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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43,825 | Culturing Physcomitrella patens | 4 | dx.doi.org/10.17504/protocols.io.bn2rmgd6 | https://www.protocols.io/view/culturing-physcomitrella-patens-bn2rmgd6 | Igem Dusseldorf | TITLE: Culturing Physcomitrella patens
AUTHORS: Igem Dusseldorf
[STEPS]
?. [Execution]
Scrape 7 – 10 days old moss protonemal tissue with spatula.
?. [Execution]
Put 4 mL of water into a (conical tube). Put in the protonemal tissue. Cut it with a Homogenizer until no big chunk is visible and the water is uniformly... | ["[Execution]\nScrape 7 – 10 days old moss protonemal tissue with spatula.", "[Execution]\nPut 4 mL of water into a (conical tube). Put in the protonemal tissue. Cut it with a Homogenizer until no big chunk is visible and the water is uniformly green.", "[Execution]\nSpread 2-3 mL of freshly fragmented protonema on the... |
68,391 | Examples of protocols on protocols.io from different disciplines | 1 | dx.doi.org/10.17504/protocols.io.4r3l2odzpv1y/v1 | https://www.protocols.io/view/examples-of-protocols-on-protocols-io-from-differe-ce2ftgbn | protocols.io team | TITLE: Examples of protocols on protocols.io from different disciplines
AUTHORS: protocols.io team
[DESCRIPTION]
We warmly welcome all research methods. While the origin of the platform was more biology/wetlab, we expanded to support all fields when we partnered with PLOS ONE in 2017.
There is now a diverse spectrum ... | ["[Molecular Biology] www.protocols.io/view/micropatterning-em-grids-for-cryo-electron-tomogra-bz22p8ge\nwww.protocols.io/view/engineering-brain-assembloids-to-interrogate-human-bznap5ae\nwww.protocols.io/view/high-quality-dna-from-fungi-for-long-read-sequenci-j8nlkky6l5r7/v11\nwww.protocols.io/view/mcscrb-seq-protocol... |
70,817 | P2 unlisted - redesign - collection | 4 | null | https://www.protocols.io/view/p2-unlisted-redesign-collection-chd9t296 | Maria Gul | TITLE: P2 unlisted - redesign - collection
AUTHORS: Maria Gul
[DESCRIPTION]
Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Integer in sapien. Praesent id justo in neque elementum ultrices. Cras elementum. Sed ac dolor sit amet purus malesuada congue. Nunc auctor. Quis autem vel eum iure reprehenderit qui i... | ["Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Integer in sapien. Praesent id justo in neque elementum ultrices. Cras elementum. Sed ac dolor sit amet purus malesuada congue. Nunc auctor. Quis autem vel eum iure reprehenderit qui in ea voluptate velit esse quam nihil molestiae consequatur, vel illum qui do... |
64,643 | Microbial Genome Editing | 4 | dx.doi.org/10.17504/protocols.io.4r3l2o173v1y/v1 | https://www.protocols.io/view/microbial-genome-editing-cbdbsi2n | contact.microbialtec | TITLE: Microbial Genome Editing
AUTHORS: contact.microbialtec
[DESCRIPTION]
Early microbial genome editing mainly focused on random screening and simple rational screening, but the shortcomings of traditional methods that are time-consuming, labor-intensive, work-intensive, and non-directional mutagenesis results ha... | ["Microbial Genome Editing Based on Rec\n\nMicrobial genome editing based on homologous recombination uses its own Rec system to carry out homologous recombination of exogenous DNA to achieve allelic replacement of target genes and recombination of genetic information between two homologous strands of DNA. By producing... |
62,876 | SMILZ CBD GUMMIES Reviews - Top Ingredients, Benefits, Pain Relief, Price & With Side Effect? | 3 | dx.doi.org/10.17504/protocols.io.5jyl89w57v2w/v1 | https://www.protocols.io/view/smilz-cbd-gummies-reviews-top-ingredients-benefits-b9m4r48w | Smilz CBD Gummies | TITLE: SMILZ CBD GUMMIES Reviews - Top Ingredients, Benefits, Pain Relief, Price & With Side Effect?
AUTHORS: Smilz CBD Gummies
[DESCRIPTION]
Smilz CBD Gummies
[STEPS] | [] |
97,344 | Phenol-chloroform DNA extraction from Sporosarcina pasteurii | 0 | dx.doi.org/10.17504/protocols.io.kqdg324eev25/v1 | https://www.protocols.io/view/phenol-chloroform-dna-extraction-from-sporosarcina-dba82ihw | Michael S. Carter, Matthew J. Tuttle, Maneesh K. Gupta | TITLE: Phenol-chloroform DNA extraction from Sporosarcina pasteurii
AUTHORS: Michael S. Carter, Matthew J. Tuttle, Maneesh K. Gupta
[DESCRIPTION]
This protocol is for extraction of genomic DNA from Sporosarcina pasteurii. It is based on a standard phenol-chloroform DNA extraction method.
[GUIDELINES]
All steps should... | ["[DNA extraction] Grow Sporosarcina pasteurii cells in 150 mL of BHI/330 mM urea at 30°C with 200 rpm shaking to an OD600 of 3.5.", "[DNA extraction] Concentrate cells by centrifugation at 15,000 x g for 10 min and pour off the supernatant.", "[DNA extraction] Resuspend cells in 10 mL of Resuspension Buffer (50 mM Tri... |
29,760 | Recording well and craniotomy for electrophysiology in head-restrained mice | 1 | dx.doi.org/10.17504/protocols.io.9a8h2hw | https://www.protocols.io/view/recording-well-and-craniotomy-for-electrophysiolog-9a8h2hw | Susu Chen, Karel Svoboda | TITLE: Recording well and craniotomy for electrophysiology in head-restrained mice
AUTHORS: Susu Chen, Karel Svoboda
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Recording well and craniotomy for acute extracellular electrophysiological recordings in head-restrained mice</div></div>
[STEPS]
?. D... | ["Disinfect all surgery tools and headbar. Anesthetize animal with 3% Isoflurane and mount it onto stereotaxic frame with homeothermic heating pad underneath the animal. During surgery, isoflurane is adjusted to 1~1.5% to achieve a steady ~1/sec breathing rate, and body temperature is maintained at . Check for absence... |
85,195 | Protocol of a systematic review and meta-analysis: blood pressure effects of chronic physical exercise in pre and post menopause women | 1 | dx.doi.org/10.17504/protocols.io.eq2lyjpkrlx9/v1 | https://www.protocols.io/view/protocol-of-a-systematic-review-and-meta-analysis-cxfjxjkn | Juliana Cristina Silva, Ana Clara Ribeiro Cunha, ana luiza amaral, Igor Mariano, Guilherme Morais Puga | TITLE: Protocol of a systematic review and meta-analysis: blood pressure effects of chronic physical exercise in pre and post menopause women
AUTHORS: Juliana Cristina Silva, Ana Clara Ribeiro Cunha, ana luiza amaral, Igor Mariano, Guilherme Morais Puga
[DESCRIPTION]
Changes in menopause affect women’s lives and the... | ["[Background] The climacteric represents the transition from the reproductive to the non-reproductive phase of a woman’s life. The marked changes in the climacteric phase include physical, hormonal, psychosocial aspects, and may affect body composition and bring cardiovascular risks, such as increased blood pressure, ... |
28,898 | Protein expression in yeast | null | dx.doi.org/10.17504/protocols.io.8gahtse | null | Jaclyn Winter | TITLE: Protein expression in yeast
AUTHORS: Jaclyn Winter
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.kqfcvtn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Quick crude protein extraction from budding or fission yeast.
[BEFORE_START]
Cool NaOH on ice before use.
[STEPS]
?.
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null | null | null | dx.doi.org/10.17504/protocols.io.jizckf6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?. | [] |
88,629 | Model Building of PI3KC3-C1/RAB1A | 4 | null | https://www.protocols.io/view/model-building-of-pi3kc3-c1-rab1a-c2svyee6 | Annan SI Cook | TITLE: Model Building of PI3KC3-C1/RAB1A
AUTHORS: Annan SI Cook
[DESCRIPTION]
Details model building of the PI3KC3-C1/RAB!A complex using chimeraX1.5-1.6 and ISOLDE. Refinement was done using Phenix real space refinement.
[STEPS]
SECTION: Generate Starting model
1. Use Alphafold2 to generate a starting model contain... | ["[Generate Starting model] Use Alphafold2 to generate a starting model containing the PI3KC3-C1 components (VPS34, VPS15, ATG14, BECN1) and RAB1A respectively.", "[Docking and model building/refinement] Dock each starting model into the experimental map", "[Docking and model building/refinement] Use ISOLDE to relax th... |
73,738 | Preparing 1% Eosin Y stock solution | 4 | null | https://www.protocols.io/view/preparing-1-eosin-y-stock-solution-cj9iur4e | joshdm | TITLE: Preparing 1% Eosin Y stock solution
AUTHORS: joshdm
[DESCRIPTION]
Preparation of 1% stock solution of Eosin Y for routine H&E staining.
[STEPS]
1. Weigh 2g of Eosin Y disodium salt and place it into a 1000mL Earlenmyer flask
2. Measure 40mL of dionized water and add it to the flask. Swirl to dissolve Eosin po... | ["Weigh 2g of Eosin Y disodium salt and place it into a 1000mL Earlenmyer flask", "Measure 40mL of dionized water and add it to the flask. Swirl to dissolve Eosin powder.", "Measure 160mL of 95% ethanol and add it to the flask. Swirl to dissolve.", "Using a p1000 Pipette, add 1mL (1000uL) of Glacial Acetic acid to the ... |
50,379 | Nucleus-highlighting (terminal/lethal) staining of adherent live U2-OS cells by Erythrosine B | 4 | dx.doi.org/10.17504/protocols.io.bvfjn3kn | https://www.protocols.io/view/nucleus-highlighting-terminal-lethal-staining-of-a-bvfjn3kn | Misha Koksharov | TITLE: Nucleus-highlighting (terminal/lethal) staining of adherent live U2-OS cells by Erythrosine B
AUTHORS: Misha Koksharov
[DESCRIPTION]
Erythrosine B (tetraiodofluorescein; ErB) is a negatively charged viability stain commonly used to assess cell viability in a hemocytometer or in adherent mammalian cell cultur... | ["[Cell staining protocol steps] Remove the culture media from the vessel (cell culture plate or well) with adherent U2-OS cells.", "[Cell staining protocol steps] Gently add a serum-free cell culture media or buffer (preferably maintaining pH 7.2-7.6 in the absence of the CO2 atmosphere) to cover the cells.", "[Cell s... |
null | null | null | dx.doi.org/10.17504/protocols.io.vh5e386 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Simple 5-minute experiment to demonstrate volume of air to children.
[STEPS]
SECTION: Preparation
?.
SECTION: Preparation
?.
SECTION: Preparation
?.
SECTION: Preparation
?.
SECTION: Preparation
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SECTION: Experiment
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SECTION: Experiment
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?.
SECT... | ["[Preparation] {\"blocks\":[{\"key\":\"2gcld\",\"text\":\"Take a large bowl and fill with water, almost to the top.\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[]},{\"key\":\"dgq2j\",\"text\":\" \",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges... |
77,834 | Methods in "The first released available genome of the common ice plant (Mesembryanthemum crystallinum L.) extended the research region on salt tolerance, C3-CAM photosynthetic conversion, and halophism" | 5 | dx.doi.org/10.17504/protocols.io.6qpvr4qdogmk/v1 | https://www.protocols.io/view/methods-in-34-the-first-released-available-genome-cp9ivr4e | Ryoma Sato, Yuri Kondo, Sakae Agarie | TITLE: Methods in "The first released available genome of the common ice plant (Mesembryanthemum crystallinum L.) extended the research region on salt tolerance, C3-CAM photosynthetic conversion, and halophism"
AUTHORS: Ryoma Sato, Yuri Kondo, Sakae Agarie
[DESCRIPTION]
The wild-type seeds of the common ic... | ["[Table of contents] ① DNA extraction, library construction, and sequencing\n② Clean read preparation and genome size estimation\n➂ De novo genome assembly and quality evaluation\n④ Phylogenetic tree creation among multiple plant species using 18S ribosomal DNA sequences\n⑤ Detection of repetitive regions\n➅ Search fo... |
37,390 | Protocol for early vigour QTL mapping | 1 | dx.doi.org/10.17504/protocols.io.bgrnjv5e | https://www.protocols.io/view/protocol-for-early-vigour-qtl-mapping-bgrnjv5e | Yumin Yang, Hongshen Wan | TITLE: Protocol for early vigour QTL mapping
AUTHORS: Yumin Yang, Hongshen Wan
[STEPS]
?. [Material preparing]
Parents, provided by CIMMYT:durum wheat DOY1 x Ae. tauschii AT333, doubled haploids Syn79 by colchicine application durum wheat DOY1 x Ae. tauschii AT428, doubled haploids Syn80 by colchicine applicationR... | ["[Material preparing]\nParents, provided by CIMMYT:durum wheat DOY1 x Ae. tauschii AT333, doubled haploids Syn79 by colchicine application durum wheat DOY1 x Ae. tauschii AT428, doubled haploids Syn80 by colchicine applicationRecombinant inbred lines (RILs):Syn79 x Syn80, single seed desent from F2 to F9, a total o... |
71,561 | A simple and economic protocol for efficient in vitro fertilization using cryopreserved mouse sperm | 4 | dx.doi.org/10.17504/protocols.io.261ge4j3yv47/v3 | https://www.protocols.io/view/a-simple-and-economic-protocol-for-efficient-in-vi-ch5ht836 | Magdalena Wigger, Simon E Tröder, Branko Zevnik | TITLE: A simple and economic protocol for efficient in vitro fertilization using cryopreserved mouse sperm
AUTHORS: Magdalena Wigger, Simon E Tröder, Branko Zevnik
[DESCRIPTION]
The advent of genome editing tools like CRISPR/Cas has substantially increased the number of genetically engineered mouse models in recent ye... | ["[Sperm cryopreservation] Prepare 20 straws for 2 sacrificed males of the same line. Use of a single male is possible as well but the number of straws and volume of media used needs to be reduced by 50%", "[Sperm cryopreservation] Mark the straws at 2.3 cm and 4.0 cm at the open end and label them at the other end (co... |
89,250 | Verification guidelines for the DDNS method for poliovirus direct detection | 3 | dx.doi.org/10.17504/protocols.io.rm7vzx54rgx1/v1 | https://www.protocols.io/view/verification-guidelines-for-the-ddns-method-for-po-c3eayjae | Joyce Akello, Alex Shaw, Catherine Troman, Erika Bujaki, Manasi Majumdar, Javier Martin, Nick Grassly | TITLE: Verification guidelines for the DDNS method for poliovirus direct detection
AUTHORS: Joyce Akello, Alex Shaw, Catherine Troman, Erika Bujaki, Manasi Majumdar, Javier Martin, Nick Grassly
[DESCRIPTION]
This document describes a pragmatic approach to conduct in-house verification of the DDNS method for detection ... | [] |
52,892 | FindingNemo Library 2: Modified RAD004 | 1 | dx.doi.org/10.17504/protocols.io.bxv4pn8w | https://www.protocols.io/view/findingnemo-library-2-modified-rad004-bxv4pn8w | Inswasti Cahyani, John Tyson, Nadine Holmes, Josh Quick, Nicholas Loman, Matthew Loose | TITLE: FindingNemo Library 2: Modified RAD004
AUTHORS: Inswasti Cahyani, John Tyson, Nadine Holmes, Josh Quick, Nicholas Loman, Matthew Loose
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This sub-protocol is designed to prepare library from extracted ultra-high molecular weight (UHMW) DNA t... | ["[Library Prep Notes]\nExtracted UHMW DNA is often difficult to quantify due to its viscosity. However, accurate measurement of DNA concentration is crucial for calculating optimum ratio of the transposase enzyme to the DNA molecules. We provide a protocol section for quantifying UHMW DNA in our 'FindingNemo' protocol... |
60,459 | CODEX® Multiplexed Imaging | Tissue Staining and Reporter Plate Preparation | 1 | dx.doi.org/10.17504/protocols.io.n92ldzro9v5b/v1 | https://www.protocols.io/view/codex-multiplexed-imaging-tissue-staining-and-repo-b7ajricn | Diane Saunders, Conrad Reihsmann, Marcela Brissova, Alvin C. Powers | TITLE: CODEX® Multiplexed Imaging | Tissue Staining and Reporter Plate Preparation
AUTHORS: Diane Saunders, Conrad Reihsmann, Marcela Brissova, Alvin C. Powers
[DESCRIPTION]
This protocol describes the staining and pre-imaging preparation currently in use by the Vanderbilt Diabetes Research Center Islet & Pancreas A... | ["[Tissue Preparation] Remove coverslip from freezer and place face up in container with layer of for 2 min to dry.", "[Tissue Preparation] Place coverslip into an individual 10-mL beaker containing acetone, making sure entire tissue area is submerged. Incubate for 10 min.", "[Tissue Preparation] Carefully remove cove... |
51,902 | Coral DNA Extraction - Modified DNeasy PowerSoil Pro Kit | 4 | dx.doi.org/10.17504/protocols.io.bww6pfhe | https://www.protocols.io/view/coral-dna-extraction-modified-dneasy-powersoil-pro-bww6pfhe | Luigi Colin | TITLE: Coral DNA Extraction - Modified DNeasy PowerSoil Pro Kit
AUTHORS: Luigi Colin
[DESCRIPTION]
DNeasy PowerSoil Pro Kit modified extraction protocol to improve yield with inhibitor heavy hard corals.
Tested and developed on Acropora corals. Optimised for all coral DNA extraction that with high quantity of inhib... | ["[Sample preparation] Gently crush a small piece of coral in a mortar and pestle (~100 mg, in order not to overload the column though). And transfer in a PowerBead Pro Tube (or 2 ml Microcentrifuge).\nNote: For improved yield focus on adding more tissue and less carbonate from the skeleton, a scalpel", "[Sample prepar... |
69,671 | carbon1d.nan | 5 | dx.doi.org/10.17504/protocols.io.eq2ly7zomlx9/v1 | https://www.protocols.io/view/carbon1d-nan-cgaftsbn | NAN-KB UGA | TITLE: carbon1d.nan
AUTHORS: NAN-KB UGA
[DESCRIPTION]
This protocol describes running a 1D carbon experiment with proton decoupling using the Bruker pulseprogram 'zgpg30'. This sequence sets the carbon pulse width to get a tip angle of 30 degrees for more rapid acqusition with a shorter relaxation delay.
The default... | ["[Create carbon1d experiment file] Starting from the 1D proton data set, click on Acquire -> 'Create Dataset' button to open dataset entry box.\nIt should increment the EXPNO to the next integer ( e.g. 2)", "[Create carbon1d experiment file] Click OK at bottom of window to create the experiment directory.\nIt will ... |
95,903 | Cytotoxicity Assay Protocol | 0 | dx.doi.org/10.17504/protocols.io.14egn35mpl5d/v1 | https://www.protocols.io/view/cytotoxicity-assay-protocol-c9v7z69n | Roshni Jaffery, Ningbo Zheng, Jiakai Hou, Ashley Guerrero, Si Chen, Chunyu Xu, Nicholas A. Egan, Ritu Bohat, Weiyi Peng | TITLE: Cytotoxicity Assay Protocol
AUTHORS: Roshni Jaffery, Ningbo Zheng, Jiakai Hou, Ashley Guerrero, Si Chen, Chunyu Xu, Nicholas A. Egan, Ritu Bohat, Weiyi Peng
[DESCRIPTION]
This is the protocol for cytotoxicity assay in cancer cell lines using flow cytometry.
[STEPS]
1. Begin T cell culturing a week prior. Grow ... | ["Begin T cell culturing a week prior. Grow and culture tumor cell lines. Ensure the cells are not over-confluent.", "Split the tumor cells the day before the assay. Perform the cytotoxic assay as described in next steps.", "Count tumor cells. Collect 3-5M cells for each cell line.", "Centrifuge the cells and wash the ... |
19,661 | UC Davis - High fat diet feeding | null | dx.doi.org/10.17504/protocols.io.xfmfjk6 | null | Kristin Evans | TITLE: UC Davis - High fat diet feeding
AUTHORS: Kristin Evans
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary</span></div><div class = "text-block">A high-fat diet of varying composition and percent fat is administered to induce obesity in mice. High-fat di... | ["High-fat diet is given ad libitum in mice. Typically mice are started on the diet at 6 weeks of age (for C57BL/6 strains). Age at diet start will be begin in consultation with the investigator needs", "A stock bag of high-fat diet should be stored in a refrigerator.", "High-fat diet placed in cages should be replac... |
83,650 | Biomarker's detection for diseases associated with metabolic disorder syndrome | 5 | dx.doi.org/10.17504/protocols.io.rm7vzxnb5gx1/v1 | https://www.protocols.io/view/biomarker-39-s-detection-for-diseases-associated-w-cvxaw7ie | Cosme E. Santiesteban Toca, Denisse Chacón, Alejandro Rojo Moreno, Saide Lizeth Medrano González, Leyla Escalante Gonzalez | TITLE: Biomarker's detection for diseases associated with metabolic disorder syndrome
AUTHORS: Cosme E. Santiesteban Toca, Denisse Chacón, Alejandro Rojo Moreno, Saide Lizeth Medrano González, Leyla Escalante Gonzalez
[DESCRIPTION]
The metabolic syndrome (MetS) is known to substantially reduce the quality of life.... | ["[Download public databases] The SRA (Sequence Read Archive) is the standard format in which all NGS data is uploades into NCBI. To download and convert SRA files into FASTQ, download SRA Toolkit", "[Download public databases] Access and download public databases. In this case, a database from the human gut metagenome... |
50,659 | PYG medium preparation (2 L) | 1 | dx.doi.org/10.17504/protocols.io.bvqbn5sn | https://www.protocols.io/view/pyg-medium-preparation-2-l-bvqbn5sn | Carrie A Flynn, Barbara Kazmierczak | TITLE: PYG medium preparation (2 L)
AUTHORS: Carrie A Flynn, Barbara Kazmierczak
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Recipe for PYG rich growth medium for </span><span style = "font-style:italic;">Acanthamoeba castellanii</span><span> trophozoites. Adapted from ATCC Medium: 712 PYG... | ["[Dry ingredients]\nTo a 2 L bottle, add:-stir bar\n[sodium citrate dihydrate]\n[yeast extract]\n[bacto peptone]", "[Water]\nBring volume to with dH2O (for our reagents, requires adding dH2O) and place on stir plate (unheated).\n1.8 L\n1.68 L", "[Liquid stock solutions]\nAdd: 0.05 M CaCl2 x 2H2O 0.4 M MgSO4 x 7H2O 0... |
87,845 | iPSCs Maintenance and Banking | 4 | dx.doi.org/10.17504/protocols.io.ewov1qd5ogr2/v1 | https://www.protocols.io/view/ipscs-maintenance-and-banking-cz2dx8a6 | Mahmoud ElAchwah, sol.diazdeleon, pangzh | TITLE: iPSCs Maintenance and Banking
AUTHORS: Mahmoud ElAchwah, sol.diazdeleon, pangzh
[DESCRIPTION]
This protocols offers a thorough description of the maintenance and banking of induced pluripotent stem cells.
[STEPS]
SECTION: Diluting Matrigel
1. Thaw Matrigel stock 9-11 µg/µL stored at -80 °C on ice
SECTION: Di... | ["[Diluting Matrigel] Thaw Matrigel stock 9-11 µg/µL stored at -80 °C on ice", "[Diluting Matrigel] Dilute 400 µL Matrigel aliquot in 40 mL of MEM (Working Concentration 90-110 µg/mL)", "[Diluting Matrigel] Mix well before use. Store at 4 °C protected from the light", "[Matrigel Coating] Coat wells with 1 mL of Matrige... |
null | null | null | dx.doi.org/10.17504/protocols.io.pv5dn86 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?. | [] |
61,848 | Generation of 3-dimensional spheroids of human umbilical vein endothelial cells and human amnion-derived mesenchymal stem cells in human platelet lysate-based gels | 4 | dx.doi.org/10.17504/protocols.io.bp2l6138kvqe/v1 | https://www.protocols.io/view/generation-of-3-dimensional-spheroids-of-human-umb-b8myru7w | Eva Rossmanith, Sabrina Summer | TITLE: Generation of 3-dimensional spheroids of human umbilical vein endothelial cells and human amnion-derived mesenchymal stem cells in human platelet lysate-based gels
AUTHORS: Eva Rossmanith, Sabrina Summer
[DESCRIPTION]
Generation of 3-dimensional spheroids containing human umbilical vein endothelial cells and hu... | ["[Harvesting of the cells] Aspirate the medium and wash the cells with 1x PBS", "[Harvesting of the cells] Add 300 µl accutase to a T-25 flask and incubate at 37 °C, 5% CO2 for 3-5 minutes", "[Harvesting of the cells] Resuspend the cells in 10 ml PBS and transfer the cell suspension to a 15-ml falcon tube", "[Harvesti... |
55,462 | Ultrasound 96 Probe Device Protocol for cancer cell treatment | 1 | dx.doi.org/10.17504/protocols.io.e6nvwkpdwvmk/v1 | https://www.protocols.io/view/ultrasound-96-probe-device-protocol-for-cancer-cel-b2eeqbbe | Aisling Field, Brijeshtiwari, James F Curtin, Julie Rose Mae Mondala, Janith Wanigasekara | TITLE: Ultrasound 96 Probe Device Protocol for cancer cell treatment
AUTHORS: Aisling Field, Brijeshtiwari, James F Curtin, Julie Rose Mae Mondala, Janith Wanigasekara
[DESCRIPTION]
Ultrasound is a sound wave with frequencies ranging between 20 kHz and 20 MHz. Ultrasound is able to temporarily and repeatedly open the... | ["Before starting the ultrasound probe system, ensure that all parts of the system/device are free from mechanical damage and that the probe is connected tightly.", "The 96-probe system is designed to fit perfectly into the 96 well plate, which can be used to grow and treat cancer cells. The retort stand is used to hol... |
54,364 | Glycerol Stock Preparation for S. elongatus | 4 | dx.doi.org/10.17504/protocols.io.bzb4p2qw | https://www.protocols.io/view/glycerol-stock-preparation-for-s-elongatus-bzb4p2qw | Akashdutta | TITLE: Glycerol Stock Preparation for S. elongatus
AUTHORS: Akashdutta
[DESCRIPTION]
Bacterial cultures in the form of agar plates or liquid cultures are not suitable for long term storage at low temperatures such as 4 degrees. Long-term storage of bacteria is best at temperatures around -80 degrees. However, agar p... | ["To make n stocks, take an aliquot of the S. elongatus culture such that the OD times the volume is at least 5n.", "Centrifuge this aliquot in a falcon at 5000 rpm, 7 min, 25 °C", "Discard the supernatant.", "Resuspend the pellet in the minimum amount of BG11 medium required to do so.", "Add n mL of 25% glycerol and ... |
38,309 | Entering the Lab (Covid-19 Shutdown Re-Entry, Srivastava Lab) | 1 | dx.doi.org/10.17504/protocols.io.bhndj5a6 | https://www.protocols.io/view/entering-the-lab-covid-19-shutdown-re-entry-srivas-bhndj5a6 | Srivastava Lab | TITLE: Entering the Lab (Covid-19 Shutdown Re-Entry, Srivastava Lab)
AUTHORS: Srivastava Lab
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Disclaimer</span><span>: The SOP presented here has been designed by the Srivastava Lab at Harvard University and is being sh... | ["Hand sanitizer pump outside the door - use before unlocking door", "Leave jacket outside of lab", "Sanitize phone/any other object that will be in the workspace with 70% ethanol wipe", "Wash hands at the sink", "Wipe bench, pipettes, pens, etc with 70% ethanol", "If it is your “high touch” day, wipe all handles (incu... |
61,467 | High Resolution Intact Proteoform Mass Spectrometry Imaging using UHMR HF Orbitrap | 6 | null | https://www.protocols.io/view/high-resolution-intact-proteoform-mass-spectrometr-b793rr8n | Kevin J. Zemaitis, Dusan Velickovic, Mowei Zhou, Ljiljana.PasaTolic | TITLE: High Resolution Intact Proteoform Mass Spectrometry Imaging using UHMR HF Orbitrap
AUTHORS: Kevin J. Zemaitis, Dusan Velickovic, Mowei Zhou, Ljiljana.PasaTolic
[DESCRIPTION]
Scope:
A detailed protocol entailing the calibration, operation, and verification of the custom UHMR Q Exactive HF Orbitrap with a Spectr... | ["[Instrument setup] At this time the sample is then loading into the MALDI source, this includes closing the beam valve and venting the source. After loading the sample both the MALDI source roughing pump is started, the beamvalve opened, and fore vacuum roughing pump is regulated to the proper pressure regimes as out... |
35,965 | Strand specific detection of overlapping transcripts via purification involving denaturation of biotinylated cDNA | null | dx.doi.org/10.17504/protocols.io.bfc5jiy6 | https://www.protocols.io/view/strand-specific-detection-of-overlapping-transcrip-bfc5jiy6 | Faizan Uddin, Madhulika Srivastava | TITLE: Strand specific detection of overlapping transcripts via purification involving denaturation of biotinylated cDNA
AUTHORS: Faizan Uddin, Madhulika Srivastava
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Reverse Transcription Polymerase Chain Reaction (RT-PCR) is the most widely employed te... | ["2µg of DNase-I treated RNA was reverse transcribed at 55ᵒC using Superscript-III First-Strand Synthesis System for RT-PCR (Invitrogen 18068-015) in 40µl RT reaction following manufacturer’s instruction. The final concentration of each biotinylated GSP was 250nM.", "50µl of Dynabeads™ MyOne™ Streptavidin C1 were trans... |
15,022 | Laboratory calibration of soil moisture sensors in porous media (repacked soils) | null | dx.doi.org/10.17504/protocols.io.swnefde | null | Soham Adla, Neeraj Rai, K Sri Harsha, Shivam Tripathi, Markus Disse, Saket Pande | TITLE: Laboratory calibration of soil moisture sensors in porous media (repacked soils)
AUTHORS: Soham Adla, Neeraj Rai, K Sri Harsha, Shivam Tripathi, Markus Disse, Saket Pande
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [References]
Czarnomski, N. M., Moore, G. W., Pypker, T. G., Licata, J., & Bond, ... | ["[References]\nCzarnomski, N. M., Moore, G. W., Pypker, T. G., Licata, J., & Bond, B. J. (2005). Precision and accuracy of three alternative instruments for measuring soil water content in two forest soils of the Pacific Northwest. Canadian Journal of Forest Research, 35(8), 1867-1876. Starr, J.L and Paltineanu, I.C. ... |
53,338 | Mycology media | 1 | null | https://www.protocols.io/view/mycology-media-byb2psqe | Yin-Tse Huang | TITLE: Mycology media
AUTHORS: Yin-Tse Huang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Mycology media</div></div>
[STEPS]
?. WA+C agar Water agar + chloramphenicol (氯黴素 kill bacteria): As an environmental isolating mediaComponentAmountAgar20gChloramphenicol0.05gDI water1000 ml
ComponentAmount... | ["WA+C agar Water agar + chloramphenicol (氯黴素 kill bacteria): As an environmental isolating mediaComponentAmountAgar20gChloramphenicol0.05gDI water1000 ml\nComponentAmountAgar20gChloramphenicol0.05gDI water1000 ml", "PDA+C agarpotato dextrose agar + chloramphenicol (氯黴素 kill bacteria): Use when WA+C agar is not working... |
38,459 | Cold-leaching extraction. A new methodology for obtaining inhibitory substances produced by bacteria in solid media. | 1 | dx.doi.org/10.17504/protocols.io.bhs3j6gn | https://www.protocols.io/view/cold-leaching-extraction-a-new-methodology-for-obt-bhs3j6gn | Catherine Cesa-Luna, Alberto Aguayo-Acosta, Antonino Baez, Jesús Muñoz-Rojas, Verónica Quintero-Hernández | TITLE: Cold-leaching extraction. A new methodology for obtaining inhibitory substances produced by bacteria in solid media.
AUTHORS: Catherine Cesa-Luna, Alberto Aguayo-Acosta, Antonino Baez, Jesús Muñoz-Rojas, Verónica Quintero-Hernández
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Inhibitory su... | [] |
79,814 | Experimental design | 4 | dx.doi.org/10.17504/protocols.io.e6nvwj7m2lmk/v1 | https://www.protocols.click/view/experimental-design-cr7ev9je | michela.deleidi, Bianca Marchetti, Federico Bertoli, Carmela Giachino | TITLE: Experimental design
AUTHORS: michela.deleidi, Bianca Marchetti, Federico Bertoli, Carmela Giachino
[DESCRIPTION]
The protocol details the experimental design.
[STEPS]
SECTION: Experimental design
1. WT and G2019S mice were exposed to intraperitoneal (ip) injections of a low dose of lipopolysaccharide LPS (0,1 ... | ["[Experimental design] WT and G2019S mice were exposed to intraperitoneal (ip) injections of a low dose of lipopolysaccharide LPS (0,1 mg kg-1 Escherichia coli serotype O111:B4) (Sigma-Aldrich), administrated twice a week for 12 weeks (Supplementary Figure 1). Treatments were performed in two different age groups, 3M ... |
20,913 | UC Davis - HbA1c Protocol | null | dx.doi.org/10.17504/protocols.io.ynrfvd6 | null | Peter Havel | TITLE: UC Davis - HbA1c 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">Direct Enzymatic HbA1c test is an enzymatic assay in which lysed whole blood samples are subjected to extensive pr... | ["Use 250 µl of lysis buffer to lyse 20 µl samples of whole blood and calibrators.IMPORTANT: Make sure the samples are totally lysed. Any solid material floating around will interfere with reading in the platereader.", "Mix R1a and R1b reagents together in a 70:30 ratio.", "Add 25 µl of each calibrator and sample to ea... |
70,055 | Sequential Microbial Biomass and Nitrogen Extraction | 6 | dx.doi.org/10.17504/protocols.io.q26g7yr6qgwz/v1 | https://www.protocols.io/view/sequential-microbial-biomass-and-nitrogen-extracti-cgnftvbn | maggie.bowman | TITLE: Sequential Microbial Biomass and Nitrogen Extraction
AUTHORS: maggie.bowman
[DESCRIPTION]
The method is modified from the Hofmockel lab at PNNL, modified from Suding Lab protocol, modified from S. E. Hobbie, 5 May 1998.
[STEPS]
SECTION: Subsample soil
1. Subsample (~8 g) place in V- bottomed conical tube labe... | ["[Subsample soil] Subsample (~8 g) place in V- bottomed conical tube labeled with Cat# and weight. Label caps with Cat#", "[Subsample soil] Gravimetric water content will also be essential for final calculations on a dry weight basis.", "[Data to Collect] Data to Collect", "[Data to Collect] Weight of soil and Cat# fo... |
32,044 | Nested Gibson Assembly | null | dx.doi.org/10.17504/protocols.io.bbikikcw | null | Erin Garza, Vincent Bielinski | TITLE: Nested Gibson Assembly
AUTHORS: Erin Garza, Vincent Bielinski
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This method can be used to increase the efficiency of Gibson Assemblies containing many pieces and/or difficult to assemble DNA fragments.</div></div>
[STEPS]
?. [Select primers]
Usi... | ["[Select primers]\nUsing the same primers that you used to amplify your DNA pieces for the Gibson Assembly, you can pick new primer pairs to amplify multiple fragments that have already been ligated together from the failed Gibson reaction.Example: By using the A-Fwd and B-Rev primers in a PCR reaction, fragments A an... |
null | null | null | dx.doi.org/10.17504/protocols.io.dri54d | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol is for purification of Cas9::NLSSV40::His6 from:<br /><span class="cit-title"><span class="cit-auth cit-auth-type-author">Paix A</span><span class="cit-sep cit-sep-separator">,</span><span class="cit-auth cit-auth-type-author"> Folkmann A</span><span class="cit-sep... | [] |
40,697 | Processing of human surgical samples for single-cell sequencing | 4 | dx.doi.org/10.17504/protocols.io.bjyzkpx6 | https://www.protocols.io/view/processing-of-human-surgical-samples-for-single-ce-bjyzkpx6 | Álvaro Quintanal-Villalonga, Viola Allaj, Andrew Chow, Nisarg Shah, Linas Mazutis, John Thomas Poirier, Triparna Sen, Dana Pe'er, Charles M. Rudin | TITLE: Processing of human surgical samples for single-cell sequencing
AUTHORS: Álvaro Quintanal-Villalonga, Viola Allaj, Andrew Chow, Nisarg Shah, Linas Mazutis, John Thomas Poirier, Triparna Sen, Dana Pe'er, Charles M. Rudin
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Human clini... | ["[Sample collection and transport to the lab]\nRapid transportation of the surgical sample to the lab after resection or biopsy is key to the success of this protocol. To maximize cell viability and sequencing data quality, processing of clinical samples in the lab should begin within an hour of surgical collection, a... |
86,097 | Preparing whole cell samples for immunoblotting | 4 | null | https://www.protocols.io/view/preparing-whole-cell-samples-for-immunoblotting-cybrxsm6 | Louise Uoselis, Louise Uoselis | TITLE: Preparing whole cell samples for immunoblotting
AUTHORS: Louise Uoselis, Louise Uoselis
[DESCRIPTION]
Protocol for preparation of HeLa cell lysates for immunoblotting
[STEPS]
1. Add an appropriate volume of 1x LDS Sample Buffer to each sample.
2. Boil each sample at 99 °C with shaking at maximum speed for 10 m... | ["Add an appropriate volume of 1x LDS Sample Buffer to each sample.", "Boil each sample at 99 °C with shaking at maximum speed for 10 min", "Allow all samples to cool to Room temperature, and quickly centrifuge the samples to collect all liquid in the bottom of the tube. Vortex each sample for ~3 seconds to ensure homo... |
null | null | null | dx.doi.org/10.17504/protocols.io.pysdpwe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The Ecuadorian territory is divided into four natural regions: the coastal lowlands, the Andean highlands, the Amazon basin and the Galapagos Islands. Each of these regions has its own ecosystems and specific vegetation. The purpose of this work is to compile an updated catal... | [] |
64,640 | Expression and purification of mCherry-NDP52 | 4 | dx.doi.org/10.17504/protocols.io.5qpvobdr9l4o/v1 | https://www.protocols.io/view/expression-and-purification-of-mcherry-ndp52-cbc8sizw | Daniel Bernklau, Dorotea Fracchiolla, Justyna Sawa-Makarska | TITLE: Expression and purification of mCherry-NDP52
AUTHORS: Daniel Bernklau, Dorotea Fracchiolla, Justyna Sawa-Makarska
[DESCRIPTION]
This protocol describes how to express in E.Coli human NDP52 N-terminally tagged with mCherry and purify it through His affinity purification followed by Size Exclusion Chromatograph... | ["[Expression] pETDuet-1_6xHis-TEV-mCh-NDP52 (Addgene ID: 187829) was transformed into E. coli Rosetta pLySS cells.", "[Expression] To express the protein grow E. coli Rosetta pLySS cells in 4 L of LB medium (w Amp/Cam) at 37°C until an OD600 nm of 0.4. Next, bring the temperature down to 18°C and grow further to an ... |
61,857 | Surface Density Calculation | 1 | dx.doi.org/10.17504/protocols.io.81wgb65nnlpk/v1 | https://www.protocols.io/view/surface-density-calculation-b8m9ru96 | Liv Jensen | TITLE: Surface Density Calculation
AUTHORS: Liv Jensen
[DESCRIPTION]
This protocol details Surface Density Calculation.
[STEPS]
SECTION: Surface Density Calculation
1. Quantify the fluorescence of a serial dilution of membrane fluorophore and of proteintag fluorophore in 1% SDS-containing buffer (10 micromolar (µM),... | ["[Surface Density Calculation] Quantify the fluorescence of a serial dilution of membrane fluorophore and of proteintag fluorophore in 1% SDS-containing buffer (10 micromolar (µM), 6 micromolar (µM), 2 micromolar (µM), 1 micromolar (µM), 0.5 micromolar (µM) of each fluor).", "[Surface Density Calculation] Compare the ... |
26,336 | Bayesian detection of piecewise linear trends in replicated time-series with application to growth data modelling | null | dx.doi.org/10.17504/protocols.io.5x8g7rw | null | Norman van Rhijn, Panagiotis Papastamoulis, Takanori Furukawa, Magnus Rattray, Mike Bromley, Elaine Bignell | TITLE: Bayesian detection of piecewise linear trends in replicated time-series with application to growth data modelling
AUTHORS: Norman van Rhijn, Panagiotis Papastamoulis, Takanori Furukawa, Magnus Rattray, Mike Bromley, Elaine Bignell
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Generall... | [] |
100,864 | Light microscopy-based neuron tracing and reconstruction | 0 | dx.doi.org/10.17504/protocols.io.5qpvokk5dl4o/v1 | https://www.protocols.io/view/light-microscopy-based-neuron-tracing-and-reconstr-deq83dzw | Rosa Villalba, Thomas Wichmann, Yoland Smith | TITLE: Light microscopy-based neuron tracing and reconstruction
AUTHORS: Rosa Villalba, Thomas Wichmann, Yoland Smith
[DESCRIPTION]
This protocol details the term ‘neuron reconstruction’ is used here to refer to the process of delineating the different components of neurons (soma, axon, dendrites, and dendritic spines... | ["[Step by step protocol (based on Neurolucida system):] Log in/switch on the computer, stage controller and joystick, microscope lamp and camera.", "[Step by step protocol (based on Neurolucida system):] Start observations at the objective lens with the lowest magnification, e.g., 2.5x.", "[Step by step protocol (base... |
null | null | null | dx.doi.org/10.17504/protocols.io.imqcc5w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes how to use a custom written MATLAB script to analyze thickness of choroid on OCT images of both eyes. </p>
[STEPS]
?.
?.
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.eiabcae | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol outlines our bacteriophage/virus taxonomy analyses. This analysis includes profiles for the average order relative abundance for each site, the phage species relative abundance profiles for each patient, and the relative abundance of specific species between sites.... | [] |
50,919 | Using polyan: a Python package for modelling polysome profiles from ribosome density data | 5 | dx.doi.org/10.17504/protocols.io.bvyfn7tn | https://www.protocols.io/view/using-polyan-a-python-package-for-modelling-polyso-bvyfn7tn | Tobias von der Haar | TITLE: Using polyan: a Python package for modelling polysome profiles from ribosome density data
AUTHORS: Tobias von der Haar
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The assessment of transcriptome-wide ribosome binding to mRNAs is useful for studying the dynamic regulation of protein synthe... | ["[General Functionality]\npolyan provides Python functions for modelling polysome profiles from input data that specify transcript abundance and ribosome occupancy of transripts for an organism or cell. Typically, such data are intended to be the result of ribosome footprinting experiments, but in principle any experi... |
70,033 | Mouse Stereotaxic Surgeries for Intracranial Viral Injection | 4 | dx.doi.org/10.17504/protocols.io.81wgby191vpk/v1 | https://www.protocols.io/view/mouse-stereotaxic-surgeries-for-intracranial-viral-cgmrtu56 | taylor.panczyk | TITLE: Mouse Stereotaxic Surgeries for Intracranial Viral Injection
AUTHORS: taylor.panczyk
[DESCRIPTION]
This procedure allows to inject a small volume of solution (in our case, either a suspension of genetically modified viruses, that will infect neurons and will induce the expression of desired proteins, often gen... | ["[Surgical Set] Prepare a clean empty mouse cage on a heating pad and a clean mouse cage with gel food for post-op care", "[Surgical Set] Set up sterile working area including stereotaxic frame", "[Surgical Set] Weigh mouse", "[Surgical Set] Anesthetize mouse in induction chamber (recommended: 2.5% isoflurane, 200ml/m... |
null | null | null | dx.doi.org/10.17504/protocols.io.dqc5sv | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is a protocol for high yield recovery of pure DNA from agarose gels, using GeneJET Gel Extraction and DNA Cleanup Micro Kit
[BEFORE_START]
Add 35 ml 100% ethanol to the <strong>Wash Buffer</strong> concentrate. Add 2.5 ml 100% ethanol to the <strong>Prewash Buffer</strong>... | [] |
29,479 | Imaging and stimulating enteric neurons in the murine large intestine | 1 | dx.doi.org/10.17504/protocols.io.82fhybn | https://www.protocols.io/view/imaging-and-stimulating-enteric-neurons-in-the-mur-82fhybn | Dante Heredia, Thomas Gould, Terence K Smith | TITLE: Imaging and stimulating enteric neurons in the murine large intestine
AUTHORS: Dante Heredia, Thomas Gould, Terence K Smith
[DESCRIPTION]
Protocol for imaging neurons within the murine myenteric plexus.
[GUIDELINES]
This protocol applies to transgenic animals expressing fluorescent calcium indicators in neu... | ["A ventral midline incision is made and the whole colon is carefully excised into a Sylguard lined dissection dish containing oxygenated Krebs-ringer solution.", "Using scissors, cut along the mesenteric border until the colonic tube is now a flat sheet.", "Carefully pin region of interest (proximal, middle or distal)... |
45,463 | R2C2 protocol draft | 4 | null | https://www.protocols.io/view/r2c2-protocol-draft-bqmxmu7n | Alison Tang | TITLE: R2C2 protocol draft
AUTHORS: Alison Tang
[DESCRIPTION]
Total RNA is reverse transcribed and PCR amplified using the smartseq2 system (with indexed oligo-dTs). Complementary DNA is then size selected for transcripts >=2.5 kb with a low melt agarose gel extraction. Size-selected cDNA and non-size-selected cDNA ar... | ["[cDNA synthesis, adding oligo-dT indexes] Add 6 µL mix #2 to each tube (10 µL total volume).", "[cDNA synthesis, adding oligo-dT indexes] Thaw oligo-dT, dNTP, DTT, Superase-In, 5x SmartScribe buffer, TSO SmartSeq primer on ice.", "[cDNA synthesis, adding oligo-dT indexes] Make mix #2, 6 µL for each reaction.", "[cDN... |
null | null | null | dx.doi.org/10.17504/protocols.io.n7qdhmw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The monthly quality control is a more extensive quality check of our 3T MRI system but also the other computers in the operator room. </p>
<p> </p>
<p>The monthly quality control consists of the following components:</p>
<ul>
<li>Virus scan on scan-computer</li>
<li>Moving ey... | [] |
39,912 | Peritoneal dialysis in extremely and low birth weight infants: a pooled analysis of case reports | 1 | dx.doi.org/10.17504/protocols.io.bi8gkhtw | https://www.protocols.io/view/peritoneal-dialysis-in-extremely-and-low-birth-wei-bi8gkhtw | Ioannis Bellos, Vasilios Karageorgiou | TITLE: Peritoneal dialysis in extremely and low birth weight infants: a pooled analysis of case reports
AUTHORS: Ioannis Bellos, Vasilios Karageorgiou
[STEPS]
?. Search strategy: Through a structured algorithm search, major databases will be searched from inception to 01 August 2020. The databases will be MEDLINE, Sco... | ["Search strategy: Through a structured algorithm search, major databases will be searched from inception to 01 August 2020. The databases will be MEDLINE, Scopus, Web of science, clinicaltrials.gov and Google Scholar. Keywords provided, with ad hoc modification, will include: peritoneal dialysis, neonate, acute kidney... |
91,121 | W-5 WATER SHIPPING | 4 | dx.doi.org/10.17504/protocols.io.ewov1qxnkgr2/v1 | https://www.protocols.io/view/w-5-water-shipping-c48ryzv6 | REDI-NET Consortium | TITLE: W-5 WATER SHIPPING
AUTHORS: REDI-NET Consortium
[DESCRIPTION]
This protocol describes water shipping.
[GUIDELINES]
OBJECTIVE
To outline steps for proper packaging and shipping of preserved water samples from a REDI-NET Silver Lab to a REDI-NET Gold Lab.
SUMMARY/SCOPE
The overarching aim of the REDI-NET is t... | ["[SAMPLE PREPARATION] Primary holding sample holding containers must be leak-proof. Samples should be preserved in appropriate preservative, if applicable (REDI-NET Water Processing SOP W-2). Ensure that the lids are tightly closed to prevent leaking of storage media while in transit.", "[SAMPLE PREPARATION] Pack vial... |
30,926 | Micro-CT imaging of rat stomach vasculature | 1 | dx.doi.org/10.17504/protocols.io.bafnibme | https://www.protocols.io/view/micro-ct-imaging-of-rat-stomach-vasculature-bafnibme | Deborah Jaffey, Logan Chesney, Terry Powley | TITLE: Micro-CT imaging of rat stomach vasculature
AUTHORS: Deborah Jaffey, Logan Chesney, Terry Powley
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes how to prepare a rat stomach for micro-CT imaging of the vasculature. A lead-containing silicone-based curable material is ... | ["[Set-up]\nFeed the rat per the details given in protocol \"Micro-CT imaging of iodine-stained rat stomach\".", "[Set-up]\nWeigh the rat to determine the appropriate dose of ketamine + xylazine cocktail. Prepared cocktail consists of 10 mL of 100 mg/mL ketamine and 1 mL of 100 mg/mL xylazine for a total volume of 11 m... |
88,641 | Conversion of Plasmid DNA to Minicircles | 1 | null | https://www.protocols.io/view/conversion-of-plasmid-dna-to-minicircles-c2s9yeh6 | Mathew Chu | TITLE: Conversion of Plasmid DNA to Minicircles
AUTHORS: Mathew Chu
[DESCRIPTION]
Plasmid DNA is conventionally the choice of vector for cloning and delivering transgenes into cells. However, for site-specific integration into the host genome, it is desirable that only the transgene sequence is transferred without ele... | ["[Adapting the Plasmid Backbone for Minicircle Production] Design a cloning site for the transgene which consists of outward-facing recognition sequences (RS) for a Type IIS restriction endonuclease:\n\n \n\nThe left and right sequences should be homologous to the transgene. A stuffer sequence of approximately 50 nt s... |
84,253 | Protocol SAM-Seq A.Thaliana | 4 | dx.doi.org/10.17504/protocols.io.8epv5x1xdg1b/v1 | https://www.protocols.io/view/protocol-sam-seq-a-thaliana-cwh5xb86 | basile.leduque, Quadrana Leandro | TITLE: Protocol SAM-Seq A.Thaliana
AUTHORS: basile.leduque, 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 present cha... | ["[Plant nuclei purification and permeabilization] Add the powder to 25 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. 675 µl Formaldehyde 37% in 25ml of EB1). Incubate 5 minutes", "[Plant ... |
42,333 | An optimised method for intact nuclei isolation from diatoms | 4 | dx.doi.org/10.17504/protocols.io.bmj5k4q6 | https://www.protocols.io/view/an-optimised-method-for-intact-nuclei-isolation-fr-bmj5k4q6 | Rossella Annunziata, Cecilia Balestra, Pina Marotta, Antonella Ruggiero, Francesco Manfellotto, Giovanna Benvenuto, Elio Biffali, Mariella Ferrante | TITLE: An optimised method for intact nuclei isolation from diatoms
AUTHORS: Rossella Annunziata, Cecilia Balestra, Pina Marotta, Antonella Ruggiero, Francesco Manfellotto, Giovanna Benvenuto, Elio Biffali, Mariella Ferrante
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Due to their abundance in t... | ["[Collection of cells ]\nPellet around 20-30 x 106cells for 15’ at 1800 xg at 18°C in 50 mL conical tubes", "[Collection of cells ]\nCollect pelleted cells in 2 mL tubes and spin 10’ at 1500 xg at 18°C; merge all cells in one 2 mL tube and spin 10’ at 1500 xg at 18°C;", "[Collection of cells ]\nPellet around 20-30 x 1... |
71,105 | Prepare agarose pad for microscopy (2022 iGEM) | 1 | dx.doi.org/10.17504/protocols.io.8epv5jze5l1b/v1 | https://www.protocols.io/view/prepare-agarose-pad-for-microscopy-2022-igem-chn9t5h6 | Team Fudan iGEM | TITLE: Prepare agarose pad for microscopy (2022 iGEM)
AUTHORS: Team Fudan iGEM
[DESCRIPTION]
This protocol describe the steps to perform fluorescence microscopy for E. coli
[BEFORE_START]
Culture cells in liquid media
[GUIDELINES]
Cells should be cultured to a late log phase to increase cell number for microscopy.
... | ["[Cell growth] Grow cells to late-log phase density (e.g. OD600 > 0.6).", "[Agarose pads] Prepare a 1% agarose in distilled water, by adding sufficient low-melting agarose to water and dissolve agarose by heating in a microwave for 30-60 seconds.\na", "[Microscopy GFP] Place the slide onto the microscope stage, with t... |
50,984 | Workflow for wooden contact samples in use-wear experiments with bronze axe replicas (MAP-protocol_B) | 1 | dx.doi.org/10.17504/protocols.io.bv2gn8bw | https://www.protocols.io/view/workflow-for-wooden-contact-samples-in-use-wear-ex-bv2gn8bw | Ulrich Thaler, Walter Gneisinger | TITLE: Workflow for wooden contact samples in use-wear experiments with bronze axe replicas (MAP-protocol_B)
AUTHORS: Ulrich Thaler, Walter Gneisinger
[DESCRIPTION]
Focussing on the role of contact materials as an element of variable control in archaeological use-wear experiments, this protocol sets out a workflow fo... | ["[Acquisition of contact material] Acquisition of contact material\n\nobtain plank of high-quality beechwood (Fagus sylvatica) in a thickness that corresponds to the intended width of your contact samples", "[Preparation of contact samples] Preparation of contact samples", "[Preparation of contact samples] Cutting of ... |
25,109 | RNA Isolation from Plant Tissue Protocol 7: pBIOZOL-LiCl Method | null | dx.doi.org/10.17504/protocols.io.4rvgv66 | null | null | TITLE: RNA Isolation from Plant Tissue Protocol 7: pBIOZOL-LiCl Method
AUTHORS:
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Implemented by: Beijing Genomics Institute </div><div class = "text-block"><span>This protocol is part of a collection of eighteen protocols used to isolate total RNA from... | ["Grind tissue to a powder in liquid nitrogen.", "Add of cold () pBIOZOL reagent for up to gram of frozen, ground tissue.\n1.3 ml\n4 °C\n100 mg", "Incubate the tube for at .\n0 Room temperature\nLay the tube down horizontally to maximize surface area during RNA extraction.", "Centrifuge at for .", "Transfer the sup... |
79,508 | Handling and Sampling Small Non-Volant Mammals - ISL Peru | 1 | dx.doi.org/10.17504/protocols.io.kxygx9xkdg8j/v1 | https://www.protocols.io/view/handling-and-sampling-small-non-volant-mammals-isl-crvuv66w | Cristian Tirapelle, Leticia Gutiérrez, Pamela Sánchez-Vendizú, Daniel Llancachahua-Tarqui, Mrinalini Watsa, Gideon Erkenswick | TITLE: Handling and Sampling Small Non-Volant Mammals - ISL Peru
AUTHORS: Cristian Tirapelle, Leticia Gutiérrez, Pamela Sánchez-Vendizú, Daniel Llancachahua-Tarqui, Mrinalini Watsa, Gideon Erkenswick
[DESCRIPTION]
Program Timing
Sample collection occurs annually during the rainforest dry season (June - August). Sampl... | ["[TRAP INSPECTION] When the team returns from trap inspection, all Sherman traps should be placed outside the tent, in shade, and protected from rain", "[PROCESSING SETUP] Setup the processing table:\nclean table surfaces (in order) with 10% diluted bleach -> water -> 70% ETOH,\ntake out enough sampling supplies for t... |
81,635 | TS Spurrs - Cell Monolayer on Thermanox coverslips (TM - 013) | 4 | dx.doi.org/10.17504/protocols.io.n92ldpk17l5b/v1 | https://www.protocols.io/view/ts-spurrs-cell-monolayer-on-thermanox-coverslips-t-ctybwpsn | sandra.crameri | TITLE: TS Spurrs - Cell Monolayer on Thermanox coverslips (TM - 013)
AUTHORS: sandra.crameri
[DESCRIPTION]
Processing a cell monolayer on Thermanox coverslips to Spurrs resin block for EM.
[GUIDELINES]
All step times are the minimum time required. Longer steps are acceptable.
[STEPS]
SECTION: HEADER
1. SAN:
SPEC N... | ["[HEADER] SAN:\n\n\nSPEC No:\n\n\nOPERATOR & STEPS:\n\n\nOPERATOR & STEPS:", "[Conventional - with reduced times for monlayer thickness] 2.5% % volume in 0.1 Molarity (M) Sorenson's phosphate buffer pH 07.2 300 mosmol/kg20 min.", "[Conventional - with reduced times for monlayer thickness] Wash buffer 5 min", "[Con... |
102,727 | NGS library preparation using Ovation RNA-Seq System V2 (M01206 v9) and Ovation Ultralow System V2 (M01437 v2) for animal tissue samples | 0 | dx.doi.org/10.17504/protocols.io.14egn6w96l5d/v1 | https://www.protocols.io/view/ngs-library-preparation-using-ovation-rna-seq-syst-dgjf3ujn | Ine Boonen, Magda Bletsa, Yiqiao Li, Philippe Lemey | TITLE: NGS library preparation using Ovation RNA-Seq System V2 (M01206 v9) and Ovation Ultralow System V2 (M01437 v2) for animal tissue samples
AUTHORS: Ine Boonen, Magda Bletsa, Yiqiao Li, Philippe Lemey
[DESCRIPTION]
This protocol is used for successful NGS library preparation from total RNA of animal tissue samples... | ["[B. First Strand cDNA Synthesis] Remove the First Strand Primer Mix (blue: A1) and First Strand Buffer mix (Blue: A2) from the freezer. Let it thaw at Room temperature. Mix by vortexing, spin down and place on ice.", "[A. Sample Preparation for Ovation RNA-Seq system V2] Remove Nuclease-free water (Green: D1) from th... |
66,327 | Recharge PM Weight Loss: Reviews, Side Effects & Precautions! | 3 | dx.doi.org/10.17504/protocols.io.14egn7qzyv5d/v1 | https://www.protocols.io/view/recharge-pm-weight-loss-reviews-side-effects-amp-p-cczxsx7n | brettlee | TITLE: Recharge PM Weight Loss: Reviews, Side Effects & Precautions!
AUTHORS: brettlee
[DESCRIPTION]
Product Name – Recharge PM
Composition –Natural Organic compound
Side-Effects–NA
Availability– Online
Rating –★★★★★
Official Website– Recharge PM.com
Weight reduction could be a tough process. Lots of people are... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.kmxcu7n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Complement activation correlates to rheumatoid arthritis disease activity, and increased amounts of the complement split product C5a is observed in synovial fluids from rheumatoid arthritis patients. Blockade of C5a or its receptor (C5aR) is efficacious in several arthritis m... | [] |
29,263 | Recordings with multiple Neuropixels probes in head-restrained mice | 1 | dx.doi.org/10.17504/protocols.io.8tphwmn | https://www.protocols.io/view/recordings-with-multiple-neuropixels-probes-in-hea-8tphwmn | Susu Chen, Karel Svoboda | TITLE: Recordings with multiple Neuropixels probes in head-restrained mice
AUTHORS: Susu Chen, Karel Svoboda
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Step-by-step instructions for electrophysiological recordings using multiple Neuropixels probes in head-fixed mice </div></div>
[STEPS]
?. Bas... | ["Based on target brain regions, set up manipulator azimuth and pitch angles before each recording session. Manipulators should be positioned to be able to reach target areas while not colliding with each other.", "Paint individual electrodes with CM-DiI (https://www.protocols.io/view/painting-neuropixels-probes-and-ot... |
27,828 | Rocky Mountain adventures in Genomic DNA sample preparation, ligation protocol optimisation / simplification and Ultra long read generation | null | dx.doi.org/10.17504/protocols.io.7euhjew | null | John Tyson | TITLE: Rocky Mountain adventures in Genomic DNA sample preparation, ligation protocol optimisation / simplification and Ultra long read generation
AUTHORS: John Tyson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">We have been playing quite a bit with native genomic DNA sequencing for a project we ... | [] |
86,063 | Transferrin uptake assay to measure Clathrin-mediated endocytosis in HIPCS derived neurons. | 4 | dx.doi.org/10.17504/protocols.io.n2bvj38d5lk5/v1 | https://www.protocols.io/view/transferrin-uptake-assay-to-measure-clathrin-media-cyapxsdn | Sakthi Kumar | TITLE: Transferrin uptake assay to measure Clathrin-mediated endocytosis in HIPCS derived neurons.
AUTHORS: Sakthi Kumar
[DESCRIPTION]
This protocol is used to measure Transferrin uptake as a way to investigate Clathrin-mediated endocytosis in HIPCS derived neurons, or other cell types.
[STEPS]
SECTION: Reagents need... | ["[Reagents needed:] 1. Human Transferrin conjugated with Alexa Fluor 647 (Thermo Fisher, Catalog no: T23366).\nNote: Transferrin conjugate is also available with Alexa Fluor 488, Alexa Fluor 546. The user may want to use a specific conjugate based on the need of their experiments. We have optimized this protocol for T... |
null | null | null | dx.doi.org/10.17504/protocols.io.h6nb9de | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?. | [] |
67,206 | Researcher led sample preparation for LC-MS using the BioMS research core facility | 2 | dx.doi.org/10.17504/protocols.io.261genmkdg47/v1 | https://www.protocols.io/view/researcher-led-sample-preparation-for-lc-ms-using-cdves63e | ronan.ocualain | TITLE: Researcher led sample preparation for LC-MS using the BioMS research core facility
AUTHORS: ronan.ocualain
[DESCRIPTION]
This is a collection of protocols that covers the processing of most biological samples for proteomics, from collection of sample, up to data acquisition using LC-MS
[BEFORE_START]
This me... | [] |
94,805 | Specificity index (pSI) calculation | 4 | dx.doi.org/10.17504/protocols.io.8epv5x8mjg1b/v1 | https://www.protocols.io/view/specificity-index-psi-calculation-c8tvzwn6 | Peter Kilfeather | TITLE: Specificity index (pSI) calculation
AUTHORS: Peter Kilfeather
[DESCRIPTION]
Specificity index (pSI) calculation from Kilfeather, Khoo et al., 2024
[STEPS]
SECTION: Protocol
1. To calculate the specificity index of genes detected within TRAP/RiboTag datasets of dopaminergic neurons and other cell types within ... | ["[Protocol] To calculate the specificity index of genes detected within TRAP/RiboTag datasets of dopaminergic neurons and other cell types within midbrain, pSI (v1.1) was used with default settings22,24,38–40,73. Genes were considered significantly specifically expressed with an FDR-adjusted P value < 0.01."] |
86,544 | Cichlid genome modification - Malawi cichlids | 4 | dx.doi.org/10.17504/protocols.io.kqdg3xxxeg25/v1 | https://www.protocols.io/view/cichlid-genome-modification-malawi-cichlids-cyrqxv5w | Scott Juntti, bethan_clark | TITLE: Cichlid genome modification - Malawi cichlids
AUTHORS: Scott Juntti, bethan_clark
[DESCRIPTION]
Here we provide a microinjection protocol for the modification of cichlid fish via CRISPR or transgenesis.
This is our forked version of the protocol provided by Scott Juntti (https://www.protocols.io/view/cichlid-... | ["[General considerations] Obtaining viable embryos can be the most trying part of generating transgenic fish. Putting in time up front to maximize survival, and to be able to get embryos on demand will be well worth your time!\nIf your cichlid species of choice is not a year-round spawner, get to know the conditions t... |
89,352 | Generating multiple stage-matched C. elegans hybrids and parental strains simultaneously | 4 | dx.doi.org/10.17504/protocols.io.5jyl8p15rg2w/v1 | https://www.protocols.io/view/generating-multiple-stage-matched-c-elegans-hybrid-c3hgyj3w | Avery Davis Bell, Francisco Valencia, Annalise Paaby | TITLE: Generating multiple stage-matched C. elegans hybrids and parental strains simultaneously
AUTHORS: Avery Davis Bell, Francisco Valencia, Annalise Paaby
[DESCRIPTION]
Here we provide a protocol for generating RNA from synchronized C. elegans F1s from crosses of multiple wild strains to a common reference strain (... | ["[Worm maintenance prior to start of experiment] In general, follow standard worm culture procedures (Stiernagle 2006). Grow worms at 18°C or cooler if any strains have known or suspected mortal germline phenotypes (Frezal et al. 2018)", "[Worm maintenance prior to start of experiment] Grow healthy cultures of each st... |
18,921 | Infrared thermography and platform vibratory - protocol | null | dx.doi.org/10.17504/protocols.io.wqhfdt6 | null | Eloá Moreira-Marconi, Marcia Cristina Moura-Fernandes, Patrícia Lopes-Souza, Ygor Teixeira-Silva, Aline Reis da Silva, Renata Marques Marchon, Eliane de Oliveira Guedes-Aguiar, Laisa Liane Paineiras-Domingos, Danúbia da Cunha de Sá-Caputo, Danielle Soares Morel, Carla Fontoura Dionello, Sérgio Oliveira de Carvalho, Mar... | TITLE: Infrared thermography and platform vibratory - protocol
AUTHORS: Eloá Moreira-Marconi, Marcia Cristina Moura-Fernandes, Patrícia Lopes-Souza, Ygor Teixeira-Silva, Aline Reis da Silva, Renata Marques Marchon, Eliane de Oliveira Guedes-Aguiar, Laisa Liane Paineiras-Domingos, Danúbia da Cunha de Sá-Caputo, Danielle... | ["[CEP]\nThe local ethics committee approved the study (Certificado de Apresentação para Apreciação Ética - CAAE - 19826413.8.0000.5259)", "[REBEC]\nThe trial registration (Registro Brasileiro de Ensaios Clínicos – REBEC - RBR-738wng)", "[Inclusion criteria]\nThe participants had to meet the following inclusion criteri... |
79,874 | Constructs and generation of stable cell lines | 1 | dx.doi.org/10.17504/protocols.io.rm7vzbr98vx1/v1 | https://www.protocols.io/view/constructs-and-generation-of-stable-cell-lines-cr9av92e | michela.deleidi | TITLE: Constructs and generation of stable cell lines
AUTHORS: michela.deleidi
[DESCRIPTION]
Protocol used to generate stable Flp-In T-REx-HEK 293 cell lines expressing WT or mutant GCase (E326K or L444P) as
a V5-FLAG-tagged protein using a tetracycline-inducible system.
[STEPS]
1. Constructs were purchased from IDT... | ["Constructs were purchased from IDT (gBlocks Gene Fragments) and subcloned into pcDNA5/frt/to (Thermo Fisher Scientific, # V652020).", "For the generation of V5-FLAG-GCase lines, the tag was positioned at the N-terminus, three aa after the cleavage site of the leader sequence. These three amino acids are repeated afte... |
null | null | null | dx.doi.org/10.17504/protocols.io.esibece | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
For use in <a href="https://www.protocols.io/view/CviJI-Purification-From-IL-3A-Virus-Infected-NC64A-er3bd8n" target="_blank">CviJI Purification From IL-3A Virus Infected NC64A Chlorella</a>.
[STEPS]
?.
?.
?. | [] |
28,727 | Ion-exchange purification of fucoidans | 1 | null | https://www.protocols.io/view/ion-exchange-purification-of-fucoidans-8axhsfn | Andreas Sichert, Jan-Hendrik Hehemann | TITLE: Ion-exchange purification of fucoidans
AUTHORS: Andreas Sichert, Jan-Hendrik Hehemann
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left"><span>Fucoidans are a diverse class of sulfated polysaccharides integral to the cell wall of brown algae and d... | ["[Buffer preparation]\nFilter all buffers through a 0.2 μm bottle top filter to remove dust", "[Prepare polysaccharide solution]\nMix 0.5 g fucoidan in 500 mL of 50 mM Tris pH 7.5 in ddH2O", "[Prepare polysaccharide solution]\nUse a magnetic stirrer and heat ~50-60°C for ~1h or until fucoidans dissolved", "[Prepare po... |
72,941 | Oral microbiome DNA extraction using Zymobiomics | 4 | null | https://www.protocols.io/view/oral-microbiome-dna-extraction-using-zymobiomics-cjgmuju6 | Thidathip Wongsurawat | TITLE: Oral microbiome DNA extraction using Zymobiomics
AUTHORS: Thidathip Wongsurawat
[DESCRIPTION]
A method of DNA extraction of oral mouthwash samples for use in microbiome studies that utilize next-generation sequencing (NGS) and/or third-generation sequencing.
[STEPS]
1. ZymoBIOMICS™ DNA Extraction (following th... | ["ZymoBIOMICS™ DNA Extraction (following the manufacturer’s instruction except for beat beating time) (reference no. 1)\n1.1. Transfer 5-10 ml collected saliva/ mouthwash sample to 15 ml sterile conical centrifuge tube\n1.2. Centrifuge the tube at 4000 rpm for 20 minutes at 4°C\n1.3. Discard supernatant as much superna... |
null | null | null | dx.doi.org/10.17504/protocols.io.p4adqse | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is a protocol to transiently transfect <em>Capsaspora owczarzaki</em>, a unicellular eukaryote</p>
[BEFORE_START]
<p><strong>Transfection Reagents preparation</strong></p>
<p> </p>
<p><strong>Growth medium (for 1 L)</strong>: 10 g Peptone (BD, #211677), 10 g Yeast Extra... | [] |
93,403 | Variant to gene to function workflow for endothelial cell programs related to CAD | 4 | null | https://www.protocols.io/view/variant-to-gene-to-function-workflow-for-endotheli-c7f3zjqn | Gavin R. Schnitzler, Helen Kang, Shi "House" Fang, ronghao, Vivian Lee, Rosa Ma, Ramcharan Angom, Jesse Engreitz, Rajat M. Gupta | TITLE: Variant to gene to function workflow for endothelial cell programs related to CAD
AUTHORS: Gavin R. Schnitzler, Helen Kang, Shi "House" Fang, ronghao, Vivian Lee, Rosa Ma, Ramcharan Angom, Jesse Engreitz, Rajat M. Gupta
[DESCRIPTION]
Linking variants from genome-wide association studies (GWAS) to underlying mec... | ["[General cell culture] Telomerase-immortalized human aortic endothelial cells (TeloHAEC) were purchased from ATCC (CRL-4052), and grown in Lifeline VEGF endothelial cell media (LL-0005) with 1x Penn/Strep. Cells were plated at a density of 0.5-1.0 x 106 cells per 10 cm plate and split before reaching 4 x 106/plate (3... |
76,484 | PacBio Isoseq samples preparation | 4 | dx.doi.org/10.17504/protocols.io.yxmvm25j6g3p/v1 | https://www.protocols.io/view/pacbio-isoseq-samples-preparation-cnxcvfiw | anita.adami | TITLE: PacBio Isoseq samples preparation
AUTHORS: anita.adami
[DESCRIPTION]
This protocol described how to prepare samples for PacBio Isoseq
[STEPS]
SECTION: RNA extraction
1. The total RNA was obtained from brain tissue samples using miRNA Easy Mini Kit (Qiagen). The manufacturer's instructions were followed step-by... | ["[RNA extraction] The total RNA was obtained from brain tissue samples using miRNA Easy Mini Kit (Qiagen). The manufacturer's instructions were followed step-by-step.", "[Samples QC evaluation] At the Nation Genomics Infrastructure of Sweden, input QC of samples was performed on the Agilent Bioanalyzer instrument, usi... |
47,330 | Cryopreservation of Microalgae | 4 | null | https://www.protocols.io/view/cryopreservation-of-microalgae-bsganbse | Lynn Doran | TITLE: Cryopreservation of Microalgae
AUTHORS: Lynn Doran
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Cryopreservation protocol for the microalgae Ostreococcus tauri for long term storage.</div><div class = "text-block">Cell viability of O. tauri at -196 for x months = unknown</div><div class =... | ["[Cryopreservation]\nVerify culture concentration daily. Cryopreservation should be made towards the end of the log phase or 1-2 days after the beginning of the stationary phase.", "[Cryopreservation]\nIn a laminar flow hood, add filter sterilized DMSO (Diméthylsulfoxyde) to a final concentration to of culture and t... |
8,933 | RNA extraction from Escherichia col | 1 | dx.doi.org/10.17504/protocols.io.kydcxs6 | https://www.protocols.io/view/rna-extraction-from-escherichia-col-kydcxs6 | Alice Pawlowski, Lutz Berwanger | TITLE: RNA extraction from Escherichia col
AUTHORS: Alice Pawlowski, Lutz Berwanger
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">RNA extraction from E. coli cells based on the method described by Chomczynski and Sacchi, 1987</div></div>
[STEPS]
?. [Cell prepartion]
centrifuge for 5 min at 4°C an... | ["[Cell prepartion]\ncentrifuge for 5 min at 4°C and 14000 x gdiscard the supernatant and resuspend the pellet in 1 ml NucleoZOL (Macherey and Nagel), place on dry iceproceed to next step or store cells at -20 or -80 °C\n4 °C", "[Cell prepartion]\nWear safety gear", "[RNA-isolation]\nincubate the sample at 65 °C and 25... |
23,809 | Tandem Mass Tag (TMT) 10-plex Labeling of Yeast Peptides | null | dx.doi.org/10.17504/protocols.io.3g9gjz6 | null | Rebecca E. Hardman, Jeffrey Lewis | TITLE: Tandem Mass Tag (TMT) 10-plex Labeling of Yeast Peptides
AUTHORS: Rebecca E. Hardman, Jeffrey Lewis
[STEPS]
?. [DAY 1: CELL LYSIS and TRYPSIN DIGEST]
Thaw frozen cells (collected in 50-ml conical tubes) at room temperature, making sure not to leave cells thawed longer than necessary. Centrifuge at max speed (4,... | ["[DAY 1: CELL LYSIS and TRYPSIN DIGEST]\nThaw frozen cells (collected in 50-ml conical tubes) at room temperature, making sure not to leave cells thawed longer than necessary. Centrifuge at max speed (4,696 rcf) in a swinging bucket rotor for 2 minutes. Carefully remove remaining media by pipetting. Suspend in 1 ml wa... |
null | null | null | dx.doi.org/10.17504/protocols.io.ihvcb66 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
30,480 | 7T MRI Protocol for response to Respiratory-gated Auricular Vagal Afferent Nerve Stimulation | 1 | dx.doi.org/10.17504/protocols.io.9zqh75w | https://www.protocols.io/view/7t-mri-protocol-for-response-to-respiratory-gated-9zqh75w | Vitaly Napadow, Roberta Sclocco, Vitaly Napadow, Roberta Sclocco | TITLE: 7T MRI Protocol for response to Respiratory-gated Auricular Vagal Afferent Nerve Stimulation
AUTHORS: Vitaly Napadow, Roberta Sclocco, Vitaly Napadow, Roberta Sclocco
[DESCRIPTION]
This is the 7T MRI protocol for a study of the subject to Respiratory-gated Auricular Vagal Afferent Nerve Stimulation in the area... | [] |
96,735 | Vaccinium floribundum Genome Assembly and Annotation Script | 0 | dx.doi.org/10.17504/protocols.io.n92ldmo4nl5b/v1 | https://www.protocols.io/view/vaccinium-floribundum-genome-assembly-and-annotati-dap72drn | Martina Albuja-Quintana, Gabriela Pozo, Milton Gordillo-Romero, Carolina E. Armijos, Maria de Lourdes Torres | TITLE: Vaccinium floribundum Genome Assembly and Annotation Script
AUTHORS: Martina Albuja-Quintana, Gabriela Pozo, Milton Gordillo-Romero, Carolina E. Armijos, Maria de Lourdes Torres
[DESCRIPTION]
Oxford Nanopore long reads and Illumina short reads obtained from sequencing the DNA of a Vaccinum floribundum specimen ... | ["[Oxford Nanopore Sequencing - Raw Reads Filtering, Trimming, and Statistics] Raw Read Adapter Filtering \nPorechop v0.2.4 (RRID:SCR_016967)", "[Oxford Nanopore Sequencing - Raw Reads Filtering, Trimming, and Statistics] Raw Read Quality and Length Trimming\nNanofilt v2.8.0 (RRID:SCR_016966)", "[Oxford Nanopore Sequen... |
60,143 | Single-Nuclei Isolation From Snap Frozen Axolotl Brain | 4 | null | https://www.protocols.io/view/single-nuclei-isolation-from-snap-frozen-axolotl-b-b6yprfvn | Ashley Maynard, Fides Zenk | TITLE: Single-Nuclei Isolation From Snap Frozen Axolotl Brain
AUTHORS: Ashley Maynard, Fides Zenk
[DESCRIPTION]
This protocol enables isolation of single nuclei from frozen pallium microdissections and whole pallium dissections (from axolotl) for the purpose of generating single-nuclei gene-expression libraries foll... | ["[Nuclei isolation] Use pre-cooled buffers and storeon ice, perform isolation steps on ice, use pre-cooled micro-centrifuge at 4 °C.", "[Nuclei isolation] Put tissue in cold 1.5 mLtube", "[Nuclei isolation] Add 50 µLof lysis buffer", "[Nuclei isolation] Using an electric grinder. Grind the tissue for 10 s (or 2-5 pul... |
null | null | null | dx.doi.org/10.17504/protocols.io.jsacnae | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Today, we are going to get you set up for your class project. You will need a class directory for putting all of your files. Also, you will need to download the data for your project (see the list of SRR numbers in D2L).</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
61,958 | Sequential Double Digest | 1 | dx.doi.org/10.17504/protocols.io.6qpvr6m72vmk/v1 | https://www.protocols.io/view/sequential-double-digest-b8rerv3e | Larissa de Clauser | TITLE: Sequential Double Digest
AUTHORS: Larissa de Clauser
[DESCRIPTION]
This is the Sequential Double Digest Protocol with Standard Restriction Enzymes. If there is no buffer in which the two enzymes exhibit > 50% activity, this sequential digest can be performed.
[BEFORE_START]
NEB's online tools, Double Digest ... | ["Set up the following reaction using the restriction endonuclease that has the lowest salt concentration in its recommended buffer (total reaction volume 50 µl).", "Mix components by pipetting the reaction mixture up and down, or by \"flicking\" the reaction tube.", "Quick (\"touch\") spin-down in a microcentrifuge. D... |
null | null | null | dx.doi.org/10.17504/protocols.io.ecjbaun | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<strong>Viral Bioinformatic Resource Centre</strong>
<ul>
<li><strong>Provide databases of viral genomic information.</strong>
<ul>
<li>Please check the <strong><em>Organisms</em></strong> menu to see which viruses we support: we’re now focusing on large DNA viruses</li>
<li>The... | [] |
68,899 | Sexual and reproductive health during Covid: a global systematic review of health system responses and service delivery adaptations | 1 | dx.doi.org/10.17504/protocols.io.36wgq7m7yvk5/v2 | https://www.protocols.io/view/sexual-and-reproductive-health-during-covid-a-glob-cfibtkan | hlconyers, Megan Srinivas, Eneyi Kpokiri, Heather Shams, Hayley Conyers | TITLE: Sexual and reproductive health during Covid: a global systematic review of health system responses and service delivery adaptations
AUTHORS: hlconyers, Megan Srinivas, Eneyi Kpokiri, Heather Shams, Hayley Conyers
[DESCRIPTION]
The COVID-19 pandemic is on-going and continues to challenge the delivery of SRH serv... | ["[Background] The COVID-19 pandemic is on-going and continues to challenge the delivery of SRH services across the globe. The impact has created imbalances in healthcare provision, disruptions of routine essential services and, in most settings, has required redeployment of scarce healthcare personnel across SRH servi... |
53,956 | SS-VIME: Single-Source Virome-Microbiome Extraction Protocol | 4 | dx.doi.org/10.17504/protocols.io.kxygxp64zl8j/v1 | https://www.protocols.io/view/ss-vime-single-source-virome-microbiome-extraction-byxcpxiw | Abdonaser Poursalavati | TITLE: SS-VIME: Single-Source Virome-Microbiome Extraction Protocol
AUTHORS: Abdonaser Poursalavati
[DESCRIPTION]
SS-VIME: Single-Source Virome-Microbiome Extraction Protocol
For simultaneous profiling of viral, bacterial, and fungal communities from a single soil sample
Naser Poursalavati, PhD Candidate in Soil Vi... | ["[Prior to Extraction Day] Sample Storage: Immediately upon arrival in the lab, freeze soil samples at -80°C (or -20°C for storage durations under 6 months). This step is crucial to preserve microbial community integrity.", "[Prior to Extraction Day] Prepare Bead Tubes: Autoclave 0.1 mm and 3 mm silica beads separatel... |
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