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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57,120 | NGS workflow with rRNA depletion for viral RNA sequencing from animal tissue specimens | 4 | dx.doi.org/10.17504/protocols.io.kqdg3p6pel25/v1 | https://www.protocols.io/view/ngs-workflow-with-rrna-depletion-for-viral-rna-seq-b3z8qp9w | Yiqiao Li, Magda Bletsa, Ine Boonen, Philippe Lemey | TITLE: NGS workflow with rRNA depletion for viral RNA sequencing from animal tissue specimens
AUTHORS: Yiqiao Li, Magda Bletsa, Ine Boonen, Philippe Lemey
[DESCRIPTION]
This NGS workflow describes how to prepare libraries from total RNA with a rRNA depletion step to increase the yield of non-host RNA transcripts... | ["[1. Pre quantity QC] The quantity of total RNA is evaluated using Qubit RNA BR assay kit (following manufacturer's protocol)", "[2. Pre quality QC] The quality of total RNA is evaluated using the Agilent RNA 6000 Nano kit in Bioanalyzer (following the manufacturer's protocol)\n(based on previous Qubit results and the... |
50,626 | Single Cell Isolation from Human Ovarian Tissue | 4 | null | https://www.protocols.io/view/single-cell-isolation-from-human-ovarian-tissue-bvpan5ie | Andrea Jones, Ariella Shikanov | TITLE: Single Cell Isolation from Human Ovarian Tissue
AUTHORS: Andrea Jones, Ariella Shikanov
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines steps to obtain a single cell suspension from fresh human ovarian tissue. Here, we do not outline steps for removing the ovarian cort... | ["[Tissue Cutting and Digest]\nStarting with 1 mm thick pieces of ovarian cortex or medulla, cut all tissue into ~1mm3 pieces either a) mechanically using a #10 blade in a glass petri dish or b) using a tissue chopper.", "[Tissue Cutting and Digest]\nAfter cutting, move tissue to a cell strainer (any pore size) and rin... |
null | null | null | dx.doi.org/10.17504/protocols.io.mgsc3we | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>RNA sequencing measures the quantitative change in gene expression over the whole transcriptome, but it lacks spatial context. On the other hand, in situ hybridization provides the location of gene expression, but only for a small number of genes. Here we detail a protocol fo... | [] |
28,229 | Measurement of Left Ventricular Hemodynamic Parameters in Intact Mice | null | dx.doi.org/10.17504/protocols.io.7tdhni6 | null | E. Dale Abel | TITLE: Measurement of Left Ventricular Hemodynamic Parameters in Intact Mice
AUTHORS: E. Dale Abel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">This protocol describes the procedure used by the DiaComp for measuring... | ["Measurement of in vivo cardiac contractile performance using a micro-manometer tipped catheter:\nIndices of left ventricular contractile performance are determined in mice under isoflurane anesthesia by percutaneously introducing a 1.4 Fr. Millar catheter into the carotid artery and gently advancing this into the lef... |
30,210 | Salmonella blood culture surveillance: SOP's ITM | null | dx.doi.org/10.17504/protocols.io.9rah52e | null | Bieke Tack | TITLE: Salmonella blood culture surveillance: SOP's ITM
AUTHORS: Bieke Tack
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Standard operating procedures for Salmonella blood culture surveillance of the unit of tropical bacteriology at the Institute of Tropical Medicine in Antwerp (Belgium):</di... | [] |
67,170 | Protocol for vagus nerve stimulation in anesthetized pigs (subject-1) | 1 | dx.doi.org/10.17504/protocols.io.x54v9yxz4g3e/v1 | https://www.protocols.io/view/protocol-for-vagus-nerve-stimulation-in-anesthetiz-cduas6se | Oliver Armitage | TITLE: Protocol for vagus nerve stimulation in anesthetized pigs (subject-1)
AUTHORS: Oliver Armitage
[DESCRIPTION]
The Vagus nerve innervates a number of thoracic and visceral organs. Exogenous nervous signal, for example, Vagus nerve stimulation (VNS) provides a route to modulating their function for therapeutic pur... | ["[Surgery] We do the nerve preparation and device implantation.", "[Data Acquisition Validation] We validate the quality of the physiological and neural signals.", "[Equipment Setup] We do the setup of the BIOS A1 System (electrophysiology).", "We install vital signs monitoring. [respiratory pressure, ECG, blood press... |
50,062 | Two forms of yawning modulation in three months old infants during the Face to Face Still Face paradigm | 1 | dx.doi.org/10.17504/protocols.io.bu5nny5e | https://www.protocols.io/view/two-forms-of-yawning-modulation-in-three-months-ol-bu5nny5e | Damiano Menin | TITLE: Two forms of yawning modulation in three months old infants during the Face to Face Still Face paradigm
AUTHORS: Damiano Menin
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The last decades have seen an increasing interest in the phenomenon of yawning and the dynamics of its modulation, yet... | ["Recruitment of participantsThe sample should include healthy infants younger than 12 months of age and a parent. In the original study only mothers were included but other studies might include both fathers and mothers. Infants should be balanced for sex.", "Data collectionParent-infant dyads participate in the FFSF ... |
32,791 | Calling Peaks on piggyBac Calling Card Data | null | dx.doi.org/10.17504/protocols.io.bb9xir7n | null | Arnav Moudgil, Rob Mitra | TITLE: Calling Peaks on piggyBac Calling Card Data
AUTHORS: Arnav Moudgil, Rob Mitra
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describes how to all peaks on mammalian calling card data using either undirected, or transcription factor fusions, to the </span><span style = "fo... | ["[Preprocessing]\nBefore calling peaks on calling card data, it is useful to create a file listing the location of every TTAA tetramer in the genome. The piggyBac transposase inserts almost exclusively into this motif. Morever, we use the presence of a TTAA adjacent to a mapped read as an internal quality check when c... |
79,729 | ONT Post-PCR Pooling & Purification for Fungal Barcoding | 4 | dx.doi.org/10.17504/protocols.io.kxygxz1yzv8j/v4 | https://www.protocols.io/view/ont-post-pcr-pooling-amp-purification-for-fungal-b-cr4rv8v6 | Stephen Douglas Russell | TITLE: ONT Post-PCR Pooling & Purification for Fungal Barcoding
AUTHORS: Stephen Douglas Russell
[DESCRIPTION]
Overview: The goals of this protocol are to pool your PCR product into a single 1.5 mL tube and to purify that product using magnetic beads.
Time required: ~45 minutes (mostly waiting)
[STEPS]
SECTION: ... | ["[Preparation] Bring magnetic beads to room temp. (Should be stored in the fridge)", "[Preparation] Heat a 1.5uL tube of molecular water to 55 °C in the heat block. ~1000uL should be sufficient in the tube. This step is optional but is helpful if a heat block is available.", "[Preparation] Create a fresh batch of 80% ... |
74,234 | CZI Pediatric Nasopharyngeal Swab Processing for 10X scRNA-seq (Illustrated Protocol) | 4 | dx.doi.org/10.17504/protocols.io.6qpvr49jogmk/v1 | https://www.protocols.io/view/czi-pediatric-nasopharyngeal-swab-processing-for-1-ckq2uvye | Jaclyn M Long, Erica M Langan, Ying Tang, Carly G.K. Ziegler, Vincent N. Miao, Andrew W. Navia, Joshua D. Bromley, Kenneth J. Wilson, Yilianys Pride, Mohammad Hasan, Taylor Christian, Hannah Laird, Anna Owings, Meredith Sloan, Haley B. Williams, Tanya O. Robinson, George E. Abraham III, Michal Senitko, Sarah C. Glover,... | TITLE: CZI Pediatric Nasopharyngeal Swab Processing for 10X scRNA-seq (Illustrated Protocol)
AUTHORS: Jaclyn M Long, Erica M Langan, Ying Tang, Carly G.K. Ziegler, Vincent N. Miao, Andrew W. Navia, Joshua D. Bromley, Kenneth J. Wilson, Yilianys Pride, Mohammad Hasan, Taylor Christian, Hannah Laird, Anna Owings, Meredit... | ["[Tube A (the cryovial)] Rapidly (within 1-2 minutes) thaw cryovial (Tube A) in thermal block set to 37 °C.", "[Tube A (the cryovial)] Remove swab from Tube A using clean forceps.", "[Tube A (the cryovial)] Dip swab in Tube B (15 mL conical) once. Swirl briefly (approximately 3 seconds) to rinse swab.", "[Tube A (the ... |
92,515 | Mouse tissue collection | 4 | null | https://www.protocols.io/view/mouse-tissue-collection-c6kbzcsn | Tae-Un Han | TITLE: Mouse tissue collection
AUTHORS: Tae-Un Han
[DESCRIPTION]
This protocol is about collecting mouse tissues for immunohistochemistry or biochemistry experiment. While it is mainly used for brain tissues, it also can be used for other visceral tissues.
[STEPS]
SECTION: Perfusion
1. Mice are anesthetized with Ave... | ["[Perfusion] Mice are anesthetized with Avertin (1mL/25g body weight).", "[Perfusion] Tissues are collected and post-fixed in 4 % volume PFA at 4°C for about 1440 min", "[Perfusion] Immobilize a mouse and cut through the skin and muscles in the lower abdomen exposing the liver using a sharp scissors.", "[Frozen tissue... |
null | null | null | dx.doi.org/10.17504/protocols.io.kujcwun | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
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30,841 | Cell Fixation and Permeabilization Protocol using 70% Ethanol | null | dx.doi.org/10.17504/protocols.io.bacziax6 | null | Sam Li | TITLE: Cell Fixation and Permeabilization Protocol using 70% Ethanol
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. Prepare 70% Ethanol and chill to -20°C.Tip: Do not freeze ethanol for long-term storage.
?. Prepare target cells of interest and wash 2X with PBS, centrifuging at 350xg for 5... | ["Prepare 70% Ethanol and chill to -20°C.Tip: Do not freeze ethanol for long-term storage.", "Prepare target cells of interest and wash 2X with PBS, centrifuging at 350xg for 5 minutes", "Discard supernatant and loosen the cell pellet by vortexing.", "Add 3ml cold 70% ethanol drop by drop to the cell pellet while vorte... |
null | null | null | dx.doi.org/10.17504/protocols.io.rnnd5de | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocol for human small intestine cell dissociation, performed on ice to reduce artifact gene expression. </p>
[BEFORE_START]
<div title="Page 1">
<p><strong>Checklist prior to beginning:</strong><br />-Centrifuges, large and small, set to 4 ºC</p>
<p>-Make enzyme stock; th... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.rdtd26n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><a href="https://www.creative-biolabs.com/car-t/cellrapeutics-chimeric-antigen-receptor-car-technology.htm" target="_blank" rel="noopener noreferrer">CAR-T therapy</a> plays a key role in cancer immunotherapy and belongs to adoptive T cell transfer (ACT). At the beginning of ... | [] |
107,559 | Preparation of B cells for scRNAseq | 0 | dx.doi.org/10.17504/protocols.io.n92ld8e1nv5b/v1 | https://www.protocols.io/view/preparation-of-b-cells-for-scrnaseq-dmaf42bn | Nicholas Pease | TITLE: Preparation of B cells for scRNAseq
AUTHORS: Nicholas Pease
[DESCRIPTION]
This protocol details activated B cell preparation and sample hashtagging for Chromium Single Cell Gene Expression (10x Genomics).
[STEPS]
SECTION: Dead cell removal
1. Pellet cells at 300xg for 10min
SECTION: Dead cell removal
2. Resus... | ["[Dead cell removal] Pellet cells at 300xg for 10min", "[Dead cell removal] Resuspend in 100uL Dead Cell Removal Buffer and filter through 40uM cell strainer", "[Dead cell removal] Add 5uL of Annexin V Cocktail to sample", "[Dead cell removal] Add 5uL of Biotin Selection Cocktail to sample, mix and incubate at RT for ... |
51,033 | Golden Gate Assembly_Perkinsus | 4 | dx.doi.org/10.17504/protocols.io.bv3zn8p6 | https://www.protocols.io/view/golden-gate-assembly-perkinsus-bv3zn8p6 | Ross F. Waller, Elin Einarsson, Imen Lassadi | TITLE: Golden Gate Assembly_Perkinsus
AUTHORS: Ross F. Waller, Elin Einarsson, Imen Lassadi
[DESCRIPTION]
The phylum Perkinsozoa is an aquatic parasite lineage that has devastating effects on commercial and natural mollusc populations, and also comprises parasites of algae, fish and amphibians. They are related t... | ["Incubate your reaction in a thermocycler for 3 cycles of 10 min 40 °C , 10 min16 °C, followed by a single cycle of 10 min 50 °C , 20 min80 °C, 4 °C forever.", "Use 5 µLof this one-pot digestion-ligation reaction product to transform E.coli cells.", "Positive clones can be selected using LB agar with an antibiotic ... |
null | null | null | dx.doi.org/10.17504/protocols.io.dxr7m5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
The diversity of ribonucleic acid (RNA) viruses in the ocean and the ongoing isolation and characterization of RNA viruses that infect important primary producers suggests that RNA viruses are active members of the marine microbial assemblage. At this point, little is known abou... | [] |
69,594 | Immunohistochemistry of rTg4510 mouse brain | 4 | dx.doi.org/10.17504/protocols.io.x54v9den4g3e/v1 | https://www.protocols.io/view/immunohistochemistry-of-rtg4510-mouse-brain-cf72trqe | Miguel Da Silva Padilha, Irina Dudanova, Itika Saha, F. Ulrich Hartl, Mark S. Hipp | TITLE: Immunohistochemistry of rTg4510 mouse brain
AUTHORS: Miguel Da Silva Padilha, Irina Dudanova, Itika Saha, F. Ulrich Hartl, Mark S. Hipp
[DESCRIPTION]
This protocol describes immunohistochemical staining of the Tau transgenic mice rTg4510 (Santacruz et al, 2005) brain section for Tau aggregates phosphorylated at... | ["Deeply anesthetize mice with 1.6% Ketamine/0.08% Xylazine and transcardially perfuse with PBS followed by 4% paraformaldehyde (PFA)(Santa Cruz) in PBS.", "Dissect brains out of the skull and post-fix in 4% PFA in PBS overnight.", "Embed fixed tissue in agarose and section into 40 μm thick sections using a vibratome (... |
55,660 | Overview of NCBI's SARS-CoV-2 submission process and the metadata required | 1 | dx.doi.org/10.17504/protocols.io.b2kkqcuw | https://www.protocols.io/view/overview-of-ncbi-39-s-sars-cov-2-submission-proces-b2kkqcuw | Ruth Timme, Emma Griffiths, Lee Katz, Michael Weigand | TITLE: Overview of NCBI's SARS-CoV-2 submission process and the metadata required
AUTHORS: Ruth Timme, Emma Griffiths, Lee Katz, Michael Weigand
[DESCRIPTION]
PURPOSE:
This protocol explains the metadata requirements for the following two protocols:
1. SARS-CoV-2 NCBI submission protocol: SRA, BioSample, and... | ["[Three templates needed for NCBI SARS-CoV-2 submission] START HERE FIRST: Read the PHA4GE contextual data specification BEFORE populating your submission templates!\n\nDirect link to the PHA4GE GitHub repository: https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification/tree/version_3_dev", "[Three template... |
72,200 | S2: Step-by-step-guide using MeshLab in the work flow. | 5 | dx.doi.org/10.17504/protocols.io.j8nlkk59dl5r/v2 | https://www.protocols.io/view/s2-step-by-step-guide-using-meshlab-in-the-work-fl-cirgud3w | Paul Kalke, Conrad Helm | TITLE: S2: Step-by-step-guide using MeshLab in the work flow.
AUTHORS: Paul Kalke, Conrad Helm
[DESCRIPTION]
How to do data refinements like repair, smooth and simplification in MeshLab and export as -ply-file.
[STEPS]
1.
•Open MeshLab
•First step is Cleaning and Repairing your mesh-irrelevant if it is generated b... | ["•Open MeshLab\n•First step is Cleaning and Repairing your mesh-irrelevant if it is generated by Image J, Amira or any other software, the steps are the same\n•Often used procedures/steps:\n-Remove Duplicate Faces\n-Remove Dublicate Vertices\n-Merge Close Vertices\n-Repair non Manifold edges by…\n•Just try out, the re... |
19,873 | U Mass - Adiponectin | null | dx.doi.org/10.17504/protocols.io.xm9fk96 | null | Jason Kim | TITLE: U Mass - Adiponectin
AUTHORS: Jason Kim
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">The adiponectin enzyme-linked immunosorbent assay (ELISA) is a standard immunoassay for the detection of total adiponectin... | ["Remove the required number of strips from the Microtiter Assay Plate. Unused strips should be resealed in the foil pouch and stored at 2-8°C.", "Assemble the strips in an empty plate holder and wash each well 3x with 300 l of diluted Wash Buffer per wash.", "Decant Wash Buffer and remove the residual amount from al... |
63,251 | Quantification of fibrosis extend and airspace availability in lung: a semi-automatic ImageJ/Fiji toolbox (step-by-step protocol) | 5 | dx.doi.org/10.17504/protocols.io.14egn7nqmv5d/v1 | https://www.protocols.io/view/quantification-of-fibrosis-extend-and-airspace-ava-b9ztr76n | Bertrand-David Ségard | TITLE: Quantification of fibrosis extend and airspace availability in lung: a semi-automatic ImageJ/Fiji toolbox (step-by-step protocol)
AUTHORS: Bertrand-David Ségard
[DESCRIPTION]
The evaluation of the structural integrity of mechanically dynamic organs such as lungs is critical for the diagnosis of numerous patholo... | ["[Sample detection] Sample detection\n\nNote: the scale of images must be defined prior to the analysis.", "[Background cleaning] Background cleaning", "[Sample detection] Open the image to be analyzed (File > Open…).", "[Sample detection] Launch the script (Plugins > Fibrosis > Sample detection).", "[Sample detection... |
null | null | null | dx.doi.org/10.17504/protocols.io.rrgd53w | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
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?. | [] |
61,899 | Bagaimana Caranya Menang Slot Pulsa Dengan Mudah Di Megalsoto | 3 | dx.doi.org/10.17504/protocols.io.14egn7mmzv5d/v1 | https://www.protocols.io/view/bagaimana-caranya-menang-slot-pulsa-dengan-mudah-d-b8pjrvkn | umar marsuky | TITLE: Bagaimana Caranya Menang Slot Pulsa Dengan Mudah Di Megalsoto
AUTHORS: umar marsuky
[DESCRIPTION]
a
[STEPS] | [] |
92,986 | Rat organotypic cultures for AAV-mediated vital labeling of the extracellular matrix | 4 | dx.doi.org/10.17504/protocols.io.e6nvwdnzzlmk/v1 | https://www.protocols.io/view/rat-organotypic-cultures-for-aav-mediated-vital-la-c622zgge | Federico N. Soria, Mario Fernandez-Ballester | TITLE: Rat organotypic cultures for AAV-mediated vital labeling of the extracellular matrix
AUTHORS: Federico N. Soria, Mario Fernandez-Ballester
[DESCRIPTION]
In this protocol we describe the preparation and maintenance of rat organotypic cultures (cortico-striatal) for AAV-infection and imaging of the extracellular ... | ["[Culture preparation] Prepare a 6-well culture plate with Millipore 0.4 µm culture inserts placed on 1 mL of organotypic medium per well, and incubate it at 37 °C and 5% CO2 to warm up.", "[Culture preparation] Prepare a p100 and p60 petri dishes with 25 mL and 5 mL, respectively, of and keep them on ice .", "[Cult... |
36,718 | Bioinformatics in Sudan-Publications | 1 | dx.doi.org/10.17504/protocols.io.bf4njqve | https://www.protocols.io/view/bioinformatics-in-sudan-publications-bf4njqve | Sabah Ibrahim, Sofia Ali, Sumaya Kambal | TITLE: Bioinformatics in Sudan-Publications
AUTHORS: Sabah Ibrahim, Sofia Ali, Sumaya Kambal
[DESCRIPTION]
This protocol shows in details how to extract Bioinformatics-related Publications from Sudan. It consists of six sections: PubMed Database Advance Search Bulider, Science Direct Database Advance Search Builder... | ["[PubMed Database Advance Search Bulider] Start buliding your search by adding Sudan (the country under subject) to the query box under the \"Affilation field\", then use the Boolean Operators (Add with AND).", "[PubMed Database Advance Search Bulider] Open PubMed Advance search bulider (https://pubmed.ncbi.nlm.nih.go... |
57,000 | Protocols from: Evolutionary analyses of visual opsin genes in frogs and toads: diversity, duplication, and positive selection | 4 | dx.doi.org/10.17504/protocols.io.b3wgqpbw | https://www.protocols.io/view/protocols-from-evolutionary-analyses-of-visual-op-b3wgqpbw | Ryan K Schott, Leah Perez, Matthew A Kwiatkowski, Vance Imhoff, Jennifer Gumm | TITLE: Protocols from: Evolutionary analyses of visual opsin genes in frogs and toads: diversity, duplication, and positive selection
AUTHORS: Ryan K Schott, Leah Perez, Matthew A Kwiatkowski, Vance Imhoff, Jennifer Gumm
[DESCRIPTION]
Protocols used to extra mRNA from frog retina, create cDNA libraries, and prepare ... | ["[mRNA Extraction] Transfer sample into a 1.5ml collection tube", "[mRNA Extraction] Pipette off RNALATER", "[mRNA Extraction] Add 600 µL Buffer RLT", "[mRNA Extraction] Add 6 µL Beta-mercaptoethanol", "[mRNA Extraction] Disrupt tissue with sterile pestle", "[mRNA Extraction] Pipette into Qiashredder column- Spin 2 mi... |
43,868 | Dose dependent test | 4 | null | https://www.protocols.io/view/dose-dependent-test-bn34mgqw | Hung Liang Pai, Cheng-Ruei Yang | TITLE: Dose dependent test
AUTHORS: Hung Liang Pai, Cheng-Ruei Yang
[STEPS]
?. [Preparation]
Sterilize the bench, and put on a labmat
?. [Preparation]
Thaw the reagents including 1. DNase/ RNase free water (store in -20°C) 2. solution A (store in -80°C) 3. solution B (store in -80°C) 4. RNase inhibitor (store in -20°C... | ["[Preparation]\nSterilize the bench, and put on a labmat", "[Preparation]\nThaw the reagents including 1. DNase/ RNase free water (store in -20°C) 2. solution A (store in -80°C) 3. solution B (store in -80°C) 4. RNase inhibitor (store in -20°C) 5.toehold switches with invertase DNA (store in 4°C) 6.miRNA as the trigge... |
105,839 | AAV Production and Purification | 0 | dx.doi.org/10.17504/protocols.io.rm7vzj5d2lx1/v2 | https://www.protocols.io/view/aav-production-and-purification-djkp4kvn | Justin T Savage | TITLE: AAV Production and Purification
AUTHORS: Justin T Savage
[DESCRIPTION]
This protocol is for the production and purification of Adeno-Associated Virus. The protocol contains the necessary steps to produce AAVs from HEK293T cell cultures.
[STEPS]
SECTION: Growing HEK 293T Cells: Day 1 -Morning
1. Make Media for... | ["[Growing HEK 293T Cells: Day 1 -Morning] Make Media for HEK293T Cells", "[Growing HEK 293T Cells: Day 1 -Morning] Thaw HEK293T Cells in 10cm Dish with 10 ml HEK Medium (One Vial into three 10cm Dish)", "[Day 3 -Morning] Split HEK293T Cells (Usually become confluent on Day 3) with 3ml Trypsin.", "[Day 3 -Morning] Use ... |
106,447 | Tri-plex staining for PAX5, CD4, and CSF1R detection in formalin-fixed, paraffin-embedded (FFPE) pig tissues | 0 | dx.doi.org/10.17504/protocols.io.eq2lyw4rwvx9/v1 | https://www.protocols.io/view/tri-plex-staining-for-pax5-cd4-and-csf1r-detection-dj7p4rmn | Jayne E Wiarda, Alyssa Ivy, Hannah Mazon, Colin Stoy, sage.becker, Crystal Loving | TITLE: Tri-plex staining for PAX5, CD4, and CSF1R detection in formalin-fixed, paraffin-embedded (FFPE) pig tissues
AUTHORS: Jayne E Wiarda, Alyssa Ivy, Hannah Mazon, Colin Stoy, sage.becker, Crystal Loving
[DESCRIPTION]
A protocol for staining of protein (PAX5) and RNA (CD4, CSF1R) in pig tissues.
[BEFORE_START]
• P... | ["[Baking] Bake slides 30 min 60 °C.", "[Baking] While slides bake:", "[Baking] Immediately before deparaffinizing:", "[Deparaffinizing] Submerge slides in fresh xylenes 5 min Room temperature.", "[Deparaffinizing] While slides deparaffinize:", "[Tissue Quenching] Unload slides from vertical slide rack and place on fla... |
46,157 | Synthesis of in vitro transcribed RNA from whole bacterial transcriptome | 4 | null | https://www.protocols.io/view/synthesis-of-in-vitro-transcribed-rna-from-whole-b-brbmm2k6 | Bhargava Reddy Morampalli, Olin Silander, Bhargava Reddy Morampalli, Olin Silander | TITLE: Synthesis of in vitro transcribed RNA from whole bacterial transcriptome
AUTHORS: Bhargava Reddy Morampalli, Olin Silander, Bhargava Reddy Morampalli, Olin Silander
[DESCRIPTION]
Identifying RNA modifications across the transcriptome has been made possible by direct RNA sequencing using nanopore sequencin... | ["[Addition of poly(A) tail to E. coli RNA] A reaction is setup in a PCR tube using the following components", "[Addition of poly(A) tail to E. coli RNA] Incubate the reaction mixture for 15 min at 37 °C in a thermocycler followed by 20 min at 65 °C for inactivation.", "[Addition of poly(A) tail to E. coli RNA] Trans... |
89,914 | Assessing autophagy using the HaloTag-LC3B cleavage assay | 4 | dx.doi.org/10.17504/protocols.io.e6nvwdo9zlmk/v1 | https://www.protocols.io/view/assessing-autophagy-using-the-halotag-lc3b-cleavag-c322yqge | Marvin Skulsuppaisarn | TITLE: Assessing autophagy using the HaloTag-LC3B cleavage assay
AUTHORS: Marvin Skulsuppaisarn
[DESCRIPTION]
Assay to detect HaloTag-LC3B during starvation autophagy based on https://doi.org/10.7554/eLife.78923.
[STEPS]
SECTION: Assessing starvation autophagy using the HaloTag-LC3B cleavage assay
1. Generate HeLa c... | ["[Assessing starvation autophagy using the HaloTag-LC3B cleavage assay] Generate HeLa cells expressing HaloTag-LC3B using pMRX-IP-HaloTag7-LC3 from Mizushima lab (Addgene #184899; DOI: 10.7554/eLife.78923).", "[Assessing starvation autophagy using the HaloTag-LC3B cleavage assay] Seed 400-450K cells in a six-well plat... |
76,905 | Indiana University adapted Akoya Phenocycler-Fusion Tissue Staining and Imaging Protocol for Fresh Frozen Kidney Samples | 1 | dx.doi.org/10.17504/protocols.io.8epv5jdbnl1b/v1 | https://www.protocols.io/view/indiana-university-adapted-akoya-phenocycler-fusio-cpchvit6 | Angela R. Sabo, Connor J Gulbronson, Daria Barwinska, Michael J. Ferkowicz, William Bowen, Seth Winfree, Tarek Ashkar | TITLE: Indiana University adapted Akoya Phenocycler-Fusion Tissue Staining and Imaging Protocol for Fresh Frozen Kidney Samples
AUTHORS: Angela R. Sabo, Connor J Gulbronson, Daria Barwinska, Michael J. Ferkowicz, William Bowen, Seth Winfree, Tarek Ashkar
[DESCRIPTION]
This protocol presents the Indiana University adap... | ["[Setup - Day 1] Prepare humidity chamber - we use an empty 1000uL tip box and place water and a wet paper towel under the tray.", "[Setup - Day 1] Prepare Drierite absorbent beads - locate a second empty box with a lid and add an even layer of beads", "[Setup - Day 1] Locate and/or label 5 plastic coplin jars for the... |
74,225 | Light-Seq Cell Barcoding | 4 | dx.doi.org/10.17504/protocols.io.eq2ly77jplx9/v3 | https://www.protocols.io/view/light-seq-cell-barcoding-ckqruvv6 | Jocelyn Y. Kishi, Ninning Liu, Emma R. West, Kuanwei Sheng, Jack J. Jordanides, Matthew Serrata, Constance L. Cepko, Sinem K. Saka, Peng Yin | TITLE: Light-Seq Cell Barcoding
AUTHORS: Jocelyn Y. Kishi, Ninning Liu, Emma R. West, Kuanwei Sheng, Jack J. Jordanides, Matthew Serrata, Constance L. Cepko, Sinem K. Saka, Peng Yin
[DESCRIPTION]
We present Light-Seq, an approach for multiplexed spatial indexing of intact biological samples using light-directed DNA ba... | ["[Protocol Overview] This protocol is for selective barcoding of cells seeded onto an Ibidi 18-well µ-slide for our Light-Seq paper. https://www.nature.com/articles/s41592-022-01604-1\n\nA separate protocol can be found for selective barcoding of tissue samples. \nhttps://www.protocols.io/view/light-seq-x54v9jno4g3e/v... |
79,497 | DENV 2 Infection | 4 | dx.doi.org/10.17504/protocols.io.j8nlkwpbdl5r/v1 | https://www.protocols.io/view/denv-2-infection-crvhv636 | Edwin Stiven Quiguanás, Delia Piedad Recalde-Reyes | TITLE: DENV 2 Infection
AUTHORS: Edwin Stiven Quiguanás, Delia Piedad Recalde-Reyes
[DESCRIPTION]
En este protocolo se describen las condiciones para el mantenimiento de las líneas celulares C6/36 HT y BHK-21, además del procedimiento de infección y plaqueo del DENV 2
[STEPS]
SECTION: Amplificación del virus
1. La i... | ["[Amplificación del virus] La infección y amplificación del DENV 2 se realiza en células C6/36 (Aedes albopictus clone C6/36 CRL-1660™ ATCC) (línea celular originaria del mosquito Aedes albopictus y utilizadas para la replicación de Flavivirus). Esta línea celular es un clon obtenido de las líneas del mosquito Aedes a... |
28,774 | Fabrication of Microneedle Patches | null | dx.doi.org/10.17504/protocols.io.8cehste | null | Stephania Konstantinidi, Hana Samet | TITLE: Fabrication of Microneedle Patches
AUTHORS: Stephania Konstantinidi, Hana Samet
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The goal is to create a microneedle. patch, which, by applying it on a leaf, will extract amplification-ready DNA.</div><div class = "text-block">All MN patches used... | ["[Mold preparation]\nClean the polydimethylsiloxane molds.", "[Mold preparation]\nHeat deionised water to 100 degrees Celsius using a becher.\n100 °C", "[Mold preparation]\nPut the mold(s) into the water and stir softly.", "[Mold preparation]\nRemove the molds and let them dry in a chemical hood for 1-2 hours.", "[M... |
36,764 | Linguistic signaling, emojis, and skin tone in trust games | null | dx.doi.org/10.17504/protocols.io.bf54jq8w | https://www.protocols.io/view/linguistic-signaling-emojis-and-skin-tone-in-trust-bf54jq8w | J Jobu Babin | TITLE: Linguistic signaling, emojis, and skin tone in trust games
AUTHORS: J Jobu Babin
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This paper reports the results of an experiment involving text-messaging and emojis in laboratory trust games executed on mobile devices. Decomposing chat logs, I f... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.hjxb4pn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocol established by Anna F. Zetler and published by Luisa F. Jiménez-Soto</p>
<p>This protocol is the final adaptation of protocols used in the laboratory of Prof. Rainer haas. The following people contributed with their ideas and experience: Benjamin Busch, Bettina Vogl-... | [] |
34,047 | Heat Inactivate FBS | null | dx.doi.org/10.17504/protocols.io.bdg7i3zn | null | Cody Roberts | TITLE: Heat Inactivate FBS
AUTHORS: Cody Roberts
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Heat inactivate FBS to denature compliment. Critical for trypanosomes but not for EA.hy 926 cells. </div></div>
[STEPS]
?. Allow serum to acclimate at room temperature for a minimum of 10 minutes or ref... | ["Allow serum to acclimate at room temperature for a minimum of 10 minutes or refrigerate overnight at 2° C to 8° C.", "The serum may then be completely thawed at room temperature. Or, you may choose to proceed by thawing the serum in a water bath at 37° C. Thawing serum at temperatures above 37° C or for an extended... |
91,252 | Passive avoidance (step-down test) | 4 | dx.doi.org/10.17504/protocols.io.5jyl8pkb9g2w/v1 | https://www.protocols.io/view/passive-avoidance-step-down-test-c5cuy2ww | Marina Lorente Picón, Núria Peñuelas, Ariadna Laguna, Miquel Vila | TITLE: Passive avoidance (step-down test)
AUTHORS: Marina Lorente Picón, Núria Peñuelas, Ariadna Laguna, Miquel Vila
[DESCRIPTION]
Passive avoidance (step-down test) for mice
[STEPS]
1. Prepare the platform: Passive Avoidance - Step Down for Mice (vibrating platform) (#40570, Ugo Basile) consisting of a platform loca... | ["Prepare the platform: Passive Avoidance - Step Down for Mice (vibrating platform) (#40570, Ugo Basile) consisting of a platform located in a controllable electrified net.", "Train the animals 24h before the test. Put the animal in the plexiglass platform located in the middle of the electrified net with 0.3 mA. If th... |
null | null | null | dx.doi.org/10.17504/protocols.io.mj5c4q6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Drop-seq is a technology we developed to enable biologists to analyze RNA expression genome-wide in thousands of individual cells at once. We first described this in <a href="http://www.sciencedirect.com/science/article/pii/S0092867415005498" target="_blank">a 2015 paper in ... | [] |
55,504 | 2,4-dinitrophenylhydrazine alpha-ketoglutarate detection assay for Prolyl Hydroxylase Domain (PHD) proteins | 4 | null | https://www.protocols.io/view/2-4-dinitrophenylhydrazine-alpha-ketoglutarate-det-b2fqqbmw | sjwong | TITLE: 2,4-dinitrophenylhydrazine alpha-ketoglutarate detection assay for Prolyl Hydroxylase Domain (PHD) proteins
AUTHORS: sjwong
[DESCRIPTION]
The 2,4-dinitrophenylhydrazine (2,4-DNPH) alpha-ketoglutarate detection assay was developed to support the study of prolyl hydroxylase domain (PHD) proteins in a substrate-... | ["[Overview of assay schematic]", "[In vitro hydroxylation assay] Prepare 5 Eppendorf tubes containing 50 µl of 10% TCA.\nLabel tubes: 0 min, 1 min, 2 min, 5 min, 15 min.", "[In vitro hydroxylation assay] Prepare cofactor solution containing HEPES/MES, catalase, DTT, ascorbic acid, FeSO4, a-ketoglutarate, and peptide i... |
21,557 | UC Davis - Femoral Vein Cannulation | null | dx.doi.org/10.17504/protocols.io.zavf2e6 | null | Jennifer Rutkowsky | TITLE: UC Davis - Femoral Vein Cannulation
AUTHORS: Jennifer Rutkowsky
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary</span></div><div class = "text-block">In multiple studies, access to the circulatory system in laboratory studies is necessary and femoral ... | ["Surgical Preparation 1. Administer a cocktail of Ketamine/Xylazine anesthesia i.p. at 90/10 mg/kg (initial dose) so animal is under deep anesthetic plane. Ketamine/Xylzine will be administered throughout the duration of the procedure at 22.5/2.5 mg/kg for subsequent doses every 30-45min after 1 hour from the initial ... |
63,478 | Isolation of ECs from Lymph node tissue for scRNAseq | 4 | null | https://www.protocols.io/view/isolation-of-ecs-from-lymph-node-tissue-for-scrnas-b98wr9xe | Guido Krähenbühl | TITLE: Isolation of ECs from Lymph node tissue for scRNAseq
AUTHORS: Guido Krähenbühl
[DESCRIPTION]
Protocols describing the isolation of murine lymph node endothelial cells
Isolation of lymphatic endothelial cells for spectral flow cytometry and scRNA-seq
Basic analysis of spectral flow cytometry data of endothelial... | ["[Preparation] Day before experiment check Antibodies to be used and prepare the following Reagents:", "[Tissue collection] Sacrifice mice using Isofluorine \n(do not use cervical dislocation as this might affect perfusion of the brain)", "[Tissue collection] Dissect inguinal, axillary, brachial and cervical lymphnode... |
null | null | null | dx.doi.org/10.17504/protocols.io.ek6bcze | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<strong>Zobell plates, 100% nutrient (1 L)</strong><br />26 g sea salts<br />1 g yeast extract<br />5 g proteose peptone no. 2<br />fill to 1 L qH<sub>2</sub>O<br />12 g agar<br /><br />Autoclave 1 L PZM for 50 min. Pour 10 ml/plate.<br /><br />Grow Pseudoalteromonas in 50% nutr... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.fyibpue | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol provides a procedure for mapping reads to co-assembled contigs using Bowtie2. </p>
[BEFORE_START]
<p>If you haven't already, you should consolidate your fasta files into their own directory (seperate from the fastq files). From /rsgrps/bh_class/username : </p>
... | [] |
9,285 | Electrophoretic Mobility Shift Assays using Infrared-Fluorescent DNA Probes | null | dx.doi.org/10.17504/protocols.io.mbdc2i6 | null | Michael Van Dyke, James Cox | TITLE: Electrophoretic Mobility Shift Assays using Infrared-Fluorescent DNA Probes
AUTHORS: Michael Van Dyke, James Cox
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protein-DNA binding interactions are critical in several biological processes, especially the regulation of gene expression at the l... | ["[PCR synthesis of IR fluorophore-labeled DNA]\nThe DNA probes used in our laboratory to study thermophile protein-DNA interactions are derived from the selection template DNA ST2R24, which was used in the identification of their preferred DNA-binding sites by the combinatorial approach REPSA. Sequence details may be ... |
38,283 | Protocol for DNA extraction from clay-rich subsoils | 4 | dx.doi.org/10.17504/protocols.io.bhmjj44n | https://www.protocols.io/view/protocol-for-dna-extraction-from-clay-rich-subsoil-bhmjj44n | Lukas Beule | TITLE: Protocol for DNA extraction from clay-rich subsoils
AUTHORS: Lukas Beule
[STEPS]
?. [Sample preparation]
Weigh in 200 ± 5 mg freeze-dried soil into a 2-mL tube.
?. [Subsoil DNA extraction]
1. Homogenize the sample by bead beating using 3 tungsten carbide beads (ø 3 mm) for 1 min at 25 Hz using a swi... | ["[Sample preparation]\nWeigh in 200 ± 5 mg freeze-dried soil into a 2-mL tube.", "[Subsoil DNA extraction]\n1. Homogenize the sample by bead beating using 3 tungsten carbide beads (ø 3 mm) for 1 min at 25 Hz using a swing mill (e.g. MM 400, Retsch, Germany).2. Add 250 µL PB buffer1 with 0.5% SDS (w/v) ... |
28,707 | Hi-Fi Gibson Assembly | null | dx.doi.org/10.17504/protocols.io.8abhsan | null | NUS iGEM | TITLE: Hi-Fi Gibson Assembly
AUTHORS: NUS iGEM
[STEPS]
?. Calculate for volumes of respective fragments to assemble based on their length and concentration
?. Add calculated volume of each fragment (maximum volume: )
5 µl
?. Add in of 2x Hi-Fi DNA Assembly Master Mix into the PCR tube
5 µl
?. Vortex to mix
?. Spin ... | ["Calculate for volumes of respective fragments to assemble based on their length and concentration", "Add calculated volume of each fragment (maximum volume: )\n5 µl", "Add in of 2x Hi-Fi DNA Assembly Master Mix into the PCR tube\n5 µl", "Vortex to mix", "Spin down PCR tube", "Incubate samples at for\n50 °C"] |
9,491 | SDS PAGE & Western Blot for Membrane proteins | null | dx.doi.org/10.17504/protocols.io.mhtc36n | null | Dennis Dienst | TITLE: SDS PAGE & Western Blot for Membrane proteins
AUTHORS: Dennis Dienst
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Prepare 4 x loading dye]
For 10 mL: final conc. 617 mg DTT 400 mM1,25 mL 2M Tris-Cl (pH 6.8) ... | ["[Prepare 4 x loading dye]\nFor 10 mL: final conc. 617 mg DTT 400 mM1,25 mL 2M Tris-Cl (pH 6.8) 250 mM4 mL Glycerol 40% (w/v) 4 mL 20% SDS 8% (w/v)ad H2O to ... |
30,849 | Anti-BrdU Staining Protocols Using DNAse with Surface and Fluorescent Proteins | null | dx.doi.org/10.17504/protocols.io.bac9iaz6 | null | Sam Li | TITLE: Anti-BrdU Staining Protocols Using DNAse with Surface and Fluorescent Proteins
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. Pulse actively dividing cells with BrdU (in vitro, cell culture media can be pulsed by adding 10-40µM of BrdU for 1-2 hours).
?. Harvest cells and centrifuge... | ["Pulse actively dividing cells with BrdU (in vitro, cell culture media can be pulsed by adding 10-40µM of BrdU for 1-2 hours).", "Harvest cells and centrifuge for 5 minutes at 1200-1500 rpm (200-300xg).", "Wash cells in Cell Staining Buffer (Cat. No. 420201) and centrifuge for 5 minutes at 1200-1500 rpm (200-300xg). D... |
73,313 | Preparação para ir ao campo | 1 | dx.doi.org/10.17504/protocols.io.dm6gpjz31gzp/v1 | https://www.protocols.io/view/prepara-o-para-ir-ao-campo-cjt9unr6 | Alicia Rafaelly Vilefort Sales, Daniel Vartanian, Maria Augusta Medeiros Andrade | TITLE: Preparação para ir ao campo
AUTHORS: Alicia Rafaelly Vilefort Sales, Daniel Vartanian, Maria Augusta Medeiros Andrade
[DESCRIPTION]
Este protocolo foi desenhado para o processo de coleta de dados do projeto de pesquisa Associações entre a duração e a qualidade do sono de gestantes no terceiro trimestre com a du... | ["[Outros materiais] Separe os itens abaixo conforme a quantidade de gestantes que irá recrutar, sempre deixando algumas cópias extras por segurança.\n\n \n\nTermo de Consentimento Livre e Esclarecido (TCLE)\n\n \n\n Formulário de campo\n\n \n\nTermo de entrega de actígrafo\n\n \n\nGuia de instruções e cuidados com o ... |
92,553 | Making Carbon-Fibre Microelectrode (CFM) for electrochemical recordings of monoamines in ex vivo mouse brain slices | 1 | dx.doi.org/10.17504/protocols.io.n2bvj84qpgk5/v2 | https://www.protocols.io/view/making-carbon-fibre-microelectrode-cfm-for-electro-c6mhzc36 | Katherine Brimblecombe, Stephanie J Cragg | TITLE: Making Carbon-Fibre Microelectrode (CFM) for electrochemical recordings of monoamines in ex vivo mouse brain slices
AUTHORS: Katherine Brimblecombe, Stephanie J Cragg
[DESCRIPTION]
This protocol is to make carbon-fibre microelectrode (CFM) for electrochemical recordings of monoamines in ex-vivo mouse brain slic... | ["[Threading Carbon Fibre] Fill test tube with acetone (flammables cupboard) and add capillary tubes.", "[Threading Carbon Fibre] Stick test tube to light box with Blu Tack.", "[Threading Carbon Fibre] Select a single carbon fibre using rubber tipped forceps.", "[Threading Carbon Fibre] Thread carbon fibre down capilla... |
33,259 | Italian set up of the program “REsilience and Activity every DaY for MS”, of outcomes, and pilot assessment of efficacy using a mixed methodology (READY-It-MS) | null | dx.doi.org/10.17504/protocols.io.bcqjivun | null | Ambra Mara Giovannetti, Alessandra Solari, Kenneth Pakenham | TITLE: Italian set up of the program “REsilience and Activity every DaY for MS”, of outcomes, and pilot assessment of efficacy using a mixed methodology (READY-It-MS)
AUTHORS: Ambra Mara Giovannetti, Alessandra Solari, Kenneth Pakenham
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Italian set up o... | [] |
62,281 | Glucagon measurement from islet populations using a TR-FRET assay | 1 | null | https://www.protocols.io/view/glucagon-measurement-from-islet-populations-using-b83hryj6 | Wesley Eaton, Michael Roper | TITLE: Glucagon measurement from islet populations using a TR-FRET assay
AUTHORS: Wesley Eaton, Michael Roper
[DESCRIPTION]
TR-FRET homogenous assay method using a microfluidic device for quantitation of glucagon secretion from human islet populations is described. A PDMS microfluidic device was used to perfuse a popu... | ["Aquire Chemicals and Reagents", "[Chemical reagents] TR-FRET glucagon assay -Cisbio (Walthan, MA)", "Polydimethylsiloxane (PDMS) prepolymer (Sylgard 184) -Dow Corning (Midland, MI)", "[Chemical reagents] Dextrose -Fisher Scientific (Pittsburg, PA)", "[Chemical reagents] Polydimethylsiloxane (PDMS) prepolymer (Sylgard... |
null | null | null | dx.doi.org/10.17504/protocols.io.qz5dx86 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
78,350 | Background and Significance (Part 1 of "Effects of Online Exercise Intervention on Physical and Mental Conditions in Young Adults with Chronic Neck Pain") | 1 | dx.doi.org/10.17504/protocols.io.rm7vzb9m2vx1/v1 | https://www.protocols.io/view/background-and-significance-part-1-of-34-effects-o-cqrnvv5e | Yiting Lin | TITLE: Background and Significance (Part 1 of "Effects of Online Exercise Intervention on Physical and Mental Conditions in Young Adults with Chronic Neck Pain")
AUTHORS: Yiting Lin
[DESCRIPTION]
This is Part 1 of "Effects of Online Exercise Intervention on Physical and Mental Conditions in Young Adults with C... | [] |
30,507 | Domestication of L0 parts for Loop type IIS (BsaI and SapI) | null | dx.doi.org/10.17504/protocols.io.92jh8cn | null | Eftychis Frangedakis, marta tomaselli, Marius Rebmann, Susana Sauret-Gueto | TITLE: Domestication of L0 parts for Loop type IIS (BsaI and SapI)
AUTHORS: Eftychis Frangedakis, marta tomaselli, Marius Rebmann, Susana Sauret-Gueto
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Domestication and cloning of L0 parts into pUAP4 for </span><a href="https://www.protocols.io/v... | ["[PCR and amplified fragments purification ]\nAmplify the parts using your preferred polymerase (e.g. Phusion, Thermo Scientigic™) following the manufacturer instructions.", "[Domestication Guide.]", "[PCR and amplified fragments purification ]\nRun your PCR product on agarose gel.", "[Fragments Assembly]\nSet up ... |
null | null | null | dx.doi.org/10.17504/protocols.io.ibwcape | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Please contact Dr. Steven Wilhelm (wilhelm@utk.edu) for more information regarding this protocol.</p>
<p> </p>
<p>Modified from Pardee, A. B., F. Jacob, and J. Monod. 1959. The genetic control and cytoplasmic expression of "inducibility" in the synthesis of ß-galactosidase in... | [] |
31,555 | Preparation of Frozen Bacteria Stock | null | dx.doi.org/10.17504/protocols.io.ba3bigin | null | Kenneth Schackart | TITLE: Preparation of Frozen Bacteria Stock
AUTHORS: Kenneth Schackart
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details how to prepare bacteria culture for deep freezing. Protocol adapted from the protocol provided as an external link.</div><div class = "text-block">Reference:</... | ["[Prepare Stocks]\nAdd sterile DMSO to sterile cryotube.\n150 µl", "[Prepare Stocks]\nAdd overnight culture to cryotube containing.\n850 µl", "[Prepare Stocks]\nVortex or invert repeatedly to mix.", "[Prepare Stocks]\nStore cryotube in deep freezer ( to )\n-40 °C\n-80 °C", "[Update Inventory]\nGo to the frozen stor... |
null | null | null | dx.doi.org/10.17504/protocols.io.rdid24e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div>
<div>
<div>
<div>
<div>
<p>This protocol was designed and developed at this laboratory.</p>
<p>The protocol specifically aims to amplify strains of Influenza B YAMAGATA virus lineage and not strains of the VICTORIA virus lineage or other virus species. The assay targets th... | [] |
92,288 | SARS-CoV-2 Whole Genome Amplicon Sequencing from Wastewater Solids or Liquid Wastewater | 4 | dx.doi.org/10.17504/protocols.io.yxmvm323bl3p/v2 | https://www.protocols.io/view/sars-cov-2-whole-genome-amplicon-sequencing-from-w-c6c8zazw | Vikram Chan-Herur, David Catoe, Dorothea Duong, Yi-Chieh Wu, Alexandria B Boehm, Bradley J White, Marlene K Wolfe | TITLE: SARS-CoV-2 Whole Genome Amplicon Sequencing from Wastewater Solids or Liquid Wastewater
AUTHORS: Vikram Chan-Herur, David Catoe, Dorothea Duong, Yi-Chieh Wu, Alexandria B Boehm, Bradley J White, Marlene K Wolfe
[DESCRIPTION]
This process instruction describes steps for whole genome amplicon sequencing of SARS-... | ["[Option 2: Viral particle concentration and RNA extraction from LIQUID wastewater] Spin down 50 mL of influent at 5,250 xg for 5 min to clarify the influent.", "[Option 2: Viral particle concentration and RNA extraction from LIQUID wastewater] Add 4.875 mL of influent sample to one well (one well per sample) of a new... |
98,449 | Donor Case Selection | HuBMAP | JHU-TMC | 0 | dx.doi.org/10.17504/protocols.io.dm6gpz8e1lzp/v2 | https://www.protocols.io/view/donor-case-selection-hubmap-jhu-tmc-dcdr2s56 | Kyu Sang Han, Joel Sunshine, Sashank Reddy, Denis Wirtz, Pei-Hsun Wu | TITLE: Donor Case Selection | HuBMAP | JHU-TMC
AUTHORS: Kyu Sang Han, Joel Sunshine, Sashank Reddy, Denis Wirtz, Pei-Hsun Wu
[DESCRIPTION]
Donor case selection protocol for Johns Hopkins TMC describes criteria for human tissue biopsy collection.
[BEFORE_START]
Patient samples are obtained from skin that is to be disc... | ["[Inclusion] Age 18-35 or 50 and over\nEnglish Speaking\nAble to provide consent\nUndergoing reconstructive or aesthetic procedures necessitating skin excision at the scalp or abdomen", "[Exclusion] Known collagen disorder\nStrong personal history of keloid formation\nDeemed unfit for general anesthesia\nActive infect... |
81,610 | Protocols from 237 CAR-T studies in a mouse ovarian tumor model (reported in Ranoa et al JITC 2023) | 2 | dx.doi.org/10.17504/protocols.io.6qpvr4jwpgmk/v1 | https://www.protocols.io/view/protocols-from-237-car-t-studies-in-a-mouse-ovaria-ctxiwpke | Diana Rose E Ranoa, Preeti Sharma, Claire P. Schane, Amber N Lewis, Edward Valdez, Edward J. Roy, David M. Kranz | TITLE: Protocols from 237 CAR-T studies in a mouse ovarian tumor model (reported in Ranoa et al JITC 2023)
AUTHORS: Diana Rose E Ranoa, Preeti Sharma, Claire P. Schane, Amber N Lewis, Edward Valdez, Edward J. Roy, David M. Kranz
[DESCRIPTION]
This is a collection of protocols from the manuscript: Ranoa, D. R. E.; Shar... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.nwfdfbn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
42,042 | Nuclei isolation from human intestinal biopsic tissue for single-cell genomic applications | 4 | dx.doi.org/10.17504/protocols.io.bma2k2ge | https://www.protocols.io/view/nuclei-isolation-from-human-intestinal-biopsic-tis-bma2k2ge | Ran Zhou, Oni Basu | TITLE: Nuclei isolation from human intestinal biopsic tissue for single-cell genomic applications
AUTHORS: Ran Zhou, Oni Basu
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol provides an efficient method to isolate nuclei from human intestinal biopsy samples for single cell applications... | ["[Sample preparation]\nRinse fresh samples in ice-cold PBS twice.\nBiopsy tissuse can be store up to 3 days in liquid nitrogen/at - 80 Celsius following the steps below:Tissues are rinsed in ice-cold PBS twiceFlash freeze the tissue in 1.7 ml Eppendorf tube in liquid nitrogenStore frozen tissue in liquid nitrogen (pre... |
null | null | null | dx.doi.org/10.17504/protocols.io.j9rcr56 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Sirius Red staining is a usefull staining to study collagen distribution. In adipose tissue development during obesity the extracellular matrix is being remodeled and this can be analyzed using Sirius Red staining. In addition, fibrosis in livers from mice suffering from non-... | [] |
91,415 | Cartilage staining | 4 | null | https://www.protocols.io/view/cartilage-staining-c5hxy37n | Satheeswaran Balasubramanian, Ekambaram Perumal | TITLE: Cartilage staining
AUTHORS: Satheeswaran Balasubramanian, Ekambaram Perumal
[DESCRIPTION]
The Alcian blue staining technique is widely used among developmental biologists to observe the development of cartilage and bone in zebrafish embryos and larvae. Alcian blue is a positively charged dye that stains the car... | ["[Larval fixation] At the desired stage, take the zebrafish larvae and wash in PBS for 5 minutes.", "[Larval fixation] Euthanize the larvae using the cold shock method (Keep at 4oC for 5-10 minutes).", "[Larval fixation] Transfer the euthanized larvae into 4% PFA and keep it in the rocker for 2 hours at room temperatu... |
null | null | null | dx.doi.org/10.17504/protocols.io.r89d9z6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is a collection of methods and protocols from the manuscript: <a href="http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2000862" target="_blank">Gonçalves et al. Commensal bacteria and essential amino acids control food choice behavior and reproductio... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.sgsebwe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>To control a disease it is essential to know its causal agent. A correct diagnosis provides a considerable amount of basic information to select correct control methods. An accurate diagnosis always starts with a representative sample of the damaged tissue, from which a porti... | [] |
28,081 | Plasmid maps and genbank files | null | dx.doi.org/10.17504/protocols.io.7nrhmd6 | null | Tamara Matute, Isaac Nuñez, Fernan Federici, Peter von Dassow | TITLE: Plasmid maps and genbank files
AUTHORS: Tamara Matute, Isaac Nuñez, Fernan Federici, Peter von Dassow
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Plasmid maps and genbank sequence files for the plasmids used in the transformation of </span><span style = "font-style:italic;">Nannochl... | [] |
39,728 | Olfactory Response as a Marker for Alzheimer’s Disease: Evidence from Perceptual and Frontal Oscillation Coherence Deficit | 4 | dx.doi.org/10.17504/protocols.io.bi2qkgdw | https://www.protocols.io/view/olfactory-response-as-a-marker-for-alzheimer-s-dis-bi2qkgdw | Mohammad Javad Sedghizadeh, Hadi Hojjati, Kiana Ezzatdoost, Hamid Aghajan, Zahra Vahabi, Heliya Tarighatnia | TITLE: Olfactory Response as a Marker for Alzheimer’s Disease: Evidence from Perceptual and Frontal Oscillation Coherence Deficit
AUTHORS: Mohammad Javad Sedghizadeh, Hadi Hojjati, Kiana Ezzatdoost, Hamid Aghajan, Zahra Vahabi, Heliya Tarighatnia
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">High... | ["[participants criteria]\nParticipants were selected among the individuals referring to the memory clinic with memory performance complaints.", "[UPSIT Test]\nThe test kit consists of 24 odors which are each exposed by scratching its corresponding strip.", "[Olfactory EEG Test]\nEEG signals were recorded using a 32-ch... |
null | null | null | dx.doi.org/10.17504/protocols.io.fvhbn36 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
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46,332 | Cyanobacterial Growth, Harvest, and Genomic DNA Prep | 4 | dx.doi.org/10.17504/protocols.io.brg4m3yw | https://www.protocols.io/view/cyanobacterial-growth-harvest-and-genomic-dna-prep-brg4m3yw | Ryan Ward, Truc Mai, Nicole Pietrasiak | TITLE: Cyanobacterial Growth, Harvest, and Genomic DNA Prep
AUTHORS: Ryan Ward, Truc Mai, Nicole Pietrasiak
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is a method for the growth of terrestrial and freshwater cyanobacteria in liquid medium and the subsequent harvesting and genomic ... | ["[Biomass growing conditions]\nTransfersterile liquid Z8 media into a sterile 250 mL polycarbonate Erlenmeyer flask (VWR® Erlenmeyer Flasks, Polycarbonate, Sterile Cat Nr. 89095-270).Label the flask with the strain ID. Inoculate with cyanobacterial specimen. Set vented cap with a 0.22µm pore-size PTFE membrane to the ... |
79,446 | How Paramedics Experience the Decision to Continue or Terminate Out-of-Hospital Resuscitation: A Scoping Review Protocol | 4 | dx.doi.org/10.17504/protocols.io.x54v9dbqpg3e/v1 | https://www.protocols.io/view/how-paramedics-experience-the-decision-to-continue-crtwv6pe | Patrick Ristau, Johanna Ristau, Andreas Wagenplast, Marcel Zill, Philipp Dahlmann, Stefan Dietsche | TITLE: How Paramedics Experience the Decision to Continue or Terminate Out-of-Hospital Resuscitation: A Scoping Review Protocol
AUTHORS: Patrick Ristau, Johanna Ristau, Andreas Wagenplast, Marcel Zill, Philipp Dahlmann, Stefan Dietsche
[DESCRIPTION]
Background
Out-of-hospital cardiac arrest (OHCA) is a frequent emerge... | ["[Statements and Declarations] Registration\n\nOpen Science Framework (https://doi.org/10.17605/OSF.IO/74D3Z)\n\nThis Scoping Review Protocol was registered on 13 March 2023 with the OSF Registries (Ristau et al., 2023).", "[Background] Out-of-hospital cardiac arrest (OHCA) is a common, acute life-threatening emergenc... |
107,736 | Small Scale IPTG Induction | Protein Expression | 0 | dx.doi.org/10.17504/protocols.io.yxmvme47og3p/v1 | https://www.protocols.io/view/small-scale-iptg-induction-protein-expression-dmfy43pw | Catherine M Gohar | TITLE: Small Scale IPTG Induction | Protein Expression
AUTHORS: Catherine M Gohar
[DESCRIPTION]
Test
[BEFORE_START]
It's best to start small-scale protein purification on a Monday or Tuesday. This protocol will take at least 3 days before the first freezing step.
[STEPS]
SECTION: Seed Culture
4. Take the BL21 glycer... | ["[Seed Culture] Take the BL21 glycerol stock from the -80 °C freezer and place immediately into the ice bucket.", "[Seed Culture] Label a 15 mLculture tube with the vector strain you will be using, and fill with 5 mL of LB broth with 1x Kanamycin antibiotic or 5ul of 1000x.", "[Seed Culture] Use a 200 µL pipette tip ... |
73,716 | DNA extraction and PCR amplification of petB gene of marine Synechococcus | 4 | dx.doi.org/10.17504/protocols.io.5qpvorkj7v4o/v1 | https://www.protocols.io/view/dna-extraction-and-pcr-amplification-of-petb-gene-cj8uurww | Denise Rui Ying Ong | TITLE: DNA extraction and PCR amplification of petB gene of marine Synechococcus
AUTHORS: Denise Rui Ying Ong
[DESCRIPTION]
This protocol was described in the paper “Nested PCR Approach for petB Gene Metabarcoding of Sorted Marine Synechococcus Populations”. The objective was to create a nested PCR approach for amplif... | ["[Primers] Primer name Sequence Reference petB-F 5'-TACGACTGGTTCCAGGAACG-3' Mazard et al. (2012) petB-R 5'-GAAGTGCATGAGCATGAA-3' Mazard et al. (2012) petB-50F 5'-CAGGACATYGCTGAY-3' Ong et al. (submitted) petB-634R 5'-GCTTVCGRATCATCARGAAG-3' Ong et al. (submitted)", "[DNA extraction of filtered sa... |
84,155 | Protein network analysis links the NSL complex to Parkinson's disease via mitochondrial and nuclear biology – Protein-protein interaction data to functional enrichment analysis | 5 | dx.doi.org/10.17504/protocols.io.5qpvorb19v4o/v3 | https://www.protocols.click/view/protein-network-analysis-links-the-nsl-complex-to-cwe3xbgn | Katie Kelly, c.manzoni, Patrick Lewis, Helene Plun-Favreau | TITLE: Protein network analysis links the NSL complex to Parkinson's disease via mitochondrial and nuclear biology – Protein-protein interaction data to functional enrichment analysis
AUTHORS: Katie Kelly, c.manzoni, Patrick Lewis, Helene Plun-Favreau
[DESCRIPTION]
Whilst the majority (~90-95%) of PD cases are sp... | ["[Downloading and merging the Protein-Protein Interaction (PPI) Data] All code can be found here : 10.5281/zenodo.7875447.\nThe general pipeline to derive the first layer interactome can be found in Figure 1.", "[Downloading and merging the Protein-Protein Interaction (PPI) Data] Collect PPIs for NSL seeds using 3 dif... |
62,874 | XP Nutrition Keto Gummies Review: Shocking Side Effects? | 1 | dx.doi.org/10.17504/protocols.io.rm7vzy13rlx1/v1 | https://www.protocols.io/view/xp-nutrition-keto-gummies-review-shocking-side-eff-b9m2r48e | xpnutritionketoreview | TITLE: XP Nutrition Keto Gummies Review: Shocking Side Effects?
AUTHORS: xpnutritionketoreview
[DESCRIPTION]
XP Nutrition Keto Gummies Review: Shocking Side Effects?
[STEPS]
1. XP Nutrition Keto Gummies Review: Shocking Side Effects?
Are you looking for a quick, easy, and effective way to exfoliate that redundant ... | ["XP Nutrition Keto Gummies Review: Shocking Side Effects?\nAre you looking for a quick, easy, and effective way to exfoliate that redundant body fat in a short period of time? Do you want to feel more and perform better? Also it’s time to try XP Nutrition Keto Gummies. You won't find a better ketogenic diet supplement... |
81,920 | Tris-Buffered Saline (TBS) | 4 | null | https://www.protocols.click/view/tris-buffered-saline-tbs-ct88wrzw | Andreas Sagen | TITLE: Tris-Buffered Saline (TBS)
AUTHORS: Andreas Sagen
[DESCRIPTION]
Tris-buffered saline (TBS) is a buffer used in certain biochemical techniques to keep the pH within a limited range. This formulation has an approximate sodium chloride concentration of 150 mM and a tris concentration of 50 mM. The pH of the buffer... | ["[1 000 mL 25xTBS] Fill 800 mL distilled water in a bottle", "[100 mL TBS with 0.1% Tween-20 (TBST)] Fill 80 mL distilled water in a glass bottle", "[1 000 mL 25xTBS] Sterilize by autoclave for 40 min", "[1 000 mL 25xTBS] Fill bottle to 1000 mL with distilled water", "[1 000 mL 25xTBS] Adjust to pH 7.6 with 12N hydroc... |
62,736 | The processing files and analysis result files | 1 | dx.doi.org/10.17504/protocols.io.b9hqr35w | https://www.protocols.io/view/the-processing-files-and-analysis-result-files-b9hqr35w | XX | TITLE: The processing files and analysis result files
AUTHORS: XX
[DESCRIPTION]
The base data for bivariate autocorrelation and geo-probe analysis and the Geodetector analysis results are included here. The GeoDA analysis results mentioned in the paper can be obtained by running the base data for bivariate autocorre... | [] |
100,128 | Slice preparation | 0 | dx.doi.org/10.17504/protocols.io.5jyl82j7rl2w/v1 | https://www.protocols.io/view/slice-preparation-ddz8279w | Nicola Biagio Mercuri | TITLE: Slice preparation
AUTHORS: Nicola Biagio Mercuri
[DESCRIPTION]
Slice preparation for electrophysiology
[STEPS]
SECTION: Animal sacrifice and surgical procedure
1. Anesthetize the animal under halothane
SECTION: Animal sacrifice and surgical procedure
2. Decapitate the animal with a guillotine
SECTION: Animal s... | ["[Animal sacrifice and surgical procedure] Anesthetize the animal under halothane", "[Animal sacrifice and surgical procedure] Decapitate the animal with a guillotine", "[Animal sacrifice and surgical procedure] Gently open the bones of the skull and remove the brain, dropping it into a beaker containing ice-cold ACSF... |
40,915 | RNA and DNA extraction (Qiagen) of frozen tissue to nanopore sequencing | 4 | dx.doi.org/10.17504/protocols.io.bj7tkrnn | https://www.protocols.io/view/rna-and-dna-extraction-qiagen-of-frozen-tissue-to-bj7tkrnn | Eric Pederson | TITLE: RNA and DNA extraction (Qiagen) of frozen tissue to nanopore sequencing
AUTHORS: Eric Pederson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">RNA extraction of extraction using the Qiagen Allprep RNA extraction kit followed by nanopore sequencing on the MinION.</div></div>
[STEPS]
?. [Pre-... | ["[Pre-experiment]\nBook RNA extraction room", "[Pre-experiment]\nSpray with ETOH and then in the fume hood", "[Pre-experiment]\nPrepare labelled 2 ml low bind tubes with 4 Zirconium Oxide Beads 2.0 mm RNase Free 4 mL beads in each", "[Pre-experiment]\nMake 3 1.5 ml eppendorf tubes for each sample; 1 with sterile wa... |
61,531 | Mehlich 2 Solution | 1 | dx.doi.org/10.17504/protocols.io.q26g74xkkgwz/v1 | https://www.protocols.io/view/mehlich-2-solution-b8b3rsqn | Hsin-Mao Wu | TITLE: Mehlich 2 Solution
AUTHORS: Hsin-Mao Wu
[DESCRIPTION]
Soil extraction
[STEPS]
SECTION: Mehlich 2 Solution
1.
在500 mL DI Water中加入0.56 g NH4F、10.7 g NH4Cl
SECTION: Mehlich 2 Solution
2. 再加1 mL HCl、11.5 mL 冰醋酸並加水至1 L
| ["[Mehlich 2 Solution] 在500 mL DI Water中加入0.56 g NH4F、10.7 g NH4Cl", "[Mehlich 2 Solution] 再加1 mL HCl、11.5 mL 冰醋酸並加水至1 L"] |
102,474 | Preparation of SARS-CoV-2 Particles in Raw Wastewater Samples for Sequencing on Illumina Platforms Using an ARTIC V4.1 Tiled Amplicon Approach | 0 | null | https://www.protocols.io/view/preparation-of-sars-cov-2-particles-in-raw-wastewa-dgbi3ske | Leah Lariscy, Amanda Sullivan, Katie Dillon, Megan Lott, Travis Glenn, Erin Lipp | TITLE: Preparation of SARS-CoV-2 Particles in Raw Wastewater Samples for Sequencing on Illumina Platforms Using an ARTIC V4.1 Tiled Amplicon Approach
AUTHORS: Leah Lariscy, Amanda Sullivan, Katie Dillon, Megan Lott, Travis Glenn, Erin Lipp
[DESCRIPTION]
This protocol describes how to prepare purified SARS-CoV-2 RNA f... | ["[cDNA Synthesis] Thaw reagents appropriately prior to use.\nThaw purified RNA samples on ice\nLunaScript RT Supermix does not require thawing and should remain at -20°C", "[cDNA Synthesis] Gently vortex and spin down reagents and samples", "[cDNA Synthesis] Prepare the cDNA synthesis reactions as follows:", "[cDNA Sy... |
33,434 | Preparation of leukocytes by differential lysis of erythrocytes | null | dx.doi.org/10.17504/protocols.io.bcv2iw8e | null | Mesut Karataş, Şenol Doğan, Emrulla Spahiu, Adna Ašić, Larisa Bešić, Yusuf Turan | TITLE: Preparation of leukocytes by differential lysis of erythrocytes
AUTHORS: Mesut Karataş, Şenol Doğan, Emrulla Spahiu, Adna Ašić, Larisa Bešić, Yusuf Turan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Leukocytes are isolated by centrifugation after specific lysis of erythrocytes</div></div>
... | ["Centrifuge EDTA blood to pellet all cells\n10 ml\nCentrifuge: 1500 33, 10 min, 4 10", "Remove plasma into a clean container and freeze.", "Restore original blood volume with 0.9% saline and transfer the blood suspension into a conical centrifuge tube.\n50 ml", "Add cold lysis buffer\n40 ml", "Stand , mixing o... |
71,294 | Culture and transfection of iPSC-derived neurons for live-imaging of axonal cargoes | 1 | dx.doi.org/10.17504/protocols.io.x54v9dj4zg3e/v1 | https://www.protocols.io/view/culture-and-transfection-of-ipsc-derived-neurons-f-chu6t6ze | Dan Dou, Alexander Boecker, Erika L.F. Holzbaur | TITLE: Culture and transfection of iPSC-derived neurons for live-imaging of axonal cargoes
AUTHORS: Dan Dou, Alexander Boecker, Erika L.F. Holzbaur
[DESCRIPTION]
Here, we plate, culture, and transfect human iPSC-derived excitatory glutamatergic neurons for the purpose of observing transport of axonal cargoes under spi... | ["[Culture and transfection of iPSCderived neurons for live-imaging of axonal cargoes] In advance, prepare 10x PLO stock.", "[Culture and transfection of iPSCderived neurons for live-imaging of axonal cargoes] The day before plating, coat imaging dishes with 1x PLO solution (10x PLO stock diluted in ddH2O).", "[Culture... |
74,611 | DStretch Tattoo Protocol: Full step-by-step protocol for identification and visualization of tattoos on preserved archaeological remains using the ImageJ plugin DStretch | 1 | dx.doi.org/10.17504/protocols.io.n92ldp52xl5b/v1 | https://www.protocols.io/view/dstretch-tattoo-protocol-full-step-by-step-protoco-ck4tuywn | Dominik Göldner, Aaron Deter-Wolf | TITLE: DStretch Tattoo Protocol: Full step-by-step protocol for identification and visualization of tattoos on preserved archaeological remains using the ImageJ plugin DStretch
AUTHORS: Dominik Göldner, Aaron Deter-Wolf
[DESCRIPTION]
Archaeological preservation of intentional skin modifications such as tattoos is ... | ["[Preparation phase] Camera setup: \n\n Charge your camera batteries and spare batteries before taking images. Digitally clean the camera image sensor on a regular basis if the option is provided by your camera model. Likewise, if necessary, manually clean your camera sensor and lens before taking pictures.\n\n ... |
null | null | null | dx.doi.org/10.17504/protocols.io.d3e8jd | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
In this virus-focused chapter, we deal primarily with the use of microarrays for expression analysis (the most popular usage) of host and virus systems during infection. We examine aspects related to array platform choice (spotted and oligonucleotide arrays), probe and array des... | [] |
67,399 | ProDentim Reviews | 3 | dx.doi.org/10.17504/protocols.io.14egn7db6v5d/v1 | https://www.protocols.io/view/prodentim-reviews-cd3fs8jn | ProDentim Reviews | TITLE: ProDentim Reviews
AUTHORS: ProDentim Reviews
[DESCRIPTION]
ProDentim Reviews
[STEPS] | [] |
45,667 | Protein Extraction and western blotting | 4 | dx.doi.org/10.17504/protocols.io.bqubmwsn | https://www.protocols.io/view/protein-extraction-and-western-blotting-bqubmwsn | t.a.mcdougall | TITLE: Protein Extraction and western blotting
AUTHORS: t.a.mcdougall
[STEPS]
?. [Protein Extraction]
Whole cell protein was extracted from cells by treating cell pellets with Radio Immunoprecipitation Assay buffer (RIPA buffer: 1M NaCl, 1% NP-40, 0.5% sodium deoxycholate, 0.1%SDS, 50mM pH 7.4 Tris in ddH2O) was prep... | ["[Protein Extraction]\nWhole cell protein was extracted from cells by treating cell pellets with Radio Immunoprecipitation Assay buffer (RIPA buffer: 1M NaCl, 1% NP-40, 0.5% sodium deoxycholate, 0.1%SDS, 50mM pH 7.4 Tris in ddH2O) was prepared according to the Cold Spring Harbor and supplemented with 1µl of Protease I... |
72,981 | High-Efficiency Yeast Electroporation | 4 | dx.doi.org/10.17504/protocols.io.5qpvorr69v4o/v2 | https://www.protocols.io/view/high-efficiency-yeast-electroporation-cjhvuj66 | Stephanie Hood, Jeffrey A Lewis | TITLE: High-Efficiency Yeast Electroporation
AUTHORS: Stephanie Hood, Jeffrey A Lewis
[DESCRIPTION]
For when extremely high transformation efficiencies are needed (e.g., for transforming plasmid DNA libraries). Adapted from An improved yeast transformation method for the generation of very large human antibody librari... | ["[2 days before starting experiment] Streak out yeast strains to be transformed onto YPD agar and grow at 30°C for 2 days.", "[Day before experiment] For each transformation, inoculate cells into 4 separate tubes containing 5 ml of YPD, and grow to saturation overnight at 30°C with 270 rpm orbital shaking.", "[Day of ... |
22,899 | Construction of high-quality rice ribosome footprint library | null | dx.doi.org/10.17504/protocols.io.2ktgcwn | null | Xiaoyu Yang, Bo Song, Jie Cui, Linlin Luo, Beixin Mo, Xuemei Chen, Lin Liu | TITLE: Construction of high-quality rice ribosome footprint library
AUTHORS: Xiaoyu Yang, Bo Song, Jie Cui, Linlin Luo, Beixin Mo, Xuemei Chen, Lin Liu
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A protocol for construction of high-quality rice ribosome footprint library is provided. Rice riboso... | ["[Isolation of rice polysomes]\nRice tissue is ground to powder with mortar and pestle in liquid nitrogen. About 1 g of the powder is resuspended in 5 mL of ice-cold polysome extraction buffer (PEB) [100 mM Tris-HCl (pH 8.0), 40 mM KCl, 20 mM MgCl2, 2% (V/V) polyoxyethylene (10) tridecyl ether (SIGMA), 0.2% (W/V) deox... |
22,978 | Immunohistochemistry- mounted slides | null | dx.doi.org/10.17504/protocols.io.2pagdie | null | John Tompkins, Don Hoover, Jeffrey Ardell, Kalyanam Shivkumar | TITLE: Immunohistochemistry- mounted slides
AUTHORS: John Tompkins, Don Hoover, Jeffrey Ardell, Kalyanam Shivkumar
[STEPS]
?. Day 1Ø Using the PAP Pen, carefully draw a water barrier circle around the tissue sections on the slide – allow this circle to dry for several seconds or up to approx. one min. Ø Rinse slides w... | ["Day 1Ø Using the PAP Pen, carefully draw a water barrier circle around the tissue sections on the slide – allow this circle to dry for several seconds or up to approx. one min. Ø Rinse slides with PBS (pH 7.3-7.4): 4 x 5 min eachØ Rinse slides with 0.5% BSA + 0.4% Triton X-100 in PBS): 1 x 10 minØ Remove slides one a... |
84,450 | Clustering of differentially expressed genes | 5 | dx.doi.org/10.17504/protocols.io.rm7vzx82rgx1/v1 | https://www.protocols.click/view/clustering-of-differentially-expressed-genes-cwqaxdse | Ahmad Husaini AHS Suhaimi | TITLE: Clustering of differentially expressed genes
AUTHORS: Ahmad Husaini AHS Suhaimi
[DESCRIPTION]
This differentially expressed genes clustering pipeline utilizes coseq v3.17 package (Rau & Maugis-Rabusseau, 2018) in R.
[STEPS]
SECTION: Clustering of differentially expressed genes (DEG) using Coseq package in R
1... | ["[Clustering of differentially expressed genes (DEG) using Coseq package in R] Load the package (coseq).", "[Clustering of differentially expressed genes (DEG) using Coseq package in R] Run Coseq on transformed and normalized counts.\nExample: \nPerforming clustering on bud data with expected clusters, K=5-16.\nCluste... |
95,902 | Cold dispase digestion of murine lungs improves recovery and culture of airway epithelial cells | 4 | dx.doi.org/10.17504/protocols.io.rm7vzxo68gx1/v2 | https://www.protocols.io/view/cold-dispase-digestion-of-murine-lungs-improves-re-c9v6z69e | piotr.janas, Caroline Chauché, Patrick Shearer, Georgia Perona-Wright, Henry J McSorley, Jürgen Schwarze | TITLE: Cold dispase digestion of murine lungs improves recovery and culture of airway epithelial cells
AUTHORS: piotr.janas, Caroline Chauché, Patrick Shearer, Georgia Perona-Wright, Henry J McSorley, Jürgen Schwarze
[DESCRIPTION]
Airway epithelial cells (AECs) play a key role in maintaining lung homeostasis, epithel... | ["[Cold dispase digestion of murine lungs improves recovery and culture of airway epithelial cells] Euthanise a mouse according to local protocols and regulations (excluding carbon dioxide).", "[Cold dispase digestion of murine lungs improves recovery and culture of airway epithelial cells] Using scissors, cut the sk... |
98,565 | Green Synthesis of Fluorescent Carbon Dots from Sweet Basil (Ocimum basilicum) Leaves via Hydrothermal Method | 0 | dx.doi.org/10.17504/protocols.io.3byl49k7ogo5/v1 | https://www.protocols.io/view/green-synthesis-of-fluorescent-carbon-dots-from-sw-dchd2t26 | Hugo Monreal-Contreras, Manoj-Kumar Arthikala, Ravichandran Manisekaran | TITLE: Green Synthesis of Fluorescent Carbon Dots from Sweet Basil (Ocimum basilicum) Leaves via Hydrothermal Method
AUTHORS: Hugo Monreal-Contreras, Manoj-Kumar Arthikala, Ravichandran Manisekaran
[DESCRIPTION]
Carbon-based materials play significant roles in the development of material science. Carbon dots (CDs), a ... | ["[Step 1: Preparation of basil leaves] Freshly collected should be sorted first to ensure only healthy leaves are chosen for the C-dots synthesis.", "[Step 1: Preparation of basil leaves] Then it is washed thoroughly and rinsed with distilled water to remove the debris, dust or any other unwanted substance attached ... |
51,677 | Selection and assessment measures used in medical school admissions: A systematic review. | 1 | dx.doi.org/10.17504/protocols.io.bwp5pdq6 | https://www.protocols.io/view/selection-and-assessment-measures-used-in-medical-bwp5pdq6 | Alec Knight, Hamda Shahzad, Ricardo Twumasi | TITLE: Selection and assessment measures used in medical school admissions: A systematic review.
AUTHORS: Alec Knight, Hamda Shahzad, Ricardo Twumasi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Introduction</span></div><br/><div class = "text-block">Patterson et... | [] |
89,762 | JMN-MSMP Notexin Muscle scRNAseq | 1 | dx.doi.org/10.17504/protocols.io.e6nvwd8r9lmk/v1 | https://www.protocols.io/view/jmn-msmp-notexin-muscle-scrnaseq-c3waypae | ccherry | TITLE: JMN-MSMP Notexin Muscle scRNAseq
AUTHORS: ccherry
[DESCRIPTION]
Murine notexin muscle injury followed by single cell RNA sequencing
[STEPS]
SECTION: Skeletal muscle injury and collection
1. In a given mouse, both tibialis anterior (TA) muscles were injected with 10 µl of notexin (10 µg/ml; Latoxan, France).
SE... | ["[Skeletal muscle injury and collection] In a given mouse, both tibialis anterior (TA) muscles were injected with 10 µl of notexin (10 µg/ml; Latoxan, France).", "[Skeletal muscle injury and collection] At various days post injury, the mouse was sacrificed and the TAs were collected. Each TA was proccessed independen... |
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