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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109,514 | AAV Production and Purification | 0 | dx.doi.org/10.17504/protocols.io.rm7vzj5d2lx1/v3 | https://www.protocols.io/view/aav-production-and-purification-dn7i5hke | 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 ... |
78,547 | Prepare sodium azide | 4 | null | https://www.protocols.io/view/prepare-sodium-azide-cqxtvxnn | Andreas Sagen | TITLE: Prepare sodium azide
AUTHORS: Andreas Sagen
[DESCRIPTION]
Prepare sodium azide solution
[STEPS]
SECTION: 50 mL 10% sodium azide
1. In a 50 mL tube, fill with 40 mL endotoxin-free water
SECTION: 50 mL 10% sodium azide
2. Empty a full bottle of 5 g Sodium azide powder in the tube
Materials:
SECTION: 50 mL... | ["[50 mL 10% sodium azide] In a 50 mL tube, fill with 40 mL endotoxin-free water", "[50 mL 10% sodium azide] Empty a full bottle of 5 g Sodium azide powder in the tube\n\nMaterials:", "[50 mL 10% sodium azide] Mix powder completely, then top-up to 50 mL endotoxin-free water", "[50 mL 10% sodium azide] Filter solution w... |
35,577 | Diagnosis and treatment of plasmablastic lymphoma, plasmablastic myeloma and plasmablastic neoplasm: protocol for a scoping review | null | dx.doi.org/10.17504/protocols.io.beyzjfx6 | null | Hirotaka Mori, Masahiko Fukatsu, Hiroshi Ohkawara, Yuka Oka, Yuki Kataoka, Shunsuke Taito, Takayuki Ikezoe | TITLE: Diagnosis and treatment of plasmablastic lymphoma, plasmablastic myeloma and plasmablastic neoplasm: protocol for a scoping review
AUTHORS: Hirotaka Mori, Masahiko Fukatsu, Hiroshi Ohkawara, Yuka Oka, Yuki Kataoka, Shunsuke Taito, Takayuki Ikezoe
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block... | [] |
57,984 | Staining Protocols for Safety Study of Wireless Fecobionics Device | 1 | dx.doi.org/10.17504/protocols.io.b4u8qwzw | https://www.protocols.io/view/staining-protocols-for-safety-study-of-wireless-fe-b4u8qwzw | Yanmin Wang, Ghassan Kassab, Hans Gregersen, Bhavesh Patel | TITLE: Staining Protocols for Safety Study of Wireless Fecobionics Device
AUTHORS: Yanmin Wang, Ghassan Kassab, Hans Gregersen, Bhavesh Patel
[DESCRIPTION]
Protocols for Hematoxylin and Eosin staining and Immunofluorescence for two SPARC datasets: Safety Study of Wireless Fecobionics Device and Safety testing of pred... | ["[Hematoxylin and Eosin Staining] Fix the tissues with 4% paraformaldehyde (pH 7.4) overnight at4 °C", "[Immunofluorescence] Put the frozen slides at room temperature for 30min.", "[Hematoxylin and Eosin Staining] Embed the tissues with Optimal Cutting Temperature (OCT) compound and freeze with liquid nitrogen.", "[He... |
48,453 | Antioxidant activity by Deoxyribose assay: in vitro protocol | 6 | dx.doi.org/10.17504/protocols.io.btjdnki6 | https://www.protocols.io/view/antioxidant-activity-by-deoxyribose-assay-in-vitro-btjdnki6 | Adrieli Sachett, Matheus Gallas-Lopes, Greicy M M Conterato, Ana Herrmann, Angelo Piato | TITLE: Antioxidant activity by Deoxyribose assay: in vitro protocol
AUTHORS: Adrieli Sachett, Matheus Gallas-Lopes, Greicy M M Conterato, Ana Herrmann, Angelo Piato
[DESCRIPTION]
<div class = "text-blocks"><div style = "text-align :; float : ;"><img style = "" src = "https://lh4.googleusercontent.com/kKFW8PRdfVBqV80Au... | ["[Preparing the reagents]\nThe first step is to prepare the reagents to be used in this protocol;", "[Preparing the reagents]\nKH2PO4-KOH buffer : 1.1.1 Weigh of monobasic potassium phosphate (KH2PO4) in a beaker of appropriate size; 1.1.2 Dissolve the salt with of ultrapure water; 1.1.3 Transfer the soluti... |
73,245 | Catalogación material no librario Biblioteca UCAM | 1 | dx.doi.org/10.17504/protocols.io.ewov1o94plr2/v1 | https://www.protocols.io/view/catalogaci-n-material-no-librario-biblioteca-ucam-cjr5um86 | Antonio Rex Alegria | TITLE: Catalogación material no librario Biblioteca UCAM
AUTHORS: Antonio Rex Alegria
[DESCRIPTION]
El objetivo de la catalogación es la selección y descripción de los elementos informativos que permiten identificar un documento así como de establecer los puntos de acceso para su posterior recuperación.
[STEPS]
1.
... | ["La adquisición de fondos bibliográficos y documentales se realiza a través del soporte. La dirección de la biblioteca aprobará la petición y pasará al Servicio de Unidad de Compras que procederá a la petición al proveedor.\n\nEl material no librario se cataloga como las monografías, añadiendo cambios en ciertos campo... |
51,913 | Hyperspectral core-logger image acquisition | 5 | null | https://www.protocols.io/view/hyperspectral-core-logger-image-acquisition-bwxhpfj6 | Kevin Jacq, Jeanne Auboiron, Kévin Humbert, Ruth Martinez-Lamas, Antonin Van Exem, Maxime Debret | TITLE: Hyperspectral core-logger image acquisition
AUTHORS: Kevin Jacq, Jeanne Auboiron, Kévin Humbert, Ruth Martinez-Lamas, Antonin Van Exem, Maxime Debret
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The following protocol describes how to acquire hyperspectral images with Specim's Single Core ... | ["[General description of the acquisition bench]", "[General description of the acquisition bench]", "[General description of the acquisition bench]", "[Core logger set-up]\nCheck that the emergency stop buttons placed along the core logger are unlocked. To do this, press and turn at the same time to unlock the buttons... |
null | null | null | dx.doi.org/10.17504/protocols.io.day2fv | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<strong>Purpose:</strong> This protocol describes how to negatively or positively stain viruses that have been deposited onto TEM grids so that they can be imaged using transmission electron microscopy (TEM). Positive staining stains the virus itself such that the virus is dark ... | [] |
74,233 | LTEE Media Recipes | 1 | dx.doi.org/10.17504/protocols.io.81wgbyr31vpk/v1 | https://www.protocols.io/view/ltee-media-recipes-ckqzuvx6 | Jesus E Chavarria-Palma, Zachary D Blount, Jeffrey E Barrick | TITLE: LTEE Media Recipes
AUTHORS: Jesus E Chavarria-Palma, Zachary D Blount, Jeffrey E Barrick
[DESCRIPTION]
This protocol describes recipes to prepare growth media and reagents used in the E. coli long-term evolution experiment (LTEE).
Section 1: DM-glucose, Davis-Mingioli liquid medium supplemented with glucose
... | ["[DM-glucose: Davis-Mingioli liquid medium supplemented with glucose] To prepare 1 L of DM, follow these steps.", "[DM-glucose: Davis-Mingioli liquid medium supplemented with glucose] Weigh dry components:\na. 5.34 g of or 7 gof \nb. 2 g of \nc. 1 g of \nd. 0.5 g of", "[DM-glucose: Davis-Mingioli liquid me... |
35,445 | Sorbitol washing complex homogenate for improved DNA extractions | null | dx.doi.org/10.17504/protocols.io.beuvjew6 | https://www.protocols.io/view/sorbitol-washing-complex-homogenate-for-improved-d-beuvjew6 | Ashley Jones, Benjamin Schwessinger | TITLE: Sorbitol washing complex homogenate for improved DNA extractions
AUTHORS: Ashley Jones, Benjamin Schwessinger
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The extraction of pure DNA can be challenging due to the presence of sugars, oils and other endogenous chemicals present within biologi... | ["[PREPARATION]\nPrepare sorbitol wash solution. Approximately 2x volume of tube capacity will be used per sample. Sample tissue should not exceed 33% of tube capacity.To prepare a 500 mL solution: ABCDE1ReagentTarget concentrationMolecular weightStock concentrationAdd from stock2D-Sorbitol0.35 M182.17powder31.88 g3PV... |
46,037 | C-SOP-501: Normalisation and Pooling of DNA Libraries for Illumina Whole Genome Sequencing | 4 | null | https://www.protocols.io/view/c-sop-501-normalisation-and-pooling-of-dna-librari-bq7vmzn6 | Mihir Kekre | TITLE: C-SOP-501: Normalisation and Pooling of DNA Libraries for Illumina Whole Genome Sequencing
AUTHORS: Mihir Kekre
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Normalisation in next-generation sequencing (NGS) is the process of equalising the concentration of multiple DNA libraries for the pu... | ["[Before Starting]\nPrior to initiating this protocol, ensure that all active workbenches are cleaned with 80% ethanol, all relevant personal protective clothing is worn and the work area is prepared according to local GLP guidelines for molecular methods.", "[Before Starting]\nEnsure that you have all of the followin... |
100,311 | NEBNext iiMS Influenza A DNA Library Prep for Oxford Nanopore | 0 | dx.doi.org/10.17504/protocols.io.n92ld8m9nv5b/v1 | https://www.protocols.io/view/nebnext-iims-influenza-a-dna-library-prep-for-oxfo-dd7x29pn | Kaylinnette Pinet, Abhinaya Srikanth, Peter Thielen, New England Biolabs, Juliet Bonnevie | TITLE: NEBNext iiMS Influenza A DNA Library Prep for Oxford Nanopore
AUTHORS: Kaylinnette Pinet, Abhinaya Srikanth, Peter Thielen, New England Biolabs, Juliet Bonnevie
[DESCRIPTION]
The NEBNext iiMS Influenza A module for Library Prep (Oxford Nanopore Technologies) includes universal Influenza A primer pairs with in... | ["[Protocol for use with Lunascript Multiplex One-Step RT-PCR Kit (E1555 S/L) with NEBNext iiMS Influenza A Primer Pairs 1-48] Note:\n1) We recommend setting up the RT-PCR reactions in a room (and ideally in a hood) separate from the library construction area to minimize cross-contamination of future reactions. \n2) We... |
103,965 | Archival DNA extraction protocol for insect specimens from museum collections | 4 | dx.doi.org/10.17504/protocols.io.81wgbybqyvpk/v2 | https://www.protocols.io/view/archival-dna-extraction-protocol-for-insect-specim-dhr53586 | Fernando Lopes, Nicole Gunter, Conrad P. D. T. Gillett, Giulio Montanaro, Michele Rossini, Federica Losacco, Gimo M. Daniel, Nicolas Straube, Sergei Tarasov | TITLE: Archival DNA extraction protocol for insect specimens from museum collections
AUTHORS: Fernando Lopes, Nicole Gunter, Conrad P. D. T. Gillett, Giulio Montanaro, Michele Rossini, Federica Losacco, Gimo M. Daniel, Nicolas Straube, Sergei Tarasov
[DESCRIPTION]
This protocol can be used to dry specimens from natura... | ["[Fundamental reading before starting] From museum drawers to a tree: phylogenomics of historical DNA sheds light on the systematics of rare dung beetles (Coleoptera: Scarabaeinae) from museum collections\n\nAuthors: Fernando Lopes, Nicole Gunter, Giulio Montanaro, Michele Rossini, Federica Losacco,\nConrad P.D.T. Gil... |
23,742 | Catalase | null | dx.doi.org/10.17504/protocols.io.3e6gjhe | null | Eva Feldman, Frank Brosius | TITLE: Catalase
AUTHORS: Eva Feldman, Frank Brosius
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Describes the protocol used by the DiaComp to detect and quantify catalase activity in a tissue. </div><div class = "t... | ["Sample Preparation:", "[TISSUE:]\n1. Homogenate tissue in 1X Reaction Buffer on ice. 2. Using a black plate, pipette 25µL of diluted standards, controls (if any) and samples into wells. (Final concentration will be fourfold lower, 0 to 10µM) 3. Prepare stock solution of 20mM H²O² then prepare a 40µM H²O² dilution by ... |
78,753 | 3D Mesh Cleanup Tutorial: Sphenodon (Intermediate) | 1 | dx.doi.org/10.17504/protocols.io.8epv5jk5nl1b/v1 | https://www.protocols.io/view/3d-mesh-cleanup-tutorial-sphenodon-intermediate-cq59vy96 | Elizabeth G. Clark, Kelsey M Jenkins, Craig R Brodersen | TITLE: 3D Mesh Cleanup Tutorial: Sphenodon (Intermediate)
AUTHORS: Elizabeth G. Clark, Kelsey M Jenkins, Craig R Brodersen
[DESCRIPTION]
This protocol details 3D mesh cleanup tutorial of sphenodon (intermediate).
[GUIDELINES]
Skills developed: Basic mesh sculpting
Even some of the nicest fossil specimens may be affe... | ["[Part 1: Making and sculpting simple shapes in Autodesk Maya 2020] Open Maya. A new scene in Maya will appear similarly to the image below.", "[Part 1: Making and sculpting simple shapes in Autodesk Maya 2020] To begin making a simple shape, select the cube from the “Poly Modeling”” tab. When you click on the cube ic... |
51,433 | Detection of Cryptosporidium in stool samples by Taq-Man qPCR | 4 | dx.doi.org/10.17504/protocols.io.bwghpbt6 | https://www.protocols.io/view/detection-of-cryptosporidium-in-stool-samples-by-t-bwghpbt6 | botchiesenyo | TITLE: Detection of Cryptosporidium in stool samples by Taq-Man qPCR
AUTHORS: botchiesenyo
[DESCRIPTION]
Detection of Cryptosporidium parvum and/or Cryptosporidium hominis from fecal samples by qPCR.
[STEPS]
SECTION: qPCR
3. Combine the following for a single qPCR sample (9μl per sample). Scale accordingly for num... | ["[qPCR] Combine the following for a single qPCR sample (9μl per sample). Scale accordingly for number of samples and technical replicates:\n\n5 μl 10 x Luna Universal Probe qPCR Master Mix\n0.25 μl 10 μM Forward Primer (ATGACGGGTAACGGGGAAT)\n0.25 μl 10 μM Reverse Primer (CCAATTACAAAACCAAAAAGTCC)\n... |
29,607 | DNA extraction from 5uL mouse blood samples (KingFisher Flex 96-well) | null | dx.doi.org/10.17504/protocols.io.86fhzbn | null | Petra Schneider, Charlotte Repton, Sarah Reece | TITLE: DNA extraction from 5uL mouse blood samples (KingFisher Flex 96-well)
AUTHORS: Petra Schneider, Charlotte Repton, Sarah Reece
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>DNA extraction from 5uL mouse blood samples, for subsequent qPCR to detect </span><span style = "font-style:itali... | ["[Sample Collection]\nDispense 150 µL of citrate saline (0.85 % w/v NaCl, 1.5% w/v trisodium citrate dihydrate) into 0.2 mL strip tubes or 96-well plates, one well per sample. Cover tubes with lids, or plate with a plastic film (the thick version, not the optical film for qPCRs – that one will NOT come off).", "[Sampl... |
43,963 | iNGN iPS Cell Differentiation to Neurons for Extracellular Vesicle Isolation | 1 | dx.doi.org/10.17504/protocols.io.bn63mhgn | https://www.protocols.io/view/ingn-ips-cell-differentiation-to-neurons-for-extra-bn63mhgn | Dima Ter-Ovanesyan, Roey Lazarovits, Wendy Trieu , Maia Norman, Emma Kowal, George Church, David Walt | TITLE: iNGN iPS Cell Differentiation to Neurons for Extracellular Vesicle Isolation
AUTHORS: Dima Ter-Ovanesyan, Roey Lazarovits, Wendy Trieu , Maia Norman, Emma Kowal, George Church, David Walt
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>We present a protocol for differentiation of human ... | ["[Thawing Cells]\nPrepare a subaliquot of mTeSR media and supplement Rock Inhibitor for a working concentration of 6 ug/mL.", "[Thawing Cells]\nPre-chill P1000 tips at -20 °C.", "[Expanding Cells]\nFeed cells daily by replacing media with fresh mTeSR.", "[Differentiating Cells]\nPrepare 250 mL of mTeSR (with mTeSR su... |
51,117 | How to find the best Cosmetic Boxes? | 1 | dx.doi.org/10.17504/protocols.io.bv6mn9c6 | https://www.protocols.io/view/how-to-find-the-best-cosmetic-boxes-bv6mn9c6 | Cosmetic Boxes | TITLE: How to find the best Cosmetic Boxes?
AUTHORS: Cosmetic Boxes
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Whether it is retail or online stores, the products go around the world. Most of the products are fragile particularly cosmetic items, and they need proper packaging for the ult... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.fvebn3e | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
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?.
?.
?. | [] |
52,348 | CITE-Seq PBMCs with demultiplexing | 1 | dx.doi.org/10.17504/protocols.io.bp2l6bwq1gqe/v1 | https://www.protocols.io/view/cite-seq-pbmcs-with-demultiplexing-bxc4piyw | Daniel V Brown | TITLE: CITE-Seq PBMCs with demultiplexing
AUTHORS: Daniel V Brown
[DESCRIPTION]
Total-Seq labelling with demultiplexing
This protocol reflects a common experimental design where PBMC samples from multiple human donors are pooled together for Total-Seq (CITE-Seq) labelling. Often multiple samples from the same donor a... | ["[Reconstituting the total-seq panel] The large panels come lyophilized e.g TotalSeq-C Human Universal Cocktail, V1.0\nThe typical staining protocol is to block 500,000 cells in 25 uL of volume (cell staining buffer + Fc blocking reagent) and then add 25 uL of the resuspended antibodies.\nTotal staining volume is 50uL... |
null | null | null | dx.doi.org/10.17504/protocols.io.jsgcnbw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><span style="font-weight: 400;">Protocol to co-culture individual colonies of different strains (e.g. transformed with different vectors) on a LB agar plate in a distributed and random manner.</span></p>
[STEPS]
?.
?.
?.
?.
?.
?. | [] |
85,380 | Acquiring and integrating data from multiple resources for meta-analysis | 1 | dx.doi.org/10.17504/protocols.io.kxygx3z9og8j/v1 | https://www.protocols.io/view/acquiring-and-integrating-data-from-multiple-resou-cxmcxk2w | Wu Huang, Alex Twyford, Peter Hollingsworth | TITLE: Acquiring and integrating data from multiple resources for meta-analysis
AUTHORS: Wu Huang, Alex Twyford, Peter Hollingsworth
[DESCRIPTION]
Acquiring sequence data generated for various purposes and repurposing it to evaluate the nature of genomic differences between plant species requires thorough dataset asse... | ["[Developing data request form] Collecting information about the file formats frequently used in the data repositories that are popular in this particular field. (Normally read >20 related publications and the picture will be clear.) Choose the most frequently used ones as input formats for the following analytical pi... |
42,192 | Lab 2 Notebook | 3 | null | https://www.protocols.io/view/lab-2-notebook-bmfqk3mw | TITLE: Lab 2 Notebook
AUTHORS:
[STEPS] | [] | |
22,566 | gmcSCRB-seq protocol | null | dx.doi.org/10.17504/protocols.io.2aegabe | null | Johannes Bagnoli, Christoph Ziegenhain, Aleksandar Janjic, Lucas Esteban Wange, Beate Vieth, Swati Parekh, Johanna Geuder, Ines Hellmann, Wolfgang Enard | TITLE: gmcSCRB-seq protocol
AUTHORS: Johannes Bagnoli, Christoph Ziegenhain, Aleksandar Janjic, Lucas Esteban Wange, Beate Vieth, Swati Parekh, Johanna Geuder, Ines Hellmann, Wolfgang Enard
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>gmcSCRB-seq is an alternative lysis protocol to mcSCRB-s... | ["[Preparation of lysis plates]\nPrepare 96 well plate(s) containing 5 μL Lysis Buffer per well.\nLysis plates should be prepared shortly before use, but can be stored for up to 1 week at room temperature. Prior to use, double check to make sure salts have not fallen out of solution or that the lysis buffer has not eva... |
59,048 | Purification of Human K560-GFP molecular motor | 4 | dx.doi.org/10.17504/protocols.io.bp2l61xrdvqe/v1 | https://www.protocols.io/view/purification-of-human-k560-gfp-molecular-motor-b5wgq7bw | Andrea M. Dickey | TITLE: Purification of Human K560-GFP molecular motor
AUTHORS: Andrea M. Dickey
[DESCRIPTION]
K560-GFP purification protocol from the Reck-Peterson Lab based on protocol from Nicholas et al. 2014. Edited for protocols.io by Andrea Dickey and Mariusz Matyszewski.
[GUIDELINES]
All protein purification steps should be p... | ["[Expression] pET17b-Kif5b(1-560)-GFP-His should be transformed into BL21(DE3)RIPL cells.", "[Expression] Make enough LB for at least 7.5 L of culture.", "[Expression] Grow an overnight starter culture.", "[Expression] Transfer starter culture into LB. Make sure to add proper antibiotics (Ampicillin for the plasmid, a... |
87,742 | Robot-based psychological intervention program for the prevention of child sexual abuse | 1 | dx.doi.org/10.17504/protocols.io.36wgq3dnxlk5/v1 | https://www.protocols.io/view/robot-based-psychological-intervention-program-for-czw6x7he | Mohammad Tahan | TITLE: Robot-based psychological intervention program for the prevention of child sexual abuse
AUTHORS: Mohammad Tahan
[DESCRIPTION]
Sexual abuse of children is an important issue with severe consequences,
so self-care education programs increase children's awareness,
knowledge, and skills against sexual abuse. It ... | ["[A Summary of the Content of the Program of Psychological Intervention with Robot for Sexual Care in Children] Starting the training program - introducing the robot - pre-testing:\n\nFirst, two groups (namely, experimental and control) complete a researcher-made questionnaire (Tahan, 2019) on the prevention of child ... |
43,699 | Gibson Assembly | 1 | dx.doi.org/10.17504/protocols.io.bnwtmfen | https://www.protocols.io/view/gibson-assembly-bnwtmfen | Zhujun Wei | TITLE: Gibson Assembly
AUTHORS: Zhujun Wei
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol includes two different kits. Choose one to use.</div></div>
[STEPS]
?. Set up a small box with ice, put DNA and Gibson Mix into it before going into the metal bath or the Bio-rad S1000TM thermoc... | ["Set up a small box with ice, put DNA and Gibson Mix into it before going into the metal bath or the Bio-rad S1000TM thermocycler cycler .", "Add the following reagent to a PCR tube (4 μl). AB1Gibson Mix2 μl2insertX μl3vectorY μl X+Y=2 ul , X : Y=3 : 1~5 : 1.Temperature : Time= 50℃ : 15-30 min\nAB1Gibson Mix2 μl2inse... |
null | null | null | dx.doi.org/10.17504/protocols.io.c64zgv | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
.
[STEPS]
?.
?. | [] |
52,010 | PBMC Isolation & Cryopreservation from Whole Blood | 4 | dx.doi.org/10.17504/protocols.io.bw2ipgce | https://www.protocols.io/view/pbmc-isolation-amp-cryopreservation-from-whole-blo-bw2ipgce | cecilia , Alessandro Sette | TITLE: PBMC Isolation & Cryopreservation from Whole Blood
AUTHORS: cecilia , Alessandro Sette
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The purpose of this procedure is to isolate and cryopreserve peripheral blood mononuclear cells (PBMC's) from 30 mL of freshly drawn whole blood.</div></div>
... | ["[Step 1: Prepare materials and supplies]\nPlace RPMI media and Ficoll in water bath. Bring to ( - ).\n0 Room temperature\n19 °C\n25 °C", "[Step 2: First Spin]\nSpin tubes at (breaks off; 5 acc 0 brake) for plasma removal.Total time for spin including acceleration and deceleration – .\nCentrifuge: 1850 33, 15 min", ... |
null | null | null | dx.doi.org/10.17504/protocols.io.t3yeqpw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
The recent international studies about psycho-educational interventions against interpersonal violence in adolescents (bullying, cyber bullying, sexual violence and dating violence) show the needs of developing comprehensive prevention programs that deal with more than once spec... | [] |
28,951 | Aptamer conjugated beads affinity assay | null | dx.doi.org/10.17504/protocols.io.8hxht7n | null | Jorge Fernández | TITLE: Aptamer conjugated beads affinity assay
AUTHORS: Jorge Fernández
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The following protocol details how to test affinity by an aptamer-conjugated particles with their targets, via target immobilization in 96-treated wells.</div></div>
[STEPS]
?. [W... | ["[Well Coatings]\nAdd to each well of the 96 maxisorp plate 100 µL of E. Coli or Streptavidin-DNA suspensions. And incubate overnight at 4 ºC.", "[Well Coatings]\nAfter incubation, remove the liquid in the plate flipping the 96-plate.q! Don't aspire the liquid in the wells with a pipette, to avoid damaging the coating... |
73,381 | Testing of Total Dissolved Solids in Coffee Samples | 1 | null | https://www.protocols.io/view/testing-of-total-dissolved-solids-in-coffee-sample-cjwdupa6 | Shannon.logan | TITLE: Testing of Total Dissolved Solids in Coffee Samples
AUTHORS: Shannon.logan
[DESCRIPTION]
Testing the total dissolved solids levels in different coffee samples
[STEPS]
1. Grind coffee to desired consistency and weigh 20g to put in cafetiere.
2. Boil kettle with 250ml of deionised water.
3. Pour boiling water in... | ["Grind coffee to desired consistency and weigh 20g to put in cafetiere.", "Boil kettle with 250ml of deionised water.", "Pour boiling water into beaker and allow to cool to 93°C, using a digital thermometer to ensure\naccuracy of temperature.", "Once the water has cooled to the desired temperature, pour into the cafet... |
52,570 | Microfluidics 3 - Mold Fabrication: 3D Printing | 1 | dx.doi.org/10.17504/protocols.io.bxj2pkqe | https://www.protocols.io/view/microfluidics-3-mold-fabrication-3d-printing-bxj2pkqe | Serhat Sevli, C. Yunus Sahan | TITLE: Microfluidics 3 - Mold Fabrication: 3D Printing
AUTHORS: Serhat Sevli, C. Yunus Sahan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left">Su8 is a photoresist resin used in MEMS technology for thick structures. PDMS microfluidic chips fabrication ... | ["[3D Printer Setup]\nMolds for PDMS microfluidic chips can be fabricated using 3D Printing technology. SLA(/DLP) printers are mostly prefered for microfluidics due to its high resolution, relative low cost, and being suitable for direct microchannel formation.NehirBT uses a SLA/DLP 3D printing technology for transferr... |
40,803 | ELISA for quantification of IL-37 in human serum. | 6 | dx.doi.org/10.17504/protocols.io.bj4bkqsn | https://www.protocols.io/view/elisa-for-quantification-of-il-37-in-human-serum-bj4bkqsn | Angel Justiz-Vaillant | TITLE: ELISA for quantification of IL-37 in human serum.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Interleukins (IL) are a type of cytokine first thought to be expressed by leukocytes alone but have later been found to be produced by many other body cells.... | ["An anti-human IL-37 coating antibody is adsorbed onto the microwells by incubation overnight at 4°C with carbonate-bicarbonate buffer.", "Add 50 µl of human serum. Human IL-37 present in the serum sample binds to antibodies adsorbed into the microwells.", "The microplate is blocked with 3% non-fat milk-PBS buffer and... |
94,535 | Production of lentiviruses in Lenti-X cells | 1 | dx.doi.org/10.17504/protocols.io.n92ldmdyol5b/v1 | https://www.protocols.io/view/production-of-lentiviruses-in-lenti-x-cells-c8jfzujn | Cole S Sitron, F Ulrich Hartl | TITLE: Production of lentiviruses in Lenti-X cells
AUTHORS: Cole S Sitron, F Ulrich Hartl
[DESCRIPTION]
This is a protocol to produce lentivirus in a HEK cell line selected to produce high-titer virus.
[STEPS]
SECTION: Transfection
1. Plate Lenti-X cells 2.5 x 10^6/10 cm 1440 min before transfection.
SECTION: Tran... | ["[Transfection] Plate Lenti-X cells 2.5 x 10^6/10 cm 1440 min before transfection.", "[Transfection] Warm OptiMEM, X-tremeGENE HP DNA Transfection Reagent, and DNA to warm to Room temperature.", "[Transfection] Add 1 mL OptiMEM to a tube.", "[Transfection] Add plasmid DNA to the OptiMEM, gently pipetting to mix.", "[T... |
57,251 | diDO-IPTL protocol | 1 | dx.doi.org/10.17504/protocols.io.b36bqran | https://www.protocols.io/view/dido-iptl-protocol-b36bqran | Jacob Waldbauer, Lichun Zhang | TITLE: diDO-IPTL protocol
AUTHORS: Jacob Waldbauer, Lichun Zhang
[DESCRIPTION]
Isobaric peptide termini labeling (IPTL) is a quantification method which permits relative quantification using quantification points distributed throughout the whole tandem mass spectrometry (MS/MS) spectrum. It is based on the complemen... | ["[DAY 1] Prepare dried MS-grade trypsin, 2ug per sample to be labeled. Note that separate aliquots of dried trypsin must be used for 16O- and 18O-labeling.", "[DAY 1] Prepare two separate N-methylmorpholine (NMM) and acetic acid O-isotope exchange buffers with 16O and 18O (>98%) enriched water. Volume ratio of buffer ... |
null | null | null | dx.doi.org/10.17504/protocols.io.fvzbn76 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><em>The EpiQuik™ Total Histone Extraction Kit</em> is a complete set of optimized buffers and reagents for extracting total core histone proteins (H2A, H2B, H3, and H4) from mammalian cells or tissues in a simple 60 minute procedure. The post-translational modifications (PTM)... | [] |
48,857 | How to dockerize an R Shiny App | 5 | null | https://www.protocols.io/view/how-to-dockerize-an-r-shiny-app-btxznpp6 | Sonia García-Ruiz | TITLE: How to dockerize an R Shiny App
AUTHORS: Sonia García-Ruiz
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol contains the steps to dockerize an R Shiny App. The Shiny App used as an example is vizER (</span><a href="https://rytenlab.com/browser/app/vizER" style = "text-decor... | ["[Docker installation]\nMake sure you have Docker Engine installed on your Operating System. To install it on CentOS: https://docs.docker.com/engine/install/centos/", "[Docker installation]\nPrepare the R Shiny App you would like to dockerize. In this example, we are going to use vizER, which can be downloaded from ht... |
98,425 | Protocols for Mountain-based Ecotourism Project | 0 | dx.doi.org/10.17504/protocols.io.j8nlk8ex5l5r/v1 | https://www.protocols.io/view/protocols-for-mountain-based-ecotourism-project-dccz2sx6 | Jayden Manalese | TITLE: Protocols for Mountain-based Ecotourism Project
AUTHORS: Jayden Manalese
[DESCRIPTION]
The mountains and valleys amongst French Polynesia have historically held a sacred role in polynesian culture and society, however the (eco) tourism industry primarily generates its income from marine and coastal-based ecosys... | ["[Protocols for Mountain-based Ecotourism Project] Community Engagement and Needs Assessment", "[Protocols for Mountain-based Ecotourism Project] Conduct meetings with local community leaders, youth groups, and stakeholders to discuss the potential development of mountain-based ecotourism in the form of an eco bike pa... |
27,964 | Protein expression using E. coli strain BL21DE3 | null | dx.doi.org/10.17504/protocols.io.7i4hkgw | null | Robert Hooftman | TITLE: Protein expression using E. coli strain BL21DE3
AUTHORS: Robert Hooftman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>In this protocol will be explained how to express proteins using </span><span style = "font-style:italic;">E. coli</span><span> strain BL21DE3 using a plasmid with a ... | ["[Day 1]\nPrepare an overnight culture of the bacterium encoding for the protein you want to express.", "[Day 2]\nPrepare an Erlenmeyer flask containing LB medium and the right antibiotics", "[Day 2]\nInoculate the Erlenmeyer flask 1:100 from your overnight culture and grow the bacteria at 37°C and 120 rpm.", "[Day 2]... |
null | null | null | dx.doi.org/10.17504/protocols.io.pfqdjmw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol was designed for collaborators with the Earth Microbiome Project to contribute samples in a standardized fashion. Raw, frozen samples are submitted in individually labeled tubes, 10 aliquots (identical replicates) per sample. Please note that unsolicited samples... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.c2wyfd | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol describes a technique to recover viruses from natural waters using iron- based flocculation and large-pore-size filtration, followed by resuspension of virus- containing precipitates in a pH 6.5 buffer. This Fe-based virus flocculation, filtration and resuspension ... | [] |
33,218 | Detection of five bacterial pathogens of rice by multiplex PCR | null | dx.doi.org/10.17504/protocols.io.bcpaivie | https://www.protocols.io/view/detection-of-five-bacterial-pathogens-of-rice-by-m-bcpaivie | Martine Bangratz, Charlotte Tollenaere | TITLE: Detection of five bacterial pathogens of rice by multiplex PCR
AUTHORS: Martine Bangratz, Charlotte Tollenaere
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This multiplex PCR protocol is used for the detection of five bacterial pathogens of rice :</span><span style = "font-style:ital... | ["The amounts described in this protocol are for one sample. Calculate the quantity you need based on your number of sample. Always prepare 10 % more mix.", "Prepare a 2% agarose gel. Load 10µl PCR product and perform the electrophoresis at 100 Volts for 90min", "Observe the gel under UV light after a ethidium bromide ... |
null | null | null | dx.doi.org/10.17504/protocols.io.fiubkew | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol details the use of various unix commands commonly used in bioinformatics. Open this protocol inside the virtual machine (details in "Start Instructions") for easy copy, paste of commands into the command line terminal window. </p>
[BEFORE_START]
<p>Before start... | [] |
40,294 | Protocol for study of the in vitro effect of purified serum anti-anti-anti-SpA antibodies (Ab-3) on cultures of Staphylococcus aureus. | 4 | dx.doi.org/10.17504/protocols.io.bjkekkte | https://www.protocols.io/view/protocol-for-study-of-the-in-vitro-effect-of-purif-bjkekkte | Angel Justiz-Vaillant, Patrick E. Akpaka | TITLE: Protocol for study of the in vitro effect of purified serum anti-anti-anti-SpA antibodies (Ab-3) on cultures of Staphylococcus aureus.
AUTHORS: Angel Justiz-Vaillant, Patrick E. Akpaka
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This test shows the ability of Ab-3 antibody to inhibit the... | ["The investigation of the neutralizing ability of purified anti-SpA antibodies is carried out as follows: One ml of brain heart infusion (BHI) broths is placed in 10 sterile test tubes.", "To each tube is added an equal volume of 10 µl of purified anti-anti-anti-SpA (Ab-3) antibodies in a concentration of 1.25-µg/µl."... |
null | null | null | dx.doi.org/10.17504/protocols.io.j8pcrvn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol presents a simplified approach for purification of viral strains directly from plaques without the need for preparation of dilutions. Using the 'Tube-free agar overlay' approach viruses are 'picked' directly from source plaques with a toothpick and streaked into mo... | ["[I. Setting up the top agar in a beaker-waterbath] Prepare a beaker-waterbath: Place bottle of top agar into a glass beaker and add water to the beaker up to the level of the top agar in the bottle; for example, a 500mL glass bottle into a 1L beaker.", "[I. Setting up the top agar in a beaker-waterbath] {\"blocks\":[... |
20,707 | UC Davis - Catalase | null | dx.doi.org/10.17504/protocols.io.ygbftsn | null | Peter Havel | TITLE: UC Davis - Catalase
AUTHORS: Peter Havel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Catalase (EC 1.11.1.6; 2H2O2 oxidoreductase) is an ubiquitous antioxidant enzyme that is present in most aerobic cells. Ca... | ["Read the absorbance at 540 nm using a plate reader.", "Formaldehyde Standard Wells - Add 100 µl of diluted Assay Buffer, 30µl of methanol, and 20µl of standard (tubes A-G) per well in the designated wells on the plate (see sample plate format, Figure 1, page 12).", "Positive Control Wells (bovine liver CAT) - Add 100... |
41,362 | Introduction to Nanopore | 3 | null | https://www.protocols.io/view/introduction-to-nanopore-bkmsku6e | TITLE: Introduction to Nanopore
AUTHORS:
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">We want students to have an excellent foundation and knowledge of nanopore sequencing. This lab will provide students with the understanding of how to sequence DNA and process and then analyze the sequence dat... | [] | |
66,462 | LAB Agarose Gel Electrophoresis Buffer Recipe | 4 | null | https://www.protocols.io/view/lab-agarose-gel-electrophoresis-buffer-recipe-cc56sy9e | Brian P Teague | TITLE: LAB Agarose Gel Electrophoresis Buffer Recipe
AUTHORS: Brian P Teague
[DESCRIPTION]
A recipe to make lithium acetate / borate agarose gel electrophoresis buffer. This buffer has a lower ionic strength than TAE, but maintains its ability to resolve both small and large bands.
Additionally, it is MUCH less expen... | ["[25X Buffer Concentrate] Weigh out 25.5 g", "[25X Buffer Concentrate] Weigh out 15.5 g .", "[25X Buffer Concentrate] Mix the lithium acetate and boric acid with deionized water to a final volume of 1 L", "[25X Buffer Concentrate] Pipette a small amount onto a . Make sure the pH is between 6.5 and 7.0.", "[1X Buffer... |
58,248 | Studying trace element nutrition without a clean room | 4 | dx.doi.org/10.17504/protocols.io.b45gqy3w | https://www.protocols.io/view/studying-trace-element-nutrition-without-a-clean-r-b45gqy3w | Sunnyjoy Dupuis | TITLE: Studying trace element nutrition without a clean room
AUTHORS: Sunnyjoy Dupuis
[DESCRIPTION]
Trace elements are key to much of the chemistry that occurs in living cells. We have investigated trace element nutrition in the eukaryotic alga Chlamydomonas reinhardtii, and describe here common best-practices for st... | ["[General best practices:] Wipe work area clean of dust, as dust is a common source of metal contamination.", "[General best practices:] Use fresh gloves when working with trace element grade chemical sources and media.", "[General best practices:] Pouring is your friend. When possible, pour chemical powders and solut... |
95,261 | alpha-Synuclein pre-formed fibrils preparation and stereotactic injection into Mus Musculus brain | 4 | dx.doi.org/10.17504/protocols.io.dm6gp3pdjvzp/v1 | https://www.protocols.io/view/alpha-synuclein-pre-formed-fibrils-preparation-and-c895zz86 | Jean-Louis Parmasad | TITLE: alpha-Synuclein pre-formed fibrils preparation and stereotactic injection into Mus Musculus brain
AUTHORS: Jean-Louis Parmasad
[DESCRIPTION]
Preparation of seed-competent alpha-Synuclein pre-formed fibrils and subsequent stereotactic injection into Mus Musculus brain as a model of synucleinopathy.
[STEPS]
SECT... | ["[Storage] Store alpha-Synuclein fibril preparations at -80 °C with appropriate biohazard precautions and labels until use.", "[PFF preparation (to be done on the same day as experiment)] On the day of usage, briefly thaw fibrils on ice.", "[PFF preparation (to be done on the same day as experiment)] Transfer required... |
90,581 | Protocol to isolate and fix nuclei from flash frozen mouse kidneys for IGVF | 4 | null | https://www.protocols.io/view/protocol-to-isolate-and-fix-nuclei-from-flash-froz-c4pvyvn6 | Elisabeth Rebboah | TITLE: Protocol to isolate and fix nuclei from flash frozen mouse kidneys for IGVF
AUTHORS: Elisabeth Rebboah
[DESCRIPTION]
This protocol describes isolation of nuclei from left and right 10 week old mouse kidneys (tissue ID: 09) from 8 founder strains (B6J, AJ, 129S1J, NZOJ, WSBJ, NODJ, PWKJ, and CASTJ), preparation ... | ["[Setup] Label tubes.", "[Setup] Pre-chill centrifuge to 4C.", "[Setup] Prepare ice buckets.", "[Setup] Prepare 40 ml lysis buffer in a 50 ml conical tube on ice. Distribute 2.5 ml into 8 gentleMACS C Tubes on ice. Add 200 ul RNase inhibitor to the lysis buffer aliquot the day of the experiment.", "[Setup] Prepare 42 ... |
75,045 | LEGACY01: INTRODUCTION | 4 | null | https://www.protocols.io/view/legacy01-introduction-cmidu4a6 | Katrina M Pollock, Calliope Dendrou | TITLE: LEGACY01: INTRODUCTION
AUTHORS: Katrina M Pollock, Calliope Dendrou
[DESCRIPTION]
This protocol provides introduction to an experimental medicine study of seasonal influenza vaccination responses in Lymph nodE single-cell Genomics in AnCestrY (LEGACY01).
[GUIDELINES]
BACKGROUND
The efficient development of va... | [] |
40,989 | Determination of C4 concentration by the Mancini test. | 6 | dx.doi.org/10.17504/protocols.io.bj95kr86 | https://www.protocols.io/view/determination-of-c4-concentration-by-the-mancini-t-bj95kr86 | Angel Justiz-Vaillant | TITLE: Determination of C4 concentration by the Mancini test.
AUTHORS: Angel Justiz-Vaillant
[STEPS]
?. An appropriate anti-C4 antiserum (antibody) is poured in the center well of an agar-containing plate.
?. Carefully circular wells are cut and detached from the plates.
?. A series of standards containing known conc... | ["An appropriate anti-C4 antiserum (antibody) is poured in the center well of an agar-containing plate.", "Carefully circular wells are cut and detached from the plates.", "A series of standards containing known concentrations of C4 are placed in separate wells, while “unknown” human serum samples and control are place... |
null | null | null | dx.doi.org/10.17504/protocols.io.ibhcaj6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Please contact Dr. Steven Wilhelm (wilhelm@utk.edu) for additional information regarding this protocol.</p>
<p> </p>
<p>Adapted from Ichimura, T. 1979 2. Isolation and culture methods of algae. 2.5.B. Freshwater algae [2. Sôrui no bunri to baiyôhô. 2.5.B. Tansui sôrui]. In Me... | [] |
50,028 | Extracellular and intracellular pH measurements in mice respiratory tract in vivo | 4 | dx.doi.org/10.17504/protocols.io.bu4knyuw | https://www.protocols.io/view/extracellular-and-intracellular-ph-measurements-in-bu4knyuw | Faten Okda, Scott Perry, Richard Webby, Charles Russell | TITLE: Extracellular and intracellular pH measurements in mice respiratory tract in vivo
AUTHORS: Faten Okda, Scott Perry, Richard Webby, Charles Russell
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>In the last century, novel respiratory viruses with pandemic potential have emerged in huma... | ["Extracellular pH measurements in live mice", "The fiber-optic microsensor, with a tip diameter of 140 μm and a tip length of 3 mm, was calibrated with six colorless pH buffer solutions (pH 4, 5, 6, 7, 8, and 9) according to the manufacturer instructions to generate a calibration curve.", "Optimizing extracellular pH ... |
43,636 | Fungal extraction from Xylosandrus compactus | 3 | dx.doi.org/10.17504/protocols.io.bnuumeww | https://www.protocols.io/view/fungal-extraction-from-xylosandrus-compactus-bnuumeww | James Skelton, Craig Bateman, Jiri Hulcr | TITLE: Fungal extraction from Xylosandrus compactus
AUTHORS: James Skelton, Craig Bateman, Jiri Hulcr
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describes how to extract ambrosia fungi from </span><span style = "font-style:italic;">Xylosandrus compactus</span><span>, the bla... | [] |
106,806 | CUT&RUN abbreviated protocol v2 | 1 | dx.doi.org/10.17504/protocols.io.8epv5rzo4g1b/v2 | https://www.protocols.io/view/cut-amp-run-abbreviated-protocol-v2-dkiw4ufe | CG - | TITLE: CUT&RUN abbreviated protocol v2
AUTHORS: CG -
[DESCRIPTION]
An abbreviated version of Henikoff/Janssens Cut&RUN protocol. We use in-house prepared pAG-MNase and standard conditions. If library quality is poor, consider using one of the high-salt or low-salt conditions offered in the original protocol.
[BE... | ["[Binding cells to beads (~30 min)] Harvest fresh culture(s) at room temperature and count cells. The same protocol can be used for up to 500,000 mammalian cells per sample and/or digestion time point.", "[Binding cells to beads (~30 min)] Centrifuge 3 min 600 x g at room temperature and withdraw liquid.\n3 min", "[Bi... |
28,371 | Generating Structural Targets | null | dx.doi.org/10.17504/protocols.io.7xthpnn | null | Courtney Comrie | TITLE: Generating Structural Targets
AUTHORS: Courtney Comrie
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol will provide a basic guide to Generating Structural Targets.</div><div class = "text-block">Note: Steps may vary based upon data.</div></div>
[STEPS]
?. [Introduction]
A few t... | ["[Introduction]\nA few things to keep in mind:This protocol will demonstrate steps that will are most commonly used by the IPA Core for creating a structural target. In this protocol we use T2 data for the example, but keep in mind that structural images can be created by using other types of data and the steps may va... |
84,907 | Immunofluorescence staining of myenteric and submucosal plexuses | 4 | dx.doi.org/10.17504/protocols.io.q26g7p85kgwz/v1 | https://www.protocols.click/view/immunofluorescence-staining-of-myenteric-and-submu-cw6jxhcn | Connor Monahan | TITLE: Immunofluorescence staining of myenteric and submucosal plexuses
AUTHORS: Connor Monahan
[DESCRIPTION]
This protocol details myenteric and submucosal plexus immunostaining.
[STEPS]
SECTION: Procedure
1.
Cut out two small regions of each plexus sheet in PBS at 4 °C.
SECTION: Procedure
2. Add each tissue sec... | ["[Procedure] Cut out two small regions of each plexus sheet in PBS at 4 °C.", "[Procedure] Add each tissue section to separate wells in a 96 well dish.", "[Procedure] Add 10% normal donkey serum (Jackson Immunoresearch, Cat #017-000-121; West Grove, PA) and 1% Triton-X in PBS. Leave in blocking solution for 60 min at ... |
72,091 | Foreskin Tissue DNA Extraction | 1 | dx.doi.org/10.17504/protocols.io.4r3l2774jg1y/v1 | https://www.protocols.io/view/foreskin-tissue-dna-extraction-cim3uc8n | Brandon Maust | TITLE: Foreskin Tissue DNA Extraction
AUTHORS: Brandon Maust
[DESCRIPTION]
Extracts total DNA from foreskin tissue, as used in Maust et al. 2022
[STEPS]
SECTION: Preparation
1. Add steel bead to 1.5 ml tube
SECTION: Preparation
2. Add 800 µL CD1 to tube
SECTION: Preparation
3. Weigh tube (with bead and solution)
SECT... | ["[Preparation] Add steel bead to 1.5 ml tube", "[Preparation] Add 800 µL CD1 to tube", "[Preparation] Weigh tube (with bead and solution)", "[Tissue] Dissect approximately 25 mg (3 mm3) piece of tissue\nFragment tissue with scalpel\nAdd tissue to tube (with bead and solution)", "[Tissue] Weigh tube and calculate net t... |
33,297 | ChIP-SICAP | null | dx.doi.org/10.17504/protocols.io.bcrriv56 | https://www.protocols.io/view/chip-sicap-bcrriv56 | Sina Rafiee, Jeroen Krijgsveld | TITLE: ChIP-SICAP
AUTHORS: Sina Rafiee, Jeroen Krijgsveld
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Chromatin immunoprecipitation combined with mass spectrometry (ChIP-MS) suffers from unexpected proteins that bind to chromatin during the cell lysis and immunoprecipitation (IP). The so-called ... | ["[Part #1-A: detach and crosslink the cells ]\nDetach the cells by Accutase. Accutase doesn’t lyse cells, so it is more suitable for single cell preparation. After detaching the cells, make sure that they are single cell by pipetting in the medium.", "[Part #1-A: detach and crosslink the cells ]\nCount the cells.", "[... |
77,625 | Closed Head Weight Drop model in mice - Whalen Lab | 4 | dx.doi.org/10.17504/protocols.io.j8nlkw2pdl5r/v1 | https://www.protocols.io/view/closed-head-weight-drop-model-in-mice-whalen-lab-cp2zvqf6 | Michael Whalen Ph. D. | TITLE: Closed Head Weight Drop model in mice - Whalen Lab
AUTHORS: Michael Whalen Ph. D.
[DESCRIPTION]
This is a protocol to describe the materials and methods utilized to perform preclinical traumatic brain injury (TBI) using a closed head injury model in mice.
The posting of this protocol is part of the mission of ... | ["Turn on anesthesia and fill the chamber for two minutes to achieve steady state mixture of isoflurane 2.5% and nitrous oxide 70%, Oxygen about 30%", "Place the mouse into the anesthesia for exactly 75 seconds.", "Ensure adequate anesthesia is achieved by use of the toe pinch test.", "Place the mouse prone onto a Kimw... |
68,322 | Methodology to Define the Origin of SARS-CoV-2 | 5 | dx.doi.org/10.17504/protocols.io.x54v9yqz4g3e/v1 | https://www.protocols.io/view/methodology-to-define-the-origin-of-sars-cov-2-ceyatfse | David Maison, Sean Cleveland, Vivek R. Nerurkar | TITLE: Methodology to Define the Origin of SARS-CoV-2
AUTHORS: David Maison, Sean Cleveland, Vivek R. Nerurkar
[DESCRIPTION]
Using the CDC-classified SARS-CoV-2 VOC (B.1.1.7, B.1.351, B.1.427, B.1.429, and P.1), identified in Hawai’i as an example, we demonstrate a method to define the origin of SARS-CoV-2 lineages an... | ["The lineage-defining sequences of SARS-CoV-2 Lineage A and Lineage B act as the most ancestral roots. Lineage A (EPI_ISL_406801) is from GISAID, and Lineage B (MN908947) is from GenBank.", "Register for a free GISAID account (https://gisaid.org/register/) to obtain EPI_ISL_406801", "GenBank MN908947 (https://www.ncbi... |
20,476 | Neural aggregate formation | null | dx.doi.org/10.17504/protocols.io.x84fryw | null | Celeste Karch, Rita Martinez, Jacob Marsh | TITLE: Neural aggregate formation
AUTHORS: Celeste Karch, Rita Martinez, Jacob Marsh
[STEPS]
?. Harvest iPSCs for neural aggregate formation when iPSCs have reached 75- 85% confluency. Aspirate medium and rinse with of DPBS.
2 ml
?. Add of Accutase. Incubate at for . Gently tap plate to dislodge cells.
1 ml
?. Dilut... | ["Harvest iPSCs for neural aggregate formation when iPSCs have reached 75- 85% confluency. Aspirate medium and rinse with of DPBS.\n2 ml", "Add of Accutase. Incubate at for . Gently tap plate to dislodge cells.\n1 ml", "Dilute Accutase with of DMEM/F12 medium and collect cell suspension in 15ml conical tube.\n4 ml",... |
null | null | null | dx.doi.org/10.17504/protocols.io.e2mbgc6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?. | [] |
18,826 | Prognostic factors associated with survival in patients with anaplastic oligodendroglioma. | null | dx.doi.org/10.17504/protocols.io.wmifc4e | null | weiduan zhuang, Shuo Liu | TITLE: Prognostic factors associated with survival in patients with anaplastic oligodendroglioma.
AUTHORS: weiduan zhuang, Shuo Liu
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Background</div><div class = "text-block">Anaplastic oligodendroglioma (AO) is a rare disease with inadequately understo... | ["[Prognostic factors associated with survival in patients with anaplastic oligodendrogliomaResults]\nThis study was conducted based on the SEER program of the National Cancer Institute. The SEER program is the largest publicly available cancer registry, which prospectively collects cancer incidence, clinicopathologica... |
63,526 | Eagle Hemp CBD Gummies [Scam Or Legit] Reviews – Check Real Fact | 1 | dx.doi.org/10.17504/protocols.io.rm7vzy2x4lx1/v1 | https://www.protocols.io/view/eagle-hemp-cbd-gummies-scam-or-legit-reviews-check-caaesabe | weightcrashers , Lucas V | TITLE: Eagle Hemp CBD Gummies [Scam Or Legit] Reviews – Check Real Fact
AUTHORS: weightcrashers , Lucas V
[DESCRIPTION]
✅ Product Name – Eagle Hemp CBD Gummies
✅ Benefits – Relief From Aches & Dangerous Pains
✅ Category – Pain Relief
✅ Side Effects - No Major Side Effects
✅ Rating - ⭐⭐⭐⭐⭐
✅ Availability – Online
✅ C... | [] |
98,805 | USDA LTAR Common Experiment measurement: Soil water potential and matric potential | 0 | dx.doi.org/10.17504/protocols.io.8epv5rzb4g1b/v1 | https://www.protocols.io/view/usda-ltar-common-experiment-measurement-soil-water-dcqv2vw6 | Andrew M O'Reilly, Claire Baffaut | TITLE: USDA LTAR Common Experiment measurement: Soil water potential and matric potential
AUTHORS: Andrew M O'Reilly, Claire Baffaut
[DESCRIPTION]
The potential of subsurface water measures the energy associated with position or internal conditions, thus representing the potential energy of a parcel of water (Hillel, ... | ["[Data collection] Equipment\n\nGravitational potential is measured simply as the vertical distance of the measurement point of interest above an established datum. Matric potential can be measured in the field and (or) laboratory using the following instruments:", "[Data collection] Tensiometer, e.g., SMS https://www... |
90,847 | DNA extraction from rectal mucosa biopsies and matched faecal samples taken from surgery for microbiome analysis | 4 | dx.doi.org/10.17504/protocols.io.eq2lyj15wlx9/v1 | https://www.protocols.io/view/dna-extraction-from-rectal-mucosa-biopsies-and-mat-c4x7yxrn | Lee Murphy, Alan Maclean, Katarzyna Hafezi | TITLE: DNA extraction from rectal mucosa biopsies and matched faecal samples taken from surgery for microbiome analysis
AUTHORS: Lee Murphy, Alan Maclean, Katarzyna Hafezi
[DESCRIPTION]
This protocol outlines the procedure for manual DNA extraction of microbiome DNA from rectal mucosa biopsy tissue and matched faecal ... | ["[DNA extraction from rectal mucosa tissue samples] Add 828 µL Sodium Phosphate buffer; 122 µL MT buffer (both from MPBio Kit), 50 µL Lysozyme (100mg/ml) and 50 µL Mutanolysin (5U/μl) to the tube, briefly vortex to mix and incubate on a heat block at 37 °C for 60 min", "[DNA extraction from rectal mucosa tissue sample... |
60,942 | Keller (K) Optimized Medium for Culturing Microalgae | 1 | dx.doi.org/10.17504/protocols.io.36wgq76z3vk5/v1 | https://www.protocols.io/view/keller-k-optimized-medium-for-culturing-microalgae-b7rnrm5e | Roscoff Culture Collection, Lynn Doran, Steven J Burgess | TITLE: Keller (K) Optimized Medium for Culturing Microalgae
AUTHORS: Roscoff Culture Collection, Lynn Doran, Steven J Burgess
[DESCRIPTION]
Medium to grow most phytoplankton species in small eukaryotes (Mamiellophyceae, Pelagophyceae etc...).
Optimized for Ostreococcus tauri. Keller Optimized Medium was developed b... | ["[Prepare Artificial Sea Water (ASW)] Prepare artificial sea water (ASW) (1 L).", "[Prepare Trace Metal Solutions] Prepare K Medium Trace Metal Working Stock Solution (7 mL).", "[Prepare f/2 Vitamin Solutions] Prepare K Medium f/2 Vitamin Working Stock Solution (100 mL).", "[Prepare Artificial Sea Water (ASW)] Weigh t... |
32,135 | Purification of DNA-dependent RNA Polymerase from Synechococcus elongatus PCC 7942 | null | dx.doi.org/10.17504/protocols.io.bbmfik3n | null | Lutz Berwanger | TITLE: Purification of DNA-dependent RNA Polymerase from Synechococcus elongatus PCC 7942
AUTHORS: Lutz Berwanger
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol can be used to purifiy DNA-dependent RNA polymerase from </span><span style = "font-style:italic;">Synechococcus elong... | ["[Prepartions]\nCulture:To get a reasonable amount of RNA polymerase it is recommended to use at least 8 litres (OD750nm = 1) culture or in other words 10 grams of cell dry cell pellet.", "[Prepartions]\nLysis buffer:10mM Tris-HCl pH 7.9150mM NaCl1 protease inhibitor cocktail tablet (Roche) per 50ml0.1 mM DTT0.1 mM ED... |
8,706 | Immunofluorescence for free-floating brain sections | 1 | dx.doi.org/10.17504/protocols.io.kracv2e | https://www.protocols.io/view/immunofluorescence-for-free-floating-brain-section-kracv2e | Jill R. Crittenden, Tomoko Yoshida, Margaret I. Davis, Ann M. Graybiel | TITLE: Immunofluorescence for free-floating brain sections
AUTHORS: Jill R. Crittenden, Tomoko Yoshida, Margaret I. Davis, Ann M. Graybiel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes how to prepare fixed brain sections and process them for immunofluorescence.</div></div>
... | ["[Brain tissue preparation]\nBrains are dissected from deeply-anesthetized mice that were trans-cardially perfused with 10 ml of room-temperature 0.9% saline followed by 60 ml of 4% PFA. PFA must be used with appropriate protection and ventilation. Brains are then post-fixed in 4% PFA in glass vials for 2 hours with g... |
69,281 | pCP20 transformation to remove Kanamycin cassette | 4 | dx.doi.org/10.17504/protocols.io.81wgbydxovpk/v1 | https://www.protocols.io/view/pcp20-transformation-to-remove-kanamycin-cassette-cfv9tn96 | Saul Moore | TITLE: pCP20 transformation to remove Kanamycin cassette
AUTHORS: Saul Moore
[DESCRIPTION]
Transformation with pCP20 to remove the Kanamycin cassette from Keio E. coli BW215113 single gene deletion mutants - Cassandra Backes (Host-Microbe Co-Metabolism Laboratory, MRC-LMS)
[STEPS]
1. Make buffer and broth the day b... | ["Make buffer and broth the day before and keep them in the fridge", "Day before: Grow O/N cultures of the strains of interest. Can also prepare buffers (see materials).", "Dilute overnight culture in LB broth at an OD = 0,2 and grow until OD595nm = 0.5 – 0.8 (mid-log phase). \nUNTIL NOW, KEEP CULTURES ON ICE", "Spin d... |
31,784 | Concentrating Viruses by Tangential Flow Filtration | null | dx.doi.org/10.17504/protocols.io.bbagiibw | null | Steven Wilhelm, Samantha Coy | TITLE: Concentrating Viruses by Tangential Flow Filtration
AUTHORS: Steven Wilhelm, Samantha Coy
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Ultracentrifugation in the WX Ultra Series can support only 30 mL samples at a time, and therefore do not significantly concentrate viruses. Tangential flo... | ["[Machine Preparation]\nSet up the tangential flow filtration (TFF) apparatus so that the Pellicon XL 30 kDa filter is attached. Both the retenate and waste tubes should empty into your waste flask.*Catalog number of Pellicon XL 30 kDA filter: PXC030C50*Refer to Figure 1 in the attached PDF.", "[Machine Preparation]\n... |
37,584 | Quantification of fungal ITS Gene Copies Using ddPCR (EvaGreen-based assay: ITS1f-ITS2) | 1 | dx.doi.org/10.17504/protocols.io.yxmvmx13ol3p/v1 | https://www.protocols.io/view/quantification-of-fungal-its-gene-copies-using-ddp-bgxqjxmw | Eva Petrova, Roey Angel | TITLE: Quantification of fungal ITS Gene Copies Using ddPCR (EvaGreen-based assay: ITS1f-ITS2)
AUTHORS: Eva Petrova, Roey Angel
[DESCRIPTION]
The protocol was designed to quantify microbial eukaryotic fungi using ITS region copy number evaluation by Droplet Digital PCR technology (ddPCR) from Bio-Rad company.
For th... | ["[ddPCR reaction mixture] All reagencies must be equilibrated to RT (do not keep them on ice). Mix each of them properly before use.", "[ddPCR reaction mixture] Prepare the master mix according to the number of samples and mix several seconds by vortexing. Transfer mix into 96-well plate à 20 µl. \n20 µL", "[ddPCR rea... |
31,800 | Honeybee DNA extractions in 96-well plates | 1 | dx.doi.org/10.17504/protocols.io.bbayiifw | https://www.protocols.io/view/honeybee-dna-extractions-in-96-well-plates-bbayiifw | Tom Harrop, Reuben McKay Vercoe | TITLE: Honeybee DNA extractions in 96-well plates
AUTHORS: Tom Harrop, Reuben McKay Vercoe
[STEPS]
?. [Prepare lysate for extraction]
Prepare lysate for extraction
?. [Prepare lysate for extraction]
Homogenise the tissue for 90 seconds at 20 Hz using a Mixer Mill or Tissue Lyser.
?. [Prepare lysate for extraction]
Pre... | ["[Prepare lysate for extraction]\nPrepare lysate for extraction", "[Prepare lysate for extraction]\nHomogenise the tissue for 90 seconds at 20 Hz using a Mixer Mill or Tissue Lyser.", "[Prepare lysate for extraction]\nPrepare 300 µL lysis buffer per well. AB1Lysis solution287 µL2RNase solution (10 mg/mL)3 µL3Proteina... |
26,363 | Reviving dead dry-erase markers | null | dx.doi.org/10.17504/protocols.io.5y3g7yn | null | Scott Barolo | TITLE: Reviving dead dry-erase markers
AUTHORS: Scott Barolo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This is a recipe for reviving dry-erase markers. It is based on the </span><a href="https://twitter.com/sbarolo/status/1155870573043572738" style = "text-decoration:underline;color:blue... | ["Tape a string to the back of the dry-erase marker as shown below.", "Spin the marker like a lasso above your head, about 25 times.(See the video here: https://www.facebook.com/sandy.owens.54/videos/10214113211493293/.)", "There should now be more life in the marker."] |
49,108 | Flow Cytometry Staining Protocol For Initial Kidney Studies | 1 | dx.doi.org/10.17504/protocols.io.bt7unrnw | https://www.protocols.io/view/flow-cytometry-staining-protocol-for-initial-kidne-bt7unrnw | Jeremy Lombardo | TITLE: Flow Cytometry Staining Protocol For Initial Kidney Studies
AUTHORS: Jeremy Lombardo
[DESCRIPTION]
Protocol for flow cytometry cell staining for initial kidney studies
[STEPS]
1. Cell suspensions were centrifugated (400xg, 5 min) and then stained concurrently with 5 μg/mL anti-mouse CD45-AF488 (clone 30-F11,... | ["Cell suspensions were centrifugated (400xg, 5 min) and then stained concurrently with 5 μg/mL anti-mouse CD45-AF488 (clone 30-F11, BioLegend, San Diego, CA), 7 μg/mL EpCAM-PE (clone G8.8, BioLegend, San Diego, CA), and 5 μg/mL TER119-AF647 (clone TER-119, BioLegend, San Diego, CA) monoclonal antibodies in PBS+1% BSA ... |
69,707 | scNMT-seq v2 | 1 | null | https://www.protocols.io/view/scnmt-seq-v2-cgbjtskn | Liyun Zhao, Thomas Lefevre, Thierry Voet, Bernard Thienpont | TITLE: scNMT-seq v2
AUTHORS: Liyun Zhao, Thomas Lefevre, Thierry Voet, Bernard Thienpont
[DESCRIPTION]
scNMT-seq (single cell Nucleosome, Methylome, and Transcriptome sequencing) allows the parallel study of a single cell chromatin status, methylation profile, and transcriptome.
Here, we are developing and testing mo... | ["[Cell isolation and GpC methylation] Prepare plates containing 2.5µl GpC methylase reaction mixture in each well: \n \n \n Component (Cinitial) Cfinal Volume Mastermix ( samples) M.CviPI reaction buffer (10x) 1x 0.25 µl M.CviPI (4U/µl) 2U 0.5 µl ... |
48,940 | Prebiotic research protocol | 1 | dx.doi.org/10.17504/protocols.io.bt2knqcw | https://www.protocols.io/view/prebiotic-research-protocol-bt2knqcw | Mohammad Abdus Salam | TITLE: Prebiotic research protocol
AUTHORS: Mohammad Abdus Salam
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The dietary chitosan promotes growth, biochemical composition, hematological parameter and morphology of internal organs by improving gut microbiota status of juvenile </span><span ... | ["[Euthanasia methods]\nPure clove oil was first dissolved in ethyl alcohol in 1:9 ratio (clove oil: ethyl alcohol)", "[Euthanasia methods]\nThis solution then diluted in water in order to obtain concentrations of 0.05 mL (50 mg), and 0.20 mL (200 mg) of clove oil per 500 mL of water", "[Euthanasia methods]\nFor hemato... |
82,647 | A single guide to impregnate samples with Golgi-Cox solution within 24hr and represent results with a set of algorithm | 4 | dx.doi.org/10.17504/protocols.io.3byl4jdrolo5/v2 | https://www.protocols.click/view/a-single-guide-to-impregnate-samples-with-golgi-co-cuxxwxpn | Avishek Roy, Binney Sharma | TITLE: A single guide to impregnate samples with Golgi-Cox solution within 24hr and represent results with a set of algorithm
AUTHORS: Avishek Roy, Binney Sharma
[DESCRIPTION]
Golgi-Cox staining is one of the old but relevant histological technique to identify neurons in superficial/ deep brain structures. The goal of... | ["[Transcardial perfusion] Perfusion setup was filled with 0.9 % NaCl (saline) 2-4 °C and the flow rate was set at a rate of 3ml/min", "[Transcardial perfusion] Rats were placed onto their back and heart was made visible by opening cardiac envelop followed by an access to plural cavity through incisions through diaphr... |
65,125 | BTI plant phenotyping system: Raspi computer and image collection | 1 | dx.doi.org/10.17504/protocols.io.j8nlkk156l5r/v1 | https://www.protocols.io/view/bti-plant-phenotyping-system-raspi-computer-and-im-cbudsns6 | Li'ang Yu | TITLE: BTI plant phenotyping system: Raspi computer and image collection
AUTHORS: Li'ang Yu
[DESCRIPTION]
Instructions on how to set up automated synching between Raspberry Pi operated PhenoRig and the server through WiFi connections
[STEPS]
SECTION: Installation RaspiOS on Raspi Computer
1. Here, we download the ar... | ["[Installation RaspiOS on Raspi Computer] Here, we download the archived RaspiOS to support the camera mode of Raspi camera. Then we used an image installer (eg: Etcher) to install the system into a micro-SD card.", "[Internet connection setup] Please use a router to set up the internet (WIFI). Here we use the LINKSYS... |
null | null | null | dx.doi.org/10.17504/protocols.io.rvbd62n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Procotol describing RNA extraction from dissected human tissue followed by reverse transcription to cDNA, PCR for detection of TMSB4X and separation of PCR products by agarose gel.</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | ["Following dissection, tissue was placed directly into RNAlater (Ambion). To extract RNA, tissue was removed from the RNAlater, placed in 1 ml TRIzol (Ambion) and ground up using a plastic tissue grinder. Samples were incubated in TRIzol for 5 mins at room temperature and centrifuged down at 12,000 g for 10 mins, tran... |
null | null | null | dx.doi.org/10.17504/protocols.io.fesbjee | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Commands for hands-on component for Qiime are found in guidelines.</p>
[GUIDELINES]
<p><strong>1. Checking mapping file format</strong></p>
<p> </p>
<div data-canvas-width="149.19595927068002">$ validate_mapping_file.py -m map_file.txt -o mapping_file_output</div>
<div data-... | [] |
52,634 | GUV assay | 1 | dx.doi.org/10.17504/protocols.io.bxm2pk8e | https://www.protocols.io/view/guv-assay-bxm2pk8e | Chunmei Chang | TITLE: GUV assay
AUTHORS: Chunmei Chang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">LC3 lipidation on GUVs</div></div>
[STEPS]
?. GUV Preparation
?. Coat cleaned coverslips with 60 μL 5% (w/w) polyvinyl alcohol (PVA) with a molecular weight of 145,000 (Millipore).
?. Place the coated coverslip... | ["GUV Preparation", "Coat cleaned coverslips with 60 μL 5% (w/w) polyvinyl alcohol (PVA) with a molecular weight of 145,000 (Millipore).", "Place the coated coverslip in a heating incubator at 60 °C to dry the PVA film for 30 min.", "Spread a lipid mixture at 1 mg/ml uniformly onto the PVA film.", "Put the lipid-coate... |
85,235 | Differentiation of human cortical neurons (CNs) from induced pluripotent stem cells (iPSCs) | 1 | dx.doi.org/10.17504/protocols.io.bp2l69qr5lqe/v1 | https://www.protocols.click/view/differentiation-of-human-cortical-neurons-cns-from-cxgtxjwn | Quyen Do, Bryan Ng, Richard Wade-Martins | TITLE: Differentiation of human cortical neurons (CNs) from induced pluripotent stem cells (iPSCs)
AUTHORS: Quyen Do, Bryan Ng, Richard Wade-Martins
[DESCRIPTION]
This protocol described the production of human cortical neurons from induced pluripotent stem cells. The differentiation protocol of cortical neurons is a... | ["[Differentiation of iPSCs into Neuronal Progenitor Cells (NPCs)] Day -2: Preparing plates for replating\nTwo days before intending on starting the differentiation (Day -2), add 1 mL/well in a 6-well plate of Geltrex one day prior to replating the iPSCs to begin the differentiation.", "[Differentiation of iPSCs into N... |
null | null | null | dx.doi.org/10.17504/protocols.io.ftpbnmn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocol for genetic manipulation of <em>Synechocystis</em> sp. PCC 6803 using the triparental mating method described in Thiel <em>et al</em>., 1988.</p>
[BEFORE_START]
<p>Pour BG11 agar plates with 5% LB.</p>
[GUIDELINES]
<p>Thiel T, Wolk CP: <strong>Conjugal Transfer of ... | [] |
53,726 | Dot Measuring (Co-localisation) (FIJI Macro) | 5 | null | https://www.protocols.io/view/dot-measuring-co-localisation-fiji-macro-byp6pvre | Condon ND | TITLE: Dot Measuring (Co-localisation) (FIJI Macro)
AUTHORS: Condon ND
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describes how to download, install, and run the ImageJ/Fiji macro for quantifying the mean fluorescence intensity of regions determined in one channel, based up... | ["[Downloading and installing the macro]\nRetrieve a copy of the macro files from the GitHub repo", "[Downloading and installing the macro]\nDownload the .ZIP copy of the entire repo to your computer, and extract the compressed file.", "[Downloading and installing the macro]\nLaunch FIJI/ImageJ on your computer.", "[Do... |
60,964 | Open-Skull Controlled Cortical Impact (CCI) model in rats | 1 | dx.doi.org/10.17504/protocols.io.5qpvobozbl4o/v1 | https://www.protocols.io/view/open-skull-controlled-cortical-impact-cci-model-in-b7scrnaw | C Edward Dixon, Nico Osier | TITLE: Open-Skull Controlled Cortical Impact (CCI) model in rats
AUTHORS: C Edward Dixon, Nico Osier
[DESCRIPTION]
This is a protocol to describe the materials and methods utilized by the submitter to perform preclinical traumatic brain injury (TBI) using the open-skull controlled cortical impact (CCI) model.
The pos... | ["Examine the CCI device and its maintenance logs to ensure that it is in proper working order and the maintenance schedule has been adhered to (see Note 1).", "Place the rat into the chamber and induce anesthesia using isoflurane (4.0%) in a 2:1 mixture of N2O:O2.", "Ensure adequate anesthesia is achieved by use of th... |
94,703 | A fast, easy, cost-free method to remove excess dye or drug from exosome solution | 1 | dx.doi.org/10.17504/protocols.io.14egn3k4pl5d/v1 | https://www.protocols.io/view/a-fast-easy-cost-free-method-to-remove-excess-dye-c8qpzvvn | Ioannis Isaioglou, Gloria Lopez-Madrigal, Jasmeen Merzaban | TITLE: A fast, easy, cost-free method to remove excess dye or drug from exosome solution
AUTHORS: Ioannis Isaioglou, Gloria Lopez-Madrigal, Jasmeen Merzaban
[DESCRIPTION]
This protocol details a cost-free method to remove excess dye or drug from exosome solution.
[GUIDELINES]
Tips:
Cells from step 5 should have sign... | ["[Protocol Steps] Collect 0.5 x 106 cells (preferably parental cells used for exosome isolation)* and wash them with\nphosphate buffered saline (PBS) or alternative buffer.", "[Protocol Steps] Add the mixture containing the stained exosomes** with the excess dye/drug to the cell pellet.", "[Protocol Steps] Pellet down... |
60,400 | Interferon signalling as a potentional therapeutic target in amyotrophic lateral sclerosis and frontotemporal dementia – protocol for a systematic review and meta-analysis | 3 | dx.doi.org/10.17504/protocols.io.bp2l61d5zvqe/v1 | https://www.protocols.io/view/interferon-signalling-as-a-potentional-therapeutic-b68qrhvw | Fergal M Waldron, Olivia Rifai, Jenna Gregory | TITLE: Interferon signalling as a potentional therapeutic target in amyotrophic lateral sclerosis and frontotemporal dementia – protocol for a systematic review and meta-analysis
AUTHORS: Fergal M Waldron, Olivia Rifai, Jenna Gregory
[DESCRIPTION]
Amyotrophic lateral sclerosis (ALS) is a rapidly progressive neurodeg... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.cdrs55 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Nucleic acid precipitation is used to concentrate and/or purify nucleic acids. The below protocol is based on the fact that nucleic acids are less soluble in alcohol than in more polar water. Addition of salt further decreases solubility by competing for water dipoles; as does l... | [] |
84,167 | Nano3P-seq Protocol | 4 | dx.doi.org/10.17504/protocols.io.3byl4j292lo5/v3 | https://www.protocols.click/view/nano3p-seq-protocol-cwffxbjn | Oguzhan Begik | TITLE: Nano3P-seq Protocol
AUTHORS: Oguzhan Begik
[DESCRIPTION]
NOTE: in this protocol version, we use LSK114 kit, replacing deprecated DCS109 kit
Here, we develop Nanopore 3’ end-capture sequencing (Nano3P-seq), a novel method that relies on nanopore cDNA sequencing to simultaneously quantify RNA abundance, tail co... | ["[Without Barcoding] Materials and consumables required\n\n●Ligation Sequencing Kit v14 (ONT, SQK-LSK114)\n●AMPure XP Reagent (Agencourt , A63881)\n●TGIRT™-III Enzyme (InGex)\n●RNase Inhibitor, Murine (NEB,M0314L)\n●RNase Cocktail Enzyme Mix (ThermoFisher,AM2286)\n●Qubit dsDNA HS Assay Kit (ThermoFisher, Q32854)\n●1... |
35,441 | Q5® Site-Directed Mutagenesis (E0552) | null | dx.doi.org/10.17504/protocols.io.beurjev6 | null | New England Biolabs | TITLE: Q5® Site-Directed Mutagenesis (E0552)
AUTHORS: New England Biolabs
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol defines methods for the Q5® Site-Directed Mutagenesis Kit without competent cells.</div></div>
[STEPS]
?. [Exponential Amplification (PCR)]
Assemble the following... | ["[Exponential Amplification (PCR)]\nAssemble the following reagents in a thin-walled PCR tube: ABC1 25 μl RXNFINAL CONC.2Q5 Hot Start High-Fidelity 2X Master Mix12.5 μl1X310 μM Forward Primer1.25 μl0.5 μM410 μM Reverse Primer1.25 μl0.5 μM5Template DNA (1–25 ng/μl)1 μl1-25 ng6Nuclease-free water9.0 μl\nABC1 25 μl RXNF... |
50,041 | Processing fallopian tube tissue for single cell sequencing analysis | 1 | dx.doi.org/10.17504/protocols.io.bu4znyx6 | https://www.protocols.io/view/processing-fallopian-tube-tissue-for-single-cell-s-bu4znyx6 | Ramlogan Sowamber, Melissa Castillo, iru.paudel , Sophia George | TITLE: Processing fallopian tube tissue for single cell sequencing analysis
AUTHORS: Ramlogan Sowamber, Melissa Castillo, iru.paudel , Sophia George
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left"><span>This protocol explains the steps used to isolate... | ["[Isolating cells from dissociated fallopian tube tissue]\nIn this step, cells isolated from fallopian tube tissues in Step 1.13 are in the form of a pellet within a 15 mL conical tube and are ready to proceed onto the following steps.", "[Isolating cells from dissociated fallopian tube tissue]\nGently re-suspend pell... |
40,789 | ELISA for quantification of IL-26 in human serum. | 6 | dx.doi.org/10.17504/protocols.io.bj3vkqn6 | https://www.protocols.io/view/elisa-for-quantification-of-il-26-in-human-serum-bj3vkqn6 | Angel Justiz-Vaillant | TITLE: ELISA for quantification of IL-26 in human serum.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Interleukins (IL) are a type of cytokine first thought to be expressed by leukocytes alone but have later been found to be produced by many other body cells. ... | ["An anti-human IL-26 coating antibody is adsorbed onto the microwells by incubation overnight at 4°C with carbonate-bicarbonate buffer.", "Add 50 µl of human serum. Human IL-26 present in the serum sample binds to antibodies adsorbed into the microwells.", "The microplate is blocked with 3% non-fat milk-PBS buffer and... |
15,735 | Building up chemostats for experimental eco-evolutionary studies | null | dx.doi.org/10.17504/protocols.io.tkxekxn | null | Ana Del Arco, Noemi Woltermann, Lutz Becks | TITLE: Building up chemostats for experimental eco-evolutionary studies
AUTHORS: Ana Del Arco, Noemi Woltermann, Lutz Becks
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left"><span>Chemostats and other flow through culture systems are a powerful tool for... | ["[BUILDING CHEMOSTATS]\nThis section for building chemostats is divided into preparing the four main parts of a chemostat (see below). Before you start assembling the different parts you should have an idea of the space you want to use and where you want to put the peristaltic pumps as some of the tubing needs to be c... |
87,055 | Qiagen RNEasy PowerMicrobiome RNA extraction kit | 4 | dx.doi.org/10.17504/protocols.io.q26g7p181gwz/v1 | https://www.protocols.io/view/qiagen-rneasy-powermicrobiome-rna-extraction-kit-cy9pxz5n | Michael Dan Siemon, Christelle Schang et al, Jessica Pardy, Richard Gibson, Dilan Joseph, Justin Donovan, christopher.degroot | TITLE: Qiagen RNEasy PowerMicrobiome RNA extraction kit
AUTHORS: Michael Dan Siemon, Christelle Schang et al, Jessica Pardy, Richard Gibson, Dilan Joseph, Justin Donovan, christopher.degroot
[DESCRIPTION]
The samples were processed using the Qiagen RNeasy PowerMicrobiome kit with the modifications described by Schang ... | ["[Qiagen RNEasy PowerMicrobiome RNA] As a substitute for vortexing described in the kit protocol, bead-beating was used. Bead-beating was conducted 4x for 30s at 4 m/s.", "[Qiagen RNEasy PowerMicrobiome RNA] Add 100 µl phenol–chloroform–isoamyl alcohol to a PowerBead Bead Tube, Glass 0.1 mm. Place 0.25 g stool or bios... |
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