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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90,825 | Proximity Ligation Assay (PLA) | 1 | dx.doi.org/10.17504/protocols.io.j8nlko6ydv5r/v1 | https://www.protocols.io/view/proximity-ligation-assay-pla-c4xhyxj6 | Leonardo A Parra-Rivas | TITLE: Proximity Ligation Assay (PLA)
AUTHORS: Leonardo A Parra-Rivas
[DESCRIPTION]
Proximity Ligation Assay (PLA)
[STEPS]
1. The PLA assay was performed as described previously with minor modifications 48. The following antibodies were used for the PLA experiments: Syn 204 against h-αSyn (Santa Cruz Biotechnology Ca... | ["The PLA assay was performed as described previously with minor modifications 48. The following antibodies were used for the PLA experiments: Syn 204 against h-αSyn (Santa Cruz Biotechnology Cat# sc-32280, RRID:AB_628319)(1:100) and EPR12790 against VAMP-2 (Abcam Cat#\nab214590)(1:300).", "The in-situ PLA was performe... |
36,552 | SPARC Pig2 acute wired ColoMOCA implantation | 1 | dx.doi.org/10.17504/protocols.io.bfxgjpjw | https://www.protocols.io/view/sparc-pig2-acute-wired-colomoca-implantation-bfxgjpjw | Brett Hanzlicek, Dennis Bourbeau, Margot Damaser | TITLE: SPARC Pig2 acute wired ColoMOCA implantation
AUTHORS: Brett Hanzlicek, Dennis Bourbeau, Margot Damaser
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">In this study, we will be using Yorkshire Pigs, 50-70kg. The purpose of this study is to develop a tool to measure bowel fullness and activit... | ["[Anesthesia Preparation]\nAnesthesia Preparation Pigs will be initially anesthetized with an intramuscular dose of telazol (4.4−6.6 mg/kg). The animals will then be intubated orotracheally and maintained on isoflurane in oxygen (1-5%; depending on anesthetic depth). Anesthetic depth will be measured by the respons... |
25,477 | Algal DNA extraction for HMW Nanopore sequencing | null | dx.doi.org/10.17504/protocols.io.45dgy26 | null | Robert Auber, Jennifer Wisecaver | TITLE: Algal DNA extraction for HMW Nanopore sequencing
AUTHORS: Robert Auber, Jennifer Wisecaver
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a protocol adapted for a haptophte algae. It is a single cellular organism lacking any type of silica or calcium carbonate armor. If your organism... | ["[Prepare equipment and reagents]\nSet water bath to 74°C", "[Prepare equipment and reagents]\nChill centrifuge to 4°C", "[Prepare equipment and reagents]\nAdd BME to premade NIB (Per Sample 35 μl BME into 35 ml premade NIB + Aliquot 1.8 ml NIB and add 200 μl Triton X-100)", "[Prepare equipment and reagents]\nCool NI... |
28,693 | Th17 Polarization of Mouse CD4+ Cells | null | dx.doi.org/10.17504/protocols.io.79vhr66 | null | Sam Li | TITLE: Th17 Polarization of Mouse CD4+ Cells
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Isolation of CD4+ Cells From Lymph Nodes]
Harvest lymph nodes (superficial cervical, mandibular, axillary, inguinal, and mesenteric) from mice.
?. [Isolation of CD4+ Cells From Lymph Nodes]
Tease l... | ["[Isolation of CD4+ Cells From Lymph Nodes]\nHarvest lymph nodes (superficial cervical, mandibular, axillary, inguinal, and mesenteric) from mice.", "[Isolation of CD4+ Cells From Lymph Nodes]\nTease lymph nodes through a sterile 70-µm nylon cell strainer to obtain single-cell suspensions in complete IMDM containing 1... |
50,701 | Gentle cell extraction from rocks for downstream single cell sorting and sequencing | 1 | dx.doi.org/10.17504/protocols.io.bvrmn546 | https://www.protocols.io/view/gentle-cell-extraction-from-rocks-for-downstream-s-bvrmn546 | Jackie Goordial, Beth Orcutt, Tim Dangelo | TITLE: Gentle cell extraction from rocks for downstream single cell sorting and sequencing
AUTHORS: Jackie Goordial, Beth Orcutt, Tim Dangelo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Method for extracting cells in a gentle manner from rocks for downstream single cell sorting and sequencing. S... | ["[Sample is started from 5 g of rock, preserved in 5 mL of glycerol TE in a 15 mL centrifuge tube]\nAdd EDTA to 15 mL tube ( containing 5 mL glyTE and 5 g crushed rock), add EDTA for final concentration of 10 mM.", "[Sample is started from 5 g of rock, preserved in 5 mL of glycerol TE in a 15 mL centrifuge tube]\nVort... |
91,851 | RNA collection, cDNA conversion and qPCR (SH-SY5Y cells) | 1 | dx.doi.org/10.17504/protocols.io.14egn3ymzl5d/v1 | https://www.protocols.io/view/rna-collection-cdna-conversion-and-qpcr-sh-sy5y-ce-c5xjy7kn | Stephanie Vrijsen, Peter Vangheluwe | TITLE: RNA collection, cDNA conversion and qPCR (SH-SY5Y cells)
AUTHORS: Stephanie Vrijsen, Peter Vangheluwe
[DESCRIPTION]
This protocol describes the isolation of RNA from SH-SY5Y cells and the subsequent conversion to cDNA for qPCR.
[STEPS]
SECTION: RNA collection
1. Cells were seeded in 10 cm dishes and used for ... | ["[RNA collection] Cells were seeded in 10 cm dishes and used for collection when reaching 70-80% confluency. \n(e.g. 3 million cells for collection after 2880 min)", "[cDNA conversion] Convert RNA to cDNA using the High-Capacity cDNA Reverse Transcription Kit (4368814, Thermo Fisher Scientific).", "[RNA collection] Sc... |
73,017 | Supplementary Material: An in silico approach to understanding the interaction between cardiovascular and pulmonary lymphatic dysfunction | 5 | dx.doi.org/10.17504/protocols.io.kxygx9zmwg8j/v1 | https://www.protocols.io/view/supplementary-material-an-in-silico-approach-to-un-cjizukf6 | Kelly Burrowes | TITLE: Supplementary Material: An in silico approach to understanding the interaction between cardiovascular and pulmonary lymphatic dysfunction
AUTHORS: Kelly Burrowes
[DESCRIPTION]
The lung is extremely sensitive to interstitial fluid balance, yet the role of pulmonary lymphatics in lung fluid homeostasis and its i... | ["[Lymphatic Model] Estimation of interstitial hydrostatic pressure (Pint)\nTo represent this a sinusoidal function was used:\n\n \nA, the amplitude, is set to the difference between the maximum and minimum elastic recoil pressures for the acinus during a breath, as given by the ventilation model. This is representati... |
62,961 | ONT Q20+ Adapter Ligation for Fungal DNA Barcoding | 4 | null | https://www.protocols.io/view/ont-q20-adapter-ligation-for-fungal-dna-barcoding-b9qrr5v6 | Stephen Douglas Russell | TITLE: ONT Q20+ Adapter Ligation for Fungal DNA Barcoding
AUTHORS: Stephen Douglas Russell
[DESCRIPTION]
This process will take your A-tailed library and add the nanopore adapters. Simply put chemicals together for a single reaction and do a bead cleanup.
Time required: ~45 minutes
[STEPS]
SECTION: Adapter Ligatio... | ["[Adapter Ligation] Spin down the Adapter Mix H (AMX H) and Quick T4 Ligase, and place on ice.\n\nAMX H - \nQuick T4 Ligase -", "[Adapter Ligation] Thaw Ligation Buffer (LNB) at room temperature, spin down and mix by pipetting. Due to viscosity, vortexing this buffer is ineffective. Place on ice immediately after tha... |
69,524 | Botanical Microfossil Extraction from Paleontological Sediments - 'Bot-MEPS' Protocol | 1 | null | https://www.protocols.io/view/botanical-microfossil-extraction-from-paleontologi-cf5utq6w | Megan C. O'Toole, Yoel E. Stuart, Jacopo Niccolo Cerasoni | TITLE: Botanical Microfossil Extraction from Paleontological Sediments - 'Bot-MEPS' Protocol
AUTHORS: Megan C. O'Toole, Yoel E. Stuart, Jacopo Niccolo Cerasoni
[DESCRIPTION]
Palaeobotanical microfossil analyses are often used to reconstruct palaeoecological histories and past environmental change. To do so, ma... | ["[Carbonate Removal (HCl)] If the sample contains carbonates, they will have to be removed for quality viewing of the microfossils.\n\nTo remove carbonates, start by pouring 50 mL of 30% into a small beaker.", "[Organics Removal (H2O2)] If the sample contains organics, they will have to be removed for quality viewin... |
98,611 | Tomogram reconstruction and sub-tomogram averaging to obtain full-length, auto-inhibited LRRK2 filaments on microtubu | 0 | dx.doi.org/10.17504/protocols.io.n92ld89zxv5b/v1 | https://www.protocols.io/view/tomogram-reconstruction-and-sub-tomogram-averaging-dcit2uen | Siyu Chen, Josh Hutchings, Digvijay Singh | TITLE: Tomogram reconstruction and sub-tomogram averaging to obtain full-length, auto-inhibited LRRK2 filaments on microtubu
AUTHORS: Siyu Chen, Josh Hutchings, Digvijay Singh
[DESCRIPTION]
This protocol describes all the data analysis steps after obtaining the LRRK2 on microtubule dataset.
[STEPS]
SECTION: Microtubu... | ["[Microtubule tracing, LRRK2 sub-tomogram picking and ab-initio model building in Dynamo] IMOD was used to manually go through all reconstructed tomograms and trace the backbone of microtubules. For each intact microtubule, make an open trajectory model by pressing the middle mouse button along the microtubule axis an... |
99,930 | Concentration technique for Viable but Non-Culturable organisms | 0 | dx.doi.org/10.17504/protocols.io.261ge53x7g47/v1 | https://www.protocols.io/view/concentration-technique-for-viable-but-non-cultura-ddt226qe | Muhammad Muhsin Fathuddin, Solomon John Obidah | TITLE: Concentration technique for Viable but Non-Culturable organisms
AUTHORS: Muhammad Muhsin Fathuddin, Solomon John Obidah
[DESCRIPTION]
This protocol is based on existing protocols, such as those for resuscitating microbes, freeze-drying, and selective isolation. It merges the parts of the three protocols to cre... | ["[Resuscitation of Microorganism] To the resuscitation broth media (e.g., peptone water, tryptic soy broth, Luria-Bertani broth, etc.), add the sample, making a 10% solution, i.e.,10 mg in90 mL.", "[Resuscitation of Microorganism] Incubate the broth culture at 37oC for 24-48 hours", "[Selective medium growth of desire... |
72,491 | Preparing multiplexed 16S/18S/ITS amplicons for the Illumina MiSeq | 4 | dx.doi.org/10.17504/protocols.io.4r3l277k3g1y/v1 | https://www.protocols.io/view/preparing-multiplexed-16s-18s-its-amplicons-for-th-ci2jugcn | André M Comeau, Alessi Kwawukume | TITLE: Preparing multiplexed 16S/18S/ITS amplicons for the Illumina MiSeq
AUTHORS: André M Comeau, Alessi Kwawukume
[DESCRIPTION]
The following detailed protocol is for the generation of paired-end sequencing reads of 16S/18S/ITS PCR amplicons with dual barcodes (i.e.: “indices”) on the Illumina MiSeq machine of lengt... | ["[Barcoded PCRs] Prepare the following PCR master-mix for PCR Plate 1 (2 and 0.2 µL) in two 1.5 mL Eppendorf tubes (one per duplicate plate; adjust if not using Phusion Plus), using either of the primer formats prepared in the IMR protocols Preparing Indexed Primer Plates (IDT Ultramers) for the Illumina MiSeq - Nexte... |
102,927 | Nuclei Isolation | 0 | dx.doi.org/10.17504/protocols.io.14egn6wryl5d/v1 | https://www.protocols.io/view/nuclei-isolation-dgrp3v5n | amanda schneeweis | TITLE: Nuclei Isolation
AUTHORS: amanda schneeweis
[DESCRIPTION]
nuclei isolation for snRNA-seq
[STEPS]
1. Prepare buffers and filter sterilize, add RNAse inhibitor fresh NP40 Lysis Buffer (NST): 0.1% NP-40 Alternative (or NP-40), 10 millimolar (mM) Tris, 146 millimolar (mM) NaCl, 1 millimolar (mM)CaCl2, 21mM MgCl2, ... | ["Prepare buffers and filter sterilize, add RNAse inhibitor fresh NP40 Lysis Buffer (NST): 0.1% NP-40 Alternative (or NP-40), 10 millimolar (mM) Tris, 146 millimolar (mM) NaCl, 1 millimolar (mM)CaCl2, 21mM MgCl2, 40U/mL of Protector RNAse inhibitor (add fresh day of) ST Wash Buffer: (10mM Tris, 146 Mass Percent NaCl, 1... |
null | null | null | dx.doi.org/10.17504/protocols.io.d9e93d | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
In this protocol we will show how to taxonomically profile 20 metagenomic shotgun samples <a href="http://www.nature.com/nature/journal/v486/n7402/full/nature11234.html" target="_blank">Human Microbiome Project</a> (HMP). Specifically, we will look at 10 samples from the buccal ... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.dn85hv | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is the protocol for DNA Assembly using the NEBuilder® HiFi DNA Assembly Master Mix (E2621).
[GUIDELINES]
<strong>Optimal Quantities</strong><br /><br />NEB recommends a total of 0.03–0.2 pmols of DNA fragments when 1 or 2 fragments are being assembled into a... | [] |
77,828 | The Cognitive Remediation of Attention in HIV Associated Disorders (HAND): A Meta-Analysis and Systematic Review | 1 | dx.doi.org/10.17504/protocols.io.5jyl8jqm7g2w/v1 | https://www.protocols.io/view/the-cognitive-remediation-of-attention-in-hiv-asso-cp9cvr2w | Sizwe Zondo | TITLE: The Cognitive Remediation of Attention in HIV Associated Disorders (HAND): A Meta-Analysis and Systematic Review
AUTHORS: Sizwe Zondo
[DESCRIPTION]
Objective: Despite medical advances in Highly Active Antiretroviral Therapy (HAART), patients living with HIV continue to be at risk for developing HIV-associated n... | ["[KEYWORDS] HIV, HAND, Attention Rehabilitation, Neuroplasticity, meta-analysis, meta-regression", "[REFERENCES] Alford, K., & Vera, J. H. (2018). Cognitive Impairment in people living with HIV in the ART era: A Review. British Medical Bulletin, 127(1), 55–68. https://doi.org/10.1093/bmb/ldy019\n\nBasterfield, C & Zon... |
55,661 | High Throughput pre-analytical processing of wastewater settled solids for SARS-CoV-2 RNA analyses | 1 | dx.doi.org/10.17504/protocols.io.b2kmqcu6 | https://www.protocols.io/view/high-throughput-pre-analytical-processing-of-waste-b2kmqcu6 | Aaron Topol, Marlene Wolfe, Brad White, Krista Wigginton, Alexandria B B Boehm | TITLE: High Throughput pre-analytical processing of wastewater settled solids for SARS-CoV-2 RNA analyses
AUTHORS: Aaron Topol, Marlene Wolfe, Brad White, Krista Wigginton, Alexandria B B Boehm
[DESCRIPTION]
This process instruction describes the steps for pre-analytical processing of primary settled solids from waste... | ["[Preparation] Process fresh samples stored at 4 °C if possible. If analyzing a frozen sample, thaw at 4 Room temperature . \nSet centrifuge temperature to 4 °C.\nSet oven temperature to 110 °C.\nRemove an aliquot of BCoV from the freezer and thaw on ice.", "[Dewater Sludge Samples by Centrifugation] Label 50 mL conic... |
69,956 | Intranasal Infection of Mice with H1N1 Virus | 1 | dx.doi.org/10.17504/protocols.io.kxygx9mndg8j/v1 | https://www.protocols.io/view/intranasal-infection-of-mice-with-h1n1-virus-cgjctuiw | Michaela Lunn, Quinton Hake-Volling, Chris Rousso, Michael G. Schlossmacher, Earl G. Brown | TITLE: Intranasal Infection of Mice with H1N1 Virus
AUTHORS: Michaela Lunn, Quinton Hake-Volling, Chris Rousso, Michael G. Schlossmacher, Earl G. Brown
[DESCRIPTION]
Objective: This SOP addresses the infection of adult mice with mouse-adapted influenza H1N1 A/FM/1/1947 strain influenza via the intranasal route
Adult ... | ["[Intranasal Infection with H1N1: Survival and Tissue Collection] Thaw one aliquot of H1N1 (stored at -80 deg). Keep on ice.", "[Intranasal Infection with H1N1: Survival and Tissue Collection] In a CL2 biosafety cabinet dilute aliquoted stock virus in phosphate buffered saline (PBS) accordingly and vortex (approximate... |
59,915 | Cell line construction and maintenance for Lyso-IP and Endo-IP analysis of amyloid precursor protein processing, version 2 | 4 | dx.doi.org/10.17504/protocols.io.4r3l24kxxg1y/v2 | https://www.protocols.io/view/cell-line-construction-and-maintenance-for-lyso-ip-b6rjrd4n | Hankum Park, Frances V Hundley, Sharan Sharan Swarup, Harper JW | TITLE: Cell line construction and maintenance for Lyso-IP and Endo-IP analysis of amyloid precursor protein processing, version 2
AUTHORS: Hankum Park, Frances V Hundley, Sharan Sharan Swarup, Harper JW
[DESCRIPTION]
Lyso-IP is a method that allows for the isolation of lysosomes for proteomics and metabolomics (dx... | ["[Cell line maintenance] Maintain 293 cells in Dulbecco’ Modifies Eagles Medium (DMEM) with 10% fetal bovine serum and optional 1% penicillin-streptomycin. Additionally, grow 293EL cells in 1.2 µg/ml puromycin and 200 µg/ml G418 to maintain selection for 3xFLAG-EEA1 and TMEM192-3XHA, respectively.", "[Endogenous taggi... |
null | null | null | dx.doi.org/10.17504/protocols.io.e9bbh2n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is part of the FOCUS™ Mitochondria Kit <a href="https://www.protocols.io/view/Collection-of-FOCUS-Mitochondria-Kit-protocols-e8tbhwn" target="_blank">collection</a>. Please refer to the appropriate protocol depending on your application.</p>
<p> </p>
<p>For faci... | [] |
35,300 | Tutorial to use the Galaxy/coral SNP STAGdb workflow | null | null | https://www.protocols.io/view/tutorial-to-use-the-galaxy-coral-snp-stagdb-workfl-beqcjdsw | Iliana Baums, Sheila Kitchen, Greg vonKustner | TITLE: Tutorial to use the Galaxy/coral SNP STAGdb workflow
AUTHORS: Iliana Baums, Sheila Kitchen, Greg vonKustner
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Tutorial to use the Galaxy coral SNP STAGdb workflow </span><a href="https://coralsnp.science.psu.edu/galaxy" style = "text-decora... | [] |
88,516 | Cryo-EM sample preparation for PI3KC3-C1~RAB1A complex | 4 | null | https://www.protocols.io/view/cryo-em-sample-preparation-for-pi3kc3-c1-rab1a-com-c2pcydiw | Annan SI Cook | TITLE: Cryo-EM sample preparation for PI3KC3-C1~RAB1A complex
AUTHORS: Annan SI Cook
[DESCRIPTION]
This protocol details cryo-EM sample preparation for PI3KC3-C1~RAB1A complex.
[STEPS]
SECTION: GTP Loading of RAB1A
1. Strip the protein of its bound divalent cations by incubating RAB1A(Q70L) with 5 millimolar (mM) EDT... | ["[GTP Loading of RAB1A] Strip the protein of its bound divalent cations by incubating RAB1A(Q70L) with 5 millimolar (mM) EDTA at Room temperature for 30 min.", "[GTP Loading of RAB1A] Add a large molar excess (50 millimolar (mM)) of GTP to the protein.", "[GTP Loading of RAB1A] Incubate the mixture for an additional 3... |
39,098 | IV catheter making | 1 | null | https://www.protocols.io/view/iv-catheter-making-bie2kbge | McKenzie Pavlich, Olivier George | TITLE: IV catheter making
AUTHORS: McKenzie Pavlich, Olivier George
[STEPS]
?.
?. Bend cannulas into a curved 90° angle making sure that the curve is not too sharp (1.5 cm from tip of bending tool)Create a ruler from tape and mark all important sections Start >> 15 cm >> Stop ** SMALL tubing should be a total ... | ["Bend cannulas into a curved 90° angle making sure that the curve is not too sharp (1.5 cm from tip of bending tool)Create a ruler from tape and mark all important sections Start >> 15 cm >> Stop ** SMALL tubing should be a total of 15 cm Make mark at 4 cm in from stopping point ** Silicone ball will be ... |
31,557 | Determination of the accuracy of micropipettes for the biochemistry lab | 1 | null | https://www.protocols.io/view/determination-of-the-accuracy-of-micropipettes-for-ba3digi6 | Chris Berndsen | TITLE: Determination of the accuracy of micropipettes for the biochemistry lab
AUTHORS: Chris Berndsen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Basic protocol to help students use the laboratory micropipettes in the range of 1 to 1000 μL. </div></div>
[STEPS]
?. [Before calibration]
Fill a b... | ["[Before calibration]\nFill a beaker with 20 mL of ddH2O.\n20 mL\nThe volume does not have to be accurate.", "[Before calibration]\nMeasure and record the temperature of the water.", "[Before calibration]\nTare the balance with the weigh boat.", "[Measuring liquid dispensing]\nSet the volume of the pipette as shown in... |
86,293 | Immunostaining Mouse Brain Tissue or Neuronal Cultures | 4 | dx.doi.org/10.17504/protocols.io.ewov1qow7gr2/v1 | https://www.protocols.io/view/immunostaining-mouse-brain-tissue-or-neuronal-cult-cyhvxt66 | Robert Edwards, Shweta Jain | TITLE: Immunostaining Mouse Brain Tissue or Neuronal Cultures
AUTHORS: Robert Edwards, Shweta Jain
[DESCRIPTION]
This protocol describes immunohistochemical and immunoctyochemical methods to analyze protein expression in mouse brain. In the protocol, we describe the fixation of tissue or cultured neurons, the immunost... | ["[Tissue fixation] Collection of fixed tissues slices from juvenile or adult mice", "[Tissue fixation] Using a perfusion pump, pierce needle into left ventricle and sever the right atrium; immediately begin perfusing cold 1X PBS followed by 4% paraformaldehyde (PFA) in PBS", "[Tissue fixation] Dissect out brain into 1... |
48,886 | High Throughput SARS-COV-2, PMMOV, and BCoV quantification in settled solids using digital RT-PCR | 1 | dx.doi.org/10.17504/protocols.io.btywnpxe | https://www.protocols.io/view/high-throughput-sars-cov-2-pmmov-and-bcov-quantifi-btywnpxe | Aaron Topol (Verily Life Sciences), marlene.wolfe , Brad White (Verily Life Sciences), Krista Wigginton, Alexandria Boehm | TITLE: High Throughput SARS-COV-2, PMMOV, and BCoV quantification in settled solids using digital RT-PCR
AUTHORS: Aaron Topol (Verily Life Sciences), marlene.wolfe , Brad White (Verily Life Sciences), Krista Wigginton, Alexandria Boehm
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This process ins... | ["[Preparation (both assays)]\nRetrieve the ddPCR One-Step RT Supermix for probes from the freezer and thaw the components .\n-20 °C\non ice", "[Preparation (both assays)]\nRetrieve ddPCR positive control aliquots (50 copies per uL gRNA and 100 copies per µL BCoV and PMMoV gene blocks) from the freezer and thaw\n-80 ... |
100,002 | 10Xv3.1 Genomics Sample Processing | 1 | dx.doi.org/10.17504/protocols.io.dm6gpwd8jlzp/v3 | https://www.protocols.io/view/10xv3-1-genomics-sample-processing-ddwa27ae | Allen Institute for Brain Science | TITLE: 10Xv3.1 Genomics Sample Processing
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
This protocol is used for the rapid generation of 3’ transcriptomic-NGS-ready- single-cell-libraries from pools of cells.
Note: Research reported in this publication was supported by the National Institute Of Mental Hea... | [] |
20,833 | UC Davis - Glucose Protocol | null | dx.doi.org/10.17504/protocols.io.yj9fur6 | null | Peter Havel | TITLE: UC Davis - Glucose Protocol
AUTHORS: Peter Havel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">
Glucose is oxidized by glucose oxidase to gluconic acid and hydrogen peroxide. The hydrogen peroxide reacts in the... | ["Reconstitute powdered reagent with only 25 ml of distilled water to make a 2X solution.", "Add 3 μl of calibrator and sample to each well.", "Add 150 μl of PBS to each well. Read at 540 nm.IMPORTANT: Make sure not to add any bubbles to the wells when dispensing reagents, this will interfere with reading in the plater... |
63,666 | Phenotyping C. elegans behaviour on E. coli bacteria supplemented with enterobactin, iron or paraquat | 4 | dx.doi.org/10.17504/protocols.io.36wgq7ybkvk5/v1 | https://www.protocols.io/view/phenotyping-c-elegans-behaviour-on-e-coli-bacteria-caessbee | Saul Moore | TITLE: Phenotyping C. elegans behaviour on E. coli bacteria supplemented with enterobactin, iron or paraquat
AUTHORS: Saul Moore
[DESCRIPTION]
Testing whether Keio Collection E. coli mutants supplemented with exogenous enterobactin, iron(III) chloride, iron(III) sulfate or paraquat elicit a behavioural response wh... | ["[Preparing 6-well plates for imaging] Add 25mL fresh LB broth to each of 2 Falcon tubes, and inoculate with the BW25113 (Keio Collection parent strain) and the E. coli gene-deletion mutant of interest, respectively", "[Preparing 6-well plates for imaging] Place inoculations to grow overnight in a shaking incubator (3... |
103,991 | FruitRescue! - Prunus phenotyping | 0 | null | https://www.protocols.io/view/fruitrescue-prunus-phenotyping-dhsx36fn | Mathieu Brisson, Amandine Cornille | TITLE: FruitRescue! - Prunus phenotyping
AUTHORS: Mathieu Brisson, Amandine Cornille
[DESCRIPTION]
The FruitRescue project aims to create a pipeline to predict fruit trees' genomic offset. To confirm the pipeline predictions, tree fitness parameters are measured in crop and wild tree orchards along a longitudinal grad... | ["[Trunk diameter] The trunk diameter is an indicator of the tree vigor (Waring 1987). Genetic information as well as environmental cues including abiotic and biotic stresses can modify the source-sink relationships and therefore modify the trunk growth during the year. Tree adaptation to its location can thus be asses... |
28,223 | Echocardiography: Mouse | null | dx.doi.org/10.17504/protocols.io.7s7hnhn | null | E. Dale Abel | TITLE: Echocardiography: Mouse
AUTHORS: E. Dale Abel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">This protocol describes the procedure used by the DiaComp for transthoracic echocardiography in awake mice. </div><div... | ["We perform transthoracic echocardiography in awake mice. If anesthesia is required we currently favor the use of inhaled isoflurane (1%), delivered via nose cone. The anesthesia flow can be titrated to minimize any reduction in heart rate. If inhaled anesthesia is not available, we have also had success with avertin ... |
69,456 | Microalgal Colony Blot - A Simple and Rapid Method for Direct Detection of Recombinant Proteins in Microalgae | 4 | dx.doi.org/10.17504/protocols.io.kxygx9k2kg8j/v1 | https://www.protocols.io/view/microalgal-colony-blot-a-simple-and-rapid-method-f-cf3qtqmw | Yasin Torres-Tiji, Francis J Fields, Stephen Mayfield | TITLE: Microalgal Colony Blot - A Simple and Rapid Method for Direct Detection of Recombinant Proteins in Microalgae
AUTHORS: Yasin Torres-Tiji, Francis J Fields, Stephen Mayfield
[DESCRIPTION]
Recombinant gene expression highly depends on the loci in which the transgene integrates and in green algae transgenes integr... | ["[Dot-Blot preparation] Grab a ruler, a pencil, scissors and an empty petri dish and wipe them with 70% ethanol. Place them inside a clean biological safety cabinet, where the Algal Immunoblot preparation will take place.", "[Dot-Blot preparation] Draw a grid on the membrane with a pencil, with care not to break the m... |
61,937 | PROTAC Design based on Bioinformatics | 6 | dx.doi.org/10.17504/protocols.io.dm6gpbox1lzp/v1 | https://www.protocols.io/view/protac-design-based-on-bioinformatics-b8qrrvv6 | boc.protac | TITLE: PROTAC Design based on Bioinformatics
AUTHORS: boc.protac
[DESCRIPTION]
In order to simplify and accelerate the discovery of PROTAC, it is necessary to grasp the design rules of PROTAC, which is helpful to establish a reliable PROTAC evaluation platform. To date, most reported PROTAC designs are based on targ... | [] |
47,808 | Time-resolved FRET in 384-well plate format to identify small molecular modifiers of mutant Huntingtin conformational inflexibility | 4 | dx.doi.org/10.17504/protocols.io.bsw8nfhw | https://www.protocols.io/view/time-resolved-fret-in-384-well-plate-format-to-ide-bsw8nfhw | Johannes Wilbertz, Julia Frappier, Barbara Calamini | TITLE: Time-resolved FRET in 384-well plate format to identify small molecular modifiers of mutant Huntingtin conformational inflexibility
AUTHORS: Johannes Wilbertz, Julia Frappier, Barbara Calamini
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">BACKGROUND</div><div class = "text-block">Huntingtin... | ["Seed 10,000 cells/well (50 ul, GM04691 fibroblasts) in DMEM + 15% FBS + PenStrep in Greiner 384 well plates according to the anticipated plating scheme. Do not seed cells in the left-most column 1. Later, this column will serve to calculate the FRET background signal. When seeding multiple plates, use a Multidrop cel... |
28,995 | Encasing LAMP mixture in paraffin | null | dx.doi.org/10.17504/protocols.io.8jbhuin | null | Niels Appelman | TITLE: Encasing LAMP mixture in paraffin
AUTHORS: Niels Appelman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol can be used to encase LAMP mastermix and primers in paraffin.</div></div>
[STEPS]
?. Prepare a 10X primermix according to the following scheme AB1Primer Concentration2 FI... | ["Prepare a 10X primermix according to the following scheme AB1Primer Concentration2 FIP 16 μM3 BIP 16 μM4 F3 2 μM5 B3 2 μM 6 LOOP F 8 μM 7 LOOP B8 μM\nAB1Primer Concentration2 FIP 16 μM3 BIP 16 μM4 F3 2 μM5 B3 2 μM 6 LOOP F 8 μM 7 LOOP B8 μM", "Add the following components to a micro centrifuge tube AB1 Component... |
22,273 | S-Basal Medium | 1 | null | https://www.protocols.io/view/s-basal-medium-zy9f7z6 | Adrien Assie, Buck Samuel | TITLE: S-Basal Medium
AUTHORS: Adrien Assie, Buck Samuel
[DESCRIPTION]
Large quantities of C. elegans can be grown in a liquid medium. Liquid cultures of C. elegans are usually grown on S Medium using concentrated E. coliOP50 as a food source. This is the S-Basal Medium recipe
[STEPS]
1. Start with 700 mL
2. 5.9 g N... | ["Start with 700 mL", "5.9 g NaCl (100 millimolar (mM))", "50 mL of 1 Molarity (M) Potassium Phosphate Buffer, pH 6.0\n\nOR\n\n1 g and 6 g", "Adjust water to 1000 mL", "Autoclave"] |
null | null | null | dx.doi.org/10.17504/protocols.io.t5aeq2e | null | null | TITLE: No Title
AUTHORS:
[STEPS] | [] |
64,642 | SARS-CoV-2 live virus neutralization assay | 4 | dx.doi.org/10.17504/protocols.io.cbdasi2e | https://www.protocols.io/view/sars-cov-2-live-virus-neutralization-assay-cbdasi2e | Ria Lassauniere, Anders Frische | TITLE: SARS-CoV-2 live virus neutralization assay
AUTHORS: Ria Lassauniere, Anders Frische
[DESCRIPTION]
Virus neutralization assays provide a means to quantitate functional antibody responses that block virus infection. These assays are instrumental in defining vaccine and therapeutic antibody potency, immune evas... | ["[Seeding Vero E6 cells into 96-well plates] Seeding Vero E6 cells (from T75 flask)", "[Seeding Vero E6 cells into 96-well plates] Verify that Vero E6 cells growing in maintenance media are actively growing (monolayer 70-95% confluent).", "[Seeding Vero E6 cells into 96-well plates] Remove the maintenance media from t... |
89,820 | Section 1: Enzymatic DNA Fragmentation (Manually) | 4 | dx.doi.org/10.17504/protocols.io.kqdg3x3m7g25/v1 | https://www.protocols.io/view/section-1-enzymatic-dna-fragmentation-manually-c3x4ypqw | Ester Kalef-Ezra, Ben Harvey, Katherine Roper, Christos Proukakis | TITLE: Section 1: Enzymatic DNA Fragmentation (Manually)
AUTHORS: Ester Kalef-Ezra, Ben Harvey, Katherine Roper, Christos Proukakis
[DESCRIPTION]
This protocol details manual enzymatic DNA Fragmentation prior to Section 2: NGS library preparation for sequencing.
[STEPS]
SECTION: Enzymatic DNA Fragmentation (Manually... | ["[Enzymatic DNA Fragmentation (Manually)] Group the samples scWGA-products of interest for library preparation based on their size length to require the same fragmentation time. The recommended fragmentation times per amplicon are suggested on Table 1.\n\nTable 1. Recommended fragmentation time based on amplicon size.... |
87,177 | Cleavage Under Targets and Release Using Nuclease (CUT&RUN) | 4 | dx.doi.org/10.17504/protocols.io.x54v9p8ppg3e/v1 | https://www.protocols.io/view/cleavage-under-targets-and-release-using-nuclease-czdhx236 | Geneva Miller, Lindsey M. Rollosson, Carrie Saada, Serenity J. Wade, Danae Schulz | TITLE: Cleavage Under Targets and Release Using Nuclease (CUT&RUN)
AUTHORS: Geneva Miller, Lindsey M. Rollosson, Carrie Saada, Serenity J. Wade, Danae Schulz
[DESCRIPTION]
This Cleavage Under Targets and Release Using Nuclease (CUT&RUN) protocol produces genomic occupancy data for a protein of interest in the prot... | ["[Prepare cells] Count parasite cultures with hemocytometer or other preferred counting method.", "[Prepare cells] Spin down cells in centrifuge at 2800 x g, 10 min.", "[Prepare cells] If needed, combine samples from multiple Eppendorf tubes so that each final tube has 75 million cells, and spin again at 2800 x g, 4 m... |
80,636 | Lakes ABPS Protocol - Optimized protocol for the extraction of fish DNA from freshwater sediments (Thomson-Laing et al., 2022) | 1 | dx.doi.org/10.17504/protocols.io.yxmvm24d6g3p/v1 | https://www.protocols.io/view/lakes-abps-protocol-optimized-protocol-for-the-ext-csy4wfyw | Georgia Thomson-Laing | TITLE: Lakes ABPS Protocol - Optimized protocol for the extraction of fish DNA from freshwater sediments (Thomson-Laing et al., 2022)
AUTHORS: Georgia Thomson-Laing
[DESCRIPTION]
DNA was extracted from lake sediment samples by an alkaline lysis method with ethanol precipitation adapted from method described by Kuwae e... | ["[Alkaline extraction] INTO a 50 mL tube add:\n10 g of sediment sample\n6 mL sodium hydroxide (0.33M)\n3 mL Tris-EDTA (pH 8)", "[Alkaline extraction] VORTEX for 1 min \n\nINCUBATE at 65 °C for 50 min", "[Alkaline extraction] ALLOW samples to cool to Room temperature \n\nCENTRIFUGE at 15000 x g for 60 min", "[Ethanol p... |
null | null | null | dx.doi.org/10.17504/protocols.io.ggcbtsw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This procedure is suitable for very low to high concentration of phosphorus (0.00001- 6 mg/l).</p>
<p style="text-align: justify;"><br /><strong>What happens to this procedure</strong>: Ammonium molybdate and potassium antimonyl tartrate react in acidic solution with orthopho... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.g4gbytw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Adapted from: Van Etten, J. (n.d.). Titering of <em>Chlorella </em>Viruses. Retrieved from http://ncv.unl.edu/vanettenlab/</p>
[GUIDELINES]
<p>For critical work, a second purification may be necessary.</p>
<p> </p>
<div>
<div>
<p>This protocol is used for Chloroviruses and m... | [] |
26,804 | Streptavidin yielding with Ponceau | null | dx.doi.org/10.17504/protocols.io.6euhbew | null | Manuela de las Casas | TITLE: Streptavidin yielding with Ponceau
AUTHORS: Manuela de las Casas
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The aim is to see if the streptavidin binds correctly to the nitrocelullose membrane. Only after achieving a positive result is recommended to proceed to the next step (the dot blo... | ["[Preparing the nitrocellulose strip]\nSet the hot plate to 100ºC or at least warm enough to melt the wax. Cut a small amount from one of the wax pencils and place it on a Petri dish. Set the Petri dish on the hot plate and wait for the wax to melt. Cut a strip from the nitrocellulose sheet with the desired size.Once... |
82,645 | Helicase-like transcription factor (HLTF)-deleted CDX/TME model of colorectal cancer increased transcription of oxidative phosphorylation genes and diverted glycolysis to boost S-glutathionylation in intravascular metastatic niches | 4 | dx.doi.org/10.17504/protocols.io.ewov1oe37lr2/v1 | https://www.protocols.click/view/helicase-like-transcription-factor-hltf-deleted-cd-cuxvwxn6 | Dalia Martinez-Marin, Rebecca A. Helmer, Gurvinder Kaur, Rachel L. Washburn, Raul Martinez-Zaguilan, Souad R. Sennone, Jannette M. Dufour, Beverly S Chilton | TITLE: Helicase-like transcription factor (HLTF)-deleted CDX/TME model of colorectal cancer increased transcription of oxidative phosphorylation genes and diverted glycolysis to boost S-glutathionylation in intravascular metastatic niches
AUTHORS: Dalia Martinez-Marin, Rebecca A. Helmer, Gurvinder Kaur, Rachel L. Washb... | ["[Reagents and kits] Microbiome collection kits were obtained from TransnetYX (Cordova, TN). McCoy’s 5a Medium (30-2007) and fetal bovine serum (30-2020) were purchased from American Type Culture Collection (ATCC, Manassas, Virginia). Puromycin (ant-pr) was purchased from InvivoGen (San Diego, CA). XenoLight D-lucifer... |
27,977 | Restriction Enzyme Digestion (Protocol for NEB CutSmart® Buffer) | null | dx.doi.org/10.17504/protocols.io.7jhhkj6 | null | Alba Balletbó | TITLE: Restriction Enzyme Digestion (Protocol for NEB CutSmart® Buffer)
AUTHORS: Alba Balletbó
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used to check if the two selected restriction enzymes can perform effective catalysis in the same solution.</div></div>
[STEPS]
?. Mix DNA ... | ["Mix DNA solution with the suitable amount of the master mix. Reaction system for a total volume of 25μL: AB1DNA solution20 μL210x NEB CutSmart® Buffer2.75 μL3Restriction enzyme1.0 μL4ddH2O1.25 μL5Total Volume25 μL\nAB1DNA solution20 μL210x NEB CutSmart® Buffer2.75 μL3Restriction enzyme1.0 μL4ddH2O1.25 μL5Total Vol... |
71,351 | SPLiT-seq Nuclei isolation for Micro-dissected Mouse Brain Tissue | 1 | dx.doi.org/10.17504/protocols.io.14egn2zkpg5d/v1 | https://www.protocols.io/view/split-seq-nuclei-isolation-for-micro-dissected-mou-chwxt7fn | Ashley B Robbins | TITLE: SPLiT-seq Nuclei isolation for Micro-dissected Mouse Brain Tissue
AUTHORS: Ashley B Robbins
[DESCRIPTION]
Protocol for nuclei isolation prior to SPLiT-seq library preparation. Specifically optimized for the storage of nuclei from micro-dissected brain regions from mice or human (50-100mg).
[GUIDELINES]
Tissu... | ["[Setup] Prepare stock lysis buffer (can be stored at 4°C for 1 week)\n\nFor 15 mL stock:\n\n\n1.641 g Sucrose\n75 µL 1M CaCl2\n45 µL 1M Mg(Ac)2\n3 µL 0.5M EDTA\n150 µL Tris-HCl, pH 8.0\n15 µL Triton X-100\n\nFill to 15 mL with UltraPure H2O (DNase-free, RNase-free)", "[Setup] Prepare wash & resuspension buffer\n\nF... |
94,413 | Optogenetic modulation of dopaminergic neurons | 1 | dx.doi.org/10.17504/protocols.io.dm6gp3kppvzp/v1 | https://www.protocols.io/view/optogenetic-modulation-of-dopaminergic-neurons-c8fmztk6 | Cristian González-Cabrera, Matthias Prigge | TITLE: Optogenetic modulation of dopaminergic neurons
AUTHORS: Cristian González-Cabrera, Matthias Prigge
[DESCRIPTION]
This protocol describes an optogenetic activation of neuromelanine-laden dopaminergic neurons in the SNc-VTA. We induce neuromelanin (NM) in the SNc-VTA through viral expression of a humane tyrosinas... | ["[Viral Injection] Stereotactic injection of viruses into DAT-Cre (JAX# 006660) animals\n\nViral Constructs:\n1.- pAAV-hSyn1-dlox-ChrimsonR_tdTomato(rev)-dlox-WPRE \n\n2.- pAAV-hSyn1-dlox-hCHR2(H134R)_mcherry(rev)-dlox-WPRE\n\n3.- pAAV_Ef1a_DIO_hTyrHA_minBack\n\nInjections: \n- Bilateral injections were performed. \n-... |
100,005 | 10x Multiome Sample Processing | 1 | dx.doi.org/10.17504/protocols.io.bp2l61mqrvqe/v2 | https://www.protocols.io/view/10x-multiome-sample-processing-ddwd27a6 | Allen Institute for Brain Science | TITLE: 10x Multiome Sample Processing
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
Protocol is used to profile all the open chromatin regions at a single nuclei level through the rapid generation of NGS-ready libraries, and for rapid generation of 3' transcriptomic-NGS-ready-single-cell-libraries from the ... | [] |
73,518 | 621.1.HTC_H&E Stain (Paraffin or Cryosections) | 1 | dx.doi.org/10.17504/protocols.io.36wgqjnq3vk5/v1 | https://www.protocols.io/view/621-1-htc-h-amp-e-stain-paraffin-or-cryosections-cj2nuqde | Gloria S Pryhuber, Cory Poole | TITLE: 621.1.HTC_H&E Stain (Paraffin or Cryosections)
AUTHORS: Gloria S Pryhuber, Cory Poole
[DESCRIPTION]
Hematoxylin and Eosin staining is the standard chemical stain used on slides to be reviewed for assessment of general histopathology and the generation of a pathology report for each donor.
(From Wikipedia) ... | ["[Staining Procedure] If sections were from tissue block embedded in paraffin, deparaffinize slides with 3 changes of Xylene for 5 minutes each.", "[Staining Procedure] Rehydrate slides by submerging them in Ethanol in the following order for 3 minutes each.\ni. 100% Ethanol, \nii. 100% Ethanol, \niii. 95% Ethanol,\... |
null | null | null | dx.doi.org/10.17504/protocols.io.gr3bv8n | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?. | [] |
73,536 | 621.1.HTC_H&E Stain (Paraffin or Cryosections) | 1 | dx.doi.org/10.17504/protocols.io.36wgqjnq3vk5/v2 | https://www.protocols.io/view/621-1-htc-h-amp-e-stain-paraffin-or-cryosections-cj28uqhw | Gloria S Pryhuber, Cory Poole, Anthony Corbett | TITLE: 621.1.HTC_H&E Stain (Paraffin or Cryosections)
AUTHORS: Gloria S Pryhuber, Cory Poole, Anthony Corbett
[DESCRIPTION]
Hematoxylin and Eosin staining is the standard chemical stain used on slides to be reviewed for assessment of general histopathology and the generation of a pathology report for each donor.
... | ["[Staining Procedure] Verify that all slides are completely dry. Slides can be dried in an 55C oven for one hour or more prior to use to prevent loss of tissue.", "[Staining Procedure] If sections were from tissue block embedded in paraffin, deparaffinize slides with 3 changes of Xylene for 5 minutes each.", "[Staini... |
64,715 | Beneficial Bio Products: Packaging protocol | 4 | null | https://www.protocols.io/view/beneficial-bio-products-packaging-protocol-cbfjsjkn | Nadine Mowoh, Stephane Fadanka | TITLE: Beneficial Bio Products: Packaging protocol
AUTHORS: Nadine Mowoh, Stephane Fadanka
[DESCRIPTION]
After production and QC (internal and External) of our products, some documents are prepared which will accompany the reagent or products whenever they are sent to a user to ensure they are used correctly to av... | ["[Gather all the information about the order at hand or product to be packaged] The information include:\nNature and quantity of products; Destination; Customers detail; Date and expected delivery date…). This information will guide on the type of packaging that will be required.", "[Print specific amounts and type of... |
52,703 | Sequencing Protocol | 4 | dx.doi.org/10.17504/protocols.io.bxp7pmrn | https://www.protocols.io/view/sequencing-protocol-bxp7pmrn | Tom Little | TITLE: Sequencing Protocol
AUTHORS: Tom Little
[DESCRIPTION]
PCR barcoding protocol for ADE samples
[STEPS]
1. Introduction to barcoding amplicons
We/you performed a first PCR using Cox-1 specific primers. These were tailed with the universal sequences given below. This tail is actually a priming site for a secon... | ["Introduction to barcoding amplicons \nWe/you performed a first PCR using Cox-1 specific primers. These were tailed with the universal sequences given below. This tail is actually a priming site for a second PCR which incorporates the Oxford Nanopore barcode sequences (we called these sequencing identifiers- I didn'... |
85,191 | Extraction and ONT MinION Library Preparation of uHMW gDNA | 4 | dx.doi.org/10.17504/protocols.io.j8nlkww11l5r/v5 | https://www.protocols.click/view/extraction-and-ont-minion-library-preparation-of-u-cxffxjjn | Kaylee S. Herzog, jfauver | TITLE: Extraction and ONT MinION Library Preparation of uHMW gDNA
AUTHORS: Kaylee S. Herzog, jfauver
[DESCRIPTION]
This custom protocol optimizes extraction, purification, and Oxford Nanopore Technologies (ONT) MinION library preparation for ultra-high molecular weight genomic DNA (uHMW gDNA) from parasitic nematodes.... | ["[Part 1: Ultra-HWM gDNA extraction | Zymo Quick-DNA HWM MagBead Plus Kit | ~3 hr] Set dry bath to 55 °C", "For each sample, add the following to a clean 1.5 mL microcentrifuge tube to create a master mix:\n 95 µL \n 95 µL \n 10 µL", "Vortex the master mix gently to mix, then spin down and keep ... |
43,595 | Analysis of CRAC Datasets | 4 | dx.doi.org/10.17504/protocols.io.bntjmekn | https://www.protocols.io/view/analysis-of-crac-datasets-bntjmekn | Clémentine Delan-Forino, David Tollervey | TITLE: Analysis of CRAC Datasets
AUTHORS: Clémentine Delan-Forino, David Tollervey
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The RNA exosome complex functions in both the accurate processing and rapid degradation of many classes of RNA in eukaryotes and Archaea. Functional and structural analy... | ["[Preprocessing Step: Demultiplexing, Quality Filtering, Trimming of Adapters]\nThe 5′ adapters mentioned in previous sections contain barcodes allowing multiplexing of several samples in a sequencing lane. In addition to barcodes, 5′ adapters contain three random nucleotides allowing removal of PCR duplicates. This a... |
58,945 | Diaminobenzidine (DAB) Staining | 4 | dx.doi.org/10.17504/protocols.io.b5s9q6h6 | https://www.protocols.io/view/diaminobenzidine-dab-staining-b5s9q6h6 | Haley Geertsma | TITLE: Diaminobenzidine (DAB) Staining
AUTHORS: Haley Geertsma
[DESCRIPTION]
This protocol is used to stain paraffin-embedded mouse brain tissue.
[STEPS]
1. To paraffin-embedded tissue, deparaffinize in 100% xylenes for 3x 5 minutes.
2. Incubate in 100% ethanol for 2x 5 minutes.
3. Incubate in 70% ethanol for 5 min... | ["To paraffin-embedded tissue, deparaffinize in 100% xylenes for 3x 5 minutes.", "Incubate in 100% ethanol for 2x 5 minutes.", "Incubate in 70% ethanol for 5 minutes.", "Incubate in 50% ethanol for 5 minutes.", "Incubate in 1X PBS for 5 minutes.", "Perform antigen retrieval by incubating tissue in 1X sodium citrate for... |
34,385 | STRIPE-seq library construction | null | dx.doi.org/10.17504/protocols.io.bdtri6m6 | null | Robert Policastro, Gabe Zentner | TITLE: STRIPE-seq library construction
AUTHORS: Robert Policastro, Gabe Zentner
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Accurate mapping of transcription start sites (TSSs) is key for understanding transcriptional regulation; however, current protocols for genome-wide TSS profiling are labor... | ["[Prepare Total RNA]\nCheck RNA quality and concentration on an Agilent TapeStation using a High-Sensitivity RNA ScreenTape.\nYou should have at least 50 to 200 ng of total RNA at a concentration of at least 30 to 125 ng/μl. Your total RNA should also not be highly degraded, as measured by the quality of the rRNA peak... |
77,086 | Proton Density Fat Fraction (PDFF) Measurement of Myelofibrosis in Mouse Tibia | 1 | dx.doi.org/10.17504/protocols.io.e6nvwjmywlmk/v1 | https://www.protocols.io/view/proton-density-fat-fraction-pdff-measurement-of-my-cph6vj9e | Thomas L Chenevert, Thomas Chenevert | TITLE: Proton Density Fat Fraction (PDFF) Measurement of Myelofibrosis in Mouse Tibia
AUTHORS: Thomas L Chenevert, Thomas Chenevert
[DESCRIPTION]
This document details procedures for PDFF measurement in MF mouse tibia to achieve stated performance claims.In this profile PDFF values are expressed in “% units” on a 0 to... | [] |
91,412 | CUTAC for FFPEs | 1 | dx.doi.org/10.17504/protocols.io.14egn292zg5d/v3 | https://www.protocols.io/view/cutac-for-ffpes-c5huy36w | Steven Henikoff | TITLE: CUTAC for FFPEs
AUTHORS: Steven Henikoff
[DESCRIPTION]
For more than a century, Formalin Fixed Paraffin Embedded (FFPE) sample preparation has been the preferred method for long-term preservation of biological material. However, the use of FFPE samples for epigenomic studies has been difficult because of chroma... | ["[REAGENT SETUP (for up to 16 samples)] Cross-link reversal buffer Mix 8 ml 1 M Tris-HCl pH8.0, 2 ml dH2O and 4 µl 0.5 mM EDTA.\n\nRinse buffer (Option 1) Mix 1 mL 1 M HEPES pH 7.5 and 1.5 mL 5 M NaCl, and bring the final volume to 50 mL with dH2O.\n\nTriton-Wash buffer Mix 1 mL 1 M HEPES pH 7.5, 1.5 mL 5 M NaCl, 250 ... |
30,125 | Radius of Curvature Measurements to Determine Best Location for Fresh Osteochondral Allograft of the Capitellum | null | dx.doi.org/10.17504/protocols.io.9nmh5c6 | null | Zachary Goldstein, Michael Robbins, Austin Thompson, Scott Yang, Adam Mirarchi | TITLE: Radius of Curvature Measurements to Determine Best Location for Fresh Osteochondral Allograft of the Capitellum
AUTHORS: Zachary Goldstein, Michael Robbins, Austin Thompson, Scott Yang, Adam Mirarchi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Osteocondritis dissecans (OCD) is a focal cha... | ["Selecting a Patient & Formatting a. Obtain all CT images from the Department of Radiology tagged \"upper extremity\" or \"elbow\" and \"lower extremity\" or \"knee\". b. Review lists and exclude patients with indication of prior intra-articular fracture, surgery, degeneration, or variations of normal anatomy. ... |
81,752 | 10x Protocols: Chromium Single Cell/Nuclei Gene Expression Flex Multiplex-- University of Minnesota TMCs (CG000527 Rev C) | 1 | dx.doi.org/10.17504/protocols.io.5jyl8jy4dg2w/v1 | https://www.protocols.click/view/10x-protocols-chromium-single-cell-nuclei-gene-exp-ct3ywqpw | 10x Genomics | TITLE: 10x Protocols: Chromium Single Cell/Nuclei Gene Expression Flex Multiplex-- University of Minnesota TMCs (CG000527 Rev C)
AUTHORS: 10x Genomics
[DESCRIPTION]
10x Genomics Chromium Single Cell Expression flex protocol for library construction.
Protocol ID# (CG) and Revision letter provided here:
10x proto... | ["https://www.10xgenomics.com/products/single-cell-gene-expression-flex\nhttps://www.10xgenomics.com/support/single-cell-gene-expression-flex", "Complete single cell or nuclei isolation and 10x fixation prior to starting this protocol", "10x Protocol CG000527, Revision C (Library Construction):"] |
59,115 | Influenza virus plaque assay | 4 | dx.doi.org/10.17504/protocols.io.n2bvj63bxlk5/v1 | https://www.protocols.io/view/influenza-virus-plaque-assay-b5yjq7un | Steven F Baker | TITLE: Influenza virus plaque assay
AUTHORS: Steven F Baker
[DESCRIPTION]
Determine virus concentration from cell culture, lung homogenates, and more. This protocol measures virus in plaque forming units per ml solution.
This protocol differs from classic flu plaque assays by using a semi-solid overlay (Avicel) as o... | ["[Seed cells (day 1)] Collect and count MDCK cells\n\nFor the following steps, MDCK cells are maintained in 10 cm dishes in 10 ml volume of D10", "[Seed cells (day 1)] Wash & collect cells \n\n- Aspirate D10, add 4 ml sterile DPBS, aspirate\n- Trypsinize cells with 1 ml 0.25% trypsin for 5-15 min at 37 C, tap gently t... |
103,142 | DNA extraction - Zooplankton - 50 tubes | 4 | dx.doi.org/10.17504/protocols.io.36wgqnm9ygk5/v1 | https://www.protocols.io/view/dna-extraction-zooplankton-50-tubes-dgye3xte | coline.royaux, Nicolas Rabet, Céline Bonillo, Myriam Georges | TITLE: DNA extraction - Zooplankton - 50 tubes
AUTHORS: coline.royaux, Nicolas Rabet, Céline Bonillo, Myriam Georges
[DESCRIPTION]
This protocol is derived from the QIAamp DNA micro kit (QIAGEN) protocol and was used to extract DNA from whole or parts of zooplanktonic freshwater crustaceans (Copepoda, Branchiopoda, ..... | ["Prepare your 50 tubes with one individual per well. Alternate genus in the wells to detect eventual contamination between wells.", "Collect one individual from a sample", "Note its genus and determine its sex with a binocular microscope", "For big individuals (more than 5 mm), dissect a few legs and put it in the wel... |
18,297 | ddPCR | null | dx.doi.org/10.17504/protocols.io.v4ze8x6 | null | Lele Sun, Xiujun Cheng, Hong Liu, Furen Zhang | TITLE: ddPCR
AUTHORS: Lele Sun, Xiujun Cheng, Hong Liu, Furen Zhang
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS] | [] |
100,201 | Digestion with NEBNext dsDNA Fragmentase (M0348) | 1 | dx.doi.org/10.17504/protocols.io.j8nlk8w75l5r/v1 | https://www.protocols.io/view/digestion-with-nebnext-dsdna-fragmentase-m0348-dd4h28t6 | New England Biolabs | TITLE: Digestion with NEBNext dsDNA Fragmentase (M0348)
AUTHORS: New England Biolabs
[DESCRIPTION]
NEBNext dsDNA Fragmentase is an enzyme-based reagent that shears DNA to produce fragments of the desired sizes in a time-dependent manner, for next generation sequencing library preparation protocols
dsDNA Fragmentase ... | ["Combine the following components in a sterile PCR tube and vortex: \n component amount DNA (5 ng–3 μg) 1–16 μl 10X Fragmentase Reaction Buffer v2 2 μl Sterile Water variable", "Add 2 µL and vortex mixture for 3 s.", "Incubate at 37 °C for the recommended times below to generate the desired fragment size:\n \... |
93,351 | KneEZ Clear: an Effective Tissue Clearing Method for Intact Mouse Joints, including the Knee | 4 | dx.doi.org/10.17504/protocols.io.14egn3oxyl5d/v1 | https://www.protocols.io/view/kneez-clear-an-effective-tissue-clearing-method-fo-c7efzjbn | Julia Younis, Taeyong Ahn, Luis Tovias, Azeez Ishola, Brendan Lee, Joshua Wythe, Nele Haelterman | TITLE: KneEZ Clear: an Effective Tissue Clearing Method for Intact Mouse Joints, including the Knee
AUTHORS: Julia Younis, Taeyong Ahn, Luis Tovias, Azeez Ishola, Brendan Lee, Joshua Wythe, Nele Haelterman
[DESCRIPTION]
KneEZ Clear is a modified version of the EZ Clear method (Hsu et al., 2022), optimized for clearing... | ["[Retro-orbital Injection] Deeply anesthetize the mouse via inhalation of 4-5% isoflurane to induce anesthesia. Toe pinch to confirm animal is not receptive to painful stimuli.", "[Retro-orbital Injection] Using an insulin syringe, inject 50 µL of conjugated lectin to the retro-orbital sinus of the right and left eye.... |
69,627 | High Efficiency Transformation | 4 | dx.doi.org/10.17504/protocols.io.14egn2bdzg5d/v1 | https://www.protocols.io/view/high-efficiency-transformation-cf83tryn | New England Biolabs | TITLE: High Efficiency Transformation
AUTHORS: New England Biolabs
[DESCRIPTION]
Protocol for high efficiency heat shock transformation of competent E. coli cells.
Source: New England Biolabs
[STEPS]
1. Thaw a tube of competent E. coli cells on ice for 10 min. Mix gently and carefully pipette 50 µL of cells into a... | ["Thaw a tube of competent E. coli cells on ice for 10 min. Mix gently and carefully pipette 50 µL of cells into a transformation tube on ice.", "Add 1 µL containing 100 ng of plasmid DNA to the cell mixture. Carefully flick the tube 4-5 times to mix cells and DNA. Do not vortex.", "Place the mixture on ice for 30 min.... |
37,725 | PBS 1X | 3 | null | https://www.protocols.io/view/pbs-1x-bg35jyq6 | Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino | TITLE: PBS 1X
AUTHORS: Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This recepe is used in the following protocols:</div><div class = "text-block">- Separation and purification o... | [] |
92,424 | Thawing Frozen Adherent Cell Lines | 4 | dx.doi.org/10.17504/protocols.io.bp2l6xz3klqe/v1 | https://www.protocols.io/view/thawing-frozen-adherent-cell-lines-c6hgzb3w | Carolina Lopez | TITLE: Thawing Frozen Adherent Cell Lines
AUTHORS: Carolina Lopez
[DESCRIPTION]
This protocol describes the procedures from thawing and expanding adherent cell lines
[STEPS]
SECTION: Protocol (Sydney Faber_2023)
1. Day 1
Prepare media ahead of time and warm to room temperature
Spray down each bottle with 70% Ethanol ... | ["[Protocol (Sydney Faber_2023)] Day 1\nPrepare media ahead of time and warm to room temperature\nSpray down each bottle with 70% Ethanol before placing it into the TC hood\nPre-cool the centrifuge to 4C\nPrepare and label a 6-well plate, and aliquot 9mL of media into a 15mL conical for each tube of cells to be thawed\... |
66,878 | Purification of human ATP13A2 for cryo-EM analysis | 1 | dx.doi.org/10.17504/protocols.io.261genmojg47/v1 | https://www.protocols.io/view/purification-of-human-atp13a2-for-cryo-em-analysis-cdi6s4he | Sue Sim, eunyong_park | TITLE: Purification of human ATP13A2 for cryo-EM analysis
AUTHORS: Sue Sim, eunyong_park
[DESCRIPTION]
Purification of GFP-tagged human ATP13A2 expressed in Sf9 cells for cryo-EM analysis
[STEPS]
SECTION: Day 1: Crude membrane preparation and solubilization
1. Thaw Sf9 cell pellets at room temperature (typical siz... | ["[Day 1: Crude membrane preparation and solubilization] Thaw Sf9 cell pellets at room temperature (typical size around 10 g from 0.7L of culture)", "[Day 1: Crude membrane preparation and solubilization] All subsequent steps performed at 4 °C", "[Day 1: Crude membrane preparation and solubilization] Resuspend each pel... |
77,069 | TMA-TNP Section Map and Slide Processing - Phase 4 | 1 | dx.doi.org/10.17504/protocols.io.ewov1o7wolr2/v1 | https://www.protocols.io/view/tma-tnp-section-map-and-slide-processing-phase-4-cphmvj46 | Heidi S Feiler | TITLE: TMA-TNP Section Map and Slide Processing - Phase 4
AUTHORS: Heidi S Feiler
[DESCRIPTION]
Human Tumor Atlas Tissue MicroArrary TNP (TMA-TNP)
The Tissue MicroArray (TMA) TNP will extend the SARDANA-TNP characterization and analytics methodologies for evaluation and validation on a large array of breast tumor ... | ["[Preparation] Verify the identity of the FFPE block to be cut against written request for sectioning. The FFPE block (TMA1) will be utilized for TMA-TNP Phase 4.", "[Preparation] Each slide was labeled with a unique OHSU Slide ID corresponding to the FFPE section map (below).\n\n Slide ID ... |
59,070 | PLOS ONE | 2 | dx.doi.org/10.17504/protocols.io.b5w6q7he | https://www.protocols.io/view/plos-one-b5w6q7he | Anna Guzek | TITLE: PLOS ONE
AUTHORS: Anna Guzek
[DESCRIPTION]
Analysis of auditory deficits of 1,012 children aged 6 to 9 confirmed the adequacy of use ofthe APD testing in 6-year-old children
[STEPS] | [] |
21,330 | Yale - Creatine Kinase Activity | null | dx.doi.org/10.17504/protocols.io.y3sfyne | null | John Stack, Gary Cline | TITLE: Yale - Creatine Kinase Activity
AUTHORS: John Stack, Gary Cline
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Procedure used to determine the creatine kinase activity in blood , serum, and plasma. Creatine kin... | ["Calibrate Cobas for the measurement of creatine kinase activity analysis by running two control serum.", "Sample handling as performed by the Cobas Mira Plus. a) Pipette 4.5 µL of sample into a cuvette slot. b) Add 175 µL of CK NADP Imidazole Reagent. c) Mixture is incubated at 37ºC and spun for 10 minutes. ... |
62,248 | Cardio Clear 7: Heart-Related Issues are Treated Quickly | 1 | dx.doi.org/10.17504/protocols.io.bp2l61r4zvqe/v1 | https://www.protocols.io/view/cardio-clear-7-heart-related-issues-are-treated-qu-b82grybw | shjfgkoza | TITLE: Cardio Clear 7: Heart-Related Issues are Treated Quickly
AUTHORS: shjfgkoza
[DESCRIPTION]
There you have it, you have the risk of being branded as a fool. As I mentioned, take Cardio Clear 7 the time to develop that incident. You might sense that I'm on a wild goose chase. Doing that would be the evil of two ... | [] |
49,797 | Sequence processing and assembly workflow using CLC workbench, SortMeRNA, and MegaHit. | 5 | dx.doi.org/10.17504/protocols.io.buvdnw26 | https://www.protocols.io/view/sequence-processing-and-assembly-workflow-using-cl-buvdnw26 | Helena Pound, Steven Wilhelm | TITLE: Sequence processing and assembly workflow using CLC workbench, SortMeRNA, and MegaHit.
AUTHORS: Helena Pound, Steven Wilhelm
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The protocol details one of many methods available to process and assemble sequence data using CLC workbench, SortMeRNA... | ["Upload sequence files to CLC workbench, indicating whether the reads are paired-end or single-end. Choose quality control parameters.", "We recommend removing failed reads and not demultiplexing.", "Trimmed reads should then be exported as fastq files, maintaining 2 files for pair-end reads.", "If multiple lanes were... |
61,025 | HuBMAP | VU TMC Eye/Pancreas | Histopathology Assessment of Human Pancreas | 1 | dx.doi.org/10.17504/protocols.io.j8nlkkdz1l5r/v1 | https://www.protocols.io/view/hubmap-vu-tmc-eye-pancreas-histopathology-assessme-b7t9rnr6 | Adel Eskaros, Jordan Wright, Annika Windon, Alvin C. Powers | TITLE: HuBMAP | VU TMC Eye/Pancreas | Histopathology Assessment of Human Pancreas
AUTHORS: Adel Eskaros, Jordan Wright, Annika Windon, Alvin C. Powers
[DESCRIPTION]
The purpose of this protocol is to outline the parameters for pathologic and morphologic assessment of human pancreatic tissue. This protocol was develope... | ["Image H&E-stained tissues prepared according to standard protocol using a whole-slide digital scanner (Aperio ScanScope or Zeiss AxioScan) at 20X magnification. Slides may also be reviewed under a light microscope (Olympus Bx41).\n \n\nDownload example H&E images (shown in Figures here):", "Assess and record patholog... |
42,917 | How to measure empowerment in sexual health? Definitions and measurement indicators. A scoping review protocol | 1 | dx.doi.org/10.17504/protocols.io.bm6dk9a6 | https://www.protocols.io/view/how-to-measure-empowerment-in-sexual-health-defini-bm6dk9a6 | Karna Coulibaly, Anne Gosselin, Annabel Desgrées du Loû | TITLE: How to measure empowerment in sexual health? Definitions and measurement indicators. A scoping review protocol
AUTHORS: Karna Coulibaly, Anne Gosselin, Annabel Desgrées du Loû
[STEPS]
?. Title and authors identificationHow to measure empowerment in sexual health? Definitions and measurement indicators. A scopin... | ["Title and authors identificationHow to measure empowerment in sexual health? Definitions and measurement indicators. A scoping review protocolKarna Coulibaly1,2, Anne Gosselin1,2,3, Annabel Desgrées du Loû1,21CEPED, Institute for Research on Sustainable Development, IRD-Université de Paris, ERL INSERM U1244 SAGESUD,... |
43,547 | Isolation of Extracellular Vesicles from Cell Culture Media by Differential Ultracentrifugation | 4 | dx.doi.org/10.17504/protocols.io.bnr3md8n | https://www.protocols.io/view/isolation-of-extracellular-vesicles-from-cell-cult-bnr3md8n | Dima Ter-Ovanesyan, Wendy Trieu , Maia Norman, Roey Lazarovits, George Church, David Walt | TITLE: Isolation of Extracellular Vesicles from Cell Culture Media by Differential Ultracentrifugation
AUTHORS: Dima Ter-Ovanesyan, Wendy Trieu , Maia Norman, Roey Lazarovits, George Church, David Walt
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Extracellular vesicles (EVs) are released by all ... | ["Culture cells under standard conditions to 50–70% confluency.", "[Day 1]\nFor adherent cells: Aspirate media from twelve 15 cm plates.", "[Day 2]\nAfter 24 hours, take off all media and divide among 50 mL falcon tubes.", "[Day 2]\nSpin at 300 x g for 10 minutes at RT to pellet the cells.", "[Day 2]\nTransfer supernat... |
81,168 | Hydroponic Seedling Culture for Low-Contaminant Wheat Tissue Collection | 4 | dx.doi.org/10.17504/protocols.io.kqdg39zmeg25/v1 | https://www.protocols.io/view/hydroponic-seedling-culture-for-low-contaminant-wh-cthqwj5w | Daniela Miller | TITLE: Hydroponic Seedling Culture for Low-Contaminant Wheat Tissue Collection
AUTHORS: Daniela Miller
[DESCRIPTION]
De-novo gene annotation of wheat genome assemblies and other RNA-seq studies require tissue collection from various tissues, including roots, for RNA extraction and sequencing. Obtaining clean tissue sa... | ["[Growth Chamber Preparation] Prepare a cover tray for the tank.", "[Transplanting Seedlings] Gently transfer a single germinated seedling into a 3\" foam slice, taking care to ensure the roots are beyond the bottom of the foam and the shoot is pointed upwards.", "[Flash-Frozen Tissue Collection] Following safety prec... |
100,998 | Preparation of ventral midbrain cells for transplantation | 0 | dx.doi.org/10.17504/protocols.io.rm7vzjjkxlx1/v1 | https://www.protocols.io/view/preparation-of-ventral-midbrain-cells-for-transpla-deve3e3e | Tyra Fraser, Lachlan Thompson | TITLE: Preparation of ventral midbrain cells for transplantation
AUTHORS: Tyra Fraser, Lachlan Thompson
[DESCRIPTION]
This protocol outlines the preparation of iPSC derived ventral midbrain progenitors for xenotransplantation.
[BEFORE_START]
D19 iPSC derived ventral midbrain progenitors are used in this protocol
[G... | ["[Experimental details] Wash wells with 1 x PBS -/- \nIncubate cells in 484 µL of Accutase per cm2 at 37 °C. Note: D19 typically dissociate between 10-20mins.\nPrepare a 15 mL falcon tube for cells. \nCheck dissociation after 6 min by using a p1000 to pipette up and down twice onto the\ncells. Observe if cells dislodg... |
null | null | null | dx.doi.org/10.17504/protocols.io.ufuetnw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?. | ["Larvae were dissected in PBS to produce muscle fillets.", "Fillets were incubated in 20 mM 2',7'-dichlorodihydrofluorescein diacetate (H2DCFDA) for 30 m at 23° C.", "Fillets were washed twice in PBS, fixed in 2% paraformaldehyde for 10 minutes at 23° C, mounted on glass slides and imaged by confocal laser scanning mi... |
76,855 | Freezing protocol for Escherichia coli | 4 | null | https://www.protocols.io/view/freezing-protocol-for-escherichia-coli-cpaxvifn | Andreas Sagen | TITLE: Freezing protocol for Escherichia coli
AUTHORS: Andreas Sagen
[DESCRIPTION]
An optimized freezing protocol of E. coli based on Zimmer and Verrinder Gibbins 1997.
[STEPS]
SECTION: Preparation of LB Freezing Buffer
6. Fill 80 mL LB-Lennox to a Duran bottle
SECTION: Freezing procedure
11. Transfer a saturated cul... | ["[Preparation of LB Freezing Buffer] Fill 80 mL LB-Lennox to a Duran bottle", "[Freezing procedure] Transfer a saturated culture of E. coli cells", "[Preparation of LB Freezing Buffer] Fill to 100 mL with LB-Lennox", "[Preparation of LB Freezing Buffer] Adjust pH to pH 7.0", "[Preparation of LB Freezing Buffer] Dissol... |
null | null | null | dx.doi.org/10.17504/protocols.io.hvib64e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Lminex Milliplex Soluble Cytokine Receptor 13-plex manufacturer's protocol</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
98,165 | Загрузка сиквенсов в базу данных коллекции (Specify 7) и экспорт данных в GenBank и GBIF | 0 | dx.doi.org/10.17504/protocols.io.3byl4975jgo5/v1 | https://www.protocols.io/view/specify-7-genbank-gbif-db4v2qw6 | Nina Filippova, Elena Zvyagina | TITLE: Загрузка сиквенсов в базу данных коллекции (Specify 7) и экспорт данных в GenBank и GBIF
AUTHORS: Nina Filippova, Elena Zvyagina
[DESCRIPTION]
Protocol for uploading sequences and their metadata into the Specify 7 database and subsequent export of data to GenBank and GBIF.
The first stage of preparing sequence... | ["[Подготовка сиквенсов] Первая стадия подготовки сиквенсов включает их первичную обработку (обрезание концов, ассемблинг, и другие операции по необходимости), сохранение готовой отредактированной последовательности и комментарии в лабораторном журнале.", "[Подготовка сиквенсов] Создать проект для первичного редактиров... |
null | null | null | dx.doi.org/10.17504/protocols.io.t5req56 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?. | ["null"] |
85,008 | Targeted analysis of 5-Fluorouracil (5-FU) and Fluoroacetate (FAC) in human plasma by automated PPT+ extraction and LC-HRMS analysis | 1 | dx.doi.org/10.17504/protocols.io.kxygx3p2kg8j/v1 | https://www.protocols.io/view/targeted-analysis-of-5-fluorouracil-5-fu-and-fluor-cw9qxh5w | Margaux Billen, Scott G Denham, Joanna P Simpson, Natalie ZM Homer | TITLE: Targeted analysis of 5-Fluorouracil (5-FU) and Fluoroacetate (FAC) in human plasma by automated PPT+ extraction and LC-HRMS analysis
AUTHORS: Margaux Billen, Scott G Denham, Joanna P Simpson, Natalie ZM Homer
[DESCRIPTION]
This protocol describes the extraction and targeted high-resolution mass spectrometry ana... | ["[Extraction Procedure] Acquire or build a sample list for the samples in Microsoft Excel including experimental details and unique sample identification codes.", "[Extraction Procedure] Complete plate map for standards and samples (make sure to place them column-wise) using the design as shown. The number of samples ... |
null | null | null | dx.doi.org/10.17504/protocols.io.g8zbzx6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Silver staining of a acrylamide gel. </p>
[GUIDELINES]
<p><span style="text-decoration: underline;"><strong>Fixate-solution:</strong></span></p>
<p>50 ml. ethanol </p>
<p>12 ml. acetic acid</p>
<p>50 µl filtered 37% formaldehyde</p>
<p> -> 100 ml. H<sub>2</sub>O</p>
<p> <... | [] |
52,107 | E. coli CRISPR Barcoding | 4 | null | https://www.protocols.io/view/e-coli-crispr-barcoding-bw5jpg4n | Leanne Hobbs | TITLE: E. coli CRISPR Barcoding
AUTHORS: Leanne Hobbs
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This is the protocol for barcoding </span><span style = "font-style:italic;">E. coli</span><span> using CRISPR for CellRepo</span></div><br/><br/></div>
[STEPS]
?. [Day 1]
Start an overnight ... | ["[Day 1]\nStart an overnight culture (37 °C) by inoculating LB medium from a single colony.", "[Day 2]\nPrepare competent cells following your favorite protocol.", "[Day 2]\nTransform E. coli cells with plasmid pREDCas9 and plate the cells at 30 °C in LB supplemented with 50 µg/mL spectinomycin.", "[Day 3]\nStart an o... |
79,752 | first-workflow-Playarists | 5 | dx.doi.org/10.17504/protocols.io.5jyl8jo1rg2w/v1 | https://www.protocols.io/view/first-workflow-playarists-cr5gv83w | Ali Ghasempouri, maddalena.ghiotto, sebastiano.giacomini | TITLE: first-workflow-Playarists
AUTHORS: Ali Ghasempouri, maddalena.ghiotto, sebastiano.giacomini
[DESCRIPTION]
In this study, we present a comprehensive workflow to assess the coverage of publications in Social Science and Humanities (SSH) journals indexed in ERIH-PLUS and their Open Access status according to the D... | ["[Retrieve OpenCitation Meta publication and Journals that are registered in ERIH-PLUS index] Starting from the ERIH-PLUS index of Social Science and Humanities approved journals dataset \n (downloaded 23/03/2023) we want to retreive all the publications belonging to one of those journals, included in OpenCitation Me... |
45,926 | Root-to-shoot organogenesis in Citrus jambhiri Lush. | 4 | dx.doi.org/10.17504/protocols.io.bq4emyte | https://www.protocols.io/view/root-to-shoot-organogenesis-in-citrus-jambhiri-lus-bq4emyte | Tongbram Roshni Devi, Madhumita Dasgupta, MANAS RANJAN SAHOO, Paresh Chandra Kole, Narendra Prakash | TITLE: Root-to-shoot organogenesis in Citrus jambhiri Lush.
AUTHORS: Tongbram Roshni Devi, Madhumita Dasgupta, MANAS RANJAN SAHOO, Paresh Chandra Kole, Narendra Prakash
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>A protocol for high-frequency direct organogenesis from root explants of </sp... | ["Plant materials and explant preparationThe mature and healthy fruits of Citrus jambhiri Lush. were collected from the Kachai village of Ukhrul District, Manipur, India. Seeds were removed from the pulp, allowed to dry at room temperature for 2-3 days (d). Such dry seeds were soaked in distilled water for 20-30 min, a... |
null | null | null | dx.doi.org/10.17504/protocols.io.ew7bfhn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol describes how to extract total RNA from flatworms. It is from:<br /><br /><em><span style="color: #222222; font-family: arial, sans-serif; font-size: 12.8px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal;... | [] |
36,062 | Mitochondrial staining of NK cells by flow cytometry | 1 | dx.doi.org/10.17504/protocols.io.e6nvw9222gmk/v1 | https://www.protocols.click/view/mitochondrial-staining-of-nk-cells-by-flow-cytomet-bff6jjre | Philippa R Kennedy | TITLE: Mitochondrial staining of NK cells by flow cytometry
AUTHORS: Philippa R Kennedy
[DESCRIPTION]
Mitotracker Green (Thermo Fisher Scientific, cat. M7514) stains mitochondrial membranes, so gives a quick measure of mitochondrial mass per cell. However, it is not always as sensitive as quantifying mitochondrial mas... | ["[Mitotracker and TMRM combined staining (keep on ice)] Resuspend 1x10^6 cells in 850 μL RPMI medium (no serum) for all tubes. Keep tubes on ice", "[Mitotracker and TMRM combined staining (keep on ice)] Before diluting reagents, set up the CCCP negative controls:\nAdd 1 μL CCCP to tubes containing 1x10^6 cells in 850... |
null | null | null | dx.doi.org/10.17504/protocols.io.jqucmww | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?. | [] |
20,237 | Chromatographic separation of neodymium isotopes in human dental enamel for Thermal Ionisation Mass Spectrometry (TIMS) analysis | null | dx.doi.org/10.17504/protocols.io.xzmfp46 | null | Esther Plomp, Richard Smeets, Janne Koornneef, Gareth Davies | TITLE: Chromatographic separation of neodymium isotopes in human dental enamel for Thermal Ionisation Mass Spectrometry (TIMS) analysis
AUTHORS: Esther Plomp, Richard Smeets, Janne Koornneef, Gareth Davies
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for sample collection, dissolution an... | ["[Enamel collection]\nSample the enamel using a micro-drill fitted with a cleaned diamond-tipped rotary burr and blade (Minilor Perceuse). Burrs and blades should be cleaned before sampling teeth from different individuals to prevent contamination: Rinse with ethanol, 3 N HNO3 (Sigma-Aldrich Company Ltd) and ultrasoun... |
42,315 | Chapter 9: Release | 4 | null | https://www.protocols.io/view/chapter-9-release-bmjjk4kn | Kerri Wolter | TITLE: Chapter 9: Release
AUTHORS: Kerri Wolter
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes when, where, and how to release vultures after successful rehabilitation.</div></div>
[STEPS]
?. When releasing a vulture, lower your body (see CHAPTER 1 for pictures), bringing t... | ["When releasing a vulture, lower your body (see CHAPTER 1 for pictures), bringing the bird’s feet to ground level, slowly allowing the bird to stand.", "Then release your grip on its entire body and neck at the same time, stepping away to give the bird some space. Be careful never to drop or throw the bird down, nor a... |
94,914 | Single Cell Sequencing 10x Chromium 5’ VDJ | 4 | dx.doi.org/10.17504/protocols.io.e6nvwdr77lmk/v1 | https://www.protocols.io/view/single-cell-sequencing-10x-chromium-5-vdj-c8xazxie | Travis Dawson, Robert Marvin, Grace Chung | TITLE: Single Cell Sequencing 10x Chromium 5’ VDJ
AUTHORS: Travis Dawson, Robert Marvin, Grace Chung
[DESCRIPTION]
Single cell RNA sequencing technique (scRNA-Seq) obtains gene expression profiles of individual cells for analysis, as opposed to comparing averaged gene expression signals between bulk samples of cells. ... | ["[GEM Generation and RT Reaction] Prepare master mix on ice. Pipette mix 15x and centrifuge briefly.", "[GEM Generation and RT Reaction] Add 37.2 μl Master Mix into each tube of a PCR 8-tube strip on ice.", "[GEM Generation and RT Reaction] Assemble Chromium Next GEM Chip G:", "[GEM Generation and RT Reaction] Load 50... |
92,360 | Non-Enzymatic Generation of Placenta Single Cells from Third Trimester Human Placenta | 1 | dx.doi.org/10.17504/protocols.io.yxmvm3b99l3p/v1 | https://www.protocols.io/view/non-enzymatic-generation-of-placenta-single-cells-c6fgzbjw | Ameloko Joy, Idowu Aimola, Fomukong A Hanneda, Reuben B. Samson, Zeenat B Kudan, Habiba H. Abubakar, Musa Kana, Benedict Anchang | TITLE: Non-Enzymatic Generation of Placenta Single Cells from Third Trimester Human Placenta
AUTHORS: Ameloko Joy, Idowu Aimola, Fomukong A Hanneda, Reuben B. Samson, Zeenat B Kudan, Habiba H. Abubakar, Musa Kana, Benedict Anchang
[DESCRIPTION]
The placenta is a heterogeneous and complex organ with multiple cell types... | ["[Placenta Single Cell Preparation Protocol] Transform placenta sections into gentle MACs C-tube containing 3000 µL of MACs running buffer.", "[Placenta Single Cell Preparation Protocol] Set up a gentle MACS dissociator program to h-cord-01 for 553 rotation per round (rpr) at\n30 s.", "[Placenta Single Cell Preparatio... |
101,222 | Directed cardiac lineage differentiation of human pluripotent stem cells | 0 | dx.doi.org/10.17504/protocols.io.x54v922bzl3e/v1 | https://www.protocols.io/view/directed-cardiac-lineage-differentiation-of-human-de4e3gte | Fan Li, Jingli Cai, Wenli Yang, Hao Wu | TITLE: Directed cardiac lineage differentiation of human pluripotent stem cells
AUTHORS: Fan Li, Jingli Cai, Wenli Yang, Hao Wu
[DESCRIPTION]
Robust cardiac lineage differentiation from human pluripotent stem cells (hPSCs) holds great potential for regenerative medicine, disease modeling, and drug discovery. Adapted f... | ["[Materials / Reagent Information] DMEM/F12: Thermofisher cat# 11330-032\nStemMACS iPS-Brew XF, human: Miltenyi Biotec cat# 130-104-368\nGeltrex‱ LDEV-Free RGF: Thermofisher cat# A1413202\nRPMI 1640: Life Technologies, cat. #11875-085 (1 L)\nB-27 (plus insulin): Life Technologies, cat. #17504-044 (10 mL) \nB-27 (minus... |
17,502 | Methods Paper Using Household survey data to identify large-scale food security patterns across Uganda | null | dx.doi.org/10.17504/protocols.io.vb6e2re | null | Jannike Wichern, Joost van Heerwaarden, Mark van Wijk | TITLE: Methods Paper Using Household survey data to identify large-scale food security patterns across Uganda
AUTHORS: Jannike Wichern, Joost van Heerwaarden, Mark van Wijk
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify">To target food security int... | ["[Spatial interpolation of household survey data]\nStep 1: Household level food availability analysisIn this step the household data are used to calculate food availability and the contributing activities on household level. To run the household level food availability analysis household survey data must be downloaded... |
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