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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null | null | null | dx.doi.org/10.17504/protocols.io.p5mdq46 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is the protocol I have developed to genterate High'ish' Molecular Weight gDNA from gram negative bacterial speices to use for ONT MinION sequencing.</p>
<p> </p>
<p>This protocol was intially developed for the high throughput extraction of bacterial gDNA for Illumina sho... | [] |
63,822 | Amyloid dye-binding analysis of α-synuclein fibrils | 4 | dx.doi.org/10.17504/protocols.io.x54v9yznpg3e/v1 | https://www.protocols.io/view/amyloid-dye-binding-analysis-of-synuclein-fibrils-cajnscme | Arpine Sokratian | TITLE: Amyloid dye-binding analysis of α-synuclein fibrils
AUTHORS: Arpine Sokratian
[DESCRIPTION]
This protocol describes the amyloid binding assay used to capture the conformational signatures in expanded cohort of a-synuclein fibrils. Specific amyloid dyes indicated in the protocol display a distinct binding affini... | ["[Dye preparation] Prepare / thaw down the dye powder at Room temperature \n , ,", "[Dye preparation] Dissolve the dyes in DMSO to final concentration 15 millimolar (mM) for NIAD-4, Nile Red and FSB, \nDissolve ThT in ddH2O to final concentration1 millimolar (mM) \nStore aliquots at -80 °C", "[Dye preparation] F... |
24,407 | Media and reagents for Seminavis robusta cultivation and experiments | null | dx.doi.org/10.17504/protocols.io.33xgqpn | null | Lev Tsypin, Aaron Turkewitz | TITLE: Media and reagents for Seminavis robusta cultivation and experiments
AUTHORS: Lev Tsypin, Aaron Turkewitz
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describes the culturing conditions used to grow </span><span style = "font-style:italic;">S. robusta </span><span>in th... | ["[Preparation of F/2 medium]\nDissolve in\n[Tropic-Marin Bioactif (TMB)]\n[MilliQ water]", "[Preparation of F/2 medium]\nAdd\n[sodium bicarbonate]", "[Preparation of F/2 medium]\nAutoclave", "[Maintenance antibiotics (200x stock)]\nDissolve , , , and in a final volume of .\n[penicillin G sodium salt]\n[ampicillin so... |
89,711 | Implementing a Health Curriculum for the Kupuna Class of Honolulu to Improve Health Literacy: An Evidence-Based Review | 1 | null | https://www.protocols.io/view/implementing-a-health-curriculum-for-the-kupuna-cl-c3upynvn | Jaymie Barnes, Rayson-Lee Egan, hannabs, Louis Langi, pakjenna, cmh, Samia Valeria Ozorio Dutra | TITLE: Implementing a Health Curriculum for the Kupuna Class of Honolulu to Improve Health Literacy: An Evidence-Based Review
AUTHORS: Jaymie Barnes, Rayson-Lee Egan, hannabs, Louis Langi, pakjenna, cmh, Samia Valeria Ozorio Dutra
[DESCRIPTION]
The absence of specialized health
education for seniors may lead to decrea... | [] |
34,623 | Ligand docking using Patchdock for Biochemistry I | 1 | null | https://www.protocols.io/view/ligand-docking-using-patchdock-for-biochemistry-i-bd27i8hn | Chris Berndsen | TITLE: Ligand docking using Patchdock for Biochemistry I
AUTHORS: Chris Berndsen
[STEPS]
?. [Docking setup]
Navigate to Patchdock
?. [Docking setup]
In Receptor molecule: Provide your PDB file as a RCSB code OR upload a .PDB file
The receptor molecule is your protein/biomolecule and is generally the larger of the two ... | ["[Docking setup]\nNavigate to Patchdock", "[Docking setup]\nIn Receptor molecule: Provide your PDB file as a RCSB code OR upload a .PDB file\nThe receptor molecule is your protein/biomolecule and is generally the larger of the two molecules.", "[Docking setup]\nIn Ligand molecule: Provide your PDB file as a RCSB code ... |
88,907 | Microindentation of Fresh Soft Biological Tissue: A Rapid Tissue Sectioning and Mounting Protocol | 1 | dx.doi.org/10.17504/protocols.io.q26g7pxm3gwz/v1 | https://www.protocols.io/view/microindentation-of-fresh-soft-biological-tissue-a-c23jygkn | Clíona M. McCarthy, Kevin L. McKevitt, Sinéad A. Connolly, Isabel Andersson, Fiona C. Leahy, Michael A. Moloney, Eamon G. Kavanagh, Eoghan M. Cunnane, Kieran D. McGourty, Michael T. Walsh, John J.E. Mulvihill | TITLE: Microindentation of Fresh Soft Biological Tissue: A Rapid Tissue Sectioning and Mounting Protocol
AUTHORS: Clíona M. McCarthy, Kevin L. McKevitt, Sinéad A. Connolly, Isabel Andersson, Fiona C. Leahy, Michael A. Moloney, Eamon G. Kavanagh, Eoghan M. Cunnane, Kieran D. McGourty, Michael T. Walsh, John J.E. Mulvihi... | ["[Procedure for the fresh biological tissue sectioning with the Compresstome® VF-210-0Z] Prepare 1X PBS for use as a solvent for the embedding solution and as a buffer during tissue sectioning.", "[Procedure for the fresh biological tissue sectioning with the Compresstome® VF-210-0Z] Place the chilling block (Figure 1... |
40,050 | Protocol 1: Micropipette | 4 | null | https://www.protocols.io/view/protocol-1-micropipette-bjcskiwe | TITLE: Protocol 1: Micropipette
AUTHORS:
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>For this lab, you will understand the </span><span style = ":UNDERLINE;">mechanics</span><span>, know how t</span><span style = ":UNDERLINE;">o use the buttons</span><span>, and understand the </span><s... | ["[Using the Micropipette]\nHold Micropipette firmly in hand.", "[Using the Micropipette]\nTurn the dial to the respective volume. Make sure you do not turn the dial past the maximum point.", "[Using the Micropipette]\nNow, gently press on the top of the pipette until you reach the first click.Release the the button to... | |
87,571 | Mechanical Dissociation using COVARIS cyroPREP | 4 | dx.doi.org/10.17504/protocols.io.eq2lyj6zrlx9/v1 | https://www.protocols.io/view/mechanical-dissociation-using-covaris-cyroprep-czrtx56n | aurelia_reynolds | TITLE: Mechanical Dissociation using COVARIS cyroPREP
AUTHORS: aurelia_reynolds
[DESCRIPTION]
Prior to nuclei isolation from frozen tissue it is necessary to pulverize the sample. The Covaris cryoPREP Dry Pulverizer allows for dry, non-contact cryopulverization of tissue samples in a closed system. The manufacturer’s ... | ["[Preparation] Clean off bench space with RNAse away then 70% EtOH.", "[Preparation] Prepare for nuclei isolation (see Nuclei Isolation Protocol).", "[Preparation] Gather dry ice bucket, wet ice bucket, and empty bucket for LN2.", "[Preparation] USING SAFETY GOGGLES AT ALL TIMES, gather LN2. Use specific LN2 container... |
54,670 | Protocol: Comparative efficacy of sedation or analgesia methods for reduction of anterior shoulder dislocation: a systematic review and network meta-analysis | 1 | dx.doi.org/10.17504/protocols.io.bzmnp45e | https://www.protocols.io/view/protocol-comparative-efficacy-of-sedation-or-analg-bzmnp45e | Minoru Hayashi, Kenichi Kano, Naoto Kuroda, Norio Yamamoto, Akihiro Shiroshita, Yuki Kataoka | TITLE: Protocol: Comparative efficacy of sedation or analgesia methods for reduction of anterior shoulder dislocation: a systematic review and network meta-analysis
AUTHORS: Minoru Hayashi, Kenichi Kano, Naoto Kuroda, Norio Yamamoto, Akihiro Shiroshita, Yuki Kataoka
[DESCRIPTION]
The objectives are as follows:
To rev... | [] |
80,210 | Desalting of Peptides to Prepare for Mass Spectrometry Analysis | 4 | dx.doi.org/10.17504/protocols.io.6qpvr4n3ogmk/v1 | https://www.protocols.io/view/desalting-of-peptides-to-prepare-for-mass-spectrom-csjswcne | Alexandra Naba, jconsi | TITLE: Desalting of Peptides to Prepare for Mass Spectrometry Analysis
AUTHORS: Alexandra Naba, jconsi
[DESCRIPTION]
Prior to proteomic analysis, peptide samples are desalted and eluted with freshly prepared 50% acetonitrile, 0.1% trifluoroacetic acid, followed by concentration in a vacuum concentrator. Peptides are t... | ["[Column Preparation] Column Preparation", "[Column Preparation] Take a Pierce peptide desalting spin column and remove the white tip (do not remove the screw cap of the tube). Place in a 2mL tube and spin column at for 1 min.", "[Column Preparation] Add 300 µLof acetonitrile. Spin at for 1 minand discard flow-thro... |
75,001 | P21.- REVISIÓN Y CONTROL DEL PROCESO DE PRESENTACIÓN PLANES DE INVESTIGACIÓN | 1 | dx.doi.org/10.17504/protocols.io.j8nlkw3w5l5r/v1 | https://www.protocols.io/view/p21-revisi-n-y-control-del-proceso-de-presentaci-n-cmgzu3x6 | cgarcia | TITLE: P21.- REVISIÓN Y CONTROL DEL PROCESO DE PRESENTACIÓN PLANES DE INVESTIGACIÓN
AUTHORS: cgarcia
[DESCRIPTION]
Atendiendo a las particularidades de la Aplicación LAUREA ACADEMIC, el proceso de presentación del Plan de Investigación inicial por parte de los doctorandos, actualmente queda únicamente bajo la supervis... | ["[P21.- REVISIÓN Y CONTROL DEL PROCESO DE PRESENTACIÓN PLANES DE INVESTIGACIÓN] DESCRIPCIÓN DEL PROCESO\n\n1.- En la primera semana de cada mes, la Secretaría de la EIDUCAM enviará un informe de estado de inscripciones de Planes de Investigación a las Comisiones Académicas. En este informe incluirá la siguiente inform... |
70,119 | Secondary Data Analysis - Creating a MycoMap Project from ONT Amplicon/Barcode Data | 5 | dx.doi.org/10.17504/protocols.io.261genybdg47/v2 | https://www.protocols.io/view/secondary-data-analysis-creating-a-mycomap-project-cgqftvtn | Stephen Douglas Russell | TITLE: Secondary Data Analysis - Creating a MycoMap Project from ONT Amplicon/Barcode Data
AUTHORS: Stephen Douglas Russell
[DESCRIPTION]
This protocol outlines many of the steps that can be taken after the primary data analysis to expedite the final analysis - turning your data into results.
Topics include c... | ["[Validate Your Data] Before any further analytical work is done, it is always a good idea to validate the fidelity of your sequences to the iNat/MO records. As a part of the primary data analysis, you linked a spreadsheet of iNat/MO numbers to the unique primer tags for each specimen. Sometimes there are systematic e... |
37,778 | 4% PFA + 2.5% Glutaraldehyde Fixative | 1 | dx.doi.org/10.17504/protocols.io.bg5sjy6e | https://www.protocols.io/view/4-pfa-2-5-glutaraldehyde-fixative-bg5sjy6e | Allen Institute for Brain Science | TITLE: 4% PFA + 2.5% Glutaraldehyde Fixative
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used to prepare 4% Paraformaldehyde (PFA) + 2.5% Glutaraldehyde Fixative. This is utilized to fix the tissue after electrophysiology recordings. </... | [] |
35,908 | Dual-light photodynamic therapy administered daily provides a sustained antibacterial effect on biofilm and prevents Streptococcus mutans adaptation | 1 | dx.doi.org/10.17504/protocols.io.bfbcjiiw | https://www.protocols.io/view/dual-light-photodynamic-therapy-administered-daily-bfbcjiiw | Sakari Nikinmaa, Tommi Patila | TITLE: Dual-light photodynamic therapy administered daily provides a sustained antibacterial effect on biofilm and prevents Streptococcus mutans adaptation
AUTHORS: Sakari Nikinmaa, Tommi Patila
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Antibacterial photodynamic therapy (aPDT) and antib... | ["[Grow the planctonic bacteria and provide a standard bacterial concentration in suspension ]\nGrow Streptococcus mutans (ATCC 25175) bacteria for 18 h in an incubator (NuAire DH autoflow 5500, NuAire inc, US), at +36 degrees C, 5% CO2in BHI broth (Bio-Rad 3564014, Bio-Rad Laboratories, Inc, US).", "[Grow the plancton... |
94,142 | Immunophenotyping of the peripheral blood immune cells by flow cytometry | 4 | dx.doi.org/10.17504/protocols.io.36wgq3zoylk5/v1 | https://www.protocols.io/view/immunophenotyping-of-the-peripheral-blood-immune-c-c766zrhe | mariangela.massarocenere, Valerio Chiurchiù | TITLE: Immunophenotyping of the peripheral blood immune cells by flow cytometry
AUTHORS: mariangela.massarocenere, Valerio Chiurchiù
[DESCRIPTION]
Protocol for immunophenotyping peripheral blood immune cells
[STEPS]
1. Deeply anesthetize the animal. Check for no reflexes and slower breathing
2. Cut the animal's tho... | ["Deeply anesthetize the animal. Check for no reflexes and slower breathing", "Cut the animal's thorax and collect peripheral blood from the left ventricle", "Lyse the whole blood with the RBC (1X) solution for 10 minutes at 37°C.", "Upon lysis, wash cells and resuspend in cold PBS for immunophenotyping", "Stain cells ... |
52,092 | Long-read plant genome assembly and annotation: annotation | 5 | null | https://www.protocols.io/view/long-read-plant-genome-assembly-and-annotation-ann-bw44pgyw | Scott Ferguson, Ashley Jones, Justin Borevitz | TITLE: Long-read plant genome assembly and annotation: annotation
AUTHORS: Scott Ferguson, Ashley Jones, Justin Borevitz
[DESCRIPTION]
With the introduction of long-read, third generation sequencing (e.g. Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio) and associated bioinformatics tools, we can... | ["[Repeat annotate] Now that your genome is complete we want to find and annotate it for repeat regions. To do this we use EDTA and RepeatMasker. EDTA is first used to build a transposon (TE) sequence library. Next, RepeatMasker is used to find all TE and simple repeats within the genome.", "[Repeat annotate: soft mask... |
86,983 | Protocol to isolate and fix nuclei from flash frozen mouse hypothalamus and pituitary gland for IGVF | 4 | null | https://www.protocols.io/view/protocol-to-isolate-and-fix-nuclei-from-flash-froz-cy7fxzjn | Elisabeth Rebboah | TITLE: Protocol to isolate and fix nuclei from flash frozen mouse hypothalamus and pituitary gland for IGVF
AUTHORS: Elisabeth Rebboah
[DESCRIPTION]
This protocol describes isolation of nuclei from 10 week old mouse hypothalamus and pituitary gland from 8 founder strains (B6J, AJ, 129S1J, NZOJ, WSBJ, NODJ, PWKJ, and C... | ["[Setup] Coat SHARE-seq nuclei prep tubes with BSA. Fill 8 1.5 ml tubes with 1.5 ml 1% BSA-DEPC and incubate for 30 minutes. After incubation, aspirate BSA solution and dry for 30 minutes. Store at 4C.", "[Setup] Label tubes.", "[Setup] Pre-chill centrifuge to 4C.", "[Setup] Prepare ice buckets.", "[Setup] Prepare lys... |
9,249 | Extraction of gDNA from Synechocystis 6803 | null | dx.doi.org/10.17504/protocols.io.k99cz96 | null | Dennis Dienst | TITLE: Extraction of gDNA from Synechocystis 6803
AUTHORS: Dennis Dienst
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Cell harvest & disruption]
[4000 g]
?. Resuspend pellet in 10 mL TE bufferrepeat centrifugation (step 1)
?.
?. Resuspend pellet in 1 mL TES bufferfreeze in liquid nitrogen
wear goggles... | ["[Cell harvest & disruption]\n[4000 g]", "Resuspend pellet in 10 mL TE bufferrepeat centrifugation (step 1)", "Resuspend pellet in 1 mL TES bufferfreeze in liquid nitrogen\nwear goggles when working with liquid nitrogenhttps://en.wikipedia.org/wiki/Liquid_nitrogen", "incubate for 1h at 60°C under gentle agitationalter... |
40,366 | Feeding of cats with hyper-immune eggs: an oral immunization protocol | 4 | dx.doi.org/10.17504/protocols.io.bjnnkmde | https://www.protocols.io/view/feeding-of-cats-with-hyper-immune-eggs-an-oral-imm-bjnnkmde | Angel Justiz-Vaillant | TITLE: Feeding of cats with hyper-immune eggs: an oral immunization protocol
AUTHORS: Angel Justiz-Vaillant
[STEPS]
?. The anti-gp120 positive eggs (hyper-immune eggs) are fed to 3 out of 5 cats. Three (3) adult cats, 2-3 years old (1 male and 4 female). A sixth cat that was a part of the control group died during t... | ["The anti-gp120 positive eggs (hyper-immune eggs) are fed to 3 out of 5 cats. Three (3) adult cats, 2-3 years old (1 male and 4 female). A sixth cat that was a part of the control group died during the experiment.", "Each cat receives on average of 2 eggs diluted in 5 volumes of soya milk weekly for 10 weeks.", "Of t... |
38,934 | 7: User-friendly protocol: Retina Tissue Sections RNA FISH | 1 | null | https://www.protocols.io/view/7-user-friendly-protocol-retina-tissue-sections-rn-bh9wj97e | Jocelyn Y. Kishi, Sylvain W. Lapan, Brian J Beliveau, Emma R. West, Allen Zhu, Hiroshi M. Sasaki, Sinem Saka, Yu Wang, Constance L Cepko, Peng Yin | TITLE: 7: User-friendly protocol: Retina Tissue Sections RNA FISH
AUTHORS: Jocelyn Y. Kishi, Sylvain W. Lapan, Brian J Beliveau, Emma R. West, Allen Zhu, Hiroshi M. Sasaki, Sinem Saka, Yu Wang, Constance L Cepko, Peng Yin
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is about SABER R... | ["[Fixation]\nDissect neural retinas in PBS and fix in (diluted from , Thermo Fisher #28908) for at .\n[ FA]\n[ FA ampule]\n0 Room temperature", "[Preparing the slide]\nPrepare PDL using dissolved in , diluted from with ddH2O.\n[PDL (sigma P7886)]\n[Borate buffer]\n[stock (Thermo Scientific, #28341)]", "[Preparing ... |
57,433 | RNAScope in situ hybridization (ISH) multiplex fluorescent protocol | 4 | dx.doi.org/10.17504/protocols.io.81wgb67o1lpk/v1 | https://www.protocols.io/view/rnascope-in-situ-hybridization-ish-multiplex-fluor-b4bzqsp6 | Roberta Marongiu, Santiago Unda | TITLE: RNAScope in situ hybridization (ISH) multiplex fluorescent protocol
AUTHORS: Roberta Marongiu, Santiago Unda
[DESCRIPTION]
Instructions to perform ISH using RNAscope kit from acdbio company
[BEFORE_START]
For Fixed Frozen Brain samples
The challenge with thicker sections (30 to 40 microns) is tissue attachm... | ["[Part 1 : Sample preparation for frozen Nodose ganglia samples] Select tissue – ~ 3 sections/sample.", "[Part 1 : Sample preparation for frozen Nodose ganglia samples] Dry tissue at Room temperature for 60 min to 120 min. \nCover the slide loosely with foil to avoid contaminations.", "[Part 1 : Sample preparation fo... |
100,133 | Fluorescence-activated nuclei sorting (FANS) for single-cell Whole Genome Sequencing (scWGS) | 0 | dx.doi.org/10.17504/protocols.io.81wgbzybygpk/v1 | https://www.protocols.io/view/fluorescence-activated-nuclei-sorting-fans-for-sin-dd2d28a6 | Ester Kalef-Ezra, Lucia Friscioni, Dominic Horner, Caoimhe Morley, George Morrow, Yanping Guo, Christos Proukakis | TITLE: Fluorescence-activated nuclei sorting (FANS) for single-cell Whole Genome Sequencing (scWGS)
AUTHORS: Ester Kalef-Ezra, Lucia Friscioni, Dominic Horner, Caoimhe Morley, George Morrow, Yanping Guo, Christos Proukakis
[DESCRIPTION]
This protocol describes the isolation steps of nuclei from human post-mortem brain... | ["[Nuclei isolation from human post-mortem brain tissue] In both cases prior use: Clean Human Tissue handling hood with 0.2 Molarity (M) NaOH, 10% Presept, 70% EtOH and dH2O.", "[Nuclei isolation from human post-mortem brain tissue] Transfer all materials needed and handle human brain samples carefully in ahuman handl... |
null | null | null | dx.doi.org/10.17504/protocols.io.giybufw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The <strong>Quick-DNA™ FFPE Kit</strong> provides a simple and reliable method for high yield/quality DNA isolation from formalin-fixed, paraffin embedded (FFPE) tissue samples and sections. The unique chemistries of the product have been optimized for maximum recovery of non... | [] |
86,446 | BIDMC TMC - low input single nuclei sequencing isolation (NNLB) | 4 | dx.doi.org/10.17504/protocols.io.x54v9pp8qg3e/v1 | https://www.protocols.io/view/bidmc-tmc-low-input-single-nuclei-sequencing-isola-cynnxvde | Luciano G Martelotto, aploumak, Shuoshuo Wang, Nikolaos Kalavros, Ioannis Vlachos | TITLE: BIDMC TMC - low input single nuclei sequencing isolation (NNLB)
AUTHORS: Luciano G Martelotto, aploumak, Shuoshuo Wang, Nikolaos Kalavros, Ioannis Vlachos
[DESCRIPTION]
Single nuclei isolation protocol used by the BIDMC TMC to isolate intact nuclei from very low input tissues. Has been used successfully by the ... | ["[Abstract] No nuclei left behind (NNLB)\n\nThe single-nuclei RNA sequencing protocol used by the Spatial Technologies Unit at the Beth Israel Deaconess Medical Center in order to isolate and sequence RNA from very small samples (<1000 cells). All steps are optimized to ensure maximum cell recovery.\n\nThis protocol h... |
null | null | null | dx.doi.org/10.17504/protocols.io.fbjbikn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is for <em>S. cerevisiae</em> and is a modification of the one developed and used by Arjun Raj and his colleagues for:</p>
<p> </p>
<p>Raj A, van den Bogaard P, Rifkin SA, van Oudenaarden A, Tyagi S. <a href="http://www.nature.com/nmeth/journal/v5/n10/full/nmeth... | [] |
35,752 | NEBNext® Ultra™ DNA Library Prep Protocol for Illumina® (E7370) | 1 | dx.doi.org/10.17504/protocols.io.j8epv5edv1bz/v3 | https://www.protocols.io/view/nebnext-ultra-dna-library-prep-protocol-for-illumi-be6gjhbw | New England Biolabs | TITLE: NEBNext® Ultra™ DNA Library Prep Protocol for Illumina® (E7370)
AUTHORS: New England Biolabs
[DESCRIPTION]
The NEBNext®Ultra™ DNA Library Prep Kit for Illumina®contains reagents for preparation of libraries for next-generation sequencing on the Illumina platform from 5 ng – 1 µg input DNA, in a streamlined w... | ["[NEBNext End Prep] Add the following components in a sterile nuclease-free tube:\n Reagent Cap Color Volume Fragmented DNA 55.5 μl End Prep Enzyme Mix Green 3.0 μl End Repair Reaction Buffer (10x) Green 6.5 μl", "[NEBNext End Prep] Place in a thermocycler, with the heated lid set to ≥ 75°C, and run the fol... |
83,010 | U54 SCENT 10X Genomics Visium Protocol | 1 | null | https://www.protocols.click/view/u54-scent-10x-genomics-visium-protocol-cvbaw2ie | Karen Abramson, Simon Gregory | TITLE: U54 SCENT 10X Genomics Visium Protocol
AUTHORS: Karen Abramson, Simon Gregory
[DESCRIPTION]
This document outlines the 10X Genomics Visium Protocol used for normal lung and colon tissues for SCENT at Duke University.
[STEPS]
SECTION: 10X Genomics Visium Protocol
1. Once slides received, the following 10x Gen... | ["[10X Genomics Visium Protocol] Once slides received, the following 10x Genomics protocol is followed: \n\nhttps://cdn.10xgenomics.com/image/upload/v1660261285/support-documents/CG000409_Demonstrated_Protocol_VisiumSpatialFFPE_Deparaffin_H_E_RevC.pdf\n\nhttps://cdn.10xgenomics.com/image/upload/v1660261285/support-docu... |
56,555 | General Taq PCR Master Mix -- CHEM 384/584 | 4 | dx.doi.org/10.17504/protocols.io.b3gjqjun | https://www.protocols.io/view/general-taq-pcr-master-mix-chem-384-584-b3gjqjun | Ken Christensen | TITLE: General Taq PCR Master Mix -- CHEM 384/584
AUTHORS: Ken Christensen
[DESCRIPTION]
SapphireAmp Fast PCR Master Mix contains a hot start PCR enzyme, optimized buffer, dNTP mixture, gel loading dye (blue), and a density reagent as a 2X premix. SapphireAmp Fast PCR Master Mix is optimized for fast PCR and offers ... | ["[Setup Reaction] To a 25 µL aliquot of a 2X Taq PCR Master Mix (e.g. TaqDog, or Sapphire Amp), add template (10-20 µl cleared lysate for colony PCR or 20-50 ng of purified DNA for typical PCR), forward and reverse primers to a final concentration of 200 nanomolar (nM). Adjust final volume to 50 µL with nuclease free... |
76,043 | All-oxide n-AZO/p-SnOx hetero-junction for flexible solar cells: A numerical approach | 1 | dx.doi.org/10.17504/protocols.io.4r3l27em3g1y/v1 | https://www.protocols.io/view/all-oxide-n-azo-p-snox-hetero-junction-for-flexibl-cnhjvb4n | MANOJ KUMAR, Syed Sadique Anwer Askari, BANOTH RAVI, BITTU KUMAR, SVS PRASAD, Santosh Kumar Choudhary, Rajesh Singh, Shamsul Hassan, PURNENDU SHEKHAR PANDEY | TITLE: All-oxide n-AZO/p-SnOx hetero-junction for flexible solar cells: A numerical approach
AUTHORS: MANOJ KUMAR, Syed Sadique Anwer Askari, BANOTH RAVI, BITTU KUMAR, SVS PRASAD, Santosh Kumar Choudhary, Rajesh Singh, Shamsul Hassan, PURNENDU SHEKHAR PANDEY
[DESCRIPTION]
Researcher needs to explore some metal oxide s... | ["Simulation studies on n-AZO/p-SnOx heterojunction thin film solar cells based on finite element analysis (FEA) using TCAD simulation software (Silvaco ATLAS TCAD tool, version 5.24.1.R) has been reported in this article.", "The effect of bulk and interface defect along with the other heterointerface phenomenon on ... |
62,997 | Oprah Winfrey Weight Loss Canada : When Does It Become Popular In Markets! | 1 | dx.doi.org/10.17504/protocols.io.j8nlkk69xl5r/v1 | https://www.protocols.io/view/oprah-winfrey-weight-loss-canada-when-does-it-beco-b9rvr566 | roxyhimr | TITLE: Oprah Winfrey Weight Loss Canada : When Does It Become Popular In Markets!
AUTHORS: roxyhimr
[DESCRIPTION]
Check Available Discount Price For Oprah Winfrey Weight Loss
AMAZING BENEFITS OF Oprah Winfrey Weight Loss
Regular intake of keto gummies offers rapid weight loss.
Keto gummies provide flattened belly a... | ["[Oprah Winfrey Weight Loss Canada]"] |
87,251 | Staining of GFAP and IBA1 in PDGFR-B/Td-tomato brain sections | 1 | dx.doi.org/10.17504/protocols.io.14egn36mml5d/v1 | https://www.protocols.io/view/staining-of-gfap-and-iba1-in-pdgfr-b-td-tomato-bra-czftx3nn | Daniel Manrique-Castano | TITLE: Staining of GFAP and IBA1 in PDGFR-B/Td-tomato brain sections
AUTHORS: Daniel Manrique-Castano
[DESCRIPTION]
This protocol is suitable for the staining of GFAP and IBA1 in PDGFR-B/Td-Tomato fixed mouse brain sections.
[GUIDELINES]
Read the entire protocol before starting the procedure.
Note that this protocol... | ["[Tissue preparation and blocking] Take out sections from -80 and place them in an incubator/plate for 20 min at 37 °C. This step is performed to ensure tissue attachment to the crystal slides.", "[Tissue preparation and blocking] 2. Draw a hydrophobic barrier on each slide using ImmEdge®Hydrophobic Barrier PAP Pen a... |
null | null | null | dx.doi.org/10.17504/protocols.io.tcqeivw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Given a set of temporal networks, from different domains and with different sizes, how can we compare them? Can we identify evolutionary patterns that are both (i) characteristic and (ii) meaningful? We address these challenges by introducing a novel temporal and topological ... | ["Extract GoT.zip.", "Enter the 'GoT' repository and run 'make'.", "Run 'GoT/gtrieScanner -s 4 -m gtrie GoT/gtries/mygtrie -g <YOUR_NET>'.", "The GoTs of each node are shown one per line (e.g, na 1 0 0 0 10 ...)"] |
57,618 | Pre-sessions description | 3 | dx.doi.org/10.17504/protocols.io.b4hsqt6e | https://www.protocols.io/view/pre-sessions-description-b4hsqt6e | Ana Rachel Pinto, Rita Matos Sousa, Maria Margarida Teles Vasconcelos Correia Neves, Joana Almeida Santos Pacheco Palha, José Miguel Moreira Pêgo, Nuno Carvalho Sousa, Paul Scoles, Peter Vincent Scoles | TITLE: Pre-sessions description
AUTHORS: Ana Rachel Pinto, Rita Matos Sousa, Maria Margarida Teles Vasconcelos Correia Neves, Joana Almeida Santos Pacheco Palha, José Miguel Moreira Pêgo, Nuno Carvalho Sousa, Paul Scoles, Peter Vincent Scoles
[DESCRIPTION]
This is a step-by-step description of the content of t... | [] |
57,866 | tdTomato iDISCO+ Protocol | 4 | dx.doi.org/10.17504/protocols.io.36wgq77m5vk5/v1 | https://www.protocols.io/view/tdtomato-idisco-protocol-b4riqv4e | Moritz Negwer | TITLE: tdTomato iDISCO+ Protocol
AUTHORS: Moritz Negwer
[DESCRIPTION]
This protocol is a supplement to our upcoming publication "FriendlyClearMap: An optimized toolkit for mouse brain mapping and analysis".
In this protocol, we describe how to prepare the samples for light-sheet imaging. Specifically, how to extract... | ["[Sample Isolation] Deeply anesthetize the mouse with Isoflurane in a closed container. Use a fume hood to prevent exposure to Isoflurane vapors. Ascertain deep anesthesia by absence of the paw pinch reflex, then quickly decapitate the animal.", "[Sample Isolation] Collect the head on an inverted petri dish on a box f... |
75,120 | A RANDOMIZED, OPEN, CONTROLLED STUDY TO EVALUATE THE EFFICACY AND SAFETY OF PEDIAFLÙ® (DIETARY SUPPLEMENT) ALONG WITH STANDARD OF CARE IN CHILDREN WITH ACUTE TONSILLOPHARYNGITIS / RHINOPHARYNGITIS VERSUS STANDARD OF CARE ONLY | 1 | null | https://www.protocols.io/view/a-randomized-open-controlled-study-to-evaluate-the-cmkqu4vw | Fabio Cardinale, Dionisio Franco Barattini, Maria Morariu Bordea, Dorina Herteg, Cristian Radu Matei | TITLE: A RANDOMIZED, OPEN, CONTROLLED STUDY TO EVALUATE THE EFFICACY AND SAFETY OF PEDIAFLÙ® (DIETARY SUPPLEMENT) ALONG WITH STANDARD OF CARE IN CHILDREN WITH ACUTE TONSILLOPHARYNGITIS / RHINOPHARYNGITIS VERSUS STANDARD OF CARE ONLY
AUTHORS: Fabio Cardinale, Dionisio Franco Barattini, Maria Morariu Bordea, Dorina Herte... | ["[A RANDOMIZED, OPEN, CONTROLLED STUDY TO EVALUATE THE EFFICACY AND SAFETY OF PEDIAFLÙ® (DIETARY SUPPLEMENT) ALONG WITH STANDARD OF CARE IN CHILDREN WITH ACUTE TONSILLOPHARYNGITIS / RHINOPHARYNGITIS VERSUS STANDARD OF CARE ONLY] A RANDOMIZED, OPEN, CONTROLLED STUDY TO EVALUATE THE EFFICACY AND SAFETY OF PEDIAFLÙ® (DIE... |
27,529 | Endometrium - Collagenase | null | dx.doi.org/10.17504/protocols.io.65hhg36 | null | Roser Vento-Tormo, Regina Hoo | TITLE: Endometrium - Collagenase
AUTHORS: Roser Vento-Tormo, Regina Hoo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describe the tissue dissociation procedures from human endometrium and pregnancy endometrium samples. This protocol is adapted from</span><span style = "font-s... | ["[Tissue dissociation and digestion]\nNote: Flash-frozen tissue with isopentane for Spatial Transcriptomics work. {optional} Note: If tissue is going to be transported, do it with preservation solution (HypoThermosol® FRS) at . Store sample for fixing in formalin (RNA Scope) & nuclei sequencing (flash-frozen) {option... |
93,350 | Quantitation of aliphatic acids from lignin-derived streams by HPLC-RID | 1 | dx.doi.org/10.17504/protocols.io.rm7vzxrn2gx1/v1 | https://www.protocols.io/view/quantitation-of-aliphatic-acids-from-lignin-derive-c7eezjbe | Stefan J. Haugen, Alexander F. Benson, Sean P. Woodworth, David Brandner, Kelsey J. Ramirez, Gregg T. Beckham | TITLE: Quantitation of aliphatic acids from lignin-derived streams by HPLC-RID
AUTHORS: Stefan J. Haugen, Alexander F. Benson, Sean P. Woodworth, David Brandner, Kelsey J. Ramirez, Gregg T. Beckham
[DESCRIPTION]
An analytical method was developed using high performance liquid chromatography with refractive index detec... | ["[Preparation of mobile phase and instrument equilibration] Instrument equilibration\n\nPurge the high performance liquid chromatography (HPLC) instrument with 0.02 N sulfuric acid mobile phase made in step 1. Ensure the instrument is purged through the entire flow path including the detector, before the analytical co... |
null | null | null | dx.doi.org/10.17504/protocols.io.hhwb37e | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
87,067 | Computational design of novel nanobodies targeting the receptor binding domain of variants of concern of SARS-CoV-2 | 5 | dx.doi.org/10.17504/protocols.io.4r3l22q4jl1y/v1 | https://www.protocols.io/view/computational-design-of-novel-nanobodies-targeting-cy93xz8n | Phoomintara Longsomboon, Thanyada Rungrotmongkol, Nongluk Plongthongkum, Kittikhun Wangkanont, Peter Wolschann, Rungtiva P. Poo-arporn | TITLE: Computational design of novel nanobodies targeting the receptor binding domain of variants of concern of SARS-CoV-2
AUTHORS: Phoomintara Longsomboon, Thanyada Rungrotmongkol, Nongluk Plongthongkum, Kittikhun Wangkanont, Peter Wolschann, Rungtiva P. Poo-arporn
[DESCRIPTION]
The COVID-19 pandemic has created an... | ["[1. Validation of protein-protein docking server] Prepare the protein datasets consisting of 29 nanobody (Nbs) and 86 antibodies (Abs) complexed with RBDs from the Protein Data Bank (PDB) (https://www.rcsb.org/) for blind docking.", "The similarity of amino acid sequences of 29 Nbs is analyzed using the Clustal Omega... |
55,697 | A multicenter survey of patients’ favorite type of nursing care and associated factors in Hebei Province, China | 1 | dx.doi.org/10.17504/protocols.io.b2mrqc56 | https://www.protocols.io/view/a-multicenter-survey-of-patients-favorite-type-of-b2mrqc56 | dryzzhang , Hongzhi Lv | TITLE: A multicenter survey of patients’ favorite type of nursing care and associated factors in Hebei Province, China
AUTHORS: dryzzhang , Hongzhi Lv
[DESCRIPTION]
Background: Nursing care service is an important part of the healthcare system; however, patients’ favorite type of nursing care remains unknown. This st... | ["A multicenter survey of patients’ favorite type of nursing care and associated factors in Hebei Province, China\n\nBackground\nNursing care service is an important part of patient care and improves a patient’s satisfaction with received healthcare [1]. Patient satisfaction is an indicator of the quality of healthcare... |
28,732 | Plasma Insulin (LINCO ELISA) | null | dx.doi.org/10.17504/protocols.io.8a4hsgw | null | Willa Hsueh, Alan Collins | TITLE: Plasma Insulin (LINCO ELISA)
AUTHORS: Willa Hsueh, Alan Collins
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">This Rat / Mouse Insulin ELISA kit is used for the non radioactive quantification of insulin in mou... | ["[Assay Procedure]\nPre-warm all reagents to room temperature immediately before setting up the assay. Dilute the 10x concentrated TBS wash buffer 10 fold by mixing the entire content of buffer with 450ml de-ionized water. Remove the microtiter assay plate from the foil pouch and wash each well 3 times with 300 ml of ... |
93,039 | Purification of rat NLRP1, rat DPP9, and rat NLRP1-DPP9 complex from Sf9 Cells for structural and biochemical studies | 1 | dx.doi.org/10.17504/protocols.io.n2bvj31zblk5/v1 | https://www.protocols.io/view/purification-of-rat-nlrp1-rat-dpp9-and-rat-nlrp1-d-c64pzgvn | Louis R R Hollingsworth | TITLE: Purification of rat NLRP1, rat DPP9, and rat NLRP1-DPP9 complex from Sf9 Cells for structural and biochemical studies
AUTHORS: Louis R R Hollingsworth
[DESCRIPTION]
Protocol associated with "Host E3 ubiquitin ligase ITCH mediates Toxoplasma gondii effector GRA35-triggered NLRP1 inflammasome activation and cell-... | ["[Bacmid production] Obtain plasmids by emailing Dr. Jeroen Saeij (jeroensaeij@gmail.com) or from Addgene (deposition details will be added as a comment once processed). These include:\nLewis rat NLRP1 (Lew-rNLRP1) allele (allele 5 Uniprot ID D9I2G4) in pFastBac (His-TEV-rNLRP1[Lew]-FLAG)\nProteolysis-deficient Lew-rN... |
67,650 | Collection: State-of-the-Art Analytical Methods of Viral Infections in Human Lung Organoids | 2 | dx.doi.org/10.17504/protocols.io.5jyl89pw6v2w/v2 | https://www.protocols.io/view/collection-state-of-the-art-analytical-methods-of-cebataie | Morris Baumgardt, Maren Hülsemann, Anna Löwa, Diana Fatykhova, Karen Hoffmann, Mirjana Kessler, Maren Mieth, Katharina Hellwig, Doris Frey, Alina Langenhagen, Anne Voss, Benedikt Obermayer, Emanuel Wyler, Simon Dökel, Achim D. Gruber, Ulf Tölch, Stefan Hippenstiel, Andreas C. Hocke, Katja Hönzke | TITLE: Collection: State-of-the-Art Analytical Methods of Viral Infections in Human Lung Organoids
AUTHORS: Morris Baumgardt, Maren Hülsemann, Anna Löwa, Diana Fatykhova, Karen Hoffmann, Mirjana Kessler, Maren Mieth, Katharina Hellwig, Doris Frey, Alina Langenhagen, Anne Voss, Benedikt Obermayer, Emanuel Wyler, Simon D... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.hgtb3wn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div class="row bibliography-item-info">
<div class="bibliography-item-copy-text content col-md-12" data-clipboard-target="copy-target-228943496" data-redirect-target="/items/228943496/copy">Van Etten, J. (n.d.). Formulation of Modified Bold's Basal Medium (MBBM). Retrieved from... | [] |
99,081 | Qubit4 Fluorometer Protocol: Invitrogen dsDNA HS Assay Kit (REF 32854) | 0 | dx.doi.org/10.17504/protocols.io.81wgbz6dngpk/v1 | https://www.protocols.io/view/qubit4-fluorometer-protocol-invitrogen-dsdna-hs-as-dczh2x36 | Jenna Brown, Mirayana Marcelino Barros, Tiago Pereira, Alejandro De Santiago Perez, Hunter Powell | TITLE: Qubit4 Fluorometer Protocol: Invitrogen dsDNA HS Assay Kit (REF 32854)
AUTHORS: Jenna Brown, Mirayana Marcelino Barros, Tiago Pereira, Alejandro De Santiago Perez, Hunter Powell
[DESCRIPTION]
Qubit4 Fluorometer Protocol: Invitrogen dsDNA HS Assay Kit (REF 32854); Qubit4 protocol used to test dsDNA concentration... | ["Prepare standards separately (Standard #1 and Standard #2): 190 µL of working solution and 10 µL of standard, to a final volume of 200 µL for each standard. \nTip: Slowly mix up and down with pipette tip.", "Prepare samples: 198 µL of working solution and 2 µL of extracted DNA, to a final volume of 200 µL for each... |
25,789 | 12 Ion Exchange | null | dx.doi.org/10.17504/protocols.io.5e5g3g6 | null | TJUSLS China | TITLE: 12 Ion Exchange
AUTHORS: TJUSLS China
[STEPS]
?. According to the predicted pI of the protein and the pH of the ion-exchange column buffer, firstly select the appropriate ion exchange column (anion exchange column or cation exchange column). The pH of buffer should deviate from the isoelectric point of the prot... | ["According to the predicted pI of the protein and the pH of the ion-exchange column buffer, firstly select the appropriate ion exchange column (anion exchange column or cation exchange column). The pH of buffer should deviate from the isoelectric point of the protein.", "The protein is concentrated with a 10KD concent... |
52,587 | Microfluidics 1 - Mold Fabrication: Spin Coating of Photoresist | 1 | dx.doi.org/10.17504/protocols.io.bxkjpkun | https://www.protocols.io/view/microfluidics-1-mold-fabrication-spin-coating-of-p-bxkjpkun | Serhat S, C. Yunus Sahan | TITLE: Microfluidics 1 - Mold Fabrication: Spin Coating of Photoresist
AUTHORS: Serhat S, C. Yunus Sahan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left">Microfluidic Lab-on-a-chip technology has several different materials and fabrication methods. PD... | ["[SpinCoater Instrument Adjustment]\nDispense 1ml of photoresist (SU8) resin for each inch (25mm) of Si wafer substrate diameter.Spin at 500 rpm for 10 seconds with an acceleration of 100 rpm/second.Spin at \"N\" rpm for 30 seconds with an acceleration of 300 rpm/second.Expected results of photoresist thickness: 40u... |
91,333 | Proteinase K digestion | 4 | dx.doi.org/10.17504/protocols.io.81wgbx9qqlpk/v1 | https://www.protocols.io/view/proteinase-k-digestion-c5fdy3i6 | Martin T. Henrich, Fanni F. Geibl | TITLE: Proteinase K digestion
AUTHORS: Martin T. Henrich, Fanni F. Geibl
[DESCRIPTION]
This protocol describes the steps for performing proteinase K digestion and subsequent visualization by immunofluorescence, which can be helpful in determining insolubility of alpha-synuclein aggregates.
[BEFORE_START]
-Prepare ... | ["[Proteinase K digestion - Procedure] -Place individual sections in 12-well-plate with netwell inserts in PB.", "[Proteinase K digestion - Procedure] -Perform PK digestion by immediately putting the filled 12-well-plate in the water bath (65 °C) followed by 10 min shaking.65 °C", "[Proteinase K digestion - Procedure] ... |
79,429 | Life Cycle Assessment for Black Soldier Fly Larvae Dried Production | 1 | dx.doi.org/10.17504/protocols.io.8epv5j54dl1b/v1 | https://www.protocols.io/view/life-cycle-assessment-for-black-soldier-fly-larvae-crtdv6i6 | Rudy Agung Nugroho | TITLE: Life Cycle Assessment for Black Soldier Fly Larvae Dried Production
AUTHORS: Rudy Agung Nugroho
[DESCRIPTION]
Background: Hermetia illucens L. has gained popularity in recent years as a potential ecologically friendly response to both the present and potential future food/feed crisis. The larvae of H. illucensL... | ["[Life cycle assessment goal and scope definition] The goal and scope definition step ensures that the LCA is performed consistently.", "[Life Cycle impact assessment]", "The following processes were evaluated: biowaste preparation for BSFL substrate, bioconversion of biowaste, production of prepupa, and production of... |
36,824 | Suggested protocol for loading a DNA Ladder/marker | 1 | dx.doi.org/10.17504/protocols.io.zkxygx6zg8j2/v2 | https://www.protocols.io/view/suggested-protocol-for-loading-a-dna-ladder-marker-bf7yjrpw | New England Biolabs | TITLE: Suggested protocol for loading a DNA Ladder/marker
AUTHORS: New England Biolabs
[DESCRIPTION]
This is the suggested protocol for use with:
Quick-Load®Purple 1 kb DNA Ladder (N0552)
Quick-Load®Purple 100 bp DNA Ladder (N0551)
Quick-Load®Purple 50 bp DNA Ladder (N0556)
Quick-Load®1 kb Extend DNA Ladder (N323... | ["Prepare loading mixture (6 μl total volume):", "Mix gently by pipetting.", "Load onto the agarose gel."] |
14,682 | Protein Expression | null | dx.doi.org/10.17504/protocols.io.sj2ecqe | null | Rengin Yamur Akbiyik, Sevval Uysalcan | TITLE: Protein Expression
AUTHORS: Rengin Yamur Akbiyik, Sevval Uysalcan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The protein expression is a process about synthesizing and modification for proteins in living</div><div class = "text-block">organisms with using several laboratory techniques an... | ["[Transform BL21 cells and plate them on Amp (Kan).]", "[Afer overnight incubation, take colonies and transfer into 6 ml LB with 6 µl Amp. Let them grow for 3-5 hours.]\n[LB]\n[Ampicillin]", "[When incubation process is done, transfer it to 1 L ZYM-5052 Medium with 1 µl Amp.]", "[Centrifuge at 6000 rpm for 10 minutes.... |
76,660 | Purification of 10xHis-SuperTEV | 4 | null | https://www.protocols.io/view/purification-of-10xhis-supertev-cn4uvgww | Kelvin Lau, Bouchra Bouchri, Florence Pojer | TITLE: Purification of 10xHis-SuperTEV
AUTHORS: Kelvin Lau, Bouchra Bouchri, Florence Pojer
[DESCRIPTION]
SuperTEV is a mutated version of TEV (Tobacco Etch Protease) a cysteine protease widely used in labs as it is highly specific to a cleavage sequence that can be genetically encoded. Depending on the lab, it has b... | ["[Growing bacterial cultures (6 L)] Transform the bacterial plasmid expressing the 10xHis-SuperTEV into BL21 (DE3) cells. Plate on to LB-Agar plates + Kanamycin. Grow overnight at 37 °C or over the weekend at 25 °C.", "[Growing bacterial cultures (6 L)] In an afternoon, pick a streak of cells and innoculate into 200 m... |
82,324 | Lentivirus production and transduction | 3 | dx.doi.org/10.17504/protocols.io.bp2l69jj1lqe/v1 | https://www.protocols.io/view/lentivirus-production-and-transduction-cumuwu6w | Shiyi Wang | TITLE: Lentivirus production and transduction
AUTHORS: Shiyi Wang
[DESCRIPTION]
Lentivirus production and transduction
[STEPS] | [] |
106,494 | Genetic interaction analysis using ERGs in D. melanogaster | 0 | dx.doi.org/10.17504/protocols.io.x54v9256pl3e/v1 | https://www.protocols.io/view/genetic-interaction-analysis-using-ergs-in-d-melan-dj864rze | Natalie Kaempf, Ayse Kilic, Patrik Verstreken | TITLE: Genetic interaction analysis using ERGs in D. melanogaster
AUTHORS: Natalie Kaempf, Ayse Kilic, Patrik Verstreken
[DESCRIPTION]
This protocols describes the recording of electroretinograms (ERGs) and calculation of genetic interactions of fly mutants for a transheterozygous screen.
[STEPS]
SECTION: Electroreti... | ["[Electroretinograms (ERGs)] For every measurement male flies are collected (including the control) 4±1 d after eclosion from the transheterozugous crosses reared in a temperature and light-controlled incubator\nat 25 °C and 12-hour light-dark cycle", "[Electroretinograms (ERGs)] Flies are sedated with CO2 and immobil... |
72,215 | Cell preparation for scRNA-Seq from diluted bodily fluids | 1 | dx.doi.org/10.17504/protocols.io.kqdg366r1g25/v2 | https://www.protocols.io/view/cell-preparation-for-scrna-seq-from-diluted-bodily-cirxud7n | Linas Mazutis, Vaidotas Kiseliovas, Adrienne Boire | TITLE: Cell preparation for scRNA-Seq from diluted bodily fluids
AUTHORS: Linas Mazutis, Vaidotas Kiseliovas, Adrienne Boire
[DESCRIPTION]
Efficient isolation of cells from complex bodily fluids is a crucial step for many biological and biomedical applications. Yet, it can become a particularly challenging when only a... | ["[Sample retrieval] Collect the bodily fluid following the protocol of choice (e.g. retrieval of cerebrospinal fluid).\nTypically one could expect to have 3-5 ml of starting fluid.", "[Concentrating cells] Divide the fluid from step #1 to microcentrifuge tubes at 0.5 ml per tube.\n\nNote: When working with large volum... |
62,986 | test 2 | 1 | dx.doi.org/10.17504/protocols.io.e6nvwkmbzvmk/v1 | https://www.protocols.io/view/test-2-b9rir54e | m.eco | TITLE: test 2
AUTHORS: m.eco
[DESCRIPTION]
fsdfdsfsdfs
[STEPS]
1.
2.
3. Add H2O | ["Add H2O"] |
63,919 | Ikaria Lean Belly Juice Australia | 1 | dx.doi.org/10.17504/protocols.io.4r3l2obxqv1y/v1 | https://www.protocols.io/view/ikaria-lean-belly-juice-australia-canpsddn | Ikarialeanbelly | TITLE: Ikaria Lean Belly Juice Australia
AUTHORS: Ikarialeanbelly
[DESCRIPTION]
Ikaria Lean Belly Juice Australia
How Does Ikaria Lean Belly Juice Work?
Ikaria Lean Belly Juice targets high uric corrosive and aggravation normally. These two are the genuine reasons for sub-optimal ability to burn calories.
Uric corro... | [] |
86,056 | Breast tissue and blood processing and storage from Komen Tissue Bank | 4 | dx.doi.org/10.17504/protocols.io.kxygx3974g8j/v1 | https://www.protocols.io/view/breast-tissue-and-blood-processing-and-storage-fro-cyagxsbw | kschneider | TITLE: Breast tissue and blood processing and storage from Komen Tissue Bank
AUTHORS: kschneider
[DESCRIPTION]
Tissue and blood was extracted and stored as in protocol 001v8.0 and 004v7.0 from the Komen Tissue Bank.
[STEPS] | [] |
99,337 | Efficient transfection protocol of rainbow trout gills epithelial (RTgill-W1) cell line through nucleofection system. | 0 | dx.doi.org/10.17504/protocols.io.8epv5x4yng1b/v2 | https://www.protocols.io/view/efficient-transfection-protocol-of-rainbow-trout-g-dc9h2z36 | Sebastián Escobar-Aguirre, Amanda Escorza, Matias Escobar-Aguirre | TITLE: Efficient transfection protocol of rainbow trout gills epithelial (RTgill-W1) cell line through nucleofection system.
AUTHORS: Sebastián Escobar-Aguirre, Amanda Escorza, Matias Escobar-Aguirre
[DESCRIPTION]
In this protocol, we optimize the experimental condition to express plasmid DNA in salmonid fish rainbow ... | ["[Cell preparation] Before electroporation, cells should be between about 70 - 90% confluent (i.e 6x10e6 cells/ml in a 175 cm2 flask).", "[Cell preparation] Neutralize cells with growth medium 9 mL into the flask.", "[Cell preparation] Wash cells monolayer 2 times with 5 mLand 1 mL", "[Electroporation] Apply 1600 vo... |
69,694 | Vertebrate Clearing and Staining - 'VCaS' Protocol | 1 | dx.doi.org/10.17504/protocols.io.x54v9de9qg3e/v1 | https://www.protocols.io/view/vertebrate-clearing-and-staining-39-vcas-39-proto-cga6tshe | Sidney E. Ryan, Kara Mia Ehler, Christina M Giudici, Yoel E. Stuart, Emily Y. Hallett, Jacopo Niccolo Cerasoni | TITLE: Vertebrate Clearing and Staining - 'VCaS' Protocol
AUTHORS: Sidney E. Ryan, Kara Mia Ehler, Christina M Giudici, Yoel E. Stuart, Emily Y. Hallett, Jacopo Niccolo Cerasoni
[DESCRIPTION]
Small v... | ["[Preparation of specimen] De-gut and de-scale/skin (optional, but recommended)\n\nThese processes should not be carried out if the specimen are too fragile or if either of the two features are of interest to the study.", "[Preparation of specimen] Label sterile containers with sample or identification assigned to spe... |
95,152 | CUT&Tag Data Processing and Analysis Tutorial for Time Series | 5 | null | https://www.protocols.io/view/cut-amp-tag-data-processing-and-analysis-tutorial-c86qzzdw | Ye Zheng, Kami Ahmad, Steven Henikoff, karina_jhingan | TITLE: CUT&Tag Data Processing and Analysis Tutorial for Time Series
AUTHORS: Ye Zheng, Kami Ahmad, Steven Henikoff, karina_jhingan
[DESCRIPTION]
This tutorial is largely based off of Ye Zheng's CUT&Tag analysis https://www.protocols.io/view/cut-amp-tag-data-processing-and-analysis-tutorial-e6nvw93x7gmk/v1?step=9 ... | ["[I. Introduction] Overview of CUT&Tag \n\nThis tutorial is a time series tweaked approach based off of a CUT&Tag processing and analysis pipeline created by Ye Zheng, https://www.protocols.io/view/cut-amp-tag-data-processing-and-analysis-tutorial-e6nvw93x7gmk/v1 (Zheng Y et al (2020). Protocol.io). Some sections and ... |
45,924 | C-SOP-301: DNA Library Preparation using the NEBNext Ultra II FS DNA Kit (≥100 ng DNA input) | 4 | null | https://www.protocols.io/view/c-sop-301-dna-library-preparation-using-the-nebnex-bq4cmysw | Mihir Kekre | TITLE: C-SOP-301: DNA Library Preparation using the NEBNext Ultra II FS DNA Kit (≥100 ng DNA input)
AUTHORS: Mihir Kekre
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span> The NEBNext</span><span style = "vertical-align:super;">®</span><span>Ultra™ II FS DNA Library Prep Kit meets the dual chall... | ["[Before Starting]\nPrior to initiating the protocol, ensure that all active workbenches are cleaned with 80% ethanol, all relevant personal protective clothing is worn and the work area is prepared according to local GLP guidelines for molecular methods.", "[Before Starting]\nCreate an organised bench space by cleari... |
null | null | null | dx.doi.org/10.17504/protocols.io.j8scrwe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>In this section we describe our method of isolation and quantification of MmuPV1 virions from papillomas arising in nude mice that can be serially passaged or used to infect other strains of mice. In our studies we have used both crude virus extracts or purified virus particl... | [] |
76,174 | Metagenomic Library Prep from fecal sample lysate | 4 | null | https://www.protocols.io/view/metagenomic-library-prep-from-fecal-sample-lysate-cnmnvc5e | Noah Noah Snyder-Mackler | TITLE: Metagenomic Library Prep from fecal sample lysate
AUTHORS: Noah Noah Snyder-Mackler
[DESCRIPTION]
Metagenomic library prep from fecal sample lysate using Illumina DNA prep kit (1/2 reactions).
[GUIDELINES]
Abbreviations
BLT: Bead-Linked Transposomes
TB1: Tagmentation Buffer 1
MM: Master Mix
TWB: Tagmentation ... | ["[Preparation] Add 18 µL of nuclease-free water and 2 µL of sample to a PCR plate", "[Tagmentation Reaction] Take out TB1 and keep on on ice. Turn on thermocycler to 37 °C", "[Tagmentation Reaction] Multiply by number of samples, for a 96 well plate use x100 and pipet mix together to create MM. Vortex BLT vigorously f... |
45,170 | Non-UDG treated double-stranded DNA library preparation for Illumina sequencing of ancient dental calculus | 1 | dx.doi.org/10.17504/protocols.io.bqcsmswe | https://www.protocols.io/view/non-udg-treated-double-stranded-dna-library-prepar-bqcsmswe | Franziska Aron, Gunnar Neumann, Christina Warinner, Guido Brandt | TITLE: Non-UDG treated double-stranded DNA library preparation for Illumina sequencing of ancient dental calculus
AUTHORS: Franziska Aron, Gunnar Neumann, Christina Warinner, Guido Brandt
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for the preparation of double-stranded genomic librari... | ["[Blunt End Repair (aDNA library preparation room)]\nPrepare a mastermix for the blunt end repair calculating . Use a new 1.5 ml LoBind tube to set up the mastermix. ABCD1ReagentStock concentrationFinal concentration1x Volume [µl]2NEB Buffer 210 x1 x53ATP10 mM1 mM54BSA20 mg/ml0.8 mg/ml25dNTPs25 mM each0.1 mM0.26T4 P... |
55,290 | sgRNA Synthesis & CRISPR-Cas9 Synthesis | 1 | dx.doi.org/10.17504/protocols.io.bz82p9ye | https://www.protocols.io/view/sgrna-synthesis-amp-crispr-cas9-synthesis-bz82p9ye | priceal , ekmatozel , parzialest | TITLE: sgRNA Synthesis & CRISPR-Cas9 Synthesis
AUTHORS: priceal , ekmatozel , parzialest
[DESCRIPTION]
A protein roadblock forms when a protein binds DNA and hinders translocation of other DNA binding proteins. These roadblocks can have significant effects on gene expression and regulation as well as DNA bindi... | ["[Preparation of sgRNA] Gather the materials used in Step 14 (See Materials section).", "[Preparation of sgRNA] Thaw EnGen 2X sgRNA Reaction Mix, S. pyogenes, and the customer-supplied target-specific oligo (1 µM). Mix and pulse each component in microfuge prior to use for 10 seconds. Store enzyme mix on ice.", "[Prep... |
50,252 | Preparation of dsRNA viruses for MinION - CLM | 1 | null | https://www.protocols.io/view/preparation-of-dsrna-viruses-for-minion-clm-bvbkn2kw | Alexander H Wilcox, Erik Delwart, Samuel L Díaz Muñoz | TITLE: Preparation of dsRNA viruses for MinION - CLM
AUTHORS: Alexander H Wilcox, Erik Delwart, Samuel L Díaz Muñoz
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Updated protocol by CLM</div></div>
[STEPS]
?. Viral lysates should be passed through a 0.22μm filter to remove host debris, then treat... | ["Viral lysates should be passed through a 0.22μm filter to remove host debris, then treated with nucleases to degrade extracapsular nucleic acids. To 1ml filtrate:25μl DNAse I, 50μl RNAse A/T1107.5 DNAse I BufferScale down for concentrated lysates, which should be in the range of 50-500uL.Incubate for 1 hour 30 minut... |
83,009 | U54 SCENT 10x Genomic Single-Cell Multiome | 1 | dx.doi.org/10.17504/protocols.io.81wgbxdpolpk/v1 | https://www.protocols.io/view/u54-scent-10x-genomic-single-cell-multiome-cva9w2h6 | Karen Abramson, Simon Gregory | TITLE: U54 SCENT 10x Genomic Single-Cell Multiome
AUTHORS: Karen Abramson, Simon Gregory
[DESCRIPTION]
This document outlines the 10X Genomics Single-Cell Multiome Protocol used for normal lung and colon tissues for SCENT at Duke University.
[STEPS]
SECTION: 10X Gemonics Single-Cell Multiome Protocol
1. Nuclei were i... | ["[10X Gemonics Single-Cell Multiome Protocol] Nuclei were isolated using this 10x Genomics kit - Chromium\nNuclei Isolation with RNase Inhibitor Kit, 16rxns, and this protocol", "[10X Gemonics Single-Cell Multiome Protocol] Multiome libraries were generated using these kits -\nChromium Next GEM Single Cell Multiome AT... |
null | null | null | dx.doi.org/10.17504/protocols.io.ccisud | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
For purifying proteins from mammalian cells for analysis by western blot.
[STEPS]
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48,781 | Ultra-Rapid Sequencing (LAMP) | 4 | null | https://www.protocols.io/view/ultra-rapid-sequencing-lamp-btvmnn46 | Jack Wadden | TITLE: Ultra-Rapid Sequencing (LAMP)
AUTHORS: Jack Wadden
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol accompanies the paper "Ultra-Rapid Somatic Variant Detection via Real-Time Threshold Sequencing." This protocol was followed to initiate a sequencing run that resulted in a somatic... | ["[Preparation]\nPrepare the LAMP reaction tube by mixing the following components in a PCR tube LAMP primer mix\n0.2 mL\n12.5 µl\n2.5 µl\n9 µl", "[Preparation]\nPrepare the DNA extraction tube by mixing the following components in a PCR tube of\n0.2 mL\n100 µl", "[DNA Extraction]\nWhen acquired, place tumor tissue... |
28,622 | Formation of gp37 LTF needle trimers-LPS complex | null | dx.doi.org/10.17504/protocols.io.77nhrme | null | Mohammad Z. Islam, Andrei Fokine, Marthandan Mahalingam, Zhihong Zhang, Carmela Garcia-Doval, Mark J. van Raaij, Michael G. Rossmann, and Venigalla B. Rao | TITLE: Formation of gp37 LTF needle trimers-LPS complex
AUTHORS: Mohammad Z. Islam, Andrei Fokine, Marthandan Mahalingam, Zhihong Zhang, Carmela Garcia-Doval, Mark J. van Raaij, Michael G. Rossmann, and Venigalla B. Rao
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Tailed bacteriophages (phages) a... | [] |
66,083 | LRRK2 Immunofluorescent staining | 4 | dx.doi.org/10.17504/protocols.io.n92ldze17v5b/v1 | https://www.protocols.io/view/lrrk2-immunofluorescent-staining-ccsbswan | sherbst | TITLE: LRRK2 Immunofluorescent staining
AUTHORS: sherbst
[DESCRIPTION]
Protocol for immunofluorescent staining for LRRK2 in cultured cells using the MJFF2 (c41-2) antibody.
[STEPS]
1. Culture cells as usual on cover slips or in a plate suitable for imaging.
If using coverslips, we recommend Ø13 mm for cells cult... | ["Culture cells as usual on cover slips or in a plate suitable for imaging.\n\nIf using coverslips, we recommend Ø13 mm for cells cultured in 24-well plates.", "Fix cells in 4 % PFA/PBS at 4 °C for 15 min.", "Permeabilise the plasma membrane by incubating samples in ice-cold MeOH for 10 min. This can be done on the ben... |
null | null | null | dx.doi.org/10.17504/protocols.io.duj6um | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is a positive control experiment (to test protocol in your hands and/or activity of your home‐made Cas9): tag <em>gtbp‐1</em> with <em>eGFP</em> or <em>mCherry</em> using <em>dpy‐10</em> co‐CRISPR.. The protocol is from:<br /><br /><span class="cit-title"><span class="cit-a... | [] |
33,169 | DNA extraction for human microbe samples. | 1 | dx.doi.org/10.17504/protocols.io.bcmriu56 | https://www.protocols.io/view/dna-extraction-for-human-microbe-samples-bcmriu56 | Lilan Hao | TITLE: DNA extraction for human microbe samples.
AUTHORS: Lilan Hao
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used to clarity the process of total DNA extration for human microbe samples.</div></div>
[STEPS]
?. 200μl samples were mixed with 500 μl TE buffer and 20 μl of 10 mg... | ["200μl samples were mixed with 500 μl TE buffer and 20 μl of 10 mg/ml lysozyme solution.", "Incubate at 37 °C for 90min. Invert the tube several times to mix every 15 minutes. Centrifuge at 13,000 rcf/min for 10 min at 4 °C and discard the supernatant.", "Add 300 μl of 20 mg/ml proteinase K and 5μl of 10% SDS. Vortex ... |
55,662 | Populating NCBI template for submissions using BioNumerics v7.6 | 1 | dx.doi.org/10.17504/protocols.io.b2knqcve | https://www.protocols.io/view/populating-ncbi-template-for-submissions-using-bio-b2knqcve | Ruth Timme, Maria Balkey, Julie Haendiges | TITLE: Populating NCBI template for submissions using BioNumerics v7.6
AUTHORS: Ruth Timme, Maria Balkey, Julie Haendiges
[DESCRIPTION]
PURPOSE: to define the standard operating procedure for collecting isolate metadata using BioNumerics for submission of food/environmental isolates to NCBI.
SCOPE: to provide a ... | ["Metadata SampleSheet preparation \n\nBefore uploading your sequencing run or linking NCBI sequencing records at the BioNumerics platform make sure to fill out the metadata spreadsheet form. \n\nPlease download the template and guidelines included in the file 'GT_BioNumerics_spreadsheet_v2.xlsx'. \n\nCreate the fiel... |
47,725 | Incidence of Acute and Chronic Post-Thoracotomy Pain in Children | 1 | dx.doi.org/10.17504/protocols.io.bsumneu6 | https://www.protocols.io/view/incidence-of-acute-and-chronic-post-thoracotomy-pa-bsumneu6 | Giuliano Marchetti, Alessandro Vittori, Fabio Ferrari, Elisa Francia, Ilaria Mascilini, Simone Piga, Valerio Pardi, Giorgia Contini, Alessandro Inserra, Sergio Giuseppe Picardo | TITLE: Incidence of Acute and Chronic Post-Thoracotomy Pain in Children
AUTHORS: Giuliano Marchetti, Alessandro Vittori, Fabio Ferrari, Elisa Francia, Ilaria Mascilini, Simone Piga, Valerio Pardi, Giorgia Contini, Alessandro Inserra, Sergio Giuseppe Picardo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-b... | ["The study has been approved by the ethics committee of the Bambino Gesù Children's Hospital IRCCS on 06/11/2013 with number 957/RA", "The study involved patients who underwent thoracotomy between 2007 and 2013 for benign diseases, with a follow-up of at least three months and who did not reach the age of majority in ... |
55,285 | Clinical characterization and treatment outcomes of intracerebral and subarachnoid hemorrhage after vaccination against COVID-19: A systematic review of the literature | 1 | dx.doi.org/10.17504/protocols.io.bz8vp9w6 | https://www.protocols.io/view/clinical-characterization-and-treatment-outcomes-o-bz8vp9w6 | Jin Pyeong Jeon, Chung Liang Chai, Jong Kook Rhim, Jeong Jin Park, Yong Jun Cho, Seung Hun Sheen | TITLE: Clinical characterization and treatment outcomes of intracerebral and subarachnoid hemorrhage after vaccination against COVID-19: A systematic review of the literature
AUTHORS: Jin Pyeong Jeon, Chung Liang Chai, Jong Kook Rhim, Jeong Jin Park, Yong Jun Cho, Seung Hun Sheen
[DESCRIPTION]
As the number of COV... | ["Review title\n\nClinical characterization and treatment outcomes of intracerebral and subarachnoid hemorrhage after vaccination against COVID-19: A systematic review of the literature", "Anticipated or actual start date\n\n20 Novermber 2021", "Anticipated completion date\n\n20 February 2022", "Stage of review at time... |
36,206 | PCR Using Q5® Hot Start High-Fidelity DNA Polymerase (M0493) | 1 | dx.doi.org/10.17504/protocols.io.bfknjkve | https://www.protocols.io/view/pcr-using-q5-hot-start-high-fidelity-dna-polymeras-bfknjkve | New England Biolabs | TITLE: PCR Using Q5® Hot Start High-Fidelity DNA Polymerase (M0493)
AUTHORS: New England Biolabs
[DESCRIPTION]
Q5®Hot Start High-Fidelity DNA Polymerase is a high-fidelity, thermostable, hot start DNA polymerase with 3´→ 5´ exonuclease activity, fused to a processivity-enhancing Sso7d domain to support robust DNA a... | ["Set up the following reaction:", "Gently mix the reaction. Collect all liquid to the bottom of the tube by a quick spin if necessary and overlay the sample with mineral oil if using a PCR machine without a heated lid.", "Transfer PCR tubes to a PCR machine and begin thermocycling: \n \nThermocycling Conditions for a ... |
12,967 | Handling of genomics samples | null | dx.doi.org/10.17504/protocols.io.qwfdxbn | null | Adriana Alberti, Julie Poulain, Stefan Engelen, Karine Labadie, Sarah Romac, Isabel Ferrera, Guillaume Albini, Jean-Marc Aury, Caroline Belser, Alexis Bertrand, Corinne Cruaud, Corinne Da Silva, Carole Dossat, Frédéric Gavory, Shahinaz Gas, Julie Guy, Maud Haquelle, E'krame Jacoby, Olivier Jaillon, Arnaud Lemainque, E... | TITLE: Handling of genomics samples
AUTHORS: Adriana Alberti, Julie Poulain, Stefan Engelen, Karine Labadie, Sarah Romac, Isabel Ferrera, Guillaume Albini, Jean-Marc Aury, Caroline Belser, Alexis Bertrand, Corinne Cruaud, Corinne Da Silva, Carole Dossat, Frédéric Gavory, Shahinaz Gas, Julie Guy, Maud Haquelle, E'krame... | [] |
39,648 | Gapclosing metagenomic islands | 1 | dx.doi.org/10.17504/protocols.io.bix8kfrw | https://www.protocols.io/view/gapclosing-metagenomic-islands-bix8kfrw | Chris Bellas | TITLE: Gapclosing metagenomic islands
AUTHORS: Chris Bellas
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol allows gapclosing of metagenomic islands which occur when mapping metagenomic reads to a phage reference genome. These gaps arise because multiple gene variants co-exist for spec... | ["1) Map metagenomic reads to virus reference contigStarting with an assembled phage contig (phage_reference_contig.fasta). i) Map trimmed, unassembled reads from a different metagenome (Query metagenome) to this reference using Bowtie2Bowtie2 -I 0 -X 800 --no-unal --very-sensitive -1 Query_metagenome_R1.fastq -2 Que... |
38,933 | 6: Protocol optimization for SABER-FISH in tissues | 1 | null | https://www.protocols.io/view/6-protocol-optimization-for-saber-fish-in-tissues-bh9vj966 | Jocelyn Y. Kishi, Sylvain W. Lapan, Brian J Beliveau, Emma R. West, Allen Zhu, Hiroshi M. Sasaki, Sinem Saka, Yu Wang, Constance L Cepko, Peng Yin | TITLE: 6: Protocol optimization for SABER-FISH in tissues
AUTHORS: Jocelyn Y. Kishi, Sylvain W. Lapan, Brian J Beliveau, Emma R. West, Allen Zhu, Hiroshi M. Sasaki, Sinem Saka, Yu Wang, Constance L Cepko, Peng Yin
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol summarizes several teste... | [] |
83,143 | U54 SCENT Histology H&E Staining | 1 | null | https://www.protocols.click/view/u54-scent-histology-h-amp-e-staining-cvffw3jn | Shannon McCall | TITLE: U54 SCENT Histology H&E Staining
AUTHORS: Shannon McCall
[DESCRIPTION]
To provide a standardized method of running, cleaning, refilling, and verifying quality of the automatic H&E stainer. Every morning before running slides for projects, a quality control slide containing brain, kidney, liver, and pancreas... | ["[Protocol - Operating Autostainer and Running Daily Quality Control] Open cover of autostainer and remove each lid of the reagents inside. Stack lids and set to the\nright side of autostainer. Close cover.", "[Protocol - Operating Autostainer and Running Daily Quality Control] Hit switch on the right side of autostai... |
null | null | null | dx.doi.org/10.17504/protocols.io.gczbsx6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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52,771 | HyDrop-ATAC v1.0 | 1 | dx.doi.org/10.17504/protocols.io.bxsbpnan | https://www.protocols.io/view/hydrop-atac-v1-0-bxsbpnan | Florian De Rop, Suresh Poovathingal, Stein Aerts | TITLE: HyDrop-ATAC v1.0
AUTHORS: Florian De Rop, Suresh Poovathingal, Stein Aerts
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Step-by-step protocol for execution of HyDrop-ATAC.</div></div>
[STEPS]
?. [Preparation Stage]
Setting up the Microfluidic FrameworkYou can perform these steps during th... | ["[Preparation Stage]\nSetting up the Microfluidic FrameworkYou can perform these steps during the tagmentation incubation.", "[Preparation Stage]\nBoot up Droplet Genomics onyx.Check syringe diameters in Onyx program. Any deviations from the true syringe diameter will result in biased flow rates, as the pump converts ... |
28,859 | Glycerol stocks | null | dx.doi.org/10.17504/protocols.io.8e3htgn | null | iGEM Dusseldorf | TITLE: Glycerol stocks
AUTHORS: iGEM Dusseldorf
[STEPS]
?. Overnight liquid culture (3mL) + Antibiotic.For E.coli (Low salt) LBFor Pichia YPD
?. 80% Glycerol: mix 20mL H2O with 80mL pure glycerol and then autoclave
?. E. coli: 812µL of cells mix with 188 µL of sterile 80% glycerol
?. Pichia: Spin 2min at 2000g. Decan... | ["Overnight liquid culture (3mL) + Antibiotic.For E.coli (Low salt) LBFor Pichia YPD", "80% Glycerol: mix 20mL H2O with 80mL pure glycerol and then autoclave", "E. coli: 812µL of cells mix with 188 µL of sterile 80% glycerol", "Pichia: Spin 2min at 2000g. Decant 2ml. Resuspend in remaining liquid. 812µL of cells mix wi... |
55,016 | Running the Titan_ClearLabs Workflow on Terra.bio | 5 | dx.doi.org/10.17504/protocols.io.bzygp7tw | https://www.protocols.io/view/running-the-titan-clearlabs-workflow-on-terra-bio-bzygp7tw | Frank J Ambrosio, Jill V Hagey, Kevin Libuit, Technical Outreach and Assistance for States Team | TITLE: Running the Titan_ClearLabs Workflow on Terra.bio
AUTHORS: Frank J Ambrosio, Jill V Hagey, Kevin Libuit, Technical Outreach and Assistance for States Team
[DESCRIPTION]
The Titan_ClearLabs workflow is a part of the Public Health Viral Genomics Titan series for SARS-CoV-2 genomic characterization. Titan_CleanL... | ["[Running the Titan_ClearLabs Workflow] To run the Titan_ClearLabs workflow, click on the 'Workflows' panel in the newly created workspace. It should bring you to your workflow page. Click on the 'Titan_ClearLabs' tile to bring up the Titan_ClearLabs assembly workflow page (if you do not see the Titan_ClearLabs workf... |
null | null | null | dx.doi.org/10.17504/protocols.io.fjtbknn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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62,744 | Immunohistochemistry Protocol for Paraffin-Embedded Sections - General | 1 | dx.doi.org/10.17504/protocols.io.kqdg3p7mql25/v1 | https://www.protocols.io/view/immunohistochemistry-protocol-for-paraffin-embedde-b9hyr37w | Julianna Tomlinson, Nathalie Lengacher | TITLE: Immunohistochemistry Protocol for Paraffin-Embedded Sections - General
AUTHORS: Julianna Tomlinson, Nathalie Lengacher
[DESCRIPTION]
This protocol details general immunohistochemistry procedure.
[STEPS]
SECTION: Day 1 - Deparaffinize
1. Dip slides in 100% Citrisolv 3 x 5 mins.
SECTION: Hydration
2. Dip in 10... | ["[Day 1 - Deparaffinize] Dip slides in 100% Citrisolv 3 x 5 mins.", "[Hydration] Dip in 100% EtOH 2 x 2 mins.", "[Hydration] Dip in 80% EtOH 2 x 2 mins.", "[Hydration] Dip in ddH2O 2 x 2 mins.", "[Quench endogenous peroxides] Incubate slides in 0.3% H2O2 in methanol for 15 min (500 µL of 30% H2O2 in 50 mL MetOH, in ... |
null | null | null | dx.doi.org/10.17504/protocols.io.j9fcr3n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Proteomics was performed to identify key factors involved in the development of symptoms. For surface-enhanced laser desorption/ionization-time of flight-mass spectrometry (SELDI-TOF MS) analysis, we centrifuged the collected human serum (200 µL) at 21,040 × <em>g</em> for 10... | [] |
47,536 | WU sc-prep Protocol for Solid Tumors v2.1 | 4 | dx.doi.org/10.17504/protocols.io.bsnqnddw | https://www.protocols.io/view/wu-sc-prep-protocol-for-solid-tumors-v2-1-bsnqnddw | Reyka Jayasinghe, Li Ding, Feng Chen | TITLE: WU sc-prep Protocol for Solid Tumors v2.1
AUTHORS: Reyka Jayasinghe, Li Ding, Feng Chen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Single-cell Isolation for solid tumors Ding Lab 2021</div></div>
[STEPS]
?. [Reagents]
-Human tumor dissociation kit(Miltenyi Biotec #130-095-929)-PBS-PBS,... | ["[Reagents]\n-Human tumor dissociation kit(Miltenyi Biotec #130-095-929)-PBS-PBS, 0.5% BSA (keep at 4°C)-(optional) Red Blood Cell (RBC) Lysis Solution ACK buffer Fisher (A1049201)-Falcon 15mL/50mL Conical Centrifuge Tubes (Corning Life Sciences DL, Fisher Scientific)-Large filter: Fisherbrand Cell Strainers. Nylon me... |
63,243 | Live-cell imaging; reactive oxygen species (Superoxide) | 4 | dx.doi.org/10.17504/protocols.io.4r3l2oyj4v1y/v1 | https://www.protocols.io/view/live-cell-imaging-reactive-oxygen-species-superoxi-b9zjr74n | Minee-Liane Choi | TITLE: Live-cell imaging; reactive oxygen species (Superoxide)
AUTHORS: Minee-Liane Choi
[DESCRIPTION]
This protocol contains the instruction for measuring superoxide using dihydroethidium (HEt) which allows the rate of superoxide generation to be measured which is present as the ratio of the oxidized form of the dye ... | ["Cells are washed and loaded 2 micromolar (µM) dihydroethidium (HEt; Thermo Fisher Scientific) in the recording buffer.", "The recording is performed using an epi-fluorescence inverted microscope equipped with 20x objective after a quick loading (2-3 min) in order to limit the intracellular accumulation of oxidized pr... |
66,350 | Bridport Health Liver Support Optimize Your Liver Health And Detox Your Fatty Liver(Work Or Hoax) | 3 | dx.doi.org/10.17504/protocols.io.rm7vzydy2lx1/v1 | https://www.protocols.io/view/bridport-health-liver-support-optimize-your-liver-cc2nsyde | Bridport Health Liver Support | TITLE: Bridport Health Liver Support Optimize Your Liver Health And Detox Your Fatty Liver(Work Or Hoax)
AUTHORS: Bridport Health Liver Support
[DESCRIPTION]
(OFFICIAL WEBSITE) Click Here To Get Bridport Health Liver Support For The Lowest Price Right Now
[STEPS] | [] |
34,909 | Cleaning an OT-2 COVID-19 Diagnostic Station | null | dx.doi.org/10.17504/protocols.io.beb5jaq6 | null | Max Marrone | TITLE: Cleaning an OT-2 COVID-19 Diagnostic Station
AUTHORS: Max Marrone
[STEPS]
?. Wipe these parts of the OT-2 down with a 1:10 dilution of bleach:The clear polycarbonate windows.The black pipette stems. (Avoid the rest of the pipettes, including the ejectors.)The aluminum deck.The removable black trash bin.
?. Wait... | ["Wipe these parts of the OT-2 down with a 1:10 dilution of bleach:The clear polycarbonate windows.The black pipette stems. (Avoid the rest of the pipettes, including the ejectors.)The aluminum deck.The removable black trash bin.", "Wait , then quickly rinse the bleach off with distilled water.\nThe aluminum on the OT-... |
70,493 | In vitro assembly of plasmid DNA for direct cloning in Lactiplantibacillus plantarum WCSF1 | 4 | dx.doi.org/10.17504/protocols.io.ewov1o82olr2/v1 | https://www.protocols.io/view/in-vitro-assembly-of-plasmid-dna-for-direct-clonin-cg35tyq6 | Marc Blanch-Asensio, Sourik Dey, Shrikrishnan Sankaran | TITLE: In vitro assembly of plasmid DNA for direct cloning in Lactiplantibacillus plantarum WCSF1
AUTHORS: Marc Blanch-Asensio, Sourik Dey, Shrikrishnan Sankaran
[DESCRIPTION]
Protocol detailing a Gibson-assembly-based direct cloning method for Lactiplatibacillus plantarum WCFS1.
[STEPS]
SECTION: MOLECULAR CLONING
1... | ["[MOLECULAR CLONING] VECTOR PCR\n\nAmplify the backbone sequence of interest. Always use a high-fidelity polymerase such as Q5 polymerase. PCR parameters: \n \n - Use 10 ng of DNA as a template.\n - Set the initial denaturation time to 1 min.\n - Set the denaturation time during the cycle... |
null | null | null | dx.doi.org/10.17504/protocols.io.f6dbra6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The purpose of this protocol is to generate Optiprep gradients for isolating viruses</p>
[STEPS]
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null | null | null | dx.doi.org/10.17504/protocols.io.eq5bdy6 | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
Materials:<br />
<p>1) <em>Chlorella</em> virus, in 50 mM Tris-HCl, pH 7.8</p>
<p>2) 100 mM Tris-HCl, pH 7.4, 10 mM EDTA, 1 M NaCl (10X TEN, pH 7.4)</p>
<p>3) 1.0% Na sarcosyl</p>
<p>4) 10 mM Tris-HCl, pH 8.0, 1 mM EDTA (1X TE)</p>
<p>5) Isopropanol, saturated with CsCl/TE buffer... | [] |
50,180 | Glufosinate ammonium (BASTA) Paint Assay for Screening for BAR Resistance Gene in Tobacco | 1 | null | https://www.protocols.io/view/glufosinate-ammonium-basta-paint-assay-for-screeni-bu9cnz2w | Lynn Doran | TITLE: Glufosinate ammonium (BASTA) Paint Assay for Screening for BAR Resistance Gene in Tobacco
AUTHORS: Lynn Doran
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Glufosinate ammonium (BASTA</span><span style = "vertical-align:super;">TM</span><span>/LIBERTY</span><span style = "vertical-al... | ["[Herbicide Dilution]\nMake a working stock of 1.5 g/L of glufosinate ammonium.", "[Herbicide Dilution]\nDetermine the amount of glufosinate ammonium active ingredient by reading the EPA herbicide label.Liberty 280 SL contains 280 g/L.", "[Herbicide Dilution]\nCalculate and perform the required dilution from the amou... |
77,401 | Phage infection and timed harvest of E. coli and B. subtilis cells | 4 | dx.doi.org/10.17504/protocols.io.j8nlkw2d5l5r/v1 | https://www.protocols.io/view/phage-infection-and-timed-harvest-of-e-coli-and-b-cptzvnp6 | Januka Athukoralage, Adair Borges | TITLE: Phage infection and timed harvest of E. coli and B. subtilis cells
AUTHORS: Januka Athukoralage, Adair Borges
[DESCRIPTION]
This protocol outlines how to infect E. coli and B. subtilis with phage T4 and SPO1, respectively, and harvest cells at set time points.
Harvesting cells at different timepoints during... | ["[Bacteriophage infection] Prepare 30 mL subcultures of E. coli and B. subtilis at 1:100 dilution (300 µL in 30 mL) and grow to a target OD600 of 0.4 in a shaking incubator (180 rpm). For both E. coli and B. subtilis this is ~2 h at 37 °C. Supplement the subculture media (LB) with 1 mM CaCl2 and 1 mM MgCl2.", "[Bacter... |
98,210 | Creating Plate Layout in FIVTools | 1 | dx.doi.org/10.17504/protocols.io.6qpvr8orolmk/v1 | https://www.protocols.io/view/creating-plate-layout-in-fivtools-db6a2rae | Jason Waligorski | TITLE: Creating Plate Layout in FIVTools
AUTHORS: Jason Waligorski
[DESCRIPTION]
Plate layout creator in FIVtools
[STEPS]
SECTION: Creating Plate Layout in FIVTools
1. Open FIVTools
SECTION: Creating Plate Layout in FIVTools
2. Click Layouts
SECTION: Creating Plate Layout in FIVTools
3. Update Exp Name field (h... | ["[Creating Plate Layout in FIVTools] Open FIVTools", "[Creating Plate Layout in FIVTools] Click Layouts", "[Creating Plate Layout in FIVTools] Update Exp Name field (highlighted in blue above) to the corresponding FIV experiment Number (make sure to keep “FIV” in the name)", "[Creating Plate Layout in FIVTools] Click ... |
74,805 | Immunostaining infiltrating spheroids as preparation for quantitative light-sheet imaging | 1 | dx.doi.org/10.17504/protocols.io.eq2ly77krlx9/v2 | https://www.protocols.io/view/immunostaining-infiltrating-spheroids-as-preparati-cmavu2e6 | Benedicte Bjørknes, Oliver Emil Neye, Petra Hamerlik, Liselotte Jauffred | TITLE: Immunostaining infiltrating spheroids as preparation for quantitative light-sheet imaging
AUTHORS: Benedicte Bjørknes, Oliver Emil Neye, Petra Hamerlik, Liselotte Jauffred
[DESCRIPTION]
Although various in vivo and in vitro models for studying glioblastoma cell invasion has progressed the field, there is still ... | [] |
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