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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61,562 | Getting started with Micro-Meta App Tutorial | 5 | null | https://www.protocols.io/view/getting-started-with-micro-meta-app-tutorial-b8c2rsye | Alessandro Rigano, Mathias Hammer, Joel Ryan, Claire M. Brown, David Grunwald, Caterina Strambio De Castillia | TITLE: Getting started with Micro-Meta App Tutorial
AUTHORS: Alessandro Rigano, Mathias Hammer, Joel Ryan, Claire M. Brown, David Grunwald, Caterina Strambio De Castillia
[DESCRIPTION]
For quality, interpretation, reproducibility, and sharing value, microscopy images should be accompanied by detailed descripti... | ["[Before the tutorial] Video introduction", "[Tutorial - 1 - Download and Install Micro-Meta App] Download Micro-Meta App\n\nFollow the instructions in this step and in Video 3 of the tutorial series to download and install the stand-alone version of the Micro-Meta App.", "[Tutorial - 1 - Download and Install Micro-Me... |
62,125 | Nuclei extraction for 10x Genomics Single Cell Multiome ATAC + Gene Expression from frozen tissue using Singulator™ 100 or 200 (S2 Genomics) V2.0 | 1 | dx.doi.org/10.17504/protocols.io.j8nlkkmq6l5r/v1 | https://www.protocols.io/view/nuclei-extraction-for-10x-genomics-single-cell-mul-b8wmrxc6 | Ignas Masilionis, Ojasvi Chaudhary, Brigita Meskauskaite Urben, Ronan Chaligne | TITLE: Nuclei extraction for 10x Genomics Single Cell Multiome ATAC + Gene Expression from frozen tissue using Singulator™ 100 or 200 (S2 Genomics) V2.0
AUTHORS: Ignas Masilionis, Ojasvi Chaudhary, Brigita Meskauskaite Urben, Ronan Chaligne
[DESCRIPTION]
This protocol describes nuclei extraction from snap frozen tissu... | ["[Preparation] - Turn on and pre-cool Singulator 10 min \n- Make sure there is sufficient number of Nuclei cartridges (or NIC+ cartridges for samples <20mg) stored / pre-cooled at 4 °C", "[Preparation] Take the tissue out of LN2 or -80C freezer and place it on dry ice to keep it frozen\nIdeally, piece should be <100mg... |
56,599 | Cloning shRNA Oligos into pLKO.1 | 1 | dx.doi.org/10.17504/protocols.io.b3hxqj7n | https://www.protocols.io/view/cloning-shrna-oligos-into-plko-1-b3hxqj7n | Addgene The Nonprofit Plasmid Repository | TITLE: Cloning shRNA Oligos into pLKO.1
AUTHORS: Addgene The Nonprofit Plasmid Repository
[DESCRIPTION]
This is the protocol accompanying the "pLKO.1 – TRC Cloning Vector". For information about the PLKO.1-TRC cloning vector and tips on designing shRNA oligos for pLKO.1 see Addgene's website: http://www.addgene.org/t... | ["[Annealing Oligos] Resuspend oligos in ddH2O to a concentration of 20 μM.", "[Annealing Oligos] Add 5ul Forward oligo \n5 1", "[Annealing Oligos] Add 5ul Reverse oligo \n5 1", "[Annealing Oligos] Add 35 μL ddH2O \n35 1", "[Annealing Oligos] Incubate for 4 minutes at 95°C in a PCR machine or in a beaker of boiling wat... |
87,387 | Sanger Tree of Life HMW DNA Extraction: Automated Plant MagAttract v.1 | 4 | dx.doi.org/10.17504/protocols.io.n2bvj3n1xlk5/v1 | https://www.protocols.io/view/sanger-tree-of-life-hmw-dna-extraction-automated-p-czj3x4qn | Edel Sheerin, Filipa Sampaio, graeme oatley, Michelle Strickland, Maja Todorovic, Caroline Howard | TITLE: Sanger Tree of Life HMW DNA Extraction: Automated Plant MagAttract v.1
AUTHORS: Edel Sheerin, Filipa Sampaio, graeme oatley, Michelle Strickland, Maja Todorovic, Caroline Howard
[DESCRIPTION]
This protocol describes the automated extraction of HMW DNA from cryogenically disrupted plant and fungi tissue samples ... | ["[Sample lysis] Prepare a lysis buffer master mix:\n Phosphate buffered saline (PBS)200 µLProteinase K20 µLRNase A4 µLBuffer AL150 µL", "[Sample lysis] Set a heat block to 50 °C.", "[Sample lysis] Transfer 50 mg of cryogenically homogenised tissue from each sample to 2 mL microcentrifuge tubes and place on dry ice to... |
100,548 | Isolation of lysosomes using the Tagless LysoIP method in PBMCs | 4 | dx.doi.org/10.17504/protocols.io.x54v9yp51g3e/v2 | https://www.protocols.io/view/isolation-of-lysosomes-using-the-tagless-lysoip-me-defc3biw | Daniel Saarela, Esther Sammler, Dario R Alessi, Francesca Tonelli | TITLE: Isolation of lysosomes using the Tagless LysoIP method in PBMCs
AUTHORS: Daniel Saarela, Esther Sammler, Dario R Alessi, Francesca Tonelli
[DESCRIPTION]
Molecular homeostasis in cells is regulated in part by protein degradation, which is facilitated by the proteasome and lysosomal proteolysis. Lysosomes are mem... | ["[Methods] Prepare a 0.5 Molarity (M) stock solution of DIFP by diluting in isopropanol under a fume hood. Stock solution can be stored in -80 °C until needed.", "[Methods] Collect blood into a BD Vacutainer sodium heparin 10-mL tubes.", "[Methods] Add density gradient medium to the SepMate tube using a 20-mL syringe ... |
94,463 | GFP-Clu-tails purification from Escherichia coli cells | 1 | dx.doi.org/10.17504/protocols.io.n2bvj3w55lk5/v1 | https://www.protocols.io/view/gfp-clu-tails-purification-from-escherichia-coli-c-c8g7ztzn | Andreas Bracher, F Ulrich Hartl | TITLE: GFP-Clu-tails purification from Escherichia coli cells
AUTHORS: Andreas Bracher, F Ulrich Hartl
[DESCRIPTION]
This protocol details how to purify the fusion protein GFP-Clu-tails from Escherichia coli.
[STEPS]
SECTION: His6-Ubiquitin-GFP-Clu-tails expression and cell lysis
1. Express His6-Ubiquitin-GFP-Clu-tai... | ["[His6-Ubiquitin-GFP-Clu-tails expression and cell lysis] Express His6-Ubiquitin-GFP-Clu-tails in E. coli Bl21 (DE3) codon+RIL cells cultured in 4 L LB Medium at 18 °C with 0.25 millimolar (mM) IPTG.", "[His6-Ubiquitin-GFP-Clu-tails expression and cell lysis] Centrifuge culture and keep pellet.", "[His6-Ubiquitin-GF... |
65,239 | Condor CBD Gummies Reviews (Shocking Exposed 2022): Beware Scam!! | 3 | dx.doi.org/10.17504/protocols.io.n2bvj613nlk5/v1 | https://www.protocols.io/view/condor-cbd-gummies-reviews-shocking-exposed-2022-b-cbxxsppn | markhussaion | TITLE: Condor CBD Gummies Reviews (Shocking Exposed 2022): Beware Scam!!
AUTHORS: markhussaion
[DESCRIPTION]
·Product Name – Condor CBD Gummies
·Composition –Natural Organic compound
·Side-Effects –NA
·Availability – Online
·Rating –★★★★★
·Official Website:- CondorCBDGummies.com
It is very important examine! It's t... | [] |
30,333 | mRNA Synthesis and Transfection | 1 | null | https://www.protocols.io/view/mrna-synthesis-and-transfection-9u5h6y6 | Yingchao Xue, Xiping Zhan, Shisheng Sun, Senthilkumar S. Karuppagounder, Shuli Xia, Valina L Dawson, Ted M Dawson, John Laterra, Jianmin Zhang, Mingyao Ying | TITLE: mRNA Synthesis and Transfection
AUTHORS: Yingchao Xue, Xiping Zhan, Shisheng Sun, Senthilkumar S. Karuppagounder, Shuli Xia, Valina L Dawson, Ted M Dawson, John Laterra, Jianmin Zhang, Mingyao Ying
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol explains the mRNA synthesis... | ["[mRNA Synthesis]\nClone coding sequence of Atoh1 into a vector containing the T7 promoter and poly(A) tail for in vitro transcription.", "[mRNA Synthesis]\nClone coding sequence of Ngn2 into a vector containing the T7 promoter and poly(A) tail for in vitro transcription.", "[mRNA Synthesis]\nLinearize Atoh1 and Ngn2 ... |
null | null | null | dx.doi.org/10.17504/protocols.io.jsucnew | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><span style="font-weight: 400;">Protocol to co-culture individual colonies of different strains (e.g. transformed with different vectors) on a LB agar plate in a distributed and random manner.</span></p>
<p> </p>
<p><span style="font-weight: 400;">This assay has been used for... | [] |
93,630 | Single cell sequencing preparation in adult Drosophila Brain | 4 | dx.doi.org/10.17504/protocols.io.261ged79dv47/v1 | https://www.protocols.io/view/single-cell-sequencing-preparation-in-adult-drosop-c7n6zmhe | Mel Feany | TITLE: Single cell sequencing preparation in adult Drosophila Brain
AUTHORS: Mel Feany
[DESCRIPTION]
This protocol covers the preparation of adult Drosophila Brains for single cell RNAseq
[STEPS]
SECTION: Fly brain dissection
1. Dissect 20 male and 20 female brains from 10-day-old flies on ice-cold Schneider’s medium... | ["[Fly brain dissection] Dissect 20 male and 20 female brains from 10-day-old flies on ice-cold Schneider’s medium with FBS (Gibco, filtered 10% FBS)", "[Fly brain dissection] After a quick spin down, remove the supernatant and wash the brains with ice-cold PBS", "[Fly brain dissection] Incubate the brain at 25 °C with... |
39,534 | Autofluorescence Reduction and Imaging Marmoset NHP Tissue with a TissueFAXS Imaging System | 1 | null | https://www.protocols.io/view/autofluorescence-reduction-and-imaging-marmoset-nh-biunkeve | Guoping Feng Lab | TITLE: Autofluorescence Reduction and Imaging Marmoset NHP Tissue with a TissueFAXS Imaging System
AUTHORS: Guoping Feng Lab
[STEPS]
?. [Autofluorescence Reduction]
1) Wash samples in 1X PBS for .
?. [Autofluorescence Reduction]
2) Stain samples free floating with TrueBlack in Ethanol for
?. [Autofluorescence Reduc... | ["[Autofluorescence Reduction]\n1) Wash samples in 1X PBS for .", "[Autofluorescence Reduction]\n2) Stain samples free floating with TrueBlack in Ethanol for", "[Autofluorescence Reduction]\n3) Rinse samples in 1X PBS for .", "[Autofluorescence Reduction]\n4) Mount samples on a slide with ProLong™ Gold Antifade Mount... |
85,485 | U54 SCENT Transcription Factor (TF)-Phosflow Flow Cytometry Panel | 1 | null | https://www.protocols.click/view/u54-scent-transcription-factor-tf-phosflow-flow-cy-cxqmxmu6 | Zachary R Healy, david murdoch, alicia cooper-volkheimer | TITLE: U54 SCENT Transcription Factor (TF)-Phosflow Flow Cytometry Panel
AUTHORS: Zachary R Healy, david murdoch, alicia cooper-volkheimer
[DESCRIPTION]
This flow cytometry panel was developed for simultaneous quantification of transcription factors, phosphorylated kinases, and endosomal β-galactosidase activity in hu... | ["[General Notes] Instrument QC, Single-Stain Controls, Fluorescence minus-one (FMO) controls, and General Protocol Notes . We routinely perform single-stain controls (using both cells and compensation beads) as well as FMO for the intracellular targets (highlighted in BOLD in materials section) prior to any batch proc... |
88,415 | Gel Electrophoresis | 4 | dx.doi.org/10.17504/protocols.io.n2bvj3dp5lk5/v1 | https://www.protocols.io/view/gel-electrophoresis-c2j7ycrn | NUS iGEM | TITLE: Gel Electrophoresis
AUTHORS: NUS iGEM
[DESCRIPTION]
2023 NUS-Singapore iGEM team followed this protocol for gel electrophoresis to isolate the DNA fragments from the PCR products.
[STEPS]
1. Set up the required apparatus:
2. Make an agarose gel by following the steps in the "Preparation of Agarose Gel" protoco... | ["Set up the required apparatus:", "Make an agarose gel by following the steps in the \"Preparation of Agarose Gel\" protocol. Usually, a 1% agarose gel is used.", "After the agarose gel has solidified in the gel tray, remove the gel tray from the gel caster and place it in a buffer tank with pre-filled 1x TAE buffer."... |
78,348 | qPCR Primer Design | 1 | null | https://www.protocols.io/view/qpcr-primer-design-cqrkvv4w | Steven J Burgess | TITLE: qPCR Primer Design
AUTHORS: Steven J Burgess
[DESCRIPTION]
Protocol for designing qPCR primers for analysis of transcript abundance using SYBR Green chemistry.
There are many good guides about how to do this online such as this, from which the following protocol is derived.
Reference for mfold/UNAfold
https:/... | ["[Identify target sequence] Decide on a gene of interest, download the transcript sequence in .gb format and upload to a new folder on Benchling for analysis.", "[Use Primer-BLAST to test for specificity] Navigate to NCBI Primer-BLAST in your browser", "[Use Primer-BLAST to test for specificity] Adjust parameters to s... |
106,642 | UDA-5'RNA-protocol | 0 | dx.doi.org/10.17504/protocols.io.6qpvr82pplmk/v2 | https://www.protocols.io/view/uda-5-39-rna-protocol-dkds4s6e | Yun Li | TITLE: UDA-5'RNA-protocol
AUTHORS: Yun Li
[DESCRIPTION]
Droplet microfluidics-based single-cell combinatorial indexing sequencing represents an attractive way to balance cost, scalability,
robustness, and accessibility. However, current methods need a tailored protocol for specific modality respectively, which may... | ["[GEM Generation & Barcoding.] Prepare Master Mix & Load Chromium Next GEM Chip K", "[GEM Generation & Barcoding.] A certain number of cells or nuclei were added to Master Mix (18.8ul RT Reagent B (2000165); 7.3ul 1.1ul Template Switch Oligo (3000228); 1.9ul Reducing Agent B (2000087) and 8.3ul RT Enzyme C(200... |
16,151 | Sanger sequencing for genes causing intellectual disability | null | dx.doi.org/10.17504/protocols.io.tzxep7n | null | Megan McSherry, Katherine E. Masih, Filiz Basak Cengiz, Daniella Nunez, Claire Sineni, Serhat Seyhan, Guney Bademci, Mustafa Tekin. | TITLE: Sanger sequencing for genes causing intellectual disability
AUTHORS: Megan McSherry, Katherine E. Masih, Filiz Basak Cengiz, Daniella Nunez, Claire Sineni, Serhat Seyhan, Guney Bademci, Mustafa Tekin.
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Sanger sequencing was performed on available... | ["[Normalize the DNA samples.]\nThe DNA concentration per sample is 20 ng/μL", "[PCR]\nCalculate the number of reactions to be performed for each assay, including recommended controls. ABCD1Component Working ConcentrationFinal Concentration25 ul reaction210x Buffer10x1x2.5 ul3dNTPs 2 mM (each)200 uM(each)2.5 ul4MgCl2... |
71,943 | HTTM : Illumina libraries | 4 | dx.doi.org/10.17504/protocols.io.n2bvj8oowgk5/v1 | https://www.protocols.io/view/httm-illumina-libraries-cihfub3n | Antoine Champie, Amélie De Grandmaison | TITLE: HTTM : Illumina libraries
AUTHORS: Antoine Champie, Amélie De Grandmaison
[DESCRIPTION]
Part three of the HTTM protocol. A low-cost and high-throughput Tn-seq protocol.
This part cover the preparation of Illumina sequencing libraries form genomic DNA.
[BEFORE_START]
All steps and master mixes need to be kept... | ["[Libraries] Transfer2.5 µL of DNA from the DNA extraction plate to a new PCR plate.", "[Libraries] Prepare a fragmentation master mix with :", "[Libraries] Add 1 µL of the fragmentation master mix to each well.", "[Libraries] Incubate in a thermocycler with the following protocol : \n15 minat 37 °C\n30 minat 65 °C", ... |
29,627 | Hatching and freezing gemmules from the freshwater sponge Ephydatia muelleri | null | dx.doi.org/10.17504/protocols.io.863hzgn | null | Sally Leys, Lauren Grombacher, April Hill | TITLE: Hatching and freezing gemmules from the freshwater sponge Ephydatia muelleri
AUTHORS: Sally Leys, Lauren Grombacher, April Hill
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Freshwater sponges are found in lakes and rivers worldwide. Many species produce an asexual cyst called a gem... | ["[Cleaning and hatching sponge gemmules ]\nSeparate gemmules from the skeletonRemove a portion of the skeleton with gemmules from the bag. Remove gemmules from the bag using sterile wide tipped forceps (wider is ideal because thinner forceps will rupture the gemmules). Sterile forceps are used in order to prevent cont... |
null | null | null | dx.doi.org/10.17504/protocols.io.rwid7ce | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>After euthanasia, testicles were obtained, tunica albuginea was removed with sterile forceps, and seminiferous tubules were treated with collagenase for 10 minutes at 37°C (5 mg/ml of collagenase, SIGMA C5138). Using a trans-illumination method, cycles of spermatogenesis were... | [] |
45,321 | 3.6 Coculturing with Astrocytes | 1 | dx.doi.org/10.17504/protocols.io.bqhhmt36 | https://www.protocols.io/view/3-6-coculturing-with-astrocytes-bqhhmt36 | Evelyn J. Sauter, Lisa K. Kutsche, Simon D. Klapper, Volker Busskamp | TITLE: 3.6 Coculturing with Astrocytes
AUTHORS: Evelyn J. Sauter, Lisa K. Kutsche, Simon D. Klapper, Volker Busskamp
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This is part 3.4 of the "</span><a href="https://www.protocols.io/private/C65DB81838BC11EBA61A0A58A9FEAC2A/protocols" style = "te... | ["[3.6 Coculturing with Astrocytes]\nIn order to increase the maturation of neurons for electrophysiological measurements, coculturing with astrocytes is highly recommended [4, 15]. We adapted the protocol from Kaech and Banker [16] to our cell culture.", "[3.6 Coculturing with Astrocytes]\nRat primary cortical astrocy... |
30,558 | BioTechniques | null | dx.doi.org/10.17504/protocols.io.936h8re | null | Francesca Lake | TITLE: BioTechniques
AUTHORS: Francesca Lake
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>A collection of protocols from </span><span style = "font-style:italic;">BioTechniques</span></div></div>
[STEPS] | [] |
99,808 | Production of Crude AAV Virus Extract | 1 | dx.doi.org/10.17504/protocols.io.yxmvmx7r9l3p/v6 | https://www.protocols.io/view/production-of-crude-aav-virus-extract-ddp825rw | Allen Institute for Brain Science | TITLE: Production of Crude AAV Virus Extract
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
This protocol is used to produce crude preps of AAV of any serotype.
Note: Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Awa... | [] |
30,756 | Tree Mapping for Leaf Collection (Megantic Only) | null | dx.doi.org/10.17504/protocols.io.baaciaaw | null | Sabine St-Jean, Anna Crofts | TITLE: Tree Mapping for Leaf Collection (Megantic Only)
AUTHORS: Sabine St-Jean, Anna Crofts
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Here, we describe the standardized protocol used by the </span><a href="http://www.caboscience.org" style = "text-decoration:underline;color:blue;cursor:... | ["[Tree Selection and Scouting]\nDuring site reconnaissance (walking between plots), pay attention to: 1) individuals of rare tree species (see attached Species List per Site and step 11 of the Canopy Trees Survey Protocol - Forests of Southern Québec), and 2) trees that meet the Leaf Spectra selection criteria.\nLeaf ... |
59,917 | Modified NEBNext® VarSkip Short SARS-CoV-2 Enrichment and library prep for Oxford Nanopore Technologies- adapted for wastewater samples | 4 | dx.doi.org/10.17504/protocols.io.3byl4bwervo5/v1 | https://www.protocols.io/view/modified-nebnext-varskip-short-sars-cov-2-enrichme-b6rmrd46 | Padmini Ramachandran, Tamara Walsky, Amanda Windsor, Chris Grim, Maria Hoffmann | TITLE: Modified NEBNext® VarSkip Short SARS-CoV-2 Enrichment and library prep for Oxford Nanopore Technologies- adapted for wastewater samples
AUTHORS: Padmini Ramachandran, Tamara Walsky, Amanda Windsor, Chris Grim, Maria Hoffmann
[DESCRIPTION]
This protocol details methods for the preparation of SARS-CoV-2 s... | ["[cDNA Synthesis] Gently mix 10 times by pipetting and spin down the LunaScript RT SuperMix reagents (contains primers). Prepare the cDNA synthesis reaction as described below:", "[cDNA Synthesis] Flick the tube or pipet up and down 10 times to mix followed by a quick spin.", "[cDNA Synthesis] For no template controls... |
null | null | null | dx.doi.org/10.17504/protocols.io.nw4dfgw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is adapted from the QIAGEN RNeasy Plant mini kit (Jan 2011). Specific modifications have been made to apply this RNA extraction to tobacco pericarp or fruit tissue.</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
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?.
... | [] |
94,473 | Tissue Cyclic Immunofluorescence (t-CyCIF)_PCA2024_spacer | 1 | dx.doi.org/10.17504/protocols.io.j8nlkoqbdv5r/v1 | https://www.protocols.io/view/tissue-cyclic-immunofluorescence-t-cycif-pca2024-s-c8hhzt36 | Jia Ren Lin, Benjamin Izar, Zoltan Maliga, Yu-An Chen, Giorgio Gaglia, Ziming Du, Clarence Yapp, Shaolin Mei, Sandro Santagata, Peter Sorger | TITLE: Tissue Cyclic Immunofluorescence (t-CyCIF)_PCA2024_spacer
AUTHORS: Jia Ren Lin, Benjamin Izar, Zoltan Maliga, Yu-An Chen, Giorgio Gaglia, Ziming Du, Clarence Yapp, Shaolin Mei, Sandro Santagata, Peter Sorger
[DESCRIPTION]
The architecture of normal and diseased tissues strongly influences the development and pr... | ["[Pre-Staining and Background Determination] Pre-staining and Background Determination takes approximately 16-24 hours.\n\nMake fluorophore bleaching solution. Combine 165 mL 1X PBS, 30 mL 30% (wt/vol) H2O2, and 4 mL 1 Molarity (M) NaOH. The final working concentration is 4.5% (wt/vol) H2O2 and 20 millimolar (mM) NaOH... |
68,551 | DAB immunostaining of thin, fixed mouse brain tissue sections using HNA or NCAM to characterize human iPSC-derived cell xenografts | 1 | dx.doi.org/10.17504/protocols.io.14egn7pb6v5d/v1 | https://www.protocols.io/view/dab-immunostaining-of-thin-fixed-mouse-brain-tissu-ce7fthjn | Benjamin Trist, Ashish Mathai, Asheeta Prasad | TITLE: DAB immunostaining of thin, fixed mouse brain tissue sections using HNA or NCAM to characterize human iPSC-derived cell xenografts
AUTHORS: Benjamin Trist, Ashish Mathai, Asheeta Prasad
[DESCRIPTION]
This protocol describes our use of chromogenic 3,3′-diaminobenzidine (DAB) immunohistochemistry to identify huma... | ["[Day 1 (~4-6 hrs)] Pre-heat oven and AR buffer to 70 °C.", "[Day 1 (~4-6 hrs)] Label scintillation vials to match labels on section storage plates (mouse and section series IDs, name, date etc.).", "[Day 1 (~4-6 hrs)] Transfer sections into scintillation vials using a transfer pipette or fine paintbrush.", "[Day 1 (~... |
null | null | null | dx.doi.org/10.17504/protocols.io.vdye27w | null | null | TITLE: No Title
AUTHORS:
[BEFORE_START]
Prepare 5 μM primer solutions.
[GUIDELINES]
Perform reactions in small batches until you are confident that there is no cross-contamination among the samples. Including isolation blanks and PCR blanks is crucial for the quality control.
ITS2 primers used in the 1st PCR:
... | ["[1st PCR] {\"blocks\":[{\"key\":\"50pu3\",\"text\":\"Prepare the mix:\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[]},{\"key\":\"7uk0e\",\"text\":\" \",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[{\"offset\":0,\"length\":1,\"key\":0}],\"da... |
99,097 | Protocol SAM-Seq Zea Mays | 4 | dx.doi.org/10.17504/protocols.io.kqdg3x25zg25/v2 | https://www.protocols.io/view/protocol-sam-seq-zea-mays-dczz2x76 | basile.leduque leduque, s Quadrana Leandro | TITLE: Protocol SAM-Seq Zea Mays
AUTHORS: basile.leduque leduque, s Quadrana Leandro
[DESCRIPTION]
Background: Epigenetic modifications, including chromatin accessibility, nucleosome positioning, and DNA methylation (5mC), are pivotal in shaping genome function. However, current short read sequencing approaches pre... | ["[Plant nuclei purification and permeabilization] Add the powder to 12.5 ml of Extraction Buffer (EB) 1 in a 50 ml falcon tube. Let sit on ice for 5 min.", "[Plant nuclei purification and permeabilization] Add 1% Formaldehyde for crosslinking (i.e. 338 µl Formaldehyde 37% in 12.5ml of EB1). Incubate 5 minutes", "[Pl... |
101,072 | DNA Extraction from 0.22µm Sterivex Filters - Qiagen Blood and Tissue with Inhibitor Removal | 1 | dx.doi.org/10.17504/protocols.io.bp2l6223dgqe/v1 | https://www.protocols.io/view/dna-extraction-from-0-22-m-sterivex-filters-qiagen-dexq3fmw | Andreas Novotny | TITLE: DNA Extraction from 0.22µm Sterivex Filters - Qiagen Blood and Tissue with Inhibitor Removal
AUTHORS: Andreas Novotny
[DESCRIPTION]
This protocol is used to extract genomic DNA from 0.22μm sterivex filters using Quiagens Blood and Tissue Kit. The protocol was developed as an equivalent replacement for the Pheno... | ["[PREPARATION] This protocol assumes that samples have been collected and preserved according to this procedure:", "[PREPARATION] Set aside ATL buffer, AL buffer, proteinase K, RNase A and anhydrous ethanol. \nPut the ATL and AL buffers in the incubator to eliminate any precipitate that may be in the solution. \nThere... |
null | null | null | dx.doi.org/10.17504/protocols.io.ddm245 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
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78,407 | Cell culture of RAW264.7 cells | 4 | dx.doi.org/10.17504/protocols.io.q26g7ynbqgwz/v1 | https://www.protocols.io/view/cell-culture-of-raw264-7-cells-cqtfvwjn | Sijia Liao, Lisa Börmel, Maria Wallert, Stefan Lorkowski | TITLE: Cell culture of RAW264.7 cells
AUTHORS: Sijia Liao, Lisa Börmel, Maria Wallert, Stefan Lorkowski
[DESCRIPTION]
RAW264.7 cells are a macrophage-like cell line that was derived from a male BALB/c mouse ascites tumor induced by Abelson Leukemia Virus (A-MuLV) [1]. Due to its rapid proliferation and ease of handlin... | ["[Passaging RAW264.7 cells] Control the cells using an inverted microscope to assess the degree of confluency, check for morphological changes, and confirm the absence of bacterial and fungal contamination.\n\nNote: Elongated cells indicate activation, non-activated cells have a round shape.", "[Seeding RAW264.7 cells... |
70,658 | Hamstring Muscle Architecture In Professional Rugby Union Players: A One Season Prospective Study | 1 | dx.doi.org/10.17504/protocols.io.6qpvr4owogmk/v1 | https://www.protocols.io/view/hamstring-muscle-architecture-in-professional-rugb-cg9atz2e | Kevin Cronin, Shane Foley, Sean Cournane, Eamonn Delahunt | TITLE: Hamstring Muscle Architecture In Professional Rugby Union Players: A One Season Prospective Study
AUTHORS: Kevin Cronin, Shane Foley, Sean Cournane, Eamonn Delahunt
[DESCRIPTION]
Hamstring injuries are very common in field sports. Muscle architecture has been suggested as a risk factor for hamstring strain inju... | [] |
106,283 | NEBNext® Poly(A) mRNA Magnetic Isolation Module NEB #E7490S/L (Express Protocol) | 0 | dx.doi.org/10.17504/protocols.io.n92ld8627v5b/v1 | https://www.protocols.io/view/nebnext-poly-a-mrna-magnetic-isolation-module-neb-dj2j4qcn | Juliet Bonnevie | TITLE: NEBNext® Poly(A) mRNA Magnetic Isolation Module NEB #E7490S/L (Express Protocol)
AUTHORS: Juliet Bonnevie
[DESCRIPTION]
The NEBNext Poly(A) mRNA Magnetic Isolation Module is designed to isolate intact poly(A)+ RNA from previously isolated total RNA. The technology is based on the coupling of Oligo d(T)25 to 1 μ... | ["[Starting Material: 1–5 μg* of DNA-free total RNA (Express Protocol)] Dilute the total RNA with nuclease-free water to a final volume of 50 µLin a nuclease-free 0.2 ml PCR tube and keep on ice.", "[Starting Material: 1–5 μg* of DNA-free total RNA (Express Protocol)] Add 20 µL NEBNext Oligo d(T)25 beads per reaction t... |
null | null | null | dx.doi.org/10.17504/protocols.io.mpac5ie | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?. | [] |
20,370 | U Mass - Uric Acid | null | dx.doi.org/10.17504/protocols.io.x5sfq6e | null | Jason Kim | TITLE: U Mass - Uric Acid
AUTHORS: Jason Kim
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">This experiment involves a spectrophotometric measurement using Roche Cobas Clinical Chemistry Analyzer. Serum uric acid lev... | ["Perform daily quality control assessment of instrumentation before analysis.", "Load each sample into a specialized micro-sample cup for the clinical chemistry analyzer.", "Select Uric acid test on display and run the analysis.", "Collect and analyze the data."] |
73,808 | ONT dA-tailing for Fungal Barcoding | 4 | dx.doi.org/10.17504/protocols.io.yxmvmnze9g3p/v3 | https://www.protocols.io/view/ont-da-tailing-for-fungal-barcoding-ckbqusmw | Stephen Douglas Russell | TITLE: ONT dA-tailing for Fungal Barcoding
AUTHORS: Stephen Douglas Russell
[DESCRIPTION]
This protocol is for dA-tailing, which is an enzymatic method for adding a non-templated nucleotide to the 3' end of a blunt, double-stranded DNA molecule. In other words, this puts A-chains on the end of our PCR product, c... | ["[End repair/A-tailing] Put a 1.5mL tube of molecular water on a heat block at 55 °C. This will be used after the cleanup step towards the end of this protocol.\n\nThaw the NEB End-prep Reaction Buffer and NEB End-prep Enzyme Mix at room temperature. (Won't take long.)\n\nAlso if you are continuing on with adapter lig... |
52,067 | Assessment of in vitro kinase activity of over-expressed and endogenous LRRK2 immunoprecipitated from cells | 1 | dx.doi.org/10.17504/protocols.io.bw4bpgsn | https://www.protocols.io/view/assessment-of-in-vitro-kinase-activity-of-over-exp-bw4bpgsn | Francesca Tonelli, Alexia Kalogeropulou, Dario Alessi | TITLE: Assessment of in vitro kinase activity of over-expressed and endogenous LRRK2 immunoprecipitated from cells
AUTHORS: Francesca Tonelli, Alexia Kalogeropulou, Dario Alessi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>We describe a non-radioactive assay that we deploy for analysing LRR... | ["[Transient transfection of HEK293 cells for analysis of over-expressed LRRK2 activity in vitro:]\nTransfect HEK293 cells at around 60-70% confluency. For a dish, add DNA (FLAG-tagged LRRK2 or FLAG empty vector) and of PEI solution to of Opti-MEMTM Reduced Serum Medium and vortex for 20/30 seconds.\n10\n10 µg\n30... |
46,710 | Build ReVisE on Ubuntu | 1 | dx.doi.org/10.17504/protocols.io.bruwm6xe | https://www.protocols.io/view/build-revise-on-ubuntu-bruwm6xe | Alexey Zhuravlev, Stepan Orlov, Егор Усик, Alexey Kuzin | TITLE: Build ReVisE on Ubuntu
AUTHORS: Alexey Zhuravlev, Stepan Orlov, Егор Усик, Alexey Kuzin
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Current protocol is intended to show how to build visualization system which is called ReVisE. Such system is aimed to provide interactive visualization of ... | ["Make sure the following ReVisE prerequisites are installedcmake >= 3.18.1gitclang >= 9.0 / gcc >= 7.4Qt >= 5.10 including QtSVG, QtWidgetsNode.jsnpmD languageCUDA Toolkit >= 11.1C++ Boost libraries", "Go to the directory where the ReVisE repository will be downloaded and built.cd", "Clone ReVisE.git clone https://git... |
88,800 | Immunofluorescence and confocal imaging protocol | 4 | dx.doi.org/10.17504/protocols.io.bp2l6x71klqe/v1 | https://www.protocols.io/view/immunofluorescence-and-confocal-imaging-protocol-c2x8yfrw | taylor.panczyk | TITLE: Immunofluorescence and confocal imaging protocol
AUTHORS: taylor.panczyk
[DESCRIPTION]
In this protocol we detail the steps needed to obtain fixed brain tissue from mice to perform immunohistochemistry and image acquisition. In particular, we detail the perfusion, dissection, brain slicing, mounting and anti-Ch... | ["[Dissection:] Decapitate the mouse with large surgical scissors.", "[Tissue Fixation Through Perfusion:] Anesthetize the mice with a mixture of ketamine (50 mg/kg) and xylazine (4.5 mg/kg).", "[Tissue Fixation Through Perfusion:] Make two additional skin incisions from the xiphoid process along the base of the ventra... |
54,211 | Plasmid Sequence Analysis from Long Reads | 1 | dx.doi.org/10.17504/protocols.io.by7bpzin | https://www.protocols.io/view/plasmid-sequence-analysis-from-long-reads-by7bpzin | David A Eccles | TITLE: Plasmid Sequence Analysis from Long Reads
AUTHORS: David A Eccles
[DESCRIPTION]
This protocol demonstrates how to assemble reads from plasmid DNA, and generate a circularised and non-repetitive consensus sequence
At the moment, this protocol uses Canu to de-novo assemble high-quality single-cut reads.
Input(... | ["[Read file preparation] Demultiplex reads as per protocol Demultiplexing Nanopore reads with LAST.\n\nIf this has been done, then the following command should produce output without errors:\n\n \n\nExample output:\n\n \n\nIf the barcode_counts.txt file is missing, the output will look like this:\n\n \n\nIf one or mor... |
null | null | null | dx.doi.org/10.17504/protocols.io.ifbcbin | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Nauplii, ie newly hatched Artmemia (3-5 days), are processed to concentrate and separate from the eggs, before a DNA extraction</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?. | [] |
42,304 | Chapter 3: Wound care | 4 | null | https://www.protocols.io/view/chapter-3-wound-care-bmi8k4hw | Kerri Wolter | TITLE: Chapter 3: Wound care
AUTHORS: Kerri Wolter
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines the steps to properly care for wounds when rehabilitating vultures.</div></div>
[STEPS]
?. [Maggots]
Observe all wounds for maggots and remove the maggots by physically picking ... | ["[Maggots]\nObserve all wounds for maggots and remove the maggots by physically picking them out.", "[Maggots]\nIf not all maggots can be removed by hand, liberally apply honey to the wound which will smother the maggots and draw them upward and out of the wound.\nEctoparasitic wound preparations, such as ‘F10 Germici... |
85,314 | DNA Extraction for Formalin Specimen | 4 | dx.doi.org/10.17504/protocols.io.e6nvwdk97lmk/v1 | https://www.protocols.click/view/dna-extraction-for-formalin-specimen-cxjaxkie | heeseung | TITLE: DNA Extraction for Formalin Specimen
AUTHORS: heeseung
[DESCRIPTION]
DNA Extraction for Formalin Specimen (Qiagen Kit: QIAamp DNA FFPE Advanced Kit)
[STEPS]
SECTION: Deparaffinization process
1. Place the tissue in a 1.5 ml or 2 ml microcentrifuge tube. Add 300 µl Deparaffinization Solution, vortex vigorously ... | ["[Deparaffinization process] Place the tissue in a 1.5 ml or 2 ml microcentrifuge tube. Add 300 µl Deparaffinization Solution, vortex vigorously for 10 s, and centrifuge briefly to bring the sample to the bottom of the tube.\n\nNote: For specimens stored only in alcohol (=not fixed in paraffin), \"deparaffinization st... |
37,462 | Transformation Protocol for BL21(DE3) Competent Cells (C2527H) | 1 | dx.doi.org/10.17504/protocols.io.bgtwjwpe | https://www.protocols.io/view/transformation-protocol-for-bl21-de3-competent-cel-bgtwjwpe | New England Biolabs | TITLE: Transformation Protocol for BL21(DE3) Competent Cells (C2527H)
AUTHORS: New England Biolabs
[DESCRIPTION]
This transformation protocol is to be performed directly in the C2527H tubes. (For the C2527I protocol, see here.)
[BEFORE_START]
Perform steps 1–8 in the tube provided.
[GUIDELINES]
Transformation Pro... | ["Thaw a tube of BL21(DE3) Competent E. coli cells on ice for 10 min.", "Add 1 µL–5 µL containing 1 pg–100 ng to the cell mixture.", "Carefully flick the tube 4–5 times to mix cells and DNA. Do not vortex.", "Place the mixture on ice for 30 min. Do not mix.", "Heat shock at exactly 42 °C for exactly 10 s. Do not mix.",... |
86,668 | Western Blot | 4 | dx.doi.org/10.17504/protocols.io.kqdg3xx3pg25/v1 | https://www.protocols.io/view/western-blot-cyvkxw4w | Beatriz E Nielsen | TITLE: Western Blot
AUTHORS: Beatriz E Nielsen
[DESCRIPTION]
This protocol describes the solutions and steps for performing western blots.
[STEPS]
SECTION: Preparation of lysate from tissues
1. Dissect the tissue with clean tools, on ice preferably, and as quickly as possible to prevent degradation by proteases.
... | ["[Preparation of lysate from tissues] Dissect the tissue with clean tools, on ice preferably, and as quickly as possible to prevent degradation by proteases.", "[Preparation of lysate from tissues] Place the pieces of tissue microcentrifuge tubes and store samples at -80 °C for later use or keep on ice for immediate h... |
103,055 | Oxford Nanopore Technologies (ONT) library preparation and sequencing of DNA prepared using droplet Multiple Displacement Amplification (dMDA) | 0 | dx.doi.org/10.17504/protocols.io.q26g71x2qgwz/v1 | https://www.protocols.io/view/oxford-nanopore-technologies-ont-library-preparati-dgvp3w5n | Nadine Holmes, Ester Kalef-Ezra, Christos Proukakis | TITLE: Oxford Nanopore Technologies (ONT) library preparation and sequencing of DNA prepared using droplet Multiple Displacement Amplification (dMDA)
AUTHORS: Nadine Holmes, Ester Kalef-Ezra, Christos Proukakis
[DESCRIPTION]
Debranching of DNA generated by Multiple Displacement Amplification (MDA) is an essential step... | ["[Section 1: DNA QC] Measure the concentration of each dMDA sample using the Qubit Fluorometer. Mix 1 µL of DNA with 199 µL of 1X dsDNA HS reagent, in a 0.5 ml Qubit tube. Vortex for 10 s, spin briefly in a microfuge and incubate at Room temperature for 2 min and measure concentration.", "[Section 1: DNA QC] (Optional... |
74,991 | Risk-Based Community Screening for the Evaluation of Atrial Fibrillation Trial (R-BEAT): a randomised controlled crossover trial protocol | 1 | dx.doi.org/10.17504/protocols.io.4r3l27nopg1y/v1 | https://www.protocols.io/view/risk-based-community-screening-for-the-evaluation-cmgpu3vn | Robert P Murphy, Ruairi Waters, Suzanne McDermott, Catriona Reddin, Alberto Alvarez-Iglesias, Michelle Canavan, Martin O'Donnell | TITLE: Risk-Based Community Screening for the Evaluation of Atrial Fibrillation Trial (R-BEAT): a randomised controlled crossover trial protocol
AUTHORS: Robert P Murphy, Ruairi Waters, Suzanne McDermott, Catriona Reddin, Alberto Alvarez-Iglesias, Michelle Canavan, Martin O'Donnell
[DESCRIPTION]
Background:
Undiagno... | ["[Background] Stroke is a leading cause of death and disability (1). Undiagnosed atrial fibrillation is a major care-gap in stroke prevention, given that about 40% of patients with acute ischemic stroke have atrial fibrillation identified at the time of acute presentation (2,3). Once identified, oral anticoagulation t... |
82,831 | Most Probable Number Fluorescence Microplate Assay | 4 | dx.doi.org/10.17504/protocols.io.q26g7yqk1gwz/v1 | https://www.protocols.click/view/most-probable-number-fluorescence-microplate-assay-cu5pwy5n | Karla Franco Meléndez, Layla Schuster, Melinda Chue Donahey, Emily Kairalla, Michael Andrew Jansen, Christopher Reisch, Adam R Rivers | TITLE: Most Probable Number Fluorescence Microplate Assay
AUTHORS: Karla Franco Meléndez, Layla Schuster, Melinda Chue Donahey, Emily Kairalla, Michael Andrew Jansen, Christopher Reisch, Adam R Rivers
[DESCRIPTION]
Here we provide a step-by-step protocol for running the MPN fluorescence microplate assay with soil samp... | ["[Inoculating soil microcosms with rfp-tagged Ralstonia] Transfer overnight culture to a 50 mL polypropylene centrifuge conical tube. Pellet sample 4000 rpm, 23 °C for 30 min.", "[Preparing cultures of rfp-tagged Ralstonia] Streak Ralstonia from a glycerol stock on casamino acid-peptone-glucose (CPG)9 agar supplement... |
88,751 | Whole mount dissection and staining of enteric nervous system | 4 | dx.doi.org/10.17504/protocols.io.14egn3wxpl5d/v1 | https://www.protocols.io/view/whole-mount-dissection-and-staining-of-enteric-ner-c2wpyfdn | Michael Henderson, Alice Prigent | TITLE: Whole mount dissection and staining of enteric nervous system
AUTHORS: Michael Henderson, Alice Prigent
[DESCRIPTION]
This protocol details whole mount dissection and staining of enteric nervous system.
[STEPS]
SECTION: Perfusion
1. Administer sodium pentobarbital through intraperitoneal injection.
SECTION: Pe... | ["[Perfusion] Administer sodium pentobarbital through intraperitoneal injection.", "[Perfusion] Place mouse back in the cage long enough for anesthesia to take effect. Apply a hard toe pinch until mouse no longer reacts, ensuring that the mouse can no longer feel pain before proceeding.", "[Perfusion] Place mouse, abd... |
50,578 | encrypting your data | 5 | null | https://www.protocols.io/view/encrypting-your-data-bvmsn46e | Alise Ponsero | TITLE: encrypting your data
AUTHORS: Alise Ponsero
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">How to encrypt a folder or a file using the command line on a linux/mac system !</div></div>
[STEPS]
?. [encrypt]
In order to encrypt your data, you'll need to zip your folder or file, creating a pass... | ["[encrypt]\nIn order to encrypt your data, you'll need to zip your folder or file, creating a password protected archive.People without the password will still be able to look at the names of the files in the archive, but won't be able to read the file.Using the command line, navigate to the folder you want to encrypt... |
40,313 | Preparation of a protein-LA conjugated to horseradish peroxidase by the periodate method. | 6 | dx.doi.org/10.17504/protocols.io.bjkzkkx6 | https://www.protocols.io/view/preparation-of-a-protein-la-conjugated-to-horsera-bjkzkkx6 | Angel Justiz-Vaillant | TITLE: Preparation of a protein-LA conjugated to horseradish peroxidase by the periodate method.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protein LA, a novel hybrid protein, structurally contains 4 of the Ig Fc-binding and 4 of the Ig Fab binding regions on Sp... | ["Horseradish peroxidase (500 µg in 50 µl NaCO3 , pH 9.6) is mixed with freshly made sodium periodate solution (1.71 mg/ml) followed by incubation in the dark for 2 h.", "Mix 500 µg of staphylococcal protein-A (SpA) with an equal amount (500 micrograms) of a mix of horseradish peroxidase-sodium periodate. On the other ... |
37,183 | Airbrushed Coral Sample Preparation for Organic Stable Carbon and Nitrogen Isotope Analyses | 1 | dx.doi.org/10.17504/protocols.io.bgi7juhn | https://www.protocols.io/view/airbrushed-coral-sample-preparation-for-organic-st-bgi7juhn | James Price, Alexandria Smith, Kerri Dobson, Andrea Grottoli | TITLE: Airbrushed Coral Sample Preparation for Organic Stable Carbon and Nitrogen Isotope Analyses
AUTHORS: James Price, Alexandria Smith, Kerri Dobson, Andrea Grottoli
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This method for separating coral tissues from algal endosymbiont (Symbiodiniaceae) ... | ["[Preparation of Coral Slurry]\nPrepare for airbrushing. Fill airbrush reservoir with 15 ml of 0.22 µm filtered ultrapure water (See Fig. 1 for the type of airbrush used). With nitrile gloves on, place coral fragment (surface area of the fragment should be approximately 2–3 cm2) in a new clean bag.", "[Preparation of ... |
null | null | null | dx.doi.org/10.17504/protocols.io.g7qbzmw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div class="page" title="Page 2">
<div class="layoutArea">
<div class="column">
<p>This protocol describes a method to determine optimal blocking conditions for NIR Western blot detection with the Odyssey family of Imagers.</p>
<p> </p>
<p>It is for use with the Millipore Immobi... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.gudbws6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocol for radioactive labelling of RNA using T7-Polymerase and α-[<sup>32</sup>P]-UTP.</p>
[STEPS]
?.
?.
?.
?. | [] |
38,824 | Coccidioides_soil_habitat_model | 3 | dx.doi.org/10.17504/protocols.io.bh6gj9bw | https://www.protocols.io/view/coccidioides-soil-habitat-model-bh6gj9bw | Robert Dobos | TITLE: Coccidioides_soil_habitat_model
AUTHORS: Robert Dobos
[STEPS] | [] |
76,674 | Using Amira to generate cell body masks in fluorescent light sheet microscopy images of EASI-FISH samples | 1 | null | https://www.protocols.io/view/using-amira-to-generate-cell-body-masks-in-fluores-cn5avg2e | Grace Park, Aubrey Weigel, Alyson Petruncio, Claire Managan, Mark Eddison, Gudrun Ihrke, Gudrun Ihrke | TITLE: Using Amira to generate cell body masks in fluorescent light sheet microscopy images of EASI-FISH samples
AUTHORS: Grace Park, Aubrey Weigel, Alyson Petruncio, Claire Managan, Mark Eddison, Gudrun Ihrke, Gudrun Ihrke
[DESCRIPTION]
This protocol describes how CellMap Project Team created the masks for cell bodie... | ["[Loading the Data] This protocol describes how the masks for cell bodies were generated to assist the RS-FISH spot-counting analysis. Please reference the Using Amira to manually segment organelles in vEM for machine learning protocol to find details of the annotation techniques and Amira software. \n\nThe raw images... |
33,661 | Skin phtocarcinogenesis by sunbed in SKH-1 mice | null | dx.doi.org/10.17504/protocols.io.bc45iyy6 | null | Francisco Jose Gomez-Garcia, Vicente Vicente Ortega | TITLE: Skin phtocarcinogenesis by sunbed in SKH-1 mice
AUTHORS: Francisco Jose Gomez-Garcia, Vicente Vicente Ortega
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">When SKH-1 mice are exposed to ultraviolet radiation three times a week for 60min each (a total of 80sessions), with a focus-skin distan... | ["Ultraviolet radiation: The mice were subjected to UV irradiation using a Philips lamp (Type HB 554/01/A) with 8 Philips Performance S 100W tubes. The lamp has an emission spectrum of 220-425 nm with a maximum peak of 364 nm (98.6% UVA and 1.4% UVB). The animals were exposed to radiation three times a week for a total... |
64,379 | Via Keto Gummies Reviews – Positive Outcomes & Legit Ingredients | 1 | dx.doi.org/10.17504/protocols.io.q26g749j3gwz/v1 | https://www.protocols.io/view/via-keto-gummies-reviews-positive-outcomes-amp-leg-ca43sgyn | ieaglehemp | TITLE: Via Keto Gummies Reviews – Positive Outcomes & Legit Ingredients
AUTHORS: ieaglehemp
[DESCRIPTION]
Via Keto GummiesAssuming you are one of the numerous people who fight to achieve their ideal body, there is another thing called Via Keto Gummies that can help you with working on the heaviness of the chief'... | [] |
20,082 | Berryhill Project 2018 | null | dx.doi.org/10.17504/protocols.io.xusfnwe | null | Michelle Altemara | TITLE: Berryhill Project 2018
AUTHORS: Michelle Altemara
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Zebrafish (Danio rerio) are a popular animal model used in a variety of research areas. As with all animal models, husbandry conditions, including environmental parameters, nutrition, and exposur... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.nuudeww | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The 16S protocol detailed here is designed to amplify prokaryotes (bacteria and archaea) using paired-end 16S community sequencing on the Illumina platform. Primers 515F-806R target the V4 region of the 16S SSU rRNA.</p>
<p> </p>
<p>For running these libraries on the MiSeq an... | [] |
18,595 | Staining/Dehydration 10 micron Rat Heart | null | dx.doi.org/10.17504/protocols.io.webfban | null | Shaina Robbins, Sean Nieves | TITLE: Staining/Dehydration 10 micron Rat Heart
AUTHORS: Shaina Robbins, Sean Nieves
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Slide retrieval]
Remove slide from freezer. Keep slide covered and allow to come to room temperature for or until frost on slide dissipates.
-80 °C
?. [Fixation]
Submerge... | ["[Slide retrieval]\nRemove slide from freezer. Keep slide covered and allow to come to room temperature for or until frost on slide dissipates.\n-80 °C", "[Fixation]\nSubmerge slide into cold acetone (kept in freezer) for\n-20 °C", "[OCT removal]\nGently dip slide 10 times into 1x PBS or until OCT appears to be was... |
53,156 | Epifluorescence-Microscopy-VLPs | 3 | dx.doi.org/10.17504/protocols.io.bx6cpraw | https://www.protocols.io/view/epifluorescence-microscopy-vlps-bx6cpraw | Josue L Castro-Mejia | TITLE: Epifluorescence-Microscopy-VLPs
AUTHORS: Josue L Castro-Mejia
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Epifluorescence Microscopy for Viral-like Particles</div><div class = "text-block">-Virome Studies-</div></div>
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.hgjb3un | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The FlowCam can be used to take quick cell density measurements of liquid samples. </p>
[BEFORE_START]
<p>Before you begin, make sure that</p>
<ol>
<li>the appropiate flow cell and syringe are mounted</li>
<li>appropiate objective and columnator, if needed, are in place</li>... | [] |
97,362 | Tissue Harvesting | HuBMAP | JHU-TMC | 0 | dx.doi.org/10.17504/protocols.io.e6nvw16p7lmk/v1 | https://www.protocols.io/view/tissue-harvesting-hubmap-jhu-tmc-dbbs2ine | Kyu Sang Han, Pei-Hsun Wu, Joel Sunshine, Ashley Kiemen, Sashank Reddy, Denis Wirtz | TITLE: Tissue Harvesting | HuBMAP | JHU-TMC
AUTHORS: Kyu Sang Han, Pei-Hsun Wu, Joel Sunshine, Ashley Kiemen, Sashank Reddy, Denis Wirtz
[DESCRIPTION]
This protocol describes how to harvest human tissue biopsy and prepare it for histological processes
[STEPS]
SECTION: Prepare tissue collection container
1. For tissue... | ["[Prepare tissue collection container] For tissue collection container, we will prefill histology containers with 10% Neutral Buffered Formalin (NBF)", "[Prepare tissue collection container] Combine 100 mL of Formaldehyde (37% - 40%), 900mL of distilled water, 4g of Sodium dihydrogen phosphate monohydrate, and 6.5g of... |
36,629 | Preparation of Gelatin Slide Coating Solution | null | dx.doi.org/10.17504/protocols.io.bfzvjp66 | https://www.protocols.io/view/preparation-of-gelatin-slide-coating-solution-bfzvjp66 | Allen Institute for Brain Science | TITLE: Preparation of Gelatin Slide Coating Solution
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the preparation of gelatin solution to be used for coating glass microscope slides.</div><div class = "text-block"><span style = "fo... | [] |
83,161 | Pole Test to assess motor coordination in parkinsonian mice | 1 | dx.doi.org/10.17504/protocols.io.dm6gp3ed8vzp/v1 | https://www.protocols.click/view/pole-test-to-assess-motor-coordination-in-parkinso-cvfzw3p6 | natalia.lopezgonzalezdelrey, Zachary Gaertner | TITLE: Pole Test to assess motor coordination in parkinsonian mice
AUTHORS: natalia.lopezgonzalezdelrey, Zachary Gaertner
[DESCRIPTION]
The pole test evaluates the motor coordination ability of a mouse by having them grasp a pole and then descend to its home cage.
[STEPS]
SECTION: Pole Test
1. Total duration: 1 da... | ["[Pole Test] Total duration: 1 day\nThree consecutive trials per animals are run.", "[Protocol] Place the animal cage in the testing room to allow the animals to acclimate. 60 min", "[Protocol] Return the mouse to its cage.", "[Analysis] The time required for the animals to orient themselves facing in a downward direc... |
null | null | null | dx.doi.org/10.17504/protocols.io.tcweixe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Female larvae of the Aedes aegypti mosquito outcompete male larvae for food. Male larvae pupate earlier and at smaller masses in vials where competition is most intense. Competition at the higher densities causes the food/larva to appear lower than the equivalent mg/larva a... | [] |
40,423 | Quick-n-Dirty electrocompetent E. coli cells | 4 | dx.doi.org/10.17504/protocols.io.bjqfkmtn | https://www.protocols.io/view/quick-n-dirty-electrocompetent-e-coli-cells-bjqfkmtn | elisa.granato | TITLE: Quick-n-Dirty electrocompetent E. coli cells
AUTHORS: elisa.granato
[STEPS]
?. Using a sterile toothpick, pipette tip or similar, pick up some cell material from the agar plate. How much, you ask? So that you have a visible amount on the tip but not more than that (better to have fewer cells than too many). Pr... | ["Using a sterile toothpick, pipette tip or similar, pick up some cell material from the agar plate. How much, you ask? So that you have a visible amount on the tip but not more than that (better to have fewer cells than too many). Probably around 2 µL volume of material. I don't know, I've never measured it. A tiny li... |
102,033 | Neural recordings of spontaneously metastasizing melanomas and melanomas with low metastatic potential | 0 | dx.doi.org/10.17504/protocols.io.81wgbzn7ngpk/v1 | https://www.protocols.io/view/neural-recordings-of-spontaneously-metastasizing-m-dfvr3n56 | Jay Shiralkar, Tiana Anthony, Grant A McCallum, Dominique Durand | TITLE: Neural recordings of spontaneously metastasizing melanomas and melanomas with low metastatic potential
AUTHORS: Jay Shiralkar, Tiana Anthony, Grant A McCallum, Dominique Durand
[DESCRIPTION]
Multiple studies report that melanomas are innervated tumors with sensory and sympathetic fibers where these neural fiber... | ["[B16-F10-Luc2 & B16-F1-Luc2 Cell Culturing Protocol] Store the vials containing cells in liquid nitrogen vapor until they are ready for use.", "[B16-F10-Luc2 & B16-F1-Luc2 Cell Culturing Protocol] Thaw in a 37°C water bath, then decontaminate by dipping in or spraying with 70% ethanol. All of the operations f... |
16,516 | Measuring CN content in leaf samples using Elementar Vario MICRO Cube | null | dx.doi.org/10.17504/protocols.io.udces2w | null | Jocelyne Ayotte, Xavier Guilbeault-Mayers, Etienne Laliberté | TITLE: Measuring CN content in leaf samples using Elementar Vario MICRO Cube
AUTHORS: Jocelyne Ayotte, Xavier Guilbeault-Mayers, Etienne Laliberté
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Here we describe the standardised protocol used by the </span><a style = "text-decoration:underline... | ["[Weighing samples and boat preparation]\nWith a microbalance, put 7 mg (+/-0.2mg) of sample in a tin boat.", "[Weighing samples and boat preparation]\nWith a microbalance, put 2 mg (+/-0.2mg) of acetanilide in a tin boat. With tweezers, gently and carefully close the boat. Using the pressing tool, slowly press the b... |
71,342 | CRISPR/Cas9 generation of knock-out iPSCs | 1 | dx.doi.org/10.17504/protocols.io.36wgqj48yvk5/v1 | https://www.protocols.io/view/crispr-cas9-generation-of-knock-out-ipscs-chwnt7de | Dan Dou, C. Alexander Boecker, Erika L.F. Holzbaur | TITLE: CRISPR/Cas9 generation of knock-out iPSCs
AUTHORS: Dan Dou, C. Alexander Boecker, Erika L.F. Holzbaur
[DESCRIPTION]
This protocol describes RNP-based CRISPR/Cas9 gene-editing to generate knock-out iPSCs. iPSCs are transfected with sgRNA, recombinant Cas9, and GFP using Lipofectamine Stem. After FACS sorting to ... | ["[Transfection with sgRNA and recombinant Cas9] Accutase-dissociate iPSCs on the morning of transfection.", "[Transfection with sgRNA and recombinant Cas9] 1 - 2 hours prior to transfection, change media to fresh, pre-warmed mTeSR + RI (2 mL/well).", "[Transfection with sgRNA and recombinant Cas9] Prepare sgRNA: \n\nR... |
21,107 | UC Davis - Non-Esterified Fatty Acids Protocol | null | dx.doi.org/10.17504/protocols.io.yutfwwn | null | Peter Havel | TITLE: UC Davis - Non-Esterified Fatty Acids Protocol
AUTHORS: Peter Havel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">
The Wako enzymatic method relies upon the acylation of coenzyme A (CoA) by the fatty acids in t... | ["Reconstitute Color Reagent A with 50 ml of Solvent A and Color Reagent B with Solvent B.", "Add 5 μl of calibrator and sample to each well.", "Add 200 μl of Reagent A to each well. Incubate at 37°C for 5 minutes. Read at 560 nm.IMPORTANT: Make sure not to add any bubbles to the wells when dispensing reagents, this wi... |
74,344 | HuBMAP | GE/Vanderbilt MALDI IMS and Cell DIVE™ Modality Overview | 1 | dx.doi.org/10.17504/protocols.io.kqdg39k41g25/v1 | https://www.protocols.io/view/hubmap-ge-vanderbilt-maldi-ims-and-cell-dive-modal-ckuguwtw | Nathan Heath Patterson, Elizabeth Neumann, Christine Surrette, Soumya Ghose, Liz McDonough, Jamie Allen, Jeff Spraggins, Fiona Ginty | TITLE: HuBMAP | GE/Vanderbilt MALDI IMS and Cell DIVE™ Modality Overview
AUTHORS: Nathan Heath Patterson, Elizabeth Neumann, Christine Surrette, Soumya Ghose, Liz McDonough, Jamie Allen, Jeff Spraggins, Fiona Ginty
[DESCRIPTION]
This is an overview of all protocols currently in use for the GE/Vanderbilt University Cel... | ["[MALDI IMS] Perform Matrix Application", "[Cell DIVE] Characterize antibodies (primary/secondary, direct conjugates, and zenon labelled antibodies) and determine any antigen effects from the Cell DIVE dye inactivation process.\n\n\nCell DIVE™ Platform | Antibody Characterization for Multiplexing \nCell DIVE™ Platform... |
66,701 | Ego-team | 1 | dx.doi.org/10.17504/protocols.io.j8nlkkjjwl5r/v1 | https://www.protocols.io/view/ego-team-cddms246 | Mantilla Cesar, Zahra Murad | TITLE: Ego-team
AUTHORS: Mantilla Cesar, Zahra Murad
[DESCRIPTION]
We study how individuals' contribution to a team production task varies depending on whether the task is ego relevant or not.
We design and conduct an experiment to test the effect of ego-relevance when the team output depends on the top- and the bot... | [] |
54,116 | Short HPLC gradient method for 20-Hydroxyecdysone (20E) quantification in malaria vectors | 6 | dx.doi.org/10.17504/protocols.io.by4cpysw | https://www.protocols.io/view/short-hplc-gradient-method-for-20-hydroxyecdysone-by4cpysw | Oswald Yedjinnavenan Djihinto, Luc S. Djogbenou, Luisa Nardini, Armorel Van Eyk, Lizette L. Koekemoer | TITLE: Short HPLC gradient method for 20-Hydroxyecdysone (20E) quantification in malaria vectors
AUTHORS: Oswald Yedjinnavenan Djihinto, Luc S. Djogbenou, Luisa Nardini, Armorel Van Eyk, Lizette L. Koekemoer
[DESCRIPTION]
Ecdysteroids are arthropod steroid hormones that are primarily involved in insect moulting. In ... | ["[Instrument] Analytical HPLC separations were performed on the Flexar LC system (Perkin Elmer) with a UV/Vis Detector and a Phenomenex Kinetex RP C18–5 µm column (4.6 x 150 mm). \nThe detection wavelength was set at 254 nm. \nThe flow rate was 1 ml/minute. \nThe mobile phase included gradient elution with Methanol:Ac... |
99,817 | EXPERIMENTO MAGNETISMO | 0 | null | https://www.protocols.io/view/experimento-magnetismo-ddqh25t6 | Keven Alexis Aispuro Bueno, Abraham Espinoza Cazares, Diego Aleiandro Malo Osuna, Eduardo Madrigal, a | TITLE: EXPERIMENTO MAGNETISMO
AUTHORS: Keven Alexis Aispuro Bueno, Abraham Espinoza Cazares, Diego Aleiandro Malo Osuna, Eduardo Madrigal, a
[DESCRIPTION]
.
[STEPS]
SECTION: Preparación del experimento
1. Primero, prensamos una agujeta de zapato con 5 imanes por un extremo.
SECTION: Preparación del experimento
2. Po... | ["[Preparación del experimento] Primero, prensamos una agujeta de zapato con 5 imanes por un extremo.", "[Preparación del experimento] Por otro extremo le pegamos un pedazo de cinta con el objetivo de poder medir la posición respecto al tiempo.", "[Preparación del experimento] Pegamos un tubo de cobre de 1 metro a una ... |
65,882 | Simpli ACV Keto Gummies ( Warning! Update 2022 ) - Does it Really Work For Diet! | 3 | dx.doi.org/10.17504/protocols.io.6qpvr6zkovmk/v1 | https://www.protocols.io/view/simpli-acv-keto-gummies-warning-update-2022-does-i-ccj2suqe | Acv keto Gummies | TITLE: Simpli ACV Keto Gummies ( Warning! Update 2022 ) - Does it Really Work For Diet!
AUTHORS: Acv keto Gummies
[DESCRIPTION]
Simpli ACV Keto Gummies
[STEPS] | [] |
95,917 | 16S Gene PCR Amplification and Sanger Sequencing | 0 | dx.doi.org/10.17504/protocols.io.3byl4qpxrvo5/v1 | https://www.protocols.io/view/16s-gene-pcr-amplification-and-sanger-sequencing-c9wmz7c6 | Carlos Goller | TITLE: 16S Gene PCR Amplification and Sanger Sequencing
AUTHORS: Carlos Goller
[DESCRIPTION]
After genomic DNA (gDNA) has been isolated and quantified, it can be used for many downstream applications. While we will use our genomic DNA samples for whole genome sequencing using Nanopore sequencing technology, we can als... | ["[Introduction] PCR Cycles Diagram indicating the three main steps: denaturation at 95-96°C, annealing at 68°C, and elongation at 72°C. Created with BioRender.com\nYou can learn about this reaction by watching the video “Polymerase Chain Reaction.” \n\nAfter completing this lab, you will gain the following lab skills:... |
null | null | null | dx.doi.org/10.17504/protocols.io.pkzdkx6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Here we describe the standardised protocol used by the <a href="http://www.caboscience.org" target="_blank" rel="noopener noreferrer">Canadian Airborne Biodiversity Observatory</a> (CABO) to measure leaf spectral reflectance and transmittance, using an integrating sphere fitt... | [] |
84,175 | Optimized conditions for whole genome sequencing of avian reoviruses. | 1 | dx.doi.org/10.17504/protocols.io.14egn38z6l5d/v1 | https://www.protocols.io/view/optimized-conditions-for-whole-genome-sequencing-o-cwfpxbmn | Sonsiray Alvarez-Narvaez, telvin_harrell, s.conrad steven_j_conrad | TITLE: Optimized conditions for whole genome sequencing of avian reoviruses.
AUTHORS: Sonsiray Alvarez-Narvaez, telvin_harrell, s.conrad steven_j_conrad
[DESCRIPTION]
Whole genome sequencing (WGS) is becoming an essential tool to characterize the genomes of avian reovirus (ARV), an emerging pathogen and growing threat... | ["[RNA extraction] We are going to use MagMAX™ Viral RNA Isolation Kit (Applied Biosystems, catalog number AM1939) to extract the RNA from the purified ARV virions.\n\n NOTE: Spray work surfaces and pipettes with an RNase decontamination solution and wipe clean.", "[Host rRNA depletion] Preparing custom ... |
null | null | null | dx.doi.org/10.17504/protocols.io.hsub6ew | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is the protocol to be used in the quantification of glial fibrillary acidic protein (GFAP) in mouse brain tissue. </p>
<p><strong> </strong></p>
[GUIDELINES]
<p><strong>TRAINING REQUIREMENTS</strong></p>
<p>Able to use a plate reader and to accurately dilute tissue samp... | [] |
17,059 | ChroDrip - ProteinG | null | dx.doi.org/10.17504/protocols.io.uwbexan | null | Alexandra Ehl, David Frommholz, Nadine Stefanczyk | TITLE: ChroDrip - ProteinG
AUTHORS: Alexandra Ehl, David Frommholz, Nadine Stefanczyk
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Purification Guide for the Isolation of Antibodies with ChroDrip Columns by DALEX Biotech.</span></div><div class = "text-block">Eas... | ["[Load and Wash]\nAdd your sample to the top of the column and let it flow through by gravity.\nFor optimal binding and purity, the pH of the sample should be 7 - 8 and should contain 150 - 300 mM NaCl. An easy way to achieve this is by adding 1/11 volume 10x PBS to your sample.Removal of particulate matter from the s... |
null | null | null | dx.doi.org/10.17504/protocols.io.c8azsd | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is the protocol we are using to assess the Light/Dark preference in flies.
[BEFORE_START]
The light source should be homogenous above the T-Maze.
[GUIDELINES]
<p>The Choice Index is calculated using the formula:<br /><br /></p>
<p>CI=((#FL×1)+(#FD×-1)+(#FE&tim... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.hjub4nw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div>
<p>This protocol is from 'Flower Ca<sup>2+</sup> channel in CME and ADBE' of Yao CK et al.</p>
<div>
<div>
<p> </p>
<p>Please see the manuscript for the full method details.</p>
</div>
</div>
</div>
[BEFORE_START]
<p>You'll need: </p>
<p> </p>
<p><strong>0 mM Ca<sup>2+</s... | [] |
18,668 | Cleaning up a biohazardous spill inside a centrifuge | null | dx.doi.org/10.17504/protocols.io.wgkfbuw | null | Steven Wilhelm, Gary LeCleir, Ashley Humphrey | TITLE: Cleaning up a biohazardous spill inside a centrifuge
AUTHORS: Steven Wilhelm, Gary LeCleir, Ashley Humphrey
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">BIOLOGICAL SPILL RESPONSE </span><span>method to be used in the event of a biosafety incident. </span><... | ["Close off the area and allow aerosols to settle.", "Notify others including supervisor.", "Wait to allow the aerosols to settle.", "Don appropriate PPE: laboratory coat, safety glasses and Nitrile gloves.", "Remove rotors and bucket and place in Biosafety Cabinet.", "Thoroughly disinfect the inside and outside of th... |
71,453 | Western Blotting (Fly Heads) | 4 | dx.doi.org/10.17504/protocols.io.8epv5j96jl1b/v1 | https://www.protocols.io/view/western-blotting-fly-heads-chz5t786 | Mel Feany | TITLE: Western Blotting (Fly Heads)
AUTHORS: Mel Feany
[DESCRIPTION]
This protocol describes how to perform a west blotting technique using fly heads.
[STEPS]
1. Homogenize desired number of fly heads in 1 X Laemmli sample buffer.
2. Heat samples to 100 °C for 10 min , spin briefly before loading.
3. Load premade ge... | ["Homogenize desired number of fly heads in 1 X Laemmli sample buffer.", "Heat samples to 100 °C for 10 min , spin briefly before loading.", "Load premade gel into western blotting apparatus. Fill reservoir with Running Buffer:\nRunning Buffer:\n6 g Tris-HCL\n28.9 g glycine\nFill to 1 L with distilled water\nAdd 5 m... |
null | null | null | dx.doi.org/10.17504/protocols.io.icscawe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Please contact Dr. Steven Wilhelm (wilhelm@utk.edu) for additional information regarding this protocol.</p>
[GUIDELINES]
<p><img id="s-mce-img" class="s-mce-img" src="https://s3.amazonaws.com/pr-journal/kdeeuxn.jpg" width="479" height="441" data-src="https://s3.amazonaws.com... | [] |
95,763 | Protein Lysate Preparation Protocol (Tissue) | 0 | dx.doi.org/10.17504/protocols.io.n2bvj3k3xlk5/v1 | https://www.protocols.io/view/protein-lysate-preparation-protocol-tissue-c9rtz56n | Scott Vermilyea | TITLE: Protein Lysate Preparation Protocol (Tissue)
AUTHORS: Scott Vermilyea
[DESCRIPTION]
This protocol details the preparation of protein lysate of the tissue sample.
[STEPS]
SECTION: Protein Lysate Preparation (Tissue)
1. If tissue stored at -80 °C, place in -20 °C for at least 240 min or prior to homogenizatio... | ["[Protein Lysate Preparation (Tissue)] If tissue stored at -80 °C, place in -20 °C for at least 240 min or prior to homogenization.", "[Protein Lysate Preparation (Tissue)] Weigh tissue out in mg.", "[Protein Lysate Preparation (Tissue)] Add in 10 volumes of 1X TNE (e.g. 10 µL of TNE per 1 mgof tissue).", "[Protein ... |
98,201 | Library Aligner and NGS Cas9 Cutting Analysis | 5 | dx.doi.org/10.17504/protocols.io.5qpvo3n89v4o/v2 | https://www.protocols.io/view/library-aligner-and-ngs-cas9-cutting-analysis-db5z2q76 | Colin Kremitzki, William J Buchser | TITLE: Library Aligner and NGS Cas9 Cutting Analysis
AUTHORS: Colin Kremitzki, William J Buchser
[DESCRIPTION]
Protocol on how to run Library Aligner in FIVTools once sequencing data has been returned to us from the Sequencing Core. It also has an option for checking the Representation of a gRNA library. Lastly, a v... | ["Open FIVTools and click on the LA tab in the upper left section of the program.", "Enter in your returned NGS link into the HTCF Link tab and the destination to download the files into Dest.", "Press Download UZ to download the files and automatically unzip them. This will deposit reads into your destination folder ... |
105,179 | Exploring Glycoproteomic Profiles in Rectal Cancer: A Comparative N-Glycocapture Analysis of Tumor and Healthy Tissues Pre- and Post-Treatment | 0 | dx.doi.org/10.17504/protocols.io.3byl49drogo5/v1 | https://www.protocols.io/view/exploring-glycoproteomic-profiles-in-rectal-cancer-dix34fqn | ABDULLAH BIN ZUBAIR, David W. Larson, Fatima Hamid, Davide Ferrari, K. L. Mathis, Tommaso Violante, Faisal Jehan, RENEE HIRTE | TITLE: Exploring Glycoproteomic Profiles in Rectal Cancer: A Comparative N-Glycocapture Analysis of Tumor and Healthy Tissues Pre- and Post-Treatment
AUTHORS: ABDULLAH BIN ZUBAIR, David W. Larson, Fatima Hamid, Davide Ferrari, K. L. Mathis, Tommaso Violante, Faisal Jehan, RENEE HIRTE
[DESCRIPTION]
This protocol outlin... | ["[Background and Rationale] Rectal cancer, a major contributor to global cancer mortality, poses a significant challenge in patient management, especially when complete surgical resection isn’t achieved. Even with advancements in treatment, many patients face disease recurrence, underscoring the urgent need for reliab... |
96,521 | Temae Golf Course Surveys | 0 | dx.doi.org/10.17504/protocols.io.ewov1qe7kgr2/v1 | https://www.protocols.io/view/temae-golf-course-surveys-dahh2b36 | Kedhar Bartlett, Bridget Bentley | TITLE: Temae Golf Course Surveys
AUTHORS: Kedhar Bartlett, Bridget Bentley
[DESCRIPTION]
This study investigates the ecological impacts of land use change, particularly focusing on the vegetation near the Temae Golf Course on Moorea, French Polynesia. Through field surveys conducted by the 2024 Island Sustainability P... | ["[Field Methods] Split group into pairs", "[Field Methods] Assign each pair a \"cultivated\" (on/near golf course) site and a \"pristine\" (anywhere else in close proximity) site", "[Field Methods] Conduct 50 meter transects at each site", "[Field Methods] Note starting point and direction of movement in field noteboo... |
77,454 | Effective and efficient cytoskeleton (actin and microtubules) fluorescence staining of adherent eukaryotic cells | 1 | dx.doi.org/10.17504/protocols.io.kxygxeerzv8j/v2 | https://www.protocols.io/view/effective-and-efficient-cytoskeleton-actin-and-mic-cpvnvn5e | Alfredo Leonardo Porfirio-Sousa, Tristan Henderson, Matthew Brown | TITLE: Effective and efficient cytoskeleton (actin and microtubules) fluorescence staining of adherent eukaryotic cells
AUTHORS: Alfredo Leonardo Porfirio-Sousa, Tristan Henderson, Matthew Brown
[DESCRIPTION]
Eukaryotic microbes, protists, are highly diverse organisms with complex cytoskeletal elements used for moveme... | ["Ensure Paraformaldehyde (8%) is at -80 Room temperature.", "Move cells onto a chamber culture slide (Lab-Tek™ II Chamber Slide - Thermo Fisher Scientific - 154461) according to how the cells are being grown, see below.", "If cells are growing on agar plates, cut block where there is dense area of cells. Place upside ... |
40,772 | ELISA for quantification of IL-13 in human serum. | 6 | dx.doi.org/10.17504/protocols.io.bj3ckqiw | https://www.protocols.io/view/elisa-for-quantification-of-il-13-in-human-serum-bj3ckqiw | Angel Justiz-Vaillant | TITLE: ELISA for quantification of IL-13 in human serum.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Interleukins (IL) are a type of cytokine first thought to be expressed by leukocytes alone but have later been found to be produced by many other body cells. T... | ["An anti-human IL-13 coating antibody is adsorbed onto microwells by incubation overnight at 4°C.", "Add 50 µl of human serum. Human IL-13 present in the serum sample binds to antibodies adsorbed to the microwells.", "The microplate is blocked with 3% non-fat milk-PBS buffer and later wash to remove unbound proteins."... |
16,998 | RNA-seq Library Construction with the KAPA mRNA HyperPrep Kit | null | dx.doi.org/10.17504/protocols.io.uueewte | null | Amanda Scholes | TITLE: RNA-seq Library Construction with the KAPA mRNA HyperPrep Kit
AUTHORS: Amanda Scholes
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>A protocol for making multiplexed RNA-seq libraries using KAPA Biosystems mRNA HyperPrep Kit, optimized for </span><span style = "font-style:italic;">Sac... | ["[Prepping mRNA Capture Beads]\n1. Resuspend the mRNA Capture Beads (stored at 4°C) by gently pipetting (try to prevent foaming).2. For each library, transfer 26.25 µL of beads (25 µL x 1.05) to an RNase-free 1.7 mL microcentrifuge tube (up to 24 total reactions per one tube).3. Place the tube with beads on a Surebead... |
49,844 | p2 11/5 | 1 | dx.doi.org/10.17504/protocols.io.buwunxew | https://www.protocols.io/view/p2-11-5-buwunxew | Maria Guliakina | TITLE: p2 11/5
AUTHORS: Maria Guliakina
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">test</div></div>
[STEPS]
?. test
{"blocks":[{"key":"ccqb3","text":"","type":"unstyled","depth":0,"inlineStyleRanges":[],"entityRanges":[],"data":[]}],"entityMap":[]} | ["test\n{\"blocks\":[{\"key\":\"ccqb3\",\"text\":\"\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[]}],\"entityMap\":[]}"] |
null | null | null | dx.doi.org/10.17504/protocols.io.cztx6m | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Modified to try to get increased yields.
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
66,894 | 10 signes révélateurs dont vous avez besoin pour obtenir un nouveau Diaetoxil Höhle Der Löwen | 1 | dx.doi.org/10.17504/protocols.io.x54v9yxjpg3e/v1 | https://www.protocols.io/view/10-signes-r-v-lateurs-dont-vous-avez-besoin-pour-o-cdjns4me | jerryballorz | TITLE: 10 signes révélateurs dont vous avez besoin pour obtenir un nouveau Diaetoxil Höhle Der Löwen
AUTHORS: jerryballorz
[DESCRIPTION]
➢Nom du product — Diaetoxil Höhle Der Löwen
➢Principaux avantages - Traite efficacement le diabete
➢Komposition – Composé Organique Naturel
➢ Sekundäre Effekte – NA
➢ Klassifizieru... | ["[10 signes révélateurs dont vous avez besoin pour obtenir un nouveau Diaetoxil Höhle Der Löwen]"] |
51,655 | High Resolution "DIY" Photogrammetry - 'HRP' Protocol | 1 | dx.doi.org/10.17504/protocols.io.bwpfpdjn | https://www.protocols.io/view/high-resolution-34-diy-34-photogrammetry-39-hrp-39-bwpfpdjn | Yu Tang, Jacopo Niccolo Cerasoni, Emily Yuko Hallett | TITLE: High Resolution "DIY" Photogrammetry - 'HRP' Protocol
AUTHORS: Yu Tang, Jacopo Niccolo Cerasoni, Emily Yuko Hallett
[DESCRIPTION]
Photogrammetry is a method of calculating the three-dimensional shape of an object from a set of images. The advantages of Photogrammetry include the ability to reco... | ["[Setting Photographic Environment] Collect and prepare equipment.", "[Photography] Place the object on the turntable or holder, make sure it is centered on the turntable. The whole object should always be within the frame of the camera. \n\nPress the shutter by remote control and rotate the turntable. Repeat this ope... |
null | null | null | dx.doi.org/10.17504/protocols.io.ig7cbzn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Description of the automated tool, which was developed for quantifying the total and air-free volume of the maxillary sinus based on computed tomography images. The quantification tool seeks to standardize maxillary sinus volume measurements, thus allowing better comparisons ... | [] |
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