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">There is a wealth of microscopy-related information online. This document lists the ones we know and like. Click on the document tab to see the list!</div><div class = "text-bl... | ["Microscopy theory and practice:iBiology Microscopy Coursehttps://www.ibiology.org/ibioeducation/taking-courses/ibiology-microscopy-course.htmlFourier transformation explained by 3Blue1Brownhttps://www.youtube.com/watch?v=spUNpyF58BYVendor websites with lots of information about microscopyhttps://www.microscopyu.com/h... |
null | null | null | dx.doi.org/10.17504/protocols.io.dpx5pm | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is a detailed outline of the extinction dilution method from: <br /><br />Nagasaki, K., and G. Bratbak. 2010. Isolation of viruses infecting photosynthetic and nonphotosynthetic protists, p. 92–101. In S. W. Wilhelm, M. G. Weinbauer, and C. A. Suttle [eds.], Manual of Aquat... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.cxfxjm | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Experiment was conducted to determine the stage at which mutant embryos arrest their development. All Drosophila melanogaster lines were crossed to balancers with a YFP marker for unambiguous identification of mutant and non-mutant embryos. Embryos were collected on apple juice ... | [] |
20,449 | Splitting 96 Well Plates for gDNA Extraction and Freezing Down | null | dx.doi.org/10.17504/protocols.io.x79frr6 | null | Celeste Karch, Rita Martinez, Jacob Marsh | TITLE: Splitting 96 Well Plates for gDNA Extraction and Freezing Down
AUTHORS: Celeste Karch, Rita Martinez, Jacob Marsh
[STEPS]
?. Aspirate media from original plate.
?. Wash with PBS and aspirate.
200 µl
?. Add of 0.05% Trypsin.
25 µl
?. Incubate at for
?. Tap to lift cells from plate.
?. Check under microscope to... | ["Aspirate media from original plate.", "Wash with PBS and aspirate.\n200 µl", "Add of 0.05% Trypsin.\n25 µl", "Incubate at for", "Tap to lift cells from plate.", "Check under microscope to ensure that cells have detached from plate.", "Add mTesR1 to plate and tap to mix.\n45 µl", "Transfer to a 96 well PCR plate, ... |
98,546 | Hafting tests on tanged blanks | 0 | dx.doi.org/10.17504/protocols.io.x54v92jmml3e/v1 | https://www.protocols.io/view/hafting-tests-on-tanged-blanks-dcgs2twe | Nassim Zejly, Bonnie Wright, Fanny Olivier, Narciso Domingos Sabao | TITLE: Hafting tests on tanged blanks
AUTHORS: Nassim Zejly, Bonnie Wright, Fanny Olivier, Narciso Domingos Sabao
[DESCRIPTION]
By the end of the Middle Pleistocene and the beginning of the Late Pleistocene (around 150,000 - 130,000 years ago), the Middle Stone Age in North Africa witnessed the emergence of tang techn... | ["[1) Animal resin preparation : here is the followed recipe] Purify the water by boiling it, then let it cool down.", "[2) Gelatine tests : 4 different test were made to find out which is best for the fake carcass] 1st test\n450ml of water for 50g of gelatine : success.", "[4) Knapping] Production of (convergent) blan... |
64,670 | ONT Post-PCR Pooling & Purification for Fungal Barcoding | 4 | dx.doi.org/10.17504/protocols.io.kxygxz1yzv8j/v2 | https://www.protocols.io/view/ont-post-pcr-pooling-amp-purification-for-fungal-b-cbd6si9e | Stephen Douglas Russell, Stephen Douglas Russell | TITLE: ONT Post-PCR Pooling & Purification for Fungal Barcoding
AUTHORS: Stephen Douglas Russell, Stephen Douglas Russell
[DESCRIPTION]
Overview: The goals of this protocol are to pool your PCR product into a single 1.5 mL tube and to purify that product using magnetic beads.
Time required: ~45 minutes... | ["[Preparation] Bring magnetic beads to room temp. (Should be stored in the fridge)", "[Preparation] Heat a 1.5uL tube of molecular water to 55 °C in the heat block. ~1000uL should be sufficient in the tube. This step is optional but is helpful if a heat block is available.", "[Preparation] Create a fresh batch of 80% ... |
108,677 | Human Pancreas Procurement and Processing of Prodo Laboratories | 0 | dx.doi.org/10.17504/protocols.io.8epv5r8kjg1b/v1 | https://www.protocols.io/view/human-pancreas-procurement-and-processing-of-prodo-dndd5a26 | Giray Eryilmaz | TITLE: Human Pancreas Procurement and Processing of Prodo Laboratories
AUTHORS: Giray Eryilmaz
[DESCRIPTION]
Human pancreas procurement and processing as described in Advances in Human Islet Processing: Manufacturing Steps to Achieve Predictable Islet Outcomes from Research Pancreases
David W. Scharp, Jayagowri Arulmo... | ["[Human Pancreas Procurement and Processing of Prodo Laboratories] Refer to this publication:\nAdvances in Human Islet Processing: Manufacturing Steps to Achieve Predictable Islet Outcomes from Research Pancreases\nDavid W. Scharp, Jayagowri Arulmoli, Kelly Morgan, Hannah Sunshine, Ergeng Hao\nReceived: October 15, 20... |
7,766 | 4% PFA for fixation | null | dx.doi.org/10.17504/protocols.io.jtwcnpe | null | Martin Thomas Jahn | TITLE: 4% PFA for fixation
AUTHORS: Martin Thomas Jahn
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Fixative for FISH and other applications</div></div>
[STEPS]
?. pour 2 g of paraformaldehyde (PFA) powder in 50 ml phosphate buffered
saline (PBS; 130 mM NaCl, 10 mM Na 2 HPO 4 /NaH 2 PO 4 , pH 7... | ["pour 2 g of paraformaldehyde (PFA) powder in 50 ml phosphate buffered \nsaline (PBS; 130 mM NaCl, 10 mM Na 2 HPO 4 /NaH 2 PO 4 , pH 7.4)\nuse mask be careful with PFA\nadjust to amount actually required", "check pH and adjust to pH 7.0", "heat to approx. 60° C (must not boil!), until suspension is clear (approx. 1/2 ... |
85,635 | The feasibility, acceptability and efficacy of an app-based intervention (the coping camp) in reducing stress among chinese school adolescents: protocol of a cluster randomised controlled tria | 1 | dx.doi.org/10.17504/protocols.io.n92ldmz69l5b/v1 | https://www.protocols.io/view/the-feasibility-acceptability-and-efficacy-of-an-a-cxvbxn2n | xiaoyun.zhou, sisira.edirippulige, sisira.edirippulige, matthew.bambling | TITLE: The feasibility, acceptability and efficacy of an app-based intervention (the coping camp) in reducing stress among chinese school adolescents: protocol of a cluster randomised controlled tria
AUTHORS: xiaoyun.zhou, sisira.edirippulige, sisira.edirippulige, matthew.bambling
[DESCRIPTION]
Background: Regardless ... | ["[Background] Stress refers to “the condition or feeling that arises when individuals perceive that the demands of a situation exceed their personal, psychological, or social resources” (1). Adolescence is a period known to be particularly sensitive to stress (2). In China, stress affects a significant portion of adol... |
46,238 | Differences in supraspinatus occupation ratio betweenthe symptomatic, the contralateral asymptomatic shoulder and control subjects: A cross-sectional study. | 1 | null | https://www.protocols.io/view/differences-in-supraspinatus-occupation-ratio-betw-brd6m29e | snl | TITLE: Differences in supraspinatus occupation ratio betweenthe symptomatic, the contralateral asymptomatic shoulder and control subjects: A cross-sectional study.
AUTHORS: snl
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify"><span style = "font-we... | [] |
55,020 | Running the Titan_Illumina_PE Workflow on Terra.bio | 5 | dx.doi.org/10.17504/protocols.io.bzykp7uw | https://www.protocols.io/view/running-the-titan-illumina-pe-workflow-on-terra-bi-bzykp7uw | Jill V Hagey, Kevin Libuit, Frank J Ambrosio, Technical Outreach and Assistance for States Team | TITLE: Running the Titan_Illumina_PE Workflow on Terra.bio
AUTHORS: Jill V Hagey, Kevin Libuit, Frank J Ambrosio, Technical Outreach and Assistance for States Team
[DESCRIPTION]
The Titan_Illumina_PE workflow is a part of the Public Health Viral Genomics Titan series for SARS-CoV-2 genomic characterization. Titan_Il... | ["[Running the Titan Illumina PE Workflow] To run the Titan workflow, click on the 'Workflows' panel in the newly created workspace. It should bring you to the following page. if you do not see the Titan_Illumina_PE workflow in your workspace, please see our video on importing a workflow to Terra.bio: https://youtu.be/... |
62,948 | P1 20/05 | 1 | null | https://www.protocols.io/view/p1-20-05-b9qcr5sw | Maria Gul, katarina | TITLE: P1 20/05
AUTHORS: Maria Gul, katarina
[DESCRIPTION]
qa
[STEPS]
1. test
Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Nam libero tempore, cum soluta nobis est eligendi optio cumque nihil impedit quo minus id quod maxime placeat facere po... | ["test \n\nLorem ipsum dolor sit amet, consectetuer adipiscing elit. Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Nam libero tempore, cum soluta nobis est eligendi optio cumque nihil impedit quo minus id quod maxime placeat facere possimus, omnis voluptas assumenda est, omnis dolor repellendus. Morbi imper... |
70,910 | ATP/NADH-enzyme coupled ATPase assay | 1 | dx.doi.org/10.17504/protocols.io.6qpvr4do2gmk/v1 | https://www.protocols.io/view/atp-nadh-enzyme-coupled-atpase-assay-chg6t3ze | Jialin Chen, Marijke De Jaeger, Nathalie Jacobs, Peter Vangheluwe | TITLE: ATP/NADH-enzyme coupled ATPase assay
AUTHORS: Jialin Chen, Marijke De Jaeger, Nathalie Jacobs, Peter Vangheluwe
[DESCRIPTION]
ATP/NADH-enzyme coupled ATPase assay to determine activation of purified ATPase protein via kinetic absorbance measurement.
[STEPS]
1. Purify the ATPase protein, flash freeze in liquid... | ["Purify the ATPase protein, flash freeze in liquid N2 and store at -80 °C until use.", "Mix the 384-well microplate for 15 s prior kinetic measurement in an absorbance plate reader, set at 25 °C.", "Measure absorbance at 340 nm, at 25 °C for30 min to 60 min. This results in at least 10 data points in the linear phas... |
41,751 | Boston Biopharma CareStart™ Rapid Diagnostic Antigen Test | 4 | dx.doi.org/10.17504/protocols.io.bkzxkx7n | https://www.protocols.io/view/boston-biopharma-carestart-rapid-diagnostic-antige-bkzxkx7n | tclark , Ahmad Hashem, Jun Yong Ha, Charlie Mize | TITLE: Boston Biopharma CareStart™ Rapid Diagnostic Antigen Test
AUTHORS: tclark , Ahmad Hashem, Jun Yong Ha, Charlie Mize
[STEPS]
?. [Temperature Equilibrium]
Allow test devices, reagents, specimens, and/or controls to equilibrate to room temperature (15~30°C) prior to testing
0 Room temperature
?. [Nasopharyngeal Sw... | ["[Temperature Equilibrium]\nAllow test devices, reagents, specimens, and/or controls to equilibrate to room temperature (15~30°C) prior to testing\n0 Room temperature", "[Nasopharyngeal Swab Specimen Collection]\nRemove a nasopharyngeal swab from the pouch.\nUse only provided or recommended nasopharyngeal swab for spe... |
100,336 | Immunohistochemical staining of wholemount major pelvic ganglia (MPG) for analysis of myelinated bladder afferents | 4 | dx.doi.org/10.17504/protocols.io.yxmvme3nbg3p/v1 | https://www.protocols.io/view/immunohistochemical-staining-of-wholemount-major-p-dd8q29vw | Janet R Keast, Peregrine B Osborne, Nicole Wiedmann | TITLE: Immunohistochemical staining of wholemount major pelvic ganglia (MPG) for analysis of myelinated bladder afferents
AUTHORS: Janet R Keast, Peregrine B Osborne, Nicole Wiedmann
[DESCRIPTION]
This protocol describes immunohistochemical procedures applied to wholemount major pelvic ganglia (MPG) for the visualizat... | ["[Immunohistochemistry] Wash whole MPGs in phosphate buffer (PB; 0.1M; pH 7.2) (3 x 30 min)", "[Immunohistochemistry] Incubate sections in blocking solution (PB; 10% horse serum; and 0.5% Triton-X) at room temperature for 2 h", "[Immunohistochemistry] Incubate sections in appropriate dilutions of primary antibodies (o... |
29,150 | Mowiol mounting media | null | dx.doi.org/10.17504/protocols.io.8p6hvre | null | Michael Economo | TITLE: Mowiol mounting media
AUTHORS: Michael Economo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This makes a low cost mounting media that preserves many fluorescent dyes very well. It is a non-hardening media.</div><div class = "text-block">This protocol first published in Cold Spring Harbor ... | ["1.Mix glycerol and Mowiol; dissolve with frequent agitation for 1 h at room temperature.", "2.Add H2O. Stir for 1 h at room temperature.", "3.Add Tris-Cl. Incubate for 2 h at 50°C with occasional stirring (e.g., for 2 min every 20 min).", "4.Centrifuge at 5000g for 15 min.", "5.Store 3-mL aliquots of the supernatant ... |
46,232 | BEAST v1.X tutorial: Mammalian timetree | 4 | dx.doi.org/10.17504/protocols.io.brdym27w | https://www.protocols.io/view/beast-v1-x-tutorial-mammalian-timetree-brdym27w | kawaoso | TITLE: BEAST v1.X tutorial: Mammalian timetree
AUTHORS: kawaoso
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify">A Bayesian inference (BI) tree is constructed using the software BEAST v.1X (Bayesian Evolutionary Analysis Sampling Trees; Suchard et ... | ["General flow\n\t\t\t\t\t\t\t .justify:after {\n\t\t\t\t\t\t\t content: \"\";\n\t\t\t\t\t\t\t display:inline-block;\n\t\t\t\t\t\t\t width: 100%;\n\t\t\t\t\t\t\t }\n\t\t\t\t\t\t\tA Bayesian inference (BI) tree is constructed using the software BEAST v.1X (Bayesian Evolutionary Analysis Sampling Trees; Suchar... |
93,034 | Validating Responsiveness of AAV-DIO-hM3Dq-DREADD | 1 | dx.doi.org/10.17504/protocols.io.6qpvr3yrpvmk/v1 | https://www.protocols.io/view/validating-responsiveness-of-aav-dio-hm3dq-dreadd-c64izgue | Katerina Rademacher, Ken Nakamura | TITLE: Validating Responsiveness of AAV-DIO-hM3Dq-DREADD
AUTHORS: Katerina Rademacher, Ken Nakamura
[DESCRIPTION]
To confirm responsiveness of AAV-DIO-hM3Dq-DREADD in DATIRESCre mice. Activation of DREADD receptors in dopamine neurons with CNO should induce a robust increase in locomotion.
[STEPS]
SECTION: Preparatio... | ["[Preparation] Mice should be at least two-weeks post-surgery.", "[Preparation] Habituate mice to wireless running wheels in individually-housed cages.", "[Preparation] See Victoria Vance, Katerina Rademacher, Ken Nakamura 2023. Behavior Tracking with Running Wheels. protocols.io https://protocols.io/view/behavior-tra... |
null | null | null | dx.doi.org/10.17504/protocols.io.ezsbf6e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is collection of BioLegend protocols for p<span data-sheets-value="{"1":2,"2":"Polarization of Mouse CD4+ Cells"}" data-sheets-userformat="{"2":897,"3":[null,0],"10":0,"11":4,"12":0}">olariza... | [] |
41,870 | FloodLAMP Inactivation Protocol v3.1 | 4 | dx.doi.org/10.17504/protocols.io.bk5nky5e | https://www.protocols.io/view/floodlamp-inactivation-protocol-v3-1-bk5nky5e | Randy True | TITLE: FloodLAMP Inactivation Protocol v3.1
AUTHORS: Randy True
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The inactivation protocol uses a chemical plus heat to break open cells (including virus, if present) and preserve the RNA. The inactivation can be done outside a lab setting, at the... | ["[Sample Preparation]\nFor dry nasal swabs add 2.5mL 1xPBS, soak swabs for 2minutes, remove and discard swabs properly", "[Inactivation]\nSpray all closed tubes with 70% ethanol", "[Inactivation]\nVortex the 100x Inactivation Solution within five minutes of use", "[Inactivation]\nAdd 100x Inactivation Solution to coll... |
null | null | null | dx.doi.org/10.17504/protocols.io.rnzd5f6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Premature ovarian failure (POF) is a refractory disease; one of the most important goals of treatment is to improve fertility. In this study, umbilical cord mesenchymal stem cells on a collagen scaffold (collagen/UC-MSCs) transplanted into the ovaries of POF mice preserved ov... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.hswb6fe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is the protocol to be used in the determination of total protein in brain tissue by the Pierce BCA method. BSA (Bovine Serum Albumin) is used as the standard and samples are prepared by sonification in 1% (w/v) SDS.</p>
<p><strong> </strong></p>
[GUIDELINES]
<p align="L... | [] |
67,394 | https://www.facebook.com/TotalKetoGummies/ | 3 | dx.doi.org/10.17504/protocols.io.x54v9y6emg3e/v1 | https://www.protocols.io/view/https-www-facebook-com-totalketogummies-cd3as8ie | sdfkmnge | TITLE: https://www.facebook.com/TotalKetoGummies/
AUTHORS: sdfkmnge
[DESCRIPTION]
https://www.facebook.com/TotalKetoGummies/
[STEPS] | [] |
78,166 | COREQ (COnsolidated criteria for REporting Qualitative research) Checklist | 1 | dx.doi.org/10.17504/protocols.io.5qpvorwdzv4o/v1 | https://www.protocols.io/view/coreq-consolidated-criteria-for-reporting-qualitat-cqjwvupe | pdgalindo, Juan Jesus Torres-Gordillo, Javier Rodríguez-Santero | TITLE: COREQ (COnsolidated criteria for REporting Qualitative research) Checklist
AUTHORS: pdgalindo, Juan Jesus Torres-Gordillo, Javier Rodríguez-Santero
[DESCRIPTION]
COREQ (COnsolidated criteria for REporting Qualitative research) Checklist, associated with article Parent-school-community relationship: A comparativ... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.frcbm2w | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
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null | null | null | dx.doi.org/10.17504/protocols.io.r7cd9iw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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null | null | null | dx.doi.org/10.17504/protocols.io.mn4c5gw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol can be used :</p>
<ul>
<li>to isolate novel cultures from natural samples</li>
<li>to isolate novel cultures from enriched samples</li>
<li>to purify existing cultures and remove contaminants</li>
<li>to obtain clonal cultures from a unialgal strain</li>
</ul>
<... | [] |
31,927 | High-Throughput Beta-glucuronidase (GUS) assay for Phaeodactylum tricornutum | null | dx.doi.org/10.17504/protocols.io.bbexijfn | null | Erin Garza, Vincent Bielinski | TITLE: High-Throughput Beta-glucuronidase (GUS) assay for Phaeodactylum tricornutum
AUTHORS: Erin Garza, Vincent Bielinski
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>A high-throughput method for measuring β-glucuronidase (GUS) activity in the diatom </span><span style = "font-style:italic... | ["[Centrifuge]\nTransfer 250 μl of each P. tricornutum culture to a 96-well plate and centrifuge at 3000 x g for 10 min. Discard supernatant.", "[Lyse]\nTo lyse the cells, add 150 µl bacterial protein extraction reagent (B-PER, ThermoFisher) to each well and mix by pipetting.", "[Centrifuge]\nCentrifuge plate for 10 mi... |
null | null | null | dx.doi.org/10.17504/protocols.io.c6czav | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
Note: complete run takes about 5 hours, most of which does not require your direct attention.
[STEPS]
?.
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36,636 | Cutting FFPE Sections for Imaging Mass Cytometry | null | dx.doi.org/10.17504/protocols.io.bfz4jp8w | https://www.protocols.io/view/cutting-ffpe-sections-for-imaging-mass-cytometry-bfz4jp8w | Marda Jorgensen, Michelle Daniel | TITLE: Cutting FFPE Sections for Imaging Mass Cytometry
AUTHORS: Marda Jorgensen, Michelle Daniel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">FFPE block are cut into thin sections. </div></div>
[STEPS]
?. [Cooling the FFPE Block]
1.1 Cool down the FFPE block a. Switch on the cooling devi... | ["[Cooling the FFPE Block]\n1.1 Cool down the FFPE block a. Switch on the cooling device and set it to 4°C b. Put the FFPE block into the cooling device.", "[Switching on the microtome]\n1.2 Prepare the microtome a. Connect the cooling unit in the back with the cable and switch it on at thefront. ... |
90,277 | Isolating Fusarium from plant material | 4 | null | https://www.protocols.io/view/isolating-fusarium-from-plant-material-c4edyta6 | Jenna Moore | TITLE: Isolating Fusarium from plant material
AUTHORS: Jenna Moore
[DESCRIPTION]
Protocol for isolating Fusarium (SDS) from soybean plants. A fresh sample is best. Incubating the root sample at 5-10 degrees Celsius encourages sporulation. Samples should be processes no later than 10 days after receiving for best isola... | ["[Isolating Fusarium from plant material] After initial observations are recorded, use pruners to cut and discard aboveground plant material (keep material from soil-line down).", "[Isolating Fusarium from plant material] Wash root system.", "[Isolating Fusarium from plant material] Observe growth after 7200 min days ... |
null | null | null | dx.doi.org/10.17504/protocols.io.pdmdi46 | null | null | TITLE: No Title
AUTHORS:
[BEFORE_START]
<p>Please wear at least the minimum required personal protective equipment.</p>
<p>Ensure that all necessary kit components are available as well as user-supplied consumables.</p>
<p>Clean all working surfaces, pipettes, and pens to remove DNA contamination.</p>
[GUIDELINES]
<... | [] |
29,425 | 3XFlag-pATn5 Protein Purification and MEDS-loading (5x scale, 2L volume) | null | dx.doi.org/10.17504/protocols.io.8yrhxv6 | null | Terri Bryson, Steven Henikoff | TITLE: 3XFlag-pATn5 Protein Purification and MEDS-loading (5x scale, 2L volume)
AUTHORS: Terri Bryson, Steven Henikoff
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Here we describe the method used to purify and load pATn5 for CUT&Tag, </span><a href="https://www.protocols.io/view/bench-top-... | ["[Day 1]\nStreak E. coli glycerol stock containing pTXB1-rbs_3XFlag-pATn5-FL plasmid onto an LB-Amp100 plate, incubate at\n37 °C", "[Day 2]\nSelect a single colony and make a patch plate for later, use within 1 week.", "[Day 3: Culture and Induce]\nEarly morning, with a sterile toothpick swipe through a bacterial pat... |
23,815 | Biometric measurements of Santa Inês meat sheep reared on Brachiaria brizantha pastures in Northeast Brazil | null | dx.doi.org/10.17504/protocols.io.3hfgj3n | null | Joelma Souza | TITLE: Biometric measurements of Santa Inês meat sheep reared on Brachiaria brizantha pastures in Northeast Brazil
AUTHORS: Joelma Souza
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ddb22m | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Purpose: to measure the infective titer (number of infective elements per mL) of from 1-5 viral samples in a quick and efficient manner.
[GUIDELINES]
<strong>(Modified from R. Fu, K. Frois-Moniz & M. Sullivan protocol)<br /><br />Materials: (assuming 2 replicates per viral ... | [] |
60,998 | Insect cell expression of wildtype and variant LRRK1full length protein | 4 | dx.doi.org/10.17504/protocols.io.rm7vzy6z2lx1/v1 | https://www.protocols.io/view/insect-cell-expression-of-wildtype-and-variant-lrr-b7ternje | Deep Chatterjee, Sebastian Mathea, Stefan Knapp | TITLE: Insect cell expression of wildtype and variant LRRK1full length protein
AUTHORS: Deep Chatterjee, Sebastian Mathea, Stefan Knapp
[DESCRIPTION]
The production of LRRK1 protein and its variants was performed using bacculovirus expression system. The method includes three major steps cloning, large scale expressi... | ["[Cloning & mutagenesis] Amplify the DNA coding for the human LRRK1 residues 20 to 2015 (OHu72031 from Genscript) using the forward primer TACTTCCAATCCGCTGTGTGTCCAGAACGTGCCATGG and the reverse primer TATCCACCTTTACTGTCACCTTCTCTTGCGAGTGCAAGCCTCC. PCR was performed by applying a touch-down protocol.\n\nThermal cyclin... |
48,592 | HIV-1 Genotyping and Drug Resistance by Next Generation Sequencing | 4 | dx.doi.org/10.17504/protocols.io.btpqnmmw | https://www.protocols.io/view/hiv-1-genotyping-and-drug-resistance-by-next-gener-btpqnmmw | Brenna McGruder Rawson, Matthew Schimenti, Jason Blanton | TITLE: HIV-1 Genotyping and Drug Resistance by Next Generation Sequencing
AUTHORS: Brenna McGruder Rawson, Matthew Schimenti, Jason Blanton
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The Florida Department of Health's Bureau of Public Health Laboratories in Jacksonville is developing a p... | ["[RNA Extraction]\nExtract RNA using the Qiagen Viral RNA Mini Kit (DSP or RUO)", "[Reverse-Transcription and Amplification]\nMaster Mix with Invitrogen SuperScript III One-Step RT-PCR System with Platinum Taq High Fidelity DNA Polymerase (cat 12574-035)\n[2x Reaction Mix]\n[HIV2252-F]\n[HIV5073-R]\n[SuperScript III P... |
95,985 | Untargeted Metabolomics & Targeted Lipidomics | 0 | dx.doi.org/10.17504/protocols.io.dm6gp37qdvzp/v1 | https://www.protocols.io/view/untargeted-metabolomics-amp-targeted-lipidomics-c9yrz7v6 | Joanna Bi | TITLE: Untargeted Metabolomics & Targeted Lipidomics
AUTHORS: Joanna Bi
[DESCRIPTION]
Protocol for untargeted metabolomics & targeted lipidomics.
[STEPS]
SECTION: Steps
1. Sample Preparation: Roughly 30 mg of flash frozen tissue were homogenized in 500 µl ice-cold methanol by bead beating (MP bioscience cat# 6913... | ["[Steps] Sample Preparation: Roughly 30 mg of flash frozen tissue were homogenized in 500 µl ice-cold methanol by bead beating (MP bioscience cat# 6913-100, Solon, OH) at 4°C (2 x 45 s). Metabolites and complex lipids were extracted using a biphasic separation with cold methyl tert-butyl ether (MTBE), methanol and wat... |
95,308 | Orexin A Analysis in Plasma | 4 | dx.doi.org/10.17504/protocols.io.kxygx365zg8j/v1 | https://www.protocols.io/view/orexin-a-analysis-in-plasma-c9bkz2kw | daniel.dautan daniel, Per Svenningsson, Wojciech Paslawski | TITLE: Orexin A Analysis in Plasma
AUTHORS: daniel.dautan daniel, Per Svenningsson, Wojciech Paslawski
[DESCRIPTION]
Mouse plasma analysis of Orexin A using Novus Biologicals ELISA kit (NBP2-80231).
[STEPS]
1. Centrifuge samples for 15 min at 1000×g at 4 °C.
2. Add50 µL of standards' working solutions and samples t... | ["Centrifuge samples for 15 min at 1000×g at 4 °C.", "Add50 µL of standards' working solutions and samples to 96-well plate in duplicates.", "Add 50 µL of biotinylated detection antibody working solution to each well. Cover with the provided plate sealer and incubate for 45 min at 37 °C.", "Decant the solution from eac... |
null | null | null | dx.doi.org/10.17504/protocols.io.fuhbnt6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Yeast is a well-characterized genome due to its small size and historical significance in genetics. The website http://yeastgenome.org/ is a dedicated resource for yeast genomics.</p>
<p> </p>
<p>For this exercise, I want you to create a "Makefile" that will execute this ent... | [] |
60,329 | Coomassie Purity Stain of Recombinant Antibodies | 4 | dx.doi.org/10.17504/protocols.io.8epv59255g1b/v1 | https://www.protocols.io/view/coomassie-purity-stain-of-recombinant-antibodies-b66hrhb6 | Addgene The Nonprofit Plasmid Repository | TITLE: Coomassie Purity Stain of Recombinant Antibodies
AUTHORS: Addgene The Nonprofit Plasmid Repository
[DESCRIPTION]
This protocol describes how to determine the purity and concentration of recombinant antibodies using ready-to-use bio-safe Coomassie G-250 stain (Addgene uses SimplyBlue SafeStain) and ImageJ softwa... | ["[SDS-PAGE] Add 5 µL of 4X sample buffer to each sample.", "[SDS-PAGE] Add 2 µL10X reducing agent to each sample.", "[SDS-PAGE] Spin the sample briefly in the microcentrifuge.", "[SDS-PAGE] Heat the samples for 10 min at 100 °C in a heat block.", "[SDS-PAGE] Spin the sample briefly in the microcentrifuge.", "[SDS-PAGE... |
17,403 | Ultrasound for Small Animal Imaging | null | dx.doi.org/10.17504/protocols.io.u83ezyn | null | Yves Sauve | TITLE: Ultrasound for Small Animal Imaging
AUTHORS: Yves Sauve
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">To obtain anatomical images that allow for measurement of structural changes in physiology, using Vevo 770,or Vevo 2100 Visual Sonics Integrated Rail System, which includes rat/mouse handli... | ["A. Specific details (eg. weight, DOB, sex, strain) of animal used for experiments are recorded on each report.B. Animal Anesthesia: Place the animal in the induction chamber and set oxygen level to 1-1.5L/minute and the Isoflurane to 1% followed with increamental increases of 0.5 % to 3.0 % to induce total anesthesia... |
72,691 | Immunohistochemical staining of CD44 core proteins in islet beta cells of formalin-fixed mouse pancreas | 1 | dx.doi.org/10.17504/protocols.io.n2bvjxr35lk5/v2 | https://www.protocols.io/view/immunohistochemical-staining-of-cd44-core-proteins-ci8tuhwn | Lora Starrs, Debra Brown, Sarah Popp, Charmaine Simeonovic | TITLE: Immunohistochemical staining of CD44 core proteins in islet beta cells of formalin-fixed mouse pancreas
AUTHORS: Lora Starrs, Debra Brown, Sarah Popp, Charmaine Simeonovic
[DESCRIPTION]
Paraffin sections (4mm thickness) of formalin-fixed mouse pancreases were treated with heat/citrate buffer for antigen retriev... | ["See Guidelines before starting", "Deparaffinize slides in each xylene for 1 min. rehydrate slides in graded alcohols beginning in absolute ethanol (10 dips)/ container of absolute ethanol), followed by 90% ethanol (10 dips) and 70% ethanol (10 dips).Wash well in running tap water for 5 min.", "Wipe around sections wi... |
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