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.iskcecw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>February, 2012, based on RNAqueous May 29, 2008 protocol revision C, TURBO DNA-free June 9, 2009 protocol 1907M revision F, phenol/chloroform protocol (http://cshprotocols.cshlp.org/content/2010/6/pdb.prot5438.full), ethanol precipitation protocol (http://cshprotocols.cshlp.o... | [] |
80,695 | GP Letter | 3 | dx.doi.org/10.17504/protocols.io.eq2ly7y3wlx9/v1 | https://www.protocols.click/view/gp-letter-cs2xwgfn | Christopher Hawthorne, Keenan Smith, Eric Jackson, Matthew Sheridan, Shona McKay, Malcolm Watson, Martin Shaw, Jonathan Cavanagh | TITLE: GP Letter
AUTHORS: Christopher Hawthorne, Keenan Smith, Eric Jackson, Matthew Sheridan, Shona McKay, Malcolm Watson, Martin Shaw, Jonathan Cavanagh
[DESCRIPTION]
Letter to participant's General Practitioner for Predicting Cognitive Decline After Spinal Surgery (PROTECT).
[STEPS] | [] |
25,009 | Transfection of Naegleria gruberi | null | dx.doi.org/10.17504/protocols.io.4nrgvd6 | null | Anastasios D.. Tsaousis, Eleanna Kazana | TITLE: Transfection of Naegleria gruberi
AUTHORS: Anastasios D.. Tsaousis, Eleanna Kazana
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Harvest Naegleria cells that have been "transformed" to flagellates, via the protocol (see below).]
Use a 100% confluent 25cm2 flask for each transformation. https://ww... | ["[Harvest Naegleria cells that have been \"transformed\" to flagellates, via the protocol (see below).]\nUse a 100% confluent 25cm2 flask for each transformation. https://www.protocols.io/view/flagellar-transformation-of-naegleria-gruberi-hnhb5b6", "[Pellet the cells by centrifugation at 1000 x g for 5 minutes]", "[Wa... |
106,521 | Bioluminescence Imaging | 0 | dx.doi.org/10.17504/protocols.io.ewov191r2lr2/v1 | https://www.protocols.io/view/bioluminescence-imaging-dj9z4r76 | Santiago Unda, Michael G. Kaplitt | TITLE: Bioluminescence Imaging
AUTHORS: Santiago Unda, Michael G. Kaplitt
[DESCRIPTION]
This protocol describes a bioluminescence stepwise imaging protocol in mice with AAV-luciferase
expression in the vagal afferents using the Ivis Lumina series III imaging system.
[STEPS]
SECTION: Preparation and In vivo imaging
1... | ["[Preparation and In vivo imaging] Induce anesthesia with isoflurane 2-3%.", "[Preparation and In vivo imaging] Shave the neck, thoracic and abdominal area.", "[Preparation and In vivo imaging] Prepare D-luciferin potassium salt (Xenogen) stock prepared in phosphate buffered saline (PBS) at 15mg/mL.", "[Software proto... |
98,298 | CODA (part 1): setting up environment and preparing sample dataset | HuBMAP | JHU-TMC | 0 | dx.doi.org/10.17504/protocols.io.q26g71rpkgwz/v2 | https://www.protocols.io/view/coda-part-1-setting-up-environment-and-preparing-s-db822rye | Kyu Sang Han, Pei-Hsun Wu, Joel Sunshine, Sashank Reddy, Ashley Kiemen, Denis Wirtz | TITLE: CODA (part 1): setting up environment and preparing sample dataset | HuBMAP | JHU-TMC
AUTHORS: Kyu Sang Han, Pei-Hsun Wu, Joel Sunshine, Sashank Reddy, Ashley Kiemen, Denis Wirtz
[DESCRIPTION]
CODA workflow part 1. setting up environment and preparing dataset
[STEPS]
SECTION: Software requirements
1. MATLAB MA... | ["[Software requirements] MATLAB MATLAB (mathworks.com)\nImage processing toolbox Image Processing Toolbox - MATLAB (mathworks.com)\nDeep learning toolbox Deep Learning Toolbox - MATLAB (mathworks.com)\nMATLAB - Resnet50 model MATLAB resnet50 (mathworks.com)", "[Software requirements] Aperio ImageScope Aperio ImageScop... |
null | null | null | dx.doi.org/10.17504/protocols.io.crsv6d | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?. | [] |
98,838 | Crystallization of Zika virus NS3 helicase | 1 | dx.doi.org/10.17504/protocols.io.e6nvw152dlmk/v1 | https://www.protocols.io/view/crystallization-of-zika-virus-ns3-helicase-dcrw2v7e | Andre Schutzer de Godoy, Peter Marples, Lizbé Koekemoer | TITLE: Crystallization of Zika virus NS3 helicase
AUTHORS: Andre Schutzer de Godoy, Peter Marples, Lizbé Koekemoer
[DESCRIPTION]
The crystallization protocol and buffer conditions used to obtain Zika NS3 helicase crystals suitable for XChem fragment screening. The Zika virus (ZIKV), discovered in Africa in 1947, swif... | ["[Crystallization experiment] Protein and buffer requirements:\n43.2 µL5 mg/mL \n4.8 mL \n4.8 mL seeds, dilution 1:100", "[Crystallization experiment] Dispense 50 µL into SwissCI 3 lens plate reservoir wells using a 100 µl multi-channel pipette.\nDispense 150 28615 mg/mL to each lens using the SPT mosquito.\nDisp... |
44,498 | Qualitative & Quantitative Assessment of Human Islets Using Dithizone (DTZ) | 4 | dx.doi.org/10.17504/protocols.io.bppsmmne | https://www.protocols.io/view/qualitative-amp-quantitative-assessment-of-human-i-bppsmmne | Human Islet Phenotyping Program (HIPP) of the IIDP | TITLE: Qualitative & Quantitative Assessment of Human Islets Using Dithizone (DTZ)
AUTHORS: Human Islet Phenotyping Program (HIPP) of the IIDP
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;font-style:italic;">This Standard Operating Procedure is adapted from the wor... | ["[Preparation of Working Dithizone]\nAssemble all items described in Materials section.", "[Preparation of Working Dithizone]\nPrepare DTZ stain as described below. Observe all safety precautions when working with DMSO.", "[Preparation of Working Dithizone]\nWearing gloves, dissolve dithizone in DMSO.\n50 mg\n10 mL"... |
null | null | null | dx.doi.org/10.17504/protocols.io.jbdcii6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Previous research in spatial cognition has often relied on simple spatial tasks in static<br />environments in order to draw inferences regarding navigation performance. These tasks<br />are typically divided into categories (e.g., egocentric or allocentric) that reflect diff... | [] |
35,844 | Simple Step to Increase Gibson Assembly Efficiency | null | dx.doi.org/10.17504/protocols.io.be9cjh2w | https://www.protocols.io/view/simple-step-to-increase-gibson-assembly-efficiency-be9cjh2w | Eric Danner | TITLE: Simple Step to Increase Gibson Assembly Efficiency
AUTHORS: Eric Danner
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The Gibson assembly solutoin is extremely toxic to some bacteria cells. </div><div class = "text-block">Doing a solution change after assembly and before transforming the b... | ["[Do Normal Assembly]\nDo a normal Gibson assembly. Incubate in the PCR machine 60 min @ 50C", "[Do Normal Assembly]\nRemove the assemblies. Do a PCR quickchange/ gel extract column. This will remove the Gibson Assembly solution but keep the 100ng (or however much) of DNA.Elute in 15u -20ull TE or water", "[Do Normal ... |
90,463 | High-throughput individual insect metabarcoding for identification and interaction data | 4 | dx.doi.org/10.17504/protocols.io.n2bvj3qrnlk5/v1 | https://www.protocols.io/view/high-throughput-individual-insect-metabarcoding-fo-c4j7yurn | Jordan P Cuff, Thomas Howells, James JN Kitson, Ben SJ Hawthorne, darren.evans | TITLE: High-throughput individual insect metabarcoding for identification and interaction data
AUTHORS: Jordan P Cuff, Thomas Howells, James JN Kitson, Ben SJ Hawthorne, darren.evans
[DESCRIPTION]
This protocol is designed for extracting DNA from individual invertebrates for metabarcoding to detect and identify ecosys... | ["[Sampling of invertebrates] Select suitable sites and locations for insect sampling. This protocol is based on hand-collected foliar and flower visitor invertebrates, but other collection methods are viable; be wary of cross-contamination and surface DNA though, and consider surface sterilisation accordingly. Conside... |
96,438 | Experimento 2: Colores | 0 | dx.doi.org/10.17504/protocols.io.e6nvwdxzdlmk/v1 | https://www.protocols.io/view/experimento-2-colores-daew2bfe | Javier Lopez, Eduardo Antonio Mancilla Pacheco, Luis Emiliano Villegas Sapiens | TITLE: Experimento 2: Colores
AUTHORS: Javier Lopez, Eduardo Antonio Mancilla Pacheco, Luis Emiliano Villegas Sapiens
[DESCRIPTION]
Este protocolo detalla un experimento diseñado para investigar la influencia del color en el cambio de temperatura. Se utilizan tres botellas de diferentes colores, y las mediciones de te... | ["[Experimento] Instalar Arduino", "[Experimento] Programar el Arduino para la recopilación de datos", "[Experimento] Conectar los sensores de temperatura", "[Experimento] Calentar agua a 80ºC", "[Experimento] Verificar que se registren las mediciones", "[Experimento] Llenar las botellas de agua caliente", "[Experiment... |
62,555 | MIBI staining | 1 | dx.doi.org/10.17504/protocols.io.dm6gprk2dvzp/v5 | https://www.protocols.io/view/mibi-staining-b9b3r2qn | Marc MB Bosse, Sean Bendall, Mike Angelo | TITLE: MIBI staining
AUTHORS: Marc MB Bosse, Sean Bendall, Mike Angelo
[DESCRIPTION]
This protocol is the standard FFPE tissue staining procedure recommended for Multiplex Ion Beam Imaging Time of Flight instrument (MIBI_TOF) developed in the Sean C. Bendall and Michael R. Angelo labs. The protocol has been successf... | ["[Slide for MIBI] FFPE or frozen sections should be deposited on special conductive slides for MIBI\nIt is recommended to use freshly cut tissue sections. Otherwise tissue section slides should be stored properly using different state of the art methods (vacuum chamber, nitrogen chamber or vacuum sealed bags)", "[Sli... |
62,211 | wafarghsg | 1 | dx.doi.org/10.17504/protocols.io.n92ldz2b9v5b/v1 | https://www.protocols.io/view/wafarghsg-b8zbrx2n | sf | TITLE: wafarghsg
AUTHORS: sf
[DESCRIPTION]
gbsfbbfgb
[STEPS]
SECTION: 21.08.2066
1. fgsgrtvsvxfdgbhgdbbgfxbxgbdfbcvbfxbgbxbggdfgxbdfgb
SECTION: 23.98.6778
2. fgdbdgnffgnbg
SECTION: 23.98.6778
2.1. | ["[21.08.2066] fgsgrtvsvxfdgbhgdbbgfxbxgbdfbcvbfxbgbxbggdfgxbdfgb", "[23.98.6778] fgdbdgnffgnbg", "[23.98.6778]"] |
20,981 | Quantitative whole-slide image analysis of CD3 and CD8 immunohistochemical stains | 1 | dx.doi.org/10.17504/protocols.io.yqvfvw6 | https://www.protocols.io/view/quantitative-whole-slide-image-analysis-of-cd3-and-yqvfvw6 | Seungyeon Yoo | TITLE: Quantitative whole-slide image analysis of CD3 and CD8 immunohistochemical stains
AUTHORS: Seungyeon Yoo
[DESCRIPTION]
Given the virtual slide images of CD3 and CD8 immunohistochemical stains, this protocol provides the following quantitative measures of tumor immune microenvironment:
Density of intraepithelial... | ["[Create a new project] After creating the project, open 'code' folder and execute 'run.bat' by double-clicking. It will automatically create the script files according to your directory setting. \n\n\n \n\nThis script do the following substitution and move all the above files to Project/Scripts (this /Scripts subfold... |
90,202 | An Open-Source System for Efficient Clinical Trial Support: the COMET study experience | 5 | dx.doi.org/10.17504/protocols.io.rm7vzxo25gx1/v1 | https://www.protocols.io/view/an-open-source-system-for-efficient-clinical-trial-c4b2ysqe | jclutton, evidoni, Dinesh Pal Mudaranthakam, Robert Neal Montgomery, Erin Blocker, Ashley Shaw, Amanda Szabo Reed | TITLE: An Open-Source System for Efficient Clinical Trial Support: the COMET study experience
AUTHORS: jclutton, evidoni, Dinesh Pal Mudaranthakam, Robert Neal Montgomery, Erin Blocker, Ashley Shaw, Amanda Szabo Reed
[DESCRIPTION]
Exercise clinical trials are complex, logistically burdensome, and require a well-coordi... | ["[Planning] Review the code (GitHub - cometstudy/OSSforEfficientClinicalTrialSupportCOMET) and plan what aspects of the project you'd like to adapt. \n\nSome possibilities include:\nFitbit data infrastructure\nDSMC reporting\nStudy staff reporting\nEmail modules\nData storage\nSome approximation of the whole project",... |
72,233 | Cryogenic (H2O)n-GCIB-SIMS imaging | 1 | dx.doi.org/10.17504/protocols.io.81wgbyynovpk/v1 | https://www.protocols.io/view/cryogenic-h2o-n-gcib-sims-imaging-cishueb6 | Hua Tian | TITLE: Cryogenic (H2O)n-GCIB-SIMS imaging
AUTHORS: Hua Tian
[DESCRIPTION]
The protocol describes the imaging of frozen-hydrated biological sample using high resolution mass spectrometry imaging, water gas cluster ion beam secondary ion mass spectrometry (H2O)n-GCIB-SIMS).
[STEPS]
1. Both (H2O)n-GCIB and C60-SIMS we... | ["Both (H2O)n-GCIB and C60-SIMS were performed on a buncher-ToF instrument, J105 3D Chemical Imager (Ionoptika, Southampton, UK. Abbv. J105). The water cluster ion beam is pulsed through a pulser in the gun column, where the distance to the sample surface is 0.533 m. Beam tuning was assisted with an oscilloscope (Tektr... |
35,926 | Protein expression of hard-to-produce proteins in the cytoplasm of Escherichia coli | 1 | dx.doi.org/10.17504/protocols.io.bfbwjipe | https://www.protocols.io/view/protein-expression-of-hard-to-produce-proteins-in-bfbwjipe | Cristina Hernandez Rollan, Kristoffer Bach Falkenberg, Maja Rennig, Andreas Birk Bertelsen, Morten Norholm | TITLE: Protein expression of hard-to-produce proteins in the cytoplasm of Escherichia coli
AUTHORS: Cristina Hernandez Rollan, Kristoffer Bach Falkenberg, Maja Rennig, Andreas Birk Bertelsen, Morten Norholm
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describes the expression ... | ["[Day 1 - Culture inoculation]\nPick a fresh colony of your BL21 (DE3) strain previously transformed with your expression vector, and inoculate it in LB medium supplemented with relevant antibiotics. Grow the culture at at 250 RPM shaking . The volume of the overnight culture depends on the volume of the expression c... |
50,784 | Illumina double-stranded DNA dual indexing for ancient DNA | 1 | dx.doi.org/10.17504/protocols.io.bvt8n6rw | https://www.protocols.io/view/illumina-double-stranded-dna-dual-indexing-for-anc-bvt8n6rw | Raphaela Stahl, Christina Warinner, Irina Velsko, Eleftheria Orfanou, Franziska Aron, Guido Brandt | TITLE: Illumina double-stranded DNA dual indexing for ancient DNA
AUTHORS: Raphaela Stahl, Christina Warinner, Irina Velsko, Eleftheria Orfanou, Franziska Aron, Guido Brandt
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol converts partially completed double-stranded DNA libraries e.g. ... | ["[Indexing preparation (aDNA library preparation room)]\nCalculate the total number of DNA molecules (total copy number) DNA concentration in each library based on qPCR performed at the end of library preparation (see Before Start). Do not use more than 1.5x10^10 copies per indexing reaction. Adjust the amount of DNA ... |
null | null | null | dx.doi.org/10.17504/protocols.io.e3vbgn6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
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null | null | null | dx.doi.org/10.17504/protocols.io.jwkcpcw | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<p>Glassware should be acid-washed and rinsed well with dH<sub>2</sub>O before use. If unable to measure small quantities accurately, either scale up the recipe or prepare stock solutions of the individual compounds.</p>
[STEPS]
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32,832 | Visualizing Calling Card Data on the WashU Epigenome Browser | null | dx.doi.org/10.17504/protocols.io.bca8ishw | null | Arnav Moudgil, Rob Mitra | TITLE: Visualizing Calling Card Data on the WashU Epigenome Browser
AUTHORS: Arnav Moudgil, Rob Mitra
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This document explains how to visualize calling card insertions as wells as density and peak tracks on the WashU Epigenome Browser. </div></div>
[STE... | ["[Introduction]\nDuring the course of a calling card experiment, or after all the analysis has been said and done, you may want to visually inspect the data. These can be the raw insertions (stored as a CCF file), insertion densities (as a bedgraph file), or the peak boundaries (as a BED file). Instructions for genera... |
70,385 | Bacterial genome annotation script using BLASTN | 5 | dx.doi.org/10.17504/protocols.io.dm6gpjrb1gzp/v1 | https://www.protocols.io/view/bacterial-genome-annotation-script-using-blastn-cgyrtxv6 | Ana Mariya Anhel, Lorea Alejaldre, Ángel Goñi-Moreno | TITLE: Bacterial genome annotation script using BLASTN
AUTHORS: Ana Mariya Anhel, Lorea Alejaldre, Ángel Goñi-Moreno
[DESCRIPTION]
This protocol uses a python based script and command-line blastn to annotate Sanger sequencing results from genome amplifications. Its main use in our lab (https://biocomputationlab.com) i... | ["[Annotation of sequencing reads] Run the following python based script with the required arguments", "[Annotation of sequencing reads] Download genome file in FASTA format and annotation file in .csv for the microbial organism to use as reference", "[Annotation of sequencing reads] Output is a folder named results_sc... |
null | null | null | dx.doi.org/10.17504/protocols.io.na8dahw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?. | [] |
70,289 | Calcium Imaging in mDA neurons | 1 | dx.doi.org/10.17504/protocols.io.3byl4j7e8lo5/v1 | https://www.protocols.io/view/calcium-imaging-in-mda-neurons-cgvrtw56 | gurvir.virdi | TITLE: Calcium Imaging in mDA neurons
AUTHORS: gurvir.virdi
[DESCRIPTION]
Calcium imaging using Fura-2, Fluo-4 and X-Rhod-1.
[STEPS]
1. To measure cytosolic calcium, 5 uM Fura-2 or Fluo-4 was added to cells at room temperature for 40 minutes made up in HBSS (Invitrogen).
To measure mitochondrial calcium, cells were ... | ["To measure cytosolic calcium, 5 uM Fura-2 or Fluo-4 was added to cells at room temperature for 40 minutes made up in HBSS (Invitrogen).\n\nTo measure mitochondrial calcium, cells were incubated with 2μM X-Rhod-1 in HBSS for 40 minutes.", "Cells are then washed 2x in HBSS at room temperature. They are now ready for im... |
83,804 | Nuclei isolation from fresh frozen human colon tissue for 10X Genomics Multi-omics (ATAC + GEX) assay | 1 | dx.doi.org/10.17504/protocols.io.5jyl8pn17g2w/v1 | https://www.protocols.click/view/nuclei-isolation-from-fresh-frozen-human-colon-tis-cv34w8qw | Antonina Mikorska, Koen Theunis, Suresh Poovathingal, sam kint, Sarah Geurs, Thierry Voet | TITLE: Nuclei isolation from fresh frozen human colon tissue for 10X Genomics Multi-omics (ATAC + GEX) assay
AUTHORS: Antonina Mikorska, Koen Theunis, Suresh Poovathingal, sam kint, Sarah Geurs, Thierry Voet
[DESCRIPTION]
Nuclei isolation protocol used for sn multi-omics assay on fresh frozen human colon tissue (full ... | ["[Sample preparation] Place the sample preparation instruments on dry ice: biopsy punch, 1.5 mL EP tube, tweezers, petri dish.", "[Experiment preparation] Prepare all buffers fresh and on wet ice. Add the the detergents, DTT and RNase inhibitor just before use.", "[Tissue homogenization] Perform all steps on wet ice. ... |
null | null | null | dx.doi.org/10.17504/protocols.io.k9icz4e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>We developed an Illumina-based pipeline, HIFI-Barcode, to produce full-length COI barcodes from pooled PCR amplicons generated by individual specimens. Using indexed primer sets and high-throughput sequencing platform strategy, and optimized analysis pipeline, the analytical ... | [] |
95,892 | Odor Threshold | 0 | dx.doi.org/10.17504/protocols.io.kqdg3xm37g25/v1 | https://www.protocols.io/view/odor-threshold-c9vuz66w | sdwalto, Jeffrey Kordower, Bryan_Killinger | TITLE: Odor Threshold
AUTHORS: sdwalto, Jeffrey Kordower, Bryan_Killinger
[DESCRIPTION]
Odor threshold optimized for mice. This test was made to test short term olfactory memory. Mice with olfactory impairment or deficits should score lower.
[GUIDELINES]
ODORANT: Propionic acid at increasing concentrations of 1:106,... | ["Prepare and empty rodent cage with no bedding.", "Prepare the odorant by diluting in mineral oil. (See guidelines)", "Acclimate mouse to setup (empty cage with odor cartridges). Place mouse in the cage and expose to empty odor cartridge for 5 mins.", "Pre-habituate mouse to a paper swab soaked in mineral oil in the o... |
null | null | null | dx.doi.org/10.17504/protocols.io.hghb3t6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol modified from: </p>
<p>Pandey A, Bhathena Z. 2014. Prevalence of PUFA Rich Thraustochytrids sps. along the<br />Coast of Mumbai for Production of Bio Oil. Journal of Food and Nutrition<br />Research 2(12): 993-999.</p>
[STEPS]
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null | null | null | dx.doi.org/10.17504/protocols.io.ti2ekge | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Genomic DNA was extracted from circulating blood leucocytes by using Gentra Puregene Blood Kits according to the manufacturer’s protocol (Qiagen) and was stored at -20°C.
The TRKB polymorphismswere genotyped by the IntegraGen company (Evry, France) using the Fluidigm®BioMarkTMH... | [] |
84,010 | Generation of stable cell lines via lentiviral transduction | 4 | dx.doi.org/10.17504/protocols.io.6qpvr3e5pvmk/v1 | https://www.protocols.io/view/generation-of-stable-cell-lines-via-lentiviral-tra-cwaixace | Elias Adriaenssens | TITLE: Generation of stable cell lines via lentiviral transduction
AUTHORS: Elias Adriaenssens
[DESCRIPTION]
Here, we describe a protocol to generate stable cell lines using a lentivirus system. Please note that necessary safety measures are to be taken in working with lentivirus.
[STEPS]
SECTION: Packaging lentivira... | ["[Packaging lentiviral plasmid into a lentiviral particles for in…] Grow HEK293T cells to 60-70% confluency in Growth media in a 6-well Petri Dish.", "[Packaging lentiviral plasmid into a lentiviral particles for in…] Prepare a transfection mix in a sterile 1.5 ml Eppendorf tube, containing: \n lentiviral vector ... |
93,136 | Sample homogenization and DNA extraction for bulk insect catches | 4 | dx.doi.org/10.17504/protocols.io.yxmvm31bbl3p/v1 | https://www.protocols.io/view/sample-homogenization-and-dna-extraction-for-bulk-c67qzhmw | nannie.persson, Håkan Johansson, Ela Iwaszkiewicz-Eggebrecht, Andreia Miraldo | TITLE: Sample homogenization and DNA extraction for bulk insect catches
AUTHORS: nannie.persson, Håkan Johansson, Ela Iwaszkiewicz-Eggebrecht, Andreia Miraldo
[DESCRIPTION]
Here we describe a protocol to homogenize and extract DNA for bulk insect catches collected via Malaise traps. By following this protocol you will... | ["[SECTION 2: Sample lysis] Add the appropriate amount of lysis buffer to each insect bottle according to Table 1 using a graduated cylinder and a small funnel to get the right amount of buffer. The funnel is important so that the lysis buffer is poured slowly and accurately from the 1L bottle into the graduated cylind... |
53,231 | Immunofluorescence of Galectin-3 Puncta after lysosomal damage with LLoMe | 1 | dx.doi.org/10.17504/protocols.io.bx8pprvn | https://www.protocols.io/view/immunofluorescence-of-galectin-3-puncta-after-lyso-bx8pprvn | Vinay V. Eapen, Sharan Swarup, Melissa Hoyer, Harper JW | TITLE: Immunofluorescence of Galectin-3 Puncta after lysosomal damage with LLoMe
AUTHORS: Vinay V. Eapen, Sharan Swarup, Melissa Hoyer, Harper JW
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Lysophagy-the selective elimination of damaged lysosomes by the autophagy pathway-is a critical hous... | ["[Immunofluorescence of Galectin-3 Puncta after lysosomal damage with LLoMe]\nPlate the cells (selected by investigator) into 12 well glass bottom dishes (No. 1.5, 14 mm glass diameter, MatTek) are grown to 50-70% confluency in media.\nFor HeLa cells, we use Dulbecco’s MEM (DMEM), high glucose (4500 mg/L), pyruvate (1... |
46,832 | Preparation of LRRK2 RCKW cryo-EM grids | 4 | dx.doi.org/10.17504/protocols.io.kxygxp7ywl8j/v1 | https://www.protocols.io/view/preparation-of-lrrk2-rckw-cryo-em-grids-bryqm7vw | Mariusz Matyszewski | TITLE: Preparation of LRRK2 RCKW cryo-EM grids
AUTHORS: Mariusz Matyszewski
[DESCRIPTION]
This is Leschziner's Lab updated protocol for making cryo-EM grids for LRRK2 RCKW. This protocol, when using lower protein concentration, results in better monomer and dimer formation than the old protocol.
[BEFORE_START]
Decide... | ["[Freezing Grids] Plasma clean grids.\nWe used UltrAuFoil Holey Gold 1.2/1.3 300 mesh grids and plasma cleaned them in the Solarus II (Gatan) using the QuantiFoil Au preset.", "[Freezing Grids] Apply protein to grids and plunge freeze.\nWe used a Vitrobot (FEI) to blot away excess sample and plunge freeze", "[Freezing... |
97,104 | USDA LTAR Common Experiment measurement: Total nitrogen (TN) and total dissolved nitrogen (TDN) concentration | 1 | dx.doi.org/10.17504/protocols.io.5jyl82rkrl2w/v1 | https://www.protocols.io/view/usda-ltar-common-experiment-measurement-total-nitr-da3q2gmw | Robert W. Malone, Amy J. Morrow, Oliva Pisani, John L. Kovar, Stephen K. Hamilton, Kevin J. Cole | TITLE: USDA LTAR Common Experiment measurement: Total nitrogen (TN) and total dissolved nitrogen (TDN) concentration
AUTHORS: Robert W. Malone, Amy J. Morrow, Oliva Pisani, John L. Kovar, Stephen K. Hamilton, Kevin J. Cole
[DESCRIPTION]
Total dissolved nitrogen (TDN) is composed of dissolved inorganic nitrogen (DIN) a... | ["[Sample collection and filtration] Return samples to the laboratory on ice.", "[Sample collection and filtration] Measure total N (TN) on unfiltered samples.", "[Sample collection and filtration] Measure TDN by filtering samples through a 0.22 or 0.45 µm pore-size filter to minimize interference from particulates bef... |
105,614 | Crystallisation protocol for SARS-CoV-2 nsp3 macrodomain in P43 | 1 | dx.doi.org/10.17504/protocols.io.e6nvw1qb2lmk/v1 | https://www.protocols.io/view/crystallisation-protocol-for-sars-cov-2-nsp3-macro-djdn4i5e | Jasmin Aschenbrenner, Peter Marples, Charlie Tomlinson, Lizbé Koekemoer, Daren Fearon | TITLE: Crystallisation protocol for SARS-CoV-2 nsp3 macrodomain in P43
AUTHORS: Jasmin Aschenbrenner, Peter Marples, Charlie Tomlinson, Lizbé Koekemoer, Daren Fearon
[DESCRIPTION]
The COVID-19 pandemic has demonstrated the need for novel therapeutic interventions and improved pandemic preparedness strategies against s... | ["[Crystallization experiment] Protein and buffer requirements:\n45 µL47 mg/mL \n2.0 mL", "[Crystallization experiment] Dispense 20 µL into SwissCI 3 lens plate reservoir wells using a 100 µl multi-channel pipette.\nDispense 150 nL47 mg/mL to each lens using the SPT mosquito.\nDispense 150 nL to each lens using th... |
58,818 | PCR with Q5® High-Fidelity 2X Master Mix - CHEM 384/584 | 1 | dx.doi.org/10.17504/protocols.io.b5paq5ie | https://www.protocols.io/view/pcr-with-q5-high-fidelity-2x-master-mix-chem-384-5-b5paq5ie | New England Biolabs | TITLE: PCR with Q5® High-Fidelity 2X Master Mix - CHEM 384/584
AUTHORS: New England Biolabs
[DESCRIPTION]
The Q5 High-Fidelity 2X Master Mix offers robust, high-fidelity performance in a convenient master mix format. The Q5 High- Fidelity 2X Master Mix features a high-fidelity, thermostable DNA polymerase with 3´→ ... | ["Set up the following reaction on ice:\n Component25 µl Reaction50 µl ReactionFinal Concentration Q5 High-Fidelity 2X Master Mix 12.5 µl 25 µl 1X 10 µM Forward Primer 1.25 µl 2.5 µl 0.5 µM 10 µM Reverse Primer 1.25 µl 2.5 µl 0.5 µM Template DNA variable variable < 1,000 ng Nuclease-Free Water to 25 µl to 50 ... |
14,542 | Determination of flavonoid content | null | dx.doi.org/10.17504/protocols.io.sfnebme | null | Jorge Carlos Ruiz Ruiz | TITLE: Determination of flavonoid content
AUTHORS: Jorge Carlos Ruiz Ruiz
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Flavonoid content determination using the aluminum chloride method.</div></div>
[STEPS]
?. An aliquot of sample (0.1 mL) was mixed with 0.4 ml distilled water in a 1.5 mL microc... | ["An aliquot of sample (0.1 mL) was mixed with 0.4 ml distilled water in a 1.5 mL microcentrifuge tube.", "0.03 mL of 5% NaNO2 was added and the mixture was allowed to react for 5 min.", "Following this, 0.03 mL of 10% AlCl3 was added and the mixture stood for a further 5 min.", "Finally, the reaction mixture was treat... |
14,859 | RNA/DNA extraction from samples of acute gastroenteritis | null | dx.doi.org/10.17504/protocols.io.srjed4n | null | Hengyun Guan, Chunrong Wang, Lanzheng Liu, Guoliang Yang | TITLE: RNA/DNA extraction from samples of acute gastroenteritis
AUTHORS: Hengyun Guan, Chunrong Wang, Lanzheng Liu, Guoliang Yang
[DESCRIPTION]
<p>Many types of sample would be collected in outbreaks of acute gastroenteritis. Therefore we have settled this protocol to extract RNA/DNA for virus detection rapidly and ef... | ["[Pretreatment of stool/anal swab]\nAdd 0.2g stool to 1.0ml phosphate buffer saline (with Mg2+ and Ca2+) in one 1.5ml Eppendorf tube with 6-8 particles of ceramic beads. Put the anal swab into 1.0ml phosphate buffer saline (with Mg2+ and Ca2+) and repeatedly squeeze it.\n Vortex for 2×20 sec at 4000rpm at room tempera... |
60,295 | Photo-oxidation Using MiniSOG with EM Preparation of Transfected Culture Cells | 1 | dx.doi.org/10.17504/protocols.io.eq2lynj8pvx9/v2 | https://www.protocols.io/view/photo-oxidation-using-minisog-with-em-preparation-b65frg3n | Mason Mackey, Xiaokun Shu, Varda Lev-Ram, Thomas J. Deerinck, Yingchuan Qi, Ericka B. Ramko, Michael W. Davidson, Yishi Jin, Mark H. Ellisman, Roger Y. Tsien | TITLE: Photo-oxidation Using MiniSOG with EM Preparation of Transfected Culture Cells
AUTHORS: Mason Mackey, Xiaokun Shu, Varda Lev-Ram, Thomas J. Deerinck, Yingchuan Qi, Ericka B. Ramko, Michael W. Davidson, Yishi Jin, Mark H. Ellisman, Roger Y. Tsien
[DESCRIPTION]
Abstract taken from Plos Biology Journal: A Gene... | ["Cells are grown on glass bottom microwell MatTek culture dishes (35 mm Glass Bottom Dishes No. 0 / Poly-d-lysine coated / γ-Irradiated) \n\n(Part no. P35G-0-14-C, MatTek Corp)", "Transfected Cells are fixed with 37oC 2% glutaraldehyde (Product No: 18426 Ted Pella, Inc.) in *0.1M sodium cacodylate (Product No. 18851 ... |
64,669 | Preparing ONT-tagged Primers and Master Mix for Fungal DNA Barcoding | 4 | null | https://www.protocols.io/view/preparing-ont-tagged-primers-and-master-mix-for-fu-cbd5si86 | Stephen Douglas Russell | TITLE: Preparing ONT-tagged Primers and Master Mix for Fungal DNA Barcoding
AUTHORS: Stephen Douglas Russell
[DESCRIPTION]
ONT primer preparation has two specific aspects that are unique when comparing to Sanger sequencing protocols. The first is that each primer needs to be "tagged" - a unique ~10-15bp sequence... | ["[Ordering ONT-tagged Primers] - Determine how many unique primers you need to order. Ex - If you are planning to utilize a Flongle cell with up to 480 specimens, you would need to order five unique forward ONT-tagged primers. If you hope to use a 10.4.1 cell with 10,000+ specimens, you would need to order at least 10... |
null | null | null | dx.doi.org/10.17504/protocols.io.gg8btzw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes basic functions to view your contigs and profiles databases in Anvi'o.</p>
[STEPS]
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25,267 | Generation and assembly of human brain region-specific organoids | null | null | https://www.protocols.io/view/generation-and-assembly-of-human-brain-region-spec-4wtgxen | Steven A. Sloan, Jimena Anderson, Anca M. Pașca, Fikri Birey, Sergiu Pasca | TITLE: Generation and assembly of human brain region-specific organoids
AUTHORS: Steven A. Sloan, Jimena Anderson, Anca M. Pașca, Fikri Birey, Sergiu Pasca
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">The ability to generate region-specific three-dimensional (3D)... | ["[MEF feeder seeding and initiation of hPSC cultures]\nCoat 10-cm cell culture dishes with 0.1% gelatin for at least at .\n0 Room temperature", "[MEF feeder seeding and initiation of hPSC cultures]\nThaw one vial of MEFs (containing ~5 × 106 cells) by placing it in a water bath at until it is 80% thawed (and for no... |
62,382 | Wastewater QC workflow in GalaxyTrakr (SSQuAWK4) | 1 | null | https://www.protocols.io/view/wastewater-qc-workflow-in-galaxytrakr-ssquawk4-b86nrzde | Jasmine Amirzadegan, Tunc Kayikcioglu, hugh.rand , Ruth Timme, Maria Balkey | TITLE: Wastewater QC workflow in GalaxyTrakr (SSQuAWK4)
AUTHORS: Jasmine Amirzadegan, Tunc Kayikcioglu, hugh.rand , Ruth Timme, Maria Balkey
[DESCRIPTION]
PURPOSE:
Step-by-step instructions for checking sequence quality for SARS-CoV-2 wastewater samples using SSQuAWK3: SARS - CoV - 2 Sequence Quality Assuranc... | ["[Account set up] Create a GalaxyTrakr account here: https://account.galaxytrakr.org/Account/Register", "[Account set up] Log into your GalaxyTrakr account: https://galaxytrakr.org", "[Create a new history] Create a new history. \n\nWe recommend creating a new history for each new MiSeq sequence set with details and d... |
98,146 | Hematoxylin & Eosin Histology of Elasmobranch skin | 0 | dx.doi.org/10.17504/protocols.io.x54v92m71l3e/v1 | https://www.protocols.io/view/hematoxylin-amp-eosin-histology-of-elasmobranch-sk-db4a2qse | Rebecca Meng, Angel Amarales, Marco Perez, Maria Elena de Bellard | TITLE: Hematoxylin & Eosin Histology of Elasmobranch skin
AUTHORS: Rebecca Meng, Angel Amarales, Marco Perez, Maria Elena de Bellard
[DESCRIPTION]
Hematoxylin and eosin stain is probably the most used staining method in histology. It provides a comprehensive and detailed picture of different types of cells and tis... | ["[Fixation:] Squalus and Leucoraja were initially preserved in formalin by Carolina Biological Supplier. We post-fixed tissues in 4% PFA for a minimum of 24 hours to improve the fixation of skin structures. We dissected 2cm blocks of skin from the head and trunks and kept them in 4%PFA. Live Urobatis halleri and Leuco... |
98,479 | ISP French Polynesia Recreational Scuba Diving | 0 | dx.doi.org/10.17504/protocols.io.q26g71bq1gwz/v1 | https://www.protocols.io/view/isp-french-polynesia-recreational-scuba-diving-dcep2tdn | Stephanie Gay | TITLE: ISP French Polynesia Recreational Scuba Diving
AUTHORS: Stephanie Gay
[DESCRIPTION]
This landscape study aims to assess the current state of the recreational diving industry in French Polynesia, particularly from a local community perspective. The main focus of study will be to investigate local perceptions of ... | ["[Background Web Research on Dive Clubs in French Polynesia] Navigate to Google Directory of dive clubs in French Polynesia through query \"Scuba diving centres in French Polynesia\"", "[Background Web Research on Dive Clubs in French Polynesia] Navigate to https://www.tahititourisme.com/activities/diving/diving-clubs... |
48,195 | Chimeric Protein-LAG and Staphylococcal Protein A sandwich ELISA | 1 | dx.doi.org/10.17504/protocols.io.btbbniin | https://www.protocols.io/view/chimeric-protein-lag-and-staphylococcal-protein-a-btbbniin | Angel Justiz-Vaillant | TITLE: Chimeric Protein-LAG and Staphylococcal Protein A sandwich ELISA
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This ELISA was used to study the interactions between protein-LAG (PLAG) and staphylococcal protein-A (SpA) with different immunoglobulin preparatio... | ["This ELISA was used to study the interactions between protein-LAG (PLAG) and staphylococcal protein-A (SpA) with different immunoglobulin preparations of mammalian and avian species. The 96 well microtiter plate was coated overnight at 4°C with 2 µg/µl per well of PLAG in carbonate-bicarbonate buffer pH 9.6.", "The p... |
76,084 | Nuclear Isolation of Post-Mortem Brain Tissue for snRNAseq | 4 | dx.doi.org/10.17504/protocols.io.yxmvm25xng3p/v1 | https://www.protocols.io/view/nuclear-isolation-of-post-mortem-brain-tissue-for-cniuvcew | Jonathan W Brenton, Carlo Sala Frigerio, Mina Ryten, Regina H Reynolds, e.gustavsson, Kylie Montgomery | TITLE: Nuclear Isolation of Post-Mortem Brain Tissue for snRNAseq
AUTHORS: Jonathan W Brenton, Carlo Sala Frigerio, Mina Ryten, Regina H Reynolds, e.gustavsson, Kylie Montgomery
[DESCRIPTION]
This protocol is used to isolate nuclei from frozen brain tissue for single nuclear RNA sequencing using 10x Genomics GEM isola... | ["[Buffer Preparation on ice for 6 samples (amount prepared for 7 to allow for waste)] ODN \n \n ODNV (µl)Stock conc Final concKCl1342.68752000mM150mMMgCl2537.0751000mM30mMTris pH 7,4 (Sigma)1074.151000mM60mMSucrose8951.25500mM250mMNuclease free water5997.3375Total Volume17902.5", "[Buffer Preparation on ice for... |
51,730 | Eric Vaughn snRNASeq Protocol | 1 | dx.doi.org/10.17504/protocols.io.bwrspd6e | https://www.protocols.io/view/eric-vaughn-snrnaseq-protocol-bwrspd6e | Eric Vaughn, Catherine Dulac | TITLE: Eric Vaughn snRNASeq Protocol
AUTHORS: Eric Vaughn, Catherine Dulac
[DESCRIPTION]
This protocol is designed to extract single nuclei for sequencing with 10X Genomics technologies.
Note: For each step, keep tissue/nuclei/reagents/centrifuge on ice/cold to reduce IEG expression and maintain nuclear integrity.
... | ["After obtaining all tissue, mince tissue 2-3 times until tissue is roughly quartered into .52mm size blocks.", "Dissect out tissue and place into tube with Hibernate A on ice (or if doing only 1-2 dissections, straight into lysis buffer).", "Transfer ~3mL lysis buffer to Potter-Elvehjem Tissue Grinder, 3 mL (manufact... |
39,050 | CRITERIA TO EVALUATE NEUROGENIC BOWEL DYSFUNCTION IN CHILDREN WITH CONGENITAL ZIKA SYNDROME | 1 | dx.doi.org/10.17504/protocols.io.bidika4e | https://www.protocols.io/view/criteria-to-evaluate-neurogenic-bowel-dysfunction-bidika4e | Valeria Azevedo De Almeida, Nancy Sotero, Rafael Pauletti Gonçalves, Edgard Morya, Lilian Lira Lisboa, Lucia Maria Costa Monteiro, Reginaldo Antônio de Oliveira Freitas Júnior | TITLE: CRITERIA TO EVALUATE NEUROGENIC BOWEL DYSFUNCTION IN CHILDREN WITH CONGENITAL ZIKA SYNDROME
AUTHORS: Valeria Azevedo De Almeida, Nancy Sotero, Rafael Pauletti Gonçalves, Edgard Morya, Lilian Lira Lisboa, Lucia Maria Costa Monteiro, Reginaldo Antônio de Oliveira Freitas Júnior
[DESCRIPTION]
<div class = "text-... | ["After confirming the inclusion criteria, the initial assessment includes 5 steps:1. Detailed clinical history, related to water intake and food routine, including any special dietetic regimen to bowel emptying.", "2. Detailed clinical history, related to bowel habits, including: Frequency of bowel emptying (evacuatio... |
19,000 | Clinical education alone is sufficient to improve strength training exercise prescription | null | dx.doi.org/10.17504/protocols.io.wsyfefw | null | A/Prof Gavin Williams, Prof Linda Denehy | TITLE: Clinical education alone is sufficient to improve strength training exercise prescription
AUTHORS: A/Prof Gavin Williams, Prof Linda Denehy
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The main cause of reduced ability to walk for the majority of people with neurological conditions is musc... | [] |
44,310 | Robust, Cost-Effective Profiling of RNA Binding Protein Targets with Single-end Enhanced Crosslinking and Immunoprecipitation (seCLIP) | 2 | dx.doi.org/10.17504/protocols.io.bphwmj7e | https://www.protocols.io/view/robust-cost-effective-profiling-of-rna-binding-pro-bphwmj7e | Eric L. Van Nostrand, Thai B. Nguyen, Chelsea Gelboin-Burkhart, Ruth Wang, Steven M. Blue, Gabriel A. Pratt, Ashley L. Louie, Gene W. Yeo | TITLE: Robust, Cost-Effective Profiling of RNA Binding Protein Targets with Single-end Enhanced Crosslinking and Immunoprecipitation (seCLIP)
AUTHORS: Eric L. Van Nostrand, Thai B. Nguyen, Chelsea Gelboin-Burkhart, Ruth Wang, Steven M. Blue, Gabriel A. Pratt, Ashley L. Louie, Gene W. Yeo
[DESCRIPTION]
<div class = "te... | [] |
35,589 | Subcutaneous Injection Adult Mouse | null | dx.doi.org/10.17504/protocols.io.bezdjf26 | null | Allen Institute for Brain Science | TITLE: Subcutaneous Injection Adult Mouse
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes general procedures used for subcutaneous injection in adult mice.</div><div class = "text-block"><span style = "font-weight:bold;">Note</span><... | [] |
36,648 | Imaging Mass Cytometer Tuning | null | dx.doi.org/10.17504/protocols.io.bf2gjqbw | https://www.protocols.io/view/imaging-mass-cytometer-tuning-bf2gjqbw | Michelle Daniel, Marda Jorgensen | TITLE: Imaging Mass Cytometer Tuning
AUTHORS: Michelle Daniel, Marda Jorgensen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This SOP describes the tuning of an Imaging Mass Cytometer (IMC). The tuning process</div><div class = "text-block">encompasses parameters such as Interface alignment, gas ... | ["[Start plasma and insert tuning slide]\n1. If the machine is running, check the “tuning log sheet.ods” and get the date of the last tuning. Ifthe last tuning was done more than two days ago proceed to step 3.3.2. Check argon supply and pressure (5 bar). Make sure that one of the argon tanks has at least25% which will... |
null | null | null | dx.doi.org/10.17504/protocols.io.mjhc4j6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Determination of apoptotic cell in lymphocyte popullation using flow-cytometry</p>
[STEPS]
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70,862 | HIV WGS - 400bp Amplicon Tiling - Oxford Nanopore Technology Protocol | 4 | dx.doi.org/10.17504/protocols.io.e6nvwj5p2lmk/v1 | https://www.protocols.io/view/hiv-wgs-400bp-amplicon-tiling-oxford-nanopore-tech-chfnt3me | Eugene Yeboah, Noah C Hull | TITLE: HIV WGS - 400bp Amplicon Tiling - Oxford Nanopore Technology Protocol
AUTHORS: Eugene Yeboah, Noah C Hull
[DESCRIPTION]
OSPHL in collaboration with APHL, will evaluate the performance of the Oxford Nanopore Technology sequencers for HIV genome sequencing using a modified protocol of the ARTIC amplicon v3:
Nano... | ["Reverse Transcription\nThe LunaScript® RT SuperMix Kit will be used to reverse transcribe HIV RNA for preparation to perform the Primer Pool PCR assay. NOTE: LunaScript® RT SuperMix will be kept in the PCR Clean room.", "Place 96-well PCR plate on an Eppendorf® PCR cooler (stored at -20oC).", "Using a repeater pipett... |
83,395 | Whole-Genome Amplification of Respiratory Syncytial Virus (RSV) using Illumina CovidSeq reagents for Next-Generation Sequencing | 4 | dx.doi.org/10.17504/protocols.io.eq2lyjzbrlx9/v1 | https://www.protocols.click/view/whole-genome-amplification-of-respiratory-syncytia-cvpbw5in | Carlos Davina-Nunez, Sonia Perez-Castro, Montse Godoy-Diz, Benito Regueiro-Garcia | TITLE: Whole-Genome Amplification of Respiratory Syncytial Virus (RSV) using Illumina CovidSeq reagents for Next-Generation Sequencing
AUTHORS: Carlos Davina-Nunez, Sonia Perez-Castro, Montse Godoy-Diz, Benito Regueiro-Garcia
[DESCRIPTION]
This protocol has been tested for amplification of RSV-positive nasopharyngeal ... | ["[Primer pools preparation] Prepare both primer mixes according to Table 1.\n\nFor a final concentration of 10uM: add 1017 ul of Nuclease-Free water to Pool 1 and 1035 ul to Pool 2.", "[RT-PCR] Two Master Mixes must be prepared per sample: one for Pool1 and one for Pool 2 (Table 2). Manipulate reagents according to th... |
101,041 | Serapure Beads Preparation and Testing | 1 | dx.doi.org/10.17504/protocols.io.3byl49952go5/v1 | https://www.protocols.io/view/serapure-beads-preparation-and-testing-dewr3fd6 | rute.carvalho Carvalho, Colleen Kellogg, Matt Lemay | TITLE: Serapure Beads Preparation and Testing
AUTHORS: rute.carvalho Carvalho, Colleen Kellogg, Matt Lemay
[DESCRIPTION]
This protocol is used to prepare low-cost SPRI beads used for Illumina Library preparations. As part of the Hakai Institute Ocean Observing Program, from 0 m to near bottom (260 m), biomolecular sam... | ["[STEPS] In a 50 mL conical using sterile stock solutions, prepare TE (10 mM Tris-HCl, 1 mM EDTA) by adding:\n 500 µL \n100 µL \nFill conical to 50 mL mark with dH20.", "[STEPS] Mix the container of and transfer 1 mL to a 1.5 mL microtube.", "[STEPS] Place SpeedBeads on amagnet stand until beads are drawn to ... |
null | null | null | dx.doi.org/10.17504/protocols.io.sefebbn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div title="Page 1">
<div>
<div>
<p>Endo F3 cleaves free or Asparagine-linked triantennary or biantennary oligosaccharides,as well as triamnnosyl chitobiose core structures. It cleaves between the two N-acetylglucosamine residues in the diacetylchitobiose core of the oligosaccha... | [] |
81,674 | Do, Q. B. et al. (2023) Early striatal hyperexcitability in an in vitro human striatal microcircuit model carrying the Parkinson’s GBA-N370S mutation | 2 | dx.doi.org/10.17504/protocols.io.x54v9dw61g3e/v1 | https://www.protocols.io/view/do-q-b-et-al-2023-early-striatal-hyperexcitability-ctziwp4e | Quyen Do, Bryan Ng, Ricardo Marquez Gomez, Dayne Beccano-Kelly, Naroa Ibarra-Aizpura, Maria-Claudia Caiazza, Charmaine Lang, Jimena Baleriola, Nora Bengoa-Vergniory, Richard Wade-Martins | TITLE: Do, Q. B. et al. (2023) Early striatal hyperexcitability in an in vitro human striatal microcircuit model carrying the Parkinson’s GBA-N370S mutation
AUTHORS: Quyen Do, Bryan Ng, Ricardo Marquez Gomez, Dayne Beccano-Kelly, Naroa Ibarra-Aizpura, Maria-Claudia Caiazza, Charmaine Lang, Jimena Baleriola, Nora Bengoa... | [] |
78,539 | 4. Workflow at a glance_ STORM chart | 1 | dx.doi.org/10.17504/protocols.io.n2bvj8e9pgk5/v1 | https://www.protocols.io/view/4-workflow-at-a-glance-storm-chart-cqxjvxkn | Haydeh Payami | TITLE: 4. Workflow at a glance_ STORM chart
AUTHORS: Haydeh Payami
[DESCRIPTION]
The protocol details the workflow at a glance, created according to STORM guidelines for reporting human microbiome data.
[STEPS] | [] |
60,287 | 2022 GenomeTrakr Proficiency Testing exercise (PulseNet Harmonized) | 1 | null | https://www.protocols.io/view/2022-genometrakr-proficiency-testing-exercise-puls-b647rgzn | Maria Balkey, Ruth Timme, Julie Haendiges | TITLE: 2022 GenomeTrakr Proficiency Testing exercise (PulseNet Harmonized)
AUTHORS: Maria Balkey, Ruth Timme, Julie Haendiges
[DESCRIPTION]
This SOP outlines guidelines on how to process the isolates for the 2022 GenomeTrakr (GT) Proficiency Testing exercise.
This SOP is applicable to all GenomeTrakr labs partici... | ["[Culture Preparation] Salmonella and Escherichia/Shigella Lyophilized cultures:\n\nDay 1\n\nDocument the isolate number(s) and the lyophilized date(s) for your records. Wipe the aluminum cover and outside of the vial with isopropyl alcohol. Using sturdy forceps, aseptically remove the aluminum cover and rubber stoppe... |
63,416 | Cardio Defend - [ITS FAKE OR REAL] Is This Supplement Safe? | 3 | dx.doi.org/10.17504/protocols.io.5qpvob259l4o/v1 | https://www.protocols.io/view/cardio-defend-its-fake-or-real-is-this-supplement-b96yr9fw | H Douglas Morris | TITLE: Cardio Defend - [ITS FAKE OR REAL] Is This Supplement Safe?
AUTHORS: H Douglas Morris
[DESCRIPTION]
The enhancement is NSF-affirmed, and that implies a free, outsider lab has checked the fixings and measurements inside the recipe.
You can contact the producers of CardioDefend by means of the accompanying:
[STE... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.viwe4fe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Optimised protocol for the isolation of non-parenchymal cells from human liver biopsies. Used on 1-2cm3 biopsies.
[GUIDELINES]
Process tissue ASAP after removal from patient to avoid excessive cell death.
[STEPS]
SECTION: Dissociation
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SECTION: Dissociation
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SECTION: Di... | ["[Dissociation] Put liver biopsy in a new 50ml tube", "[Dissociation] Cut finely with scissors", "[Dissociation] {\"blocks\":[{\"key\":\"8bcaa\",\"text\":\"Add RPMI containing enzymes (1mg\\/ml Collagenase A & 10U\\/ml DNase)\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[{\"offset\":... |
60,144 | Single-Nuclei Isolation From Snap Frozen Axolotl Brain with Injected EdU | 4 | null | https://www.protocols.io/view/single-nuclei-isolation-from-snap-frozen-axolotl-b-b6yqrfvw | Ashley Maynard, Fides Zenk | TITLE: Single-Nuclei Isolation From Snap Frozen Axolotl Brain with Injected EdU
AUTHORS: Ashley Maynard, Fides Zenk
[DESCRIPTION]
This protocol enables isolation of single nuclei with EdU incorporation from frozen pallium dissections (from axolotl) for the purpose of generating single-nuclei gene-expression librarie... | ["[Nuclei isolation] Use pre-cooled buffers and storeon ice, perform isolation steps on ice, use pre-cooled micro-centrifuge at 4 °C.", "[Nuclei isolation] Put tissue in cold 1.5 mLtube", "[Nuclei isolation] Add 50 µLof lysis buffer", "[Nuclei isolation] Using an electric grinder. Grind the tissue for 10 s (or 2-5 pul... |
21,032 | Feather colour affect aggressive behaviour of chickens with same genotype on dominant white (I) locus | null | dx.doi.org/10.17504/protocols.io.ysgfwbw | null | Changsheng Nie, Liping Ban, Zhonghua Ning, Lujiang Qu | TITLE: Feather colour affect aggressive behaviour of chickens with same genotype on dominant white (I) locus
AUTHORS: Changsheng Nie, Liping Ban, Zhonghua Ning, Lujiang Qu
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Aggression in chickens is a serious economic and welfare issue. Pigmentation tra... | ["[ Animals and Behavioural tests]\nThese behaviours were counted separately (attacker or victim) for the red and white featherStiff body posture towards another bird, the birds stands", "[Genotyping candidate genes for feather colour]\nThe polymerase chain reactions (PCRs) were performed using an Applied Biosystems Ve... |
98,304 | Social and Ecological Benefits of Public Transportation System on Mo'orea | 0 | dx.doi.org/10.17504/protocols.io.5jyl82m8rl2w/v1 | https://www.protocols.io/view/social-and-ecological-benefits-of-public-transport-db882rzw | Marcella Welter | TITLE: Social and Ecological Benefits of Public Transportation System on Mo'orea
AUTHORS: Marcella Welter
[DESCRIPTION]
Mo’orea is arguably a car-centric island, with one main road wrapping 60 km all the way around the island, with many roads branching off into the island. In January 2024, a private transportatio... | ["[Qualitative Data Collection: How Public Transport Supports Communities] Interview Protocol", "[Qualitative Data Collection: How Public Transport Supports Communities] Find local community members to interview, including students, families, workers who commute to the ferry station. Post flyers around the island at st... |
40,855 | Study Population (Part 4 of Phase 3 study of Vaccine Candidate for COVID-19) | 1 | dx.doi.org/10.17504/protocols.io.bj5xkq7n | https://www.protocols.io/view/study-population-part-4-of-phase-3-study-of-vaccin-bj5xkq7n | Chris Ockenhouse, Chris Gast, Renee Holt, Jorge Flores | TITLE: Study Population (Part 4 of Phase 3 study of Vaccine Candidate for COVID-19)
AUTHORS: Chris Ockenhouse, Chris Gast, Renee Holt, Jorge Flores
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This is Part 4 of "Phase 3 randomized, double-blinded, placebo-controlled trial to evaluate the sa... | ["[Participant inclusion criteria]\nWillingness to provide a signed, printed, and dated informed consent form.", "[Participant inclusion criteria]\nStated willingness to comply with all study procedures and availability for the duration of the study.", "[Participant inclusion criteria]\nBe a male or female 18 years of ... |
null | null | null | dx.doi.org/10.17504/protocols.io.qjcduiw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Electroporation strategy used in the transformation of Aurantiochytrium limacinum (ATCC MYA-1381; Stramenopile/ Heterokont, Thraustochytrid). This protocol is following the guidance of Ono et al. 2011. US Patent # 7,888,123 B2. </p>
[STEPS]
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?.... | [] |
68,779 | ACE-inhibitory activity assay: IC50 | 6 | dx.doi.org/10.17504/protocols.io.q26g74q5kgwz/v1 | https://www.protocols.io/view/ace-inhibitory-activity-assay-ic50-cfejtjcn | Ezequiel Coscueta, & Maria Manuela Pintado | TITLE: ACE-inhibitory activity assay: IC50
AUTHORS: Ezequiel Coscueta, & Maria Manuela Pintado
[DESCRIPTION]
This protocol describes the procedure for the determination of the IC50 in inhibition on angiotensin-I converting enzyme (ACE) activity. ACE is also known as peptidyl dipeptidase A because it removes C-terminal... | ["[Analysis]", "[Analysis] Add 80 µL to blank (BLK)", "[Analysis] Add 40 µL to control (CTL) and sample blank (SPLB)", "[Analysis] Add 40 µL to sample (SPL) and sample blank (SPLB)", "[Analysis] Add 40 µL to control (CTL) and sample (SPL)", "[Analysis] Add 160 µL to control all wells", "[Analysis] Incubate at 37 °C 30 ... |
73,578 | Enteric neuron activity in the mouse colon and responses to lumbosacral stimulation | 4 | dx.doi.org/10.17504/protocols.io.ewov1o817lr2/v1 | https://www.protocols.io/view/enteric-neuron-activity-in-the-mouse-colon-and-res-cj4iuque | Kristen Smith-Edwards | TITLE: Enteric neuron activity in the mouse colon and responses to lumbosacral stimulation
AUTHORS: Kristen Smith-Edwards
[DESCRIPTION]
This protocol describes the steps for calcium imaging activity in the enteric nervous system (ENS) and interstitial cells of Cajal (ICC) in isolated colons and ex vivo lumbosacral spi... | ["[Isolated Colon Preparation] Euthanize EIIa-GCaMP mice (offspring from the pairing of B6.FVB-Tg(EIIa-cre)C5379Lmgd/J [RRID:IMSR_JAX:003724; cat. 003724; Jax Labs] and B6J.Cg-Gt(ROSA)26Sortm95.1(CAG-GCaMP6f)Hze/MwarJ [RRID:IMSR_JAX:028866; cat. 028865; Jax Labs]), by inhalation of isoflurane and thoracotomy. Remove th... |
null | null | null | dx.doi.org/10.17504/protocols.io.n95dh86 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Host Decoy Traps (HDT) sample outdoor-biting mosquitoes and have potential as a monitoring malaria vectors. The trap emits human odour, is visually conspicuous and heated to human body temperature, thus mimicking a human host, and therefore, it catches a proportion of the num... | [] |
67,668 | Protocols for Molecular Characterization of the Female Reproductive System | 4 | dx.doi.org/10.17504/protocols.io.kqdg3pj37l25/v1 | https://www.protocols.io/view/protocols-for-molecular-characterization-of-the-fe-cebutanw | Stephen Fisher, Marielena Grijalva, Rong Guo, sarahjoh, Hieu Nguyen, John Renz, Jean G Rosario, Steven Rudich, Brian Gregory, Junhyong Kim, Kate O'Neill | TITLE: Protocols for Molecular Characterization of the Female Reproductive System
AUTHORS: Stephen Fisher, Marielena Grijalva, Rong Guo, sarahjoh, Hieu Nguyen, John Renz, Jean G Rosario, Steven Rudich, Brian Gregory, Junhyong Kim, Kate O'Neill
[DESCRIPTION]
Here we describe our multi-step protocol to generate a compre... | ["Preparation and Preservation of the Female Reproductive System (ovaries, Fallopian tubes and uterus) Prior to Procurement\nhttps://dx.doi.org/10.17504/protocols.io.ewov1nr57gr2/v1", "Removal of the Female Reproductive SystemEn Bloc\nhttps://dx.doi.org/10.17504/protocols.io.bp2l61jrzvqe/v1", "Post-Surgical Dissection ... |
null | null | null | dx.doi.org/10.17504/protocols.io.fw2bpge | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?. | [] |
50,417 | Protocol to process Gastruloids for FACS (reporters only) | 4 | dx.doi.org/10.17504/protocols.io.bvgrn3v6 | https://www.protocols.io/view/protocol-to-process-gastruloids-for-facs-reporters-bvgrn3v6 | Stefano Vianello, Tania Hübscher, Giuliana Rossi, Matthias Lutolf | TITLE: Protocol to process Gastruloids for FACS (reporters only)
AUTHORS: Stefano Vianello, Tania Hübscher, Giuliana Rossi, Matthias Lutolf
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol to process reporter Gastruloids for FACS analysis of their endogenous reporters.</div></div>
[STEPS]
... | ["[Gastruloid collection]\nOnce all Gastruloids have settled to the bottom of the tube, aspirate out the supernatant (N2B27 medium carried over with each Gastruloids)", "[Gastruloid collection]\nResuspend the Gastruloids in 5mL PBS-/-, to wash away traces of N2B27", "[Gastruloid collection]\nOnce all Gastruloids have r... |
68,923 | Adult mouse pancreas cell dissociation (on ice) | 1 | dx.doi.org/10.17504/protocols.io.ewov1yj6kvr2/v2 | https://www.protocols.io/view/adult-mouse-pancreas-cell-dissociation-on-ice-cfi3tkgn | Andrew Potter | TITLE: Adult mouse pancreas cell dissociation (on ice)
AUTHORS: Andrew Potter
[DESCRIPTION]
Note: In testing several different enzymes to dissociate pancreas tissue on ice, Collagenase Type 4 appeared to be most effective. However, the results of the dissociation have been variable, with significant debris in some pre... | ["Dissect pancreas and place in ice-cold PBS.", "Mince tissue thoroughly on petri dish on ice (2 min) until fine paste. \n2 min", "Weigh out 18 mg tissue and add to tube with 1 mL Type 4 collagenase enzyme mix. \n18 5", "Incubate on ice. Shake vigorously every 30 seconds for the first two min to re-suspend tissue. \n30... |
28,608 | Isolation of total RNA from Synechocystis | null | dx.doi.org/10.17504/protocols.io.768hrhw | null | iGEM Dusseldorf | TITLE: Isolation of total RNA from Synechocystis
AUTHORS: iGEM Dusseldorf
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-style:italic;">Isolation of total RNA from Synechocystis sp. PCC 6803 Can be used for further work, like qPCR Always work fast, with ice and RNase-free (wear... | [] |
59,922 | Immunofluorescence of RAB5 and FLAG-EEA1 puncta after Dynamin-1 and -2 inhibition with Dyngo4a | 1 | dx.doi.org/10.17504/protocols.io.ewov146xkvr2/v2 | https://www.protocols.io/view/immunofluorescence-of-rab5-and-flag-eea1-puncta-af-b6rsrd6e | Hankum Park, Frances V Hundley, Harper JW | TITLE: Immunofluorescence of RAB5 and FLAG-EEA1 puncta after Dynamin-1 and -2 inhibition with Dyngo4a
AUTHORS: Hankum Park, Frances V Hundley, Harper JW
[DESCRIPTION]
Selective purification of early endosomes can be achieved through affinity capture of the early endosome-associated protein EEA1 (termed Endo-IP) (P... | ["[Preparation of coverslips] Coat No.1.5 coverslips in 0.01% poly-L-lysine solution. Incubate at 37 °C for 15 min", "[Preparation of coverslips] Aspirate poly-L-lysine solution and wash coverslips three times with sterile DPBS.", "[Preparation of coverslips] Dry coverslips at 37 °C for 15 min .", "[Seed cells] Spli... |
null | null | null | dx.doi.org/10.17504/protocols.io.eznbf5e | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<p><strong>Reagent List:</strong></p>
<p> </p>
<ul>
<li>Sterile PBS</li>
<li>Cell culture medium (RPMI 1640 supplemented with 10% FBS)</li>
<li>Sterile 12-well plate</li>
<li>Sterile 6-well plate</li>
<li>RBC Lysis Buffer (Cat. No. 420301)</li>
<li>Anti-mouse CD3ε, clone 145-2C11... | [] |
9,020 | Microscope video recording | null | dx.doi.org/10.17504/protocols.io.k24cygw | null | Daniel Vaulot | TITLE: Microscope video recording
AUTHORS: Daniel Vaulot
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol to record videos on SBR Microscope</div></div>
[STEPS]
?. [First steps]
Prepare your sample
- Cultures flask
- Drop between slide and coverslip and invert the slide so that the objecti... | ["[First steps]\nPrepare your sample\n- Cultures flask\n- Drop between slide and coverslip and invert the slide so that the objective is on side of coverslipUse x 40 objective for most cultures and x20 for dinoflagellatesInstall and start Infinitity Capture software", "[Acquisition with Infinity Capture]\nInfinity X - ... |
32,561 | Removal of Single-Stranded Extension using Mung Bean Nuclease (M0250) | 1 | dx.doi.org/10.17504/protocols.io.bb2riqd6 | https://www.protocols.io/view/removal-of-single-stranded-extension-using-mung-be-bb2riqd6 | New England Biolabs | TITLE: Removal of Single-Stranded Extension using Mung Bean Nuclease (M0250)
AUTHORS: New England Biolabs
[DESCRIPTION]
This is the protocol for the removal of single-stranded extension using Mung Bean Nuclease (M0250).
[STEPS]
1. Suspend DNA (0.1 μg/μl) in 1X Mung Bean Nuclease Buffer or 1X NEBuffer 1.1, 2.1 or ... | ["Suspend DNA (0.1 μg/μl) in 1X Mung Bean Nuclease Buffer or 1X NEBuffer 1.1, 2.1 or CutSmart®.", "Add 1.0 unit of Mung Bean Nuclease per μg DNA.", "Incubate at 30 °C for 30 min.", "Inactivate the enzyme by phenol/chloroform extraction or by addition of SDS to 0.01%.", "Recover the DNA by ethanol precipitation."] |
90,942 | Dung Spherulite Analysis and pH Testing | 1 | dx.doi.org/10.17504/protocols.io.36wgq3ew3lk5/v1 | https://www.protocols.io/view/dung-spherulite-analysis-and-ph-testing-c426yyhe | bubest, natalia.vanzojais, dejonge, Kali R Wade | TITLE: Dung Spherulite Analysis and pH Testing
AUTHORS: bubest, natalia.vanzojais, dejonge, Kali R Wade
[DESCRIPTION]
The dung spherulite and pH testing methods used for sediment samples from Yavne, Israel, based upon the methods from Smith et al. 2019.
[STEPS]
SECTION: Fail-Safe Practices
1. Wiping down all equipme... | ["[Fail-Safe Practices] Wiping down all equipment, surfaces, and tools used with soap and water followed by acetone (beginning and end of every day of the project).", "[Fail-Safe Practices] Plating one slide of Cargille Immersion Oil (Type B) and viewing them under microscopy to ensure no contamination.", "[Fail-Safe P... |
30,353 | Power in a single case multiple baseline design | null | dx.doi.org/10.17504/protocols.io.9vrh656 | null | Samantha Bouwmeester, Joran Jongerling | TITLE: Power in a single case multiple baseline design
AUTHORS: Samantha Bouwmeester, Joran Jongerling
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:center"></div></div><div class = "text-block">A randomization test can be used to statistically test hypot... | [] |
53,003 | Variant (E484K) ALERT - Ligation-Dependent Loop-Mediated Isothermal Amplification | 4 | dx.doi.org/10.17504/protocols.io.bxzjpp4n | https://www.protocols.io/view/variant-e484k-alert-ligation-dependent-loop-mediat-bxzjpp4n | Ali Bektas, Anitha Jayaprakash | TITLE: Variant (E484K) ALERT - Ligation-Dependent Loop-Mediated Isothermal Amplification
AUTHORS: Ali Bektas, Anitha Jayaprakash
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A 2-hour, 2-temperature protocol, using RNA templated DNA ligation, for the visual detection of the E484K mutation of conce... | ["[Ligation ]\nX1 Ligation mix (multiply for number of samples processed) E484K-Donor (100nM) E484K-Acceptor (100nM)SplintR Buffer (NEB) (NEB) molecular biology grade wateradd RNA per of reaction mix for a reaction volume\n2 µl\n2 µl\n1 µl\n0.2 µl\n1.8 µl\n3 µl\n7 µl\n10 µl", "[Ligation ]\nIncubate at for followed... |
57,522 | Pavlovian Conditioned Approach | 1 | dx.doi.org/10.17504/protocols.io.x54v9yjx4g3e/v1 | https://www.protocols.io/view/pavlovian-conditioned-approach-b4esqtee | lukehann , cpking , Paul Meyer | TITLE: Pavlovian Conditioned Approach
AUTHORS: lukehann , cpking , Paul Meyer
[DESCRIPTION]
Through their association with rewards, reward associated stimuli “cues” can acquire incentive motivational properties (aka incentive value), and thus the ability to attract, reinforce, and motivate behavior (Robinson and Be... | ["[Reward Habituation] Give each subject ~25 banana flavored pellets/day in their home cage for the 2 days preceding the start of the Pre-training.", "[Pre-Training] Pre-training consists of a single, ~17.5 minute session (time varies between banana pellets on a VI-30s schedule).", "[Pre-Training] Remove subject from t... |
null | null | null | dx.doi.org/10.17504/protocols.io.g5pby5n | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
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?. | [] |
46,779 | cDNA library preparation from total RNA extracts of Single-cell marine protists (e.g. Acantharia, Strombidium basimorphum, and Prymnesium parvum) for transcriptome sequencing | 4 | dx.doi.org/10.17504/protocols.io.brw3m7gn | https://www.protocols.io/view/cdna-library-preparation-from-total-rna-extracts-o-brw3m7gn | Joost Mansour, Konstantinos Anestis, Fabrice Not, Uwe John | TITLE: cDNA library preparation from total RNA extracts of Single-cell marine protists (e.g. Acantharia, Strombidium basimorphum, and Prymnesium parvum) for transcriptome sequencing
AUTHORS: Joost Mansour, Konstantinos Anestis, Fabrice Not, Uwe John
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">... | ["[cDNA synthesis preparations]\nLabel for each sample a tube .", "[cDNA synthesis preparations]\nPrepare a 72°C incubator (e.g. a thermocycler)", "[cDNA synthesis preparations]\nThaw other reagents – except SmartScribe Reverse Transcriptase, take that from the freezer only once needed.\non ice", "[cDNA synthesis prep... |
null | null | null | dx.doi.org/10.17504/protocols.io.t5eeq3e | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ntfdejn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
19,210 | kiwifruits in response to Pseudomonas syringae pv. Actinidiae | null | dx.doi.org/10.17504/protocols.io.wziff4e | null | yalin song | TITLE: kiwifruits in response to Pseudomonas syringae pv. Actinidiae
AUTHORS: yalin song
[STEPS]
?. [Psa inoculation]
Psa was cultured on beef peptone medium for 24 h at 20°C.
?. [Psa inoculation]
The microbial concentration of Psa was diluted to 10 8 colony-forming units (cfu)/ml prior to inoculation.
?. [Psa inocula... | ["[Psa inoculation]\nPsa was cultured on beef peptone medium for 24 h at 20°C.", "[Psa inoculation]\nThe microbial concentration of Psa was diluted to 10\u001f8 colony-forming units (cfu)/ml prior to inoculation.", "[Psa inoculation]\nFor inoculation, the detached shoots were surface sterilized with chlorine and then c... |
98,352 | Processing frozen archival human DNA samples for large-scale SQK-LSK114 Oxford Nanopore long-read DNA sequencing SOP v1 | 1 | dx.doi.org/10.17504/protocols.io.5jyl82morl2w/v1 | https://www.protocols.io/view/processing-frozen-archival-human-dna-samples-for-l-dcaq2sdw | Alicia Wenghöfer, Kimberly Paquette, Laksh Malik, Breeana Baker, Cedric Kouam, Kimberley J Billingsley, on behalf of the CARD Long-read Team | TITLE: Processing frozen archival human DNA samples for large-scale SQK-LSK114 Oxford Nanopore long-read DNA sequencing SOP v1
AUTHORS: Alicia Wenghöfer, Kimberly Paquette, Laksh Malik, Breeana Baker, Cedric Kouam, Kimberley J Billingsley, on behalf of the CARD Long-read Team
[DESCRIPTION]
Abstract:
As part of the GP... | ["Part 1: Thaw DNA samples on ice (~5 min)\n\nNote: Ideally for best results, DNA needs to be extracted with high-molecular weight methods straight from tissue. See dx.doi.org/10.17504/protocols.io.5qpvo3639v4o/v1 or dx.doi.org/10.17504/protocols.io.6qpvr347bvmk/v1 or dx.doi.org/10.17504/protocols.io.kxygx3zzog8j/v1 ba... |
70,253 | Estimating microbial population data from optical density | 4 | dx.doi.org/10.17504/protocols.io.8epv5j6wjl1b/v2 | https://www.protocols.io/view/estimating-microbial-population-data-from-optical-cgumtwu6 | Pamela Yeh, Portia M Mira | TITLE: Estimating microbial population data from optical density
AUTHORS: Pamela Yeh, Portia M Mira
[DESCRIPTION]
The spectrophotometer has been used for decades to measure the density of bacterial populations as the turbidity expressed as optical density – OD. However, the OD alone is an unreliable metric and is onl... | ["Calibration\nGrow a sufficient volume of limited culture to provide at least 10 OD units. For oxygen limited cultures\nthis may require several 10 ml cultures. If so, combine the cultures. Check the OD of the combined\nculture to see that there are about 10 OD units.", "Preparation\n\nWhen calibrating a microtiter pl... |
36,454 | Protocol for Use with Standard Insert Libraries (370-420 bp) (NEB#E7120) | 1 | dx.doi.org/10.17504/protocols.io.bfuejnte | https://www.protocols.io/view/protocol-for-use-with-standard-insert-libraries-37-bfuejnte | New England Biolabs | TITLE: Protocol for Use with Standard Insert Libraries (370-420 bp) (NEB#E7120)
AUTHORS: New England Biolabs
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details how to construct DNA libraries from start to finish using NEBNext reagents.</div><div class = "text-block"><span>The cor... | ["[DNA Preparation (Section 1.1)]\nDNA PreparationCombine 10 ng-200 ng of genomic DNA with control DNAs, CpG methylated pUC19 (lilac) and unmethylated lambda DNA (lilac) in made up with 0.1X TE . The amount of control DNA added is dependent on the number of reads required.\nStarting materials is 10 ng-200 ng DNA\n50 µ... |
94,963 | Bovine necropsy | 4 | dx.doi.org/10.17504/protocols.io.n2bvj344wlk5/v1 | https://www.protocols.io/view/bovine-necropsy-c8ytzxwn | Laetitia Dorso | TITLE: Bovine necropsy
AUTHORS: Laetitia Dorso
[DESCRIPTION]
A necropsy is the final medical diagnostic procedure performed on a deceased animal to determine the cause of death.
The aim of a necropsy is to investigate and define as precisely as possible the cause of death of the animal, or to identify and confirm the ... | ["[Anamnesis] Breeding: \nRearing method, number and age of animals\nFeed\nBreeding health plan, vaccines, deworming, others (nature, dates)\nMorbidity, mortality (diagnosis, number and %)", "[Anamnesis] Animal: \nDate of introduction in the herd\nSymptoms (description, chronology, duration)\nConditions, date and time ... |
68,558 | Tissue Preparation for Intact Proteoform MALDI-MSI on Human Tissue | 1 | dx.doi.org/10.17504/protocols.io.6qpvr61x2vmk/v1 | https://www.protocols.io/view/tissue-preparation-for-intact-proteoform-maldi-msi-ce7nthme | Kevin J. Zemaitis, Dusan Velickovic, Ljiljana.PasaTolic | TITLE: Tissue Preparation for Intact Proteoform MALDI-MSI on Human Tissue
AUTHORS: Kevin J. Zemaitis, Dusan Velickovic, Ljiljana.PasaTolic
[DESCRIPTION]
Scope:
A detailed protocol entailing the overall protocols developed for human tissue sections for the UHMR HF Orbitrap platform. This includes QC metrics for tissue ... | ["[Tissue sectioning and metrics] Tissue either sectioned by PNNL-TTD or provided by others and are stored at -80 °C , these slides have undergone either high-resolution bright-field (BF) light microscopy or auto-fluorescence (AF) microscopy prior to cold storage (e.g., AF for kidney) for the evaluation of tissue integ... |
104,839 | qPCR to measure mRNA expression in S. rosetta | 0 | dx.doi.org/10.17504/protocols.io.n2bvjnjongk5/v1 | https://www.protocols.io/view/qpcr-to-measure-mrna-expression-in-s-rosetta-dimf4c3n | Fredrick leon, David Booth | TITLE: qPCR to measure mRNA expression in S. rosetta
AUTHORS: Fredrick leon, David Booth
[DESCRIPTION]
This protocol tailors common qPCR methods for quantifying transcript abundance in S. rosetta. The protocol covers primer design, synthesis of ssDNA standards, and assembling the qPCR reaction. It builds upon the pref... | ["[Primer design] Search for your gene of interest here https://protists.ensembl.org/Salpingoeca_rosetta_gca_000188695/Info/Index \nAfter opening the gene page, click the \"Sequence\" tab on the left-hand column to display the gene's exons. From there click download sequence and select \"cDNA\". Reference the exon sequ... |
34,618 | Electroporation Protocol | 1 | dx.doi.org/10.17504/protocols.io.bd22i8ge | https://www.protocols.io/view/electroporation-protocol-bd22i8ge | New England Biolabs | TITLE: Electroporation Protocol
AUTHORS: New England Biolabs
[DESCRIPTION]
This protocol may be used with electrocompetent cells prepared according to this protocol.
[BEFORE_START]
For control electroporation dilute pUC19 to 10 pg/μl with Milli-Q water.
The electroporation protocol will vary depending on the stra... | ["Turn on electroporator and set to 1.7-2.5 kv (optimize for strain), 200 ohms and 25 µF.", "Place recovery SOC in 37 °C water bath.", "Pre-warm LB-antibiotic plates at 37 °C.", "Thaw cells on ice for 10 min or use freshly made cells.", "Place appropriate number of microcentrifuge tubes and 1 mm-electroporation cuvette... |
65,183 | Pure Calms CBD Gummies Reviews |SCAM Or Legit | 1 | dx.doi.org/10.17504/protocols.io.n92ldz19ov5b/v1 | https://www.protocols.io/view/pure-calms-cbd-gummies-reviews-scam-or-legit-cbv7sn9n | testolutraty | TITLE: Pure Calms CBD Gummies Reviews |SCAM Or Legit
AUTHORS: testolutraty
[DESCRIPTION]
Expecting you are one of the numerous people who necessities to add CBD to their step by step ordinary practice, there is another thing called Pure Calms CBD Gummies that you could have to organize immediately. This bewildering ... | [] |
76,211 | Post a draft | 4 | null | https://www.protocols.io/view/post-a-draft-cnntvden | Emma Ganley | TITLE: Post a draft
AUTHORS: Emma Ganley
[DESCRIPTION]
test
[STEPS]
1. My table
2.
| ["My table"] |
103,797 | Optimizing the Effect of Additives on qPCR Detection | 0 | dx.doi.org/10.17504/protocols.io.j8nlk8nkxl5r/v1 | https://www.protocols.io/view/optimizing-the-effect-of-additives-on-qpcr-detecti-dhkv34w6 | Jonathan Phillips, Gregor Blaha | TITLE: Optimizing the Effect of Additives on qPCR Detection
AUTHORS: Jonathan Phillips, Gregor Blaha
[DESCRIPTION]
Optimizing qPCR reactions has two key objectives: (1) to handle a wider range of samples, and (2) to minimize variability between replicates. [Anonymous 2009; Minas K., et al. 2011; Nolan T., et al. 2006... | [] |
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