id float64 1.55k 110k ⌀ | title stringlengths 1 256 ⌀ | template_id float64 0 6 ⌀ | doi stringlengths 39 49 ⌀ | url stringlengths 40 92 ⌀ | authors stringlengths 1 933 ⌀ | protocol_text stringlengths 34 1.08M | steps_list stringlengths 2 269k |
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null | null | null | dx.doi.org/10.17504/protocols.io.dmf43m | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<strong>PFGE Protocol is from Griffith 2000</strong><br /><br /><strong>PFGE Modifications (Schwalbach 2002): </strong><br />- 1% Seakem Gold agarose gels are used. Gel is poured after it has cooled to below 45°C. <br />- Instead of using 1:10 TE for the 3 microcon rinse... | [] |
46,211 | HA Filtration of Wastewater for SARS-CoV-2 detection | 4 | null | https://www.protocols.io/view/ha-filtration-of-wastewater-for-sars-cov-2-detecti-brdbm22n | Vbarua , Md Ariful Islam Juel, Neha Mittal, Nick Stark, Cynthia Gibas, jschluet , Mariya Munir | TITLE: HA Filtration of Wastewater for SARS-CoV-2 detection
AUTHORS: Vbarua , Md Ariful Islam Juel, Neha Mittal, Nick Stark, Cynthia Gibas, jschluet , Mariya Munir
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol provides the information on how to concentrate SARS-CoV-2 virus in wastewa... | ["Put on proper PPE (lab coat, N95 fitted masks, gloves, face shield) before handling the wastewater sample.", "The biosafety cabinet should be properly sterilized (UV light for 20 minutes and the surface should be cleaned with 70% ethanol). Gloves should be sprayed with 70% ethanol prior to starting.", "Place a 40 mL ... |
null | null | null | dx.doi.org/10.17504/protocols.io.gzfbx3n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Ligation protocol. Do ligation using a vector:insert molar ratio of 1:3.</p>
[STEPS]
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93,401 | Western Blot | 4 | null | https://www.protocols.io/view/western-blot-c7fzzjp6 | Yiqin Shen | TITLE: Western Blot
AUTHORS: Yiqin Shen
[DESCRIPTION]
This is a protocol of Leo Parra-Rivas, PhD.
[STEPS]
SECTION: Preparing Proteins
1. Dilute protein samples to 1.25 µg/µL. For running a 10-well gel, each loading sample should be around 15 µLto 20 µL.
SECTION: Transferring the Gel
5. Assemble the module according ... | ["[Preparing Proteins] Dilute protein samples to 1.25 µg/µL. For running a 10-well gel, each loading sample should be around 15 µLto 20 µL.", "[Transferring the Gel] Assemble the module according to instructions (membrane = 0.2ul pores; gel needs to be flipped). Ensure all bubbles are removed. \nAdd transfer buffer (ic... |
29,102 | Longitudinal bidirectional relations between body dissatisfaction and depressive symptoms among Black adolescents: A cross-lagged panel analysis | null | dx.doi.org/10.17504/protocols.io.8nnhvde | null | Yan Wang, Sarah D. Lynne, Dawn Witherspoon, Maureen M. Black | TITLE: Longitudinal bidirectional relations between body dissatisfaction and depressive symptoms among Black adolescents: A cross-lagged panel analysis
AUTHORS: Yan Wang, Sarah D. Lynne, Dawn Witherspoon, Maureen M. Black
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style... | ["Purpose1) To compare body dissatisfaction and depressive symptoms by weight status (overweight/obesity vs. healthy weight) among Black adolescents 12-13 years old.2) To investigate the relationship between body dissatisfaction and depressive symptoms among Black adolescents 12-13 years old, who were overweight or obe... |
52,245 | Prediction of ligand binding using FunFOLD2 | 1 | null | https://www.protocols.io/view/prediction-of-ligand-binding-using-funfold2-bw9vph66 | Chris Berndsen | TITLE: Prediction of ligand binding using FunFOLD2
AUTHORS: Chris Berndsen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Clues to functionality can be gleaned from comparing unknown or predicted structures with previously characterized structures of known function and characteristics. These scans ... | ["[Uploading sequence]\nNavigate to the FunFOLD2 server submission form.", "[Uploading sequence]\nPaste in your sequence in single letter amino acid code.", "[Uploading sequence]\nProvide an email address and a short name for your protein. Record the short name as a note in this step.", "[Uploading sequence]\nPress Pr... |
41,475 | Dry cell weight by centrifugation | 4 | null | https://www.protocols.io/view/dry-cell-weight-by-centrifugation-bkrbkv2n | Joao Vitor Molino | TITLE: Dry cell weight by centrifugation
AUTHORS: Joao Vitor Molino
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocols describe the steps required for dry cell weight measurements using microcentrifugal tubes. </div></div>
[STEPS]
?. [Material]
Analytical balance with high precision (Th... | ["[Material]\nAnalytical balance with high precision (The higher the precision the better. For example a balance with a 0.1mg readability, could account to approximately 10% error alone in a measurement of 1mL sample of a culture at 1g/L) Microcentrifugal tubesMicrocentrifuge", "[Tubes preparation]\nLabel microcentrifu... |
null | null | null | dx.doi.org/10.17504/protocols.io.r8rd9v6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This procedure is used to dissociate adult (10 wk.) mouse pancreas into single cells. The procedure is carried out on ice in order to maintain a more authentic gene expression profile. It is a two-layered dissociation, with each layer consisting of 5 mg/mL type 4 collagenase.... | [] |
91,860 | Protocol for the development of coarse-grained structures for macromolecular simulation using GROMACS | 5 | dx.doi.org/10.17504/protocols.io.kxygx92rdg8j/v2 | https://www.protocols.io/view/protocol-for-the-development-of-coarse-grained-str-c5xuy7nw | M Purushotham Rao, Akshay Uttarkar, Vidya Niranjan | TITLE: Protocol for the development of coarse-grained structures for macromolecular simulation using GROMACS
AUTHORS: M Purushotham Rao, Akshay Uttarkar, Vidya Niranjan
[DESCRIPTION]
This paper presents a protocol for the development of coarse-grained (CG) structures for macromolecular simulation using the GROMACS s... | ["[DOWNLOAD NECESSARY PROTEIN] DOWNLOAD THE PDB FILE FROM https://www.rcsb.org/\nHere, in this tutorial DUSP28 https://www.rcsb.org/structure/5Y15 is used.\nPreprocess the pdb to remove all ions and B chain or can obtained from here https://drive.google.com/file/d/1YDJV2hKtZ5dJrl8S6A_4AFdTt_lVJFMv/view?usp=sharing", "[... |
10,213 | Empty protocol reagent | null | dx.doi.org/10.17504/protocols.io.m8dc9s6 | null | Darja Darja | TITLE: Empty protocol reagent
AUTHORS: Darja Darja
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Sneguje</div></div>
[STEPS]
?. Po podatkih uprave za zaščito in reševanje so nedeljska neurja prizadela območja 46 občin, zaznali so več kot 100 dogodkov. Najhuje je bilo v občinah Zagorje, Rogatec i... | ["Po podatkih uprave za zaščito in reševanje so nedeljska neurja prizadela območja 46 občin, zaznali so več kot 100 dogodkov. Najhuje je bilo v občinah Zagorje, Rogatec in Rogaška Slatina, kjer sta zaradi povečanega pretoka poplavljali reki Medija in Sotla, hudo je bilo tudi na Ptuju, kjer je v nedeljo popoldne kar 12... |
59,320 | Isolation of Ashbya from bugs | 4 | null | https://www.protocols.click/view/isolation-of-ashbya-from-bugs-b56yq9fw | Amy Gladfelter | TITLE: Isolation of Ashbya from bugs
AUTHORS: Amy Gladfelter
[DESCRIPTION]
Protocol to isolate Ashbya gossypii from milkweed and box elder bugs.
[STEPS]
2. To collect bugs put them in any sealable container. I like to use a 50 or 15ml conical with a few small holes in the lid but I've also used clean mason jars or th... | ["To collect bugs put them in any sealable container. I like to use a 50 or 15ml conical with a few small holes in the lid but I've also used clean mason jars or the disposable coffee cups at conferences. In my experience live bugs work best. If possible record the species of insect, the location of collection, the dat... |
40,153 | Vesselucida 360 Protocol for Segmenting and Analyzing Human Islet Microvasculature | 1 | dx.doi.org/10.17504/protocols.io.bjfzkjp6 | https://www.protocols.io/view/vesselucida-360-protocol-for-segmenting-and-analyz-bjfzkjp6 | Martha Campbell Thompson, Malavika Nair, Aidan Sullivan | TITLE: Vesselucida 360 Protocol for Segmenting and Analyzing Human Islet Microvasculature
AUTHORS: Martha Campbell Thompson, Malavika Nair, Aidan Sullivan
[STEPS]
?. [Set-up]
Download and install Vesselucida 360 application (RRID:SCR_017320).
?. [Set-up]
Launch the application and set-up SciCrunch connection.
?. [Set-... | ["[Set-up]\nDownload and install Vesselucida 360 application (RRID:SCR_017320).", "[Set-up]\nLaunch the application and set-up SciCrunch connection.", "[Set-up]\nGo to https://scicrunch.org/ and click REGISTER in the top menu. Fill out the registration form to create an account. From \"My account\", click API KEYS. Cli... |
null | null | null | dx.doi.org/10.17504/protocols.io.kwpcxdn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocol details how to create and merge Anvi'o profiles to view them using anvi-interactive. </p>
[STEPS]
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45,902 | Transformation of Diplonema papillatum by electroporation | 1 | dx.doi.org/10.17504/protocols.io.bq3nmyme | https://www.protocols.io/view/transformation-of-diplonema-papillatum-by-electrop-bq3nmyme | Matus Valach | TITLE: Transformation of Diplonema papillatum by electroporation
AUTHORS: Matus Valach
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Variant protocol for transformation of </span><span style = "font-style:italic;">Diplonema papillatum</span><span> by electroporation using a "home-made" trans... | ["Prepare the transformation (cytomix-like) buffer. AB1ComponentFinal concentration2HEPES pH7.525 mM3KCl25 mM4CaCl20.155NaH2PO4 pH7.5106MgCl22.57EDTA18glucose30 mM (0.5%)9sucrose145 mM (4.35%)10bovine serum albumin (BSA)0.1 mg/mL11inosine triphosphate (ITP) [or hypoxanthine]1 mM\nAB1ComponentFinal concentration2HEPES ... |
43,111 | Benefits of Makerspaces: Building An Enhanced Flight Mill for the Study of Tethered Insect Flight | 1 | dx.doi.org/10.17504/protocols.io.bncfmatn | https://www.protocols.io/view/benefits-of-makerspaces-building-an-enhanced-fligh-bncfmatn | Anastasia Bernat | TITLE: Benefits of Makerspaces: Building An Enhanced Flight Mill for the Study of Tethered Insect Flight
AUTHORS: Anastasia Bernat
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Makerspaces have a high potential of enabling researchers to develop new techniques and work with novel species in ecolog... | ["Build the Flight Mill in a Makerspace", "[Laser cut and assemble the acrylic plastic support structure.]\nUse eight 304.8 mm by 609.6 mm, 3.175 mm thick transparent acrylic sheets to construct the acrylic plastic support structure. Ensure that the material is not polycarbonate, which looks similar to acrylic but will... |
null | null | null | dx.doi.org/10.17504/protocols.io.e27bghn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is essentially the same as a standard ELISA protocol, with one major exception – all animal compounds must be avoided in buffers, etc. because they contain Neu5Gc, which will interfere with antibody activity and result in misleading data. Essentially, the glycoc... | [] |
97,102 | USDA LTAR Common Experiment measurement: Natural pest suppression | 1 | dx.doi.org/10.17504/protocols.io.rm7vzjm14lx1/v1 | https://www.protocols.io/view/usda-ltar-common-experiment-measurement-natural-pe-da3n2gme | Nate Haan | TITLE: USDA LTAR Common Experiment measurement: Natural pest suppression
AUTHORS: Nate Haan
[DESCRIPTION]
Pest suppression is a key ecosystem service worth billions of dollars annually, and it can vary with local management practices and landscape context. We propose to measure biocontrol services by deploying plastic... | ["[Overview] Green plasticine caterpillars (3 cm × 15 cm) will be prepared and mounted on small wooden stakes in advance at a centralized location and mailed to each LTAR Site.", "[Overview] At each site, several caterpillars will be placed in the alternative and prevailing treatments at the plot and field scales.", "[... |
98,442 | CODA (part 4): register the deep learning labelled images and Construct 3D tissue matrix | HuBMAP | JHU-TMC | 0 | dx.doi.org/10.17504/protocols.io.yxmvme7eog3p/v2 | https://www.protocols.io/view/coda-part-4-register-the-deep-learning-labelled-im-dcdi2s4e | Kyu Sang Han, Pei-Hsun Wu, Joel Sunshine, Ashley Kiemen, Sashank Reddy, Denis Wirtz | TITLE: CODA (part 4): register the deep learning labelled images and Construct 3D tissue matrix | HuBMAP | JHU-TMC
AUTHORS: Kyu Sang Han, Pei-Hsun Wu, Joel Sunshine, Ashley Kiemen, Sashank Reddy, Denis Wirtz
[DESCRIPTION]
CODA (part 4): register the deep learning labelled images and Construct 3D tissue matrix
[STEPS]... | ["[Register the deep learning labelled images] Using the registration transformations calculated in low-resolution (as described in CODA-part2), register the segmentation masks of the high-resolution tif images generated in CODA-part3.", "[Function requirements] High-resolution images from CODA-part3 (pthclassified)", ... |
93,856 | Spore measurements using ImageJ | 4 | dx.doi.org/10.17504/protocols.io.kxygx3xj4g8j/v1 | https://www.protocols.io/view/spore-measurements-using-imagej-c7v8zn9w | Nhu Nguyen | TITLE: Spore measurements using ImageJ
AUTHORS: Nhu Nguyen
[DESCRIPTION]
Measurement of spore size and particles can be very tedious and time-consuming. This protocol leverages the particle analysis function in ImageJ to measure spores. It will be able to measure spore length, width, and area.
[STEPS]
SECTION: Photog... | ["[Photographing the spores] Mount the specimen of interest under appropriate objective lens size (typically a 40X objective lens or 400X magnification will suffice). The best area for photography should have abundant spores, little background materials other than the spores, positioned on a single plane, not overlappi... |
92,253 | High-performance liquid chromatography with electrochemical detection of monoamine neurotransmitters and metabolites | 1 | dx.doi.org/10.17504/protocols.io.8epv5xkz4g1b/v1 | https://www.protocols.io/view/high-performance-liquid-chromatography-with-electr-c6b5zaq6 | Emanuel F Lopes, Stephanie J Cragg | TITLE: High-performance liquid chromatography with electrochemical detection of monoamine neurotransmitters and metabolites
AUTHORS: Emanuel F Lopes, Stephanie J Cragg
[DESCRIPTION]
This protocol describes a method to identify and quantify the content of the monoamine neurotransmitters dopamine (DA) and norepinephrine... | ["[Obtaining tissue punches] Dispense 200 µL of 0.1 M PCA solution (see Materials) into Eppendorf tubes. We generally use each Eppendorf to prepare material from 2 tissue punches.", "[Obtaining tissue punches] Lay acute coronal striatal slices (slice thickness is 300 µm) flat on a cutting mat, and use a micro punch to ... |
26,936 | Preparation of extracted DNA for long-read library prep | 1 | null | https://www.protocols.io/view/preparation-of-extracted-dna-for-long-read-library-6iyhcfw | Natalie Solonenko, Marie Burris | TITLE: Preparation of extracted DNA for long-read library prep
AUTHORS: Natalie Solonenko, Marie Burris
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details steps to prepare DNA for long-read library prep, including clean-up and shearing.</div></div>
[STEPS]
?. [Shear DNA]
Load at ... | ["[Shear DNA]\nLoad at least 90ul of high molecular weight DNA into the top of a Covaris g-TUBE. Loading less than 90ul will result in poorly sheared DNA.", "[Shear DNA]\nTo shear DNA to 15kb, centrifuge at 4,700 rpm for 60 sec in an Eppendorf 5424 centrifuge with a 24 position rotor. Flip the g-TUBE upside-down and r... |
60,897 | Rotarod assay to detect motor phenotypes in mice | 4 | dx.doi.org/10.17504/protocols.io.j8nlkkd1dl5r/v1 | https://www.protocols.io/view/rotarod-assay-to-detect-motor-phenotypes-in-mice-b7p9rmr6 | William Hancock-Cerutti, Pietro De Camilli | TITLE: Rotarod assay to detect motor phenotypes in mice
AUTHORS: William Hancock-Cerutti, Pietro De Camilli
[DESCRIPTION]
This protocol describes an assay to detect motor deficits in mice by testing how long they can stay on a rotating rod before falling.
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.e4ebgte | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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49,253 | HuBMAP UF TMC - FACS Sorting of Live CD45 negative Cells for 10x scRNASeq | 1 | dx.doi.org/10.17504/protocols.io.bucdnss6 | https://www.protocols.io/view/hubmap-uf-tmc-facs-sorting-of-live-cd45-negative-c-bucdnss6 | Maigan Brusko | TITLE: HuBMAP UF TMC - FACS Sorting of Live CD45 negative Cells for 10x scRNASeq
AUTHORS: Maigan Brusko
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This standard operating procedure (SOP) provides instructions for staining and sorting live cells. This SOP applies to cryopreserved cells that are ... | ["[Thaw Cryopreserved Cells]\na. In a 15 mL conical tube, warm 10 mL of cDMEM in a bead bath set to 37 o Cb. Thaw the cells in the cryovials in a water bath set at 37 o Cc. Immediately, resuspend the cells in 10 ml of RT cDMEM i. First, add 1 mL of cDMEM to the cryovial ii. Then, transfer the cells from the cryov... |
63,325 | BioLogic Trim Keto Gummies Reviews - Fake Or Trusted? | 1 | dx.doi.org/10.17504/protocols.io.j8nlkk6z6l5r/v1 | https://www.protocols.io/view/biologic-trim-keto-gummies-reviews-fake-or-trusted-b935r8q6 | biologictrimketoreviews | TITLE: BioLogic Trim Keto Gummies Reviews - Fake Or Trusted?
AUTHORS: biologictrimketoreviews
[DESCRIPTION]
BioLogic Trim Keto Gummies Reviews - Fake Or Trusted?
[STEPS]
1. BioLogic Trim Keto Gummies Reviews - Fake Or Trusted?
Multitudinous promising exploration studies have proven that it's possible to lose weigh... | ["BioLogic Trim Keto Gummies Reviews - Fake Or Trusted?\nMultitudinous promising exploration studies have proven that it's possible to lose weight snappily in moment's ultramodern world. There are numerous myths about weight loss. Then is how to avoid them. Rotundity doesn't have to be a habitual problem that requires ... |
61,930 | Guardian Blood Balance Australia | 3 | dx.doi.org/10.17504/protocols.io.261genx2wg47/v1 | https://www.protocols.io/view/guardian-blood-balance-australia-b8qirvue | health | TITLE: Guardian Blood Balance Australia
AUTHORS: health
[DESCRIPTION]
Guardian Botanicals Blood Balance Australia is, in my opinion a great product! This pill will assist your body to repair itself. You can trust your judgement to make the right choice.
You will live a happier, healthier life. It is a great trea... | [] |
55,841 | Pancreatic Islet RNA Extraction | 4 | dx.doi.org/10.17504/protocols.io.b2r9qd96 | https://www.protocols.io/view/pancreatic-islet-rna-extraction-b2r9qd96 | Islet and Pancreas Analysis Core | TITLE: Pancreatic Islet RNA Extraction
AUTHORS: Islet and Pancreas Analysis Core
[DESCRIPTION]
This SOP defines the methods used by the Vanderbilt Diabetes Center Islet and Pancreas Analysis (IPA) Core for RNA extraction of pancreatic islets isolated from mouse or human tissue.
[BEFORE_START]
Prepare all working sur... | ["[Reagent preparation] RNAqueous Kit – Can be stored at 4 °C up to 6 months.", "[Reagent preparation] DNase Kit – Can be stored at -20 °C up to 6 months.", "[RNA extraction procedure] Pick at least 75 islets into an RNase-free microcentrifuge tube. Islets should be free of acinar tissue and other debris.\n\nFor more i... |
37,447 | Diagnostic yield of an ambulatory patch monitor in Emergency Department syncope patients unexplained after Emergency Department evaluation – a pilot study (PATCH-ED). | null | dx.doi.org/10.17504/protocols.io.bgtfjwjn | https://www.protocols.io/view/diagnostic-yield-of-an-ambulatory-patch-monitor-in-bgtfjwjn | Christopher J. Weir, Matt Reed, Kirsty Simpson, Chris Lang, Neil Grubb, Alasdair Gray | TITLE: Diagnostic yield of an ambulatory patch monitor in Emergency Department syncope patients unexplained after Emergency Department evaluation – a pilot study (PATCH-ED).
AUTHORS: Christopher J. Weir, Matt Reed, Kirsty Simpson, Chris Lang, Neil Grubb, Alasdair Gray
[DESCRIPTION]
<div class = "text-blocks"><div clas... | ["1.Short project summary: Syncope is a common Emergency Department (ED) presentation but the underlying diagnosis is not apparent in 60% of patients after assessment and serious adverse event rate is 7% at one month with most having acute cardiovascularevents, also more likely to be unexplained after ED assessment. Ma... |
41,851 | Copy of Corona Detective User Protocol V1.0 | 1 | dx.doi.org/10.17504/protocols.io.bk43kyyn | https://www.protocols.io/view/copy-of-corona-detective-user-protocol-v1-0-bk43kyyn | Rachel Aronoff, Guy Aidelberg | TITLE: Copy of Corona Detective User Protocol V1.0
AUTHORS: Rachel Aronoff, Guy Aidelberg
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Corona Detective</span><span> is based upon a molecular amplification strategy inspired by the ‘</span><a href="https://gmodetec... | ["Sample Extraction: Three options are possible A: 'direct reactions' with addition of TBE to 1x and (after incubation at for ) addition of detergent (Tween 20 to 0.5%)B: 'concentrated reactions' using a variant of the glass-milk protocol of Rabe and CepkoC: 'Magnetic Beads' as described.The B/C methods are especia... |
68,253 | Manual Tissue Dissociation for Multiome Analysis | 4 | dx.doi.org/10.17504/protocols.io.8epv59y34g1b/v1 | https://www.protocols.io/view/manual-tissue-dissociation-for-multiome-analysis-cev5te86 | Stephen Fisher, Marielena Grijalva, Rong Guo, sarahjoh, Hieu Nguyen, John Renz, Jean G Rosario, Steven Rudich, Brian Gregory, Junhyong Kim, Kate O'Neill | TITLE: Manual Tissue Dissociation for Multiome Analysis
AUTHORS: Stephen Fisher, Marielena Grijalva, Rong Guo, sarahjoh, Hieu Nguyen, John Renz, Jean G Rosario, Steven Rudich, Brian Gregory, Junhyong Kim, Kate O'Neill
[DESCRIPTION]
This protocol describes dissociation of snap-frozen ovarian tissue in order to isolate ... | ["[Methods] Keep snap-frozen tissue specimen on dry ice, after removing from freezer and until ready to begin.", "[Methods] Using a disposable weigh boat, quickly weigh the tissue specimen while still frozen.", "[Methods] Mince tissue with a fresh scalpel until tissue is the size of dry rice grains (or smaller) and tra... |
59,657 | Plant assemble - Plant de novo genome assembly: quality assessment | 5 | dx.doi.org/10.17504/protocols.io.e6nvw578zvmk/v2 | https://www.protocols.io/view/plant-assemble-plant-de-novo-genome-assembly-quali-b6hhrb36 | Scott Ferguson, Ashley Jones, Justin Borevitz | TITLE: Plant assemble - Plant de novo genome assembly: quality assessment
AUTHORS: Scott Ferguson, Ashley Jones, Justin Borevitz
[DESCRIPTION]
With the advancement of long-read sequencing technologies and associated bioinformatics tools, it has now become possible to de novo assemble complex plant genomes with unri... | ["[Genome quality assessment] Having assembled a genome we want to assess how good it is. The three major considerations here are contiguity, accuracy and completeness.\n\nContiguity we can assess with numerical statistics: \nN50.\nE-size.\nnumber of sequences.\nN50 and E-size are both ways of trying to express genome ... |
95,360 | Human and mouse alpha-synuclein protein expression and purification | 4 | null | https://www.protocols.io/view/human-and-mouse-alpha-synuclein-protein-expression-c9c8z2zw | andrew.west, arpine.sokratian | TITLE: Human and mouse alpha-synuclein protein expression and purification
AUTHORS: andrew.west, arpine.sokratian
[DESCRIPTION]
The protocol for is designed for high-yield purification of recombinant α-synuclein monomer. It is recommended to always store the protein on ice, and once the purification process has starte... | ["[Transformation] Thaw down an aliquot of plasmid construct (pRK172) encoding WT-human-a-synuclein or mouse-a-synuclein 0.3 mg/mL on ice", "[Transformation] Thaw down on ice an aliquot of BL21 (DE3) RIL competent E Coli cells", "[Transformation] Add 1 µL of plasmid construct to the thawed competent cells and gently ... |
null | null | null | dx.doi.org/10.17504/protocols.io.c38yrv | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Modified after V. Rich, 2/10/07: DNA extraction protocol from 25 mm 0.2 μm filters – Low-throughput, using DNeasy columns (based on lab Steripak filter extraction protocol and the Suzuki et al. 2001 protocol)
[GUIDELINES]
<strong>Materials: </strong><br /><br />
<... | [] |
68,696 | Immunoblotting analysis of samples from GolgiTAG (TMEM115-3HA) immunoprecipitation | 1 | dx.doi.org/10.17504/protocols.io.bp2l61oxdvqe/v1 | https://www.protocols.io/view/immunoblotting-analysis-of-samples-from-golgitag-t-cfbytipw | Rotimi Fasimoye, Dario R Alessi | TITLE: Immunoblotting analysis of samples from GolgiTAG (TMEM115-3HA) immunoprecipitation
AUTHORS: Rotimi Fasimoye, Dario R Alessi
[DESCRIPTION]
Analysis of the expression of organelle-specific markers is essential to verify the efficiency of any Golgi immunoprecipitation (IP) protocol. Here, we describe our immunoblo... | ["[Preparation of IP samples or whole cell lysates samples:] For a detailed description of our method for Golgi immunoprecipitation, refer to dx.doi.org/10.17504/protocols.io.6qpvrdjrogmk/v1 (Introducing GolgiTag to Cells and Immunoprecipitation of Golgi). This also includes a description of how to prepare whole cell l... |
21,040 | Experiment protocol: a syringe-filter based DNA extraction | null | dx.doi.org/10.17504/protocols.io.ysqfwdw | null | Sungwoo Bae | TITLE: Experiment protocol: a syringe-filter based DNA extraction
AUTHORS: Sungwoo Bae
[STEPS]
?. Prepare the following solutionsa. TE buffer (10 mM Tris-HCl and 1 mM EDTA)b. TE/lysozyme (TL) buffer (10 mM Tris-HCl, 1 mM EDTA, and 7.5 mg/mL lysozyme)c. TE/proteinase K/SDS (TPS) buffer (10 mM Tris-HCl, 1 mM EDTA, 300 µ... | ["Prepare the following solutionsa. TE buffer (10 mM Tris-HCl and 1 mM EDTA)b. TE/lysozyme (TL) buffer (10 mM Tris-HCl, 1 mM EDTA, and 7.5 mg/mL lysozyme)c. TE/proteinase K/SDS (TPS) buffer (10 mM Tris-HCl, 1 mM EDTA, 300 µg/mL proteinase K, and 1% SDS[w/v])", "Filtration The 10 mL sample or 100ml was passed through a... |
null | null | null | dx.doi.org/10.17504/protocols.io.ir7cd9n | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?. | [] |
63,339 | Melodious CBD Gummies Results, 100 Percent Safe And Risk Free! | 3 | dx.doi.org/10.17504/protocols.io.n2bvj6q5xlk5/v1 | https://www.protocols.io/view/melodious-cbd-gummies-results-100-percent-safe-and-b94jr8un | Melodious CBD Gummies | TITLE: Melodious CBD Gummies Results, 100 Percent Safe And Risk Free!
AUTHORS: Melodious CBD Gummies
[DESCRIPTION]
Melodious CBD Gummies Reviews: Nowadays, stress and uneasiness have become a vital part of one's life, bringing forth numerous wellbeing problems and in any event, misshaping your wellness.
[STEPS] | [] |
62,203 | Mouse model of post-colitis (DNBS) chronic visceral hypersensitivity. | 1 | dx.doi.org/10.17504/protocols.io.14egn7mpqv5d/v1 | https://www.protocols.io/view/mouse-model-of-post-colitis-dnbs-chronic-visceral-b8y3rxyn | Andrea Harrington | TITLE: Mouse model of post-colitis (DNBS) chronic visceral hypersensitivity.
AUTHORS: Andrea Harrington
[DESCRIPTION]
This protocol is used to administer DNBS (Dinitrobenzene sulfonic acid) to the colorectum of mice via intracolonic enema administration to induce mild colonic inflammation.
[STEPS]
1. Fast mice over... | ["Fast mice overnight by removing bedding and food from cages and placing a wire fasting rack at the bottom of cage. Provide 5% glucose drinking water. Record weight before fasting.", "Weigh mouse following overnight fasting, if mouse has lost more than 10% of prefast weight, or is under 22 grams do not treat animal, r... |
75,340 | Single-moclecule Immunofluorescence Tissue Staining Protocol for Oligomer Imaging | 4 | dx.doi.org/10.17504/protocols.io.5qpvorp6bv4o/v1 | https://www.protocols.io/view/single-moclecule-immunofluorescence-tissue-stainin-cmtku6kw | Rebecca Andrews | TITLE: Single-moclecule Immunofluorescence Tissue Staining Protocol for Oligomer Imaging
AUTHORS: Rebecca Andrews
[DESCRIPTION]
This protocol details about immunofluorescence staining for oligomer imaging.
[GUIDELINES]
Use only clean bottles, flasks, magnetic stirrers, tweezers, weighing spatulas, measuring cylinders... | ["[Immunofluorescences staining protocol for oligomer imaging] Cut tissue sections on a microtome and load onto glass slides.", "[Immunofluorescences staining protocol for oligomer imaging] Dry slides 10 min at 37 °C – cover over the top.", "[Immunofluorescences staining protocol for oligomer imaging] Before staining... |
106,083 | Quantification of pathological protein accumulation (aSyn and tau) in transplanted human iPSC-derived dopamine neurons | 0 | dx.doi.org/10.17504/protocols.io.n92ld86z9v5b/v1 | https://www.protocols.io/view/quantification-of-pathological-protein-accumulatio-djub4nsn | Giselle Sagredo, Hongyun Li, YuHong Fu, Glenda Halliday | TITLE: Quantification of pathological protein accumulation (aSyn and tau) in transplanted human iPSC-derived dopamine neurons
AUTHORS: Giselle Sagredo, Hongyun Li, YuHong Fu, Glenda Halliday
[DESCRIPTION]
This protocol details the immunohistochemistry protocol and subsequent imaging analysis protocols for quantifying ... | ["[Tissue processing and immunofluorescence staining] Day 1\nTissue Prep\nPour sections into well insert in well-plate to separate the cryoprotectant storage solution from\nthe sections. \nMove well-insert to well-plate containing approximately 6 mLof 1 x phosphate buffered saline (PBS)\nin each well. \nWash sections f... |
null | null | null | dx.doi.org/10.17504/protocols.io.n57dg9n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is provided to synthesize single-stranded cDNA from total RNA samples using the TaqMan® MicroRNA Reverse Transcription Kit and quantification of miRNA using the comparative Cycle threshold (Ct) method. Endogenous controls are used to normalize the expression lev... | [] |
45,975 | Assessment of the impact on future risk of diseases associated with low birth weight: overview of reviews | 1 | dx.doi.org/10.17504/protocols.io.bq5xmy7n | https://www.protocols.io/view/assessment-of-the-impact-on-future-risk-of-disease-bq5xmy7n | Yoshiko Yamamoto, Yasushi Tsujimoto, Shunsuke Taito, Yusuke Tsutsumi, Yoshitaka Wada, Yasutaka Kuniyoshi, Takashi Ariie, Daishi Hirano, Masahiro Banno | TITLE: Assessment of the impact on future risk of diseases associated with low birth weight: overview of reviews
AUTHORS: Yoshiko Yamamoto, Yasushi Tsujimoto, Shunsuke Taito, Yusuke Tsutsumi, Yoshitaka Wada, Yasutaka Kuniyoshi, Takashi Ariie, Daishi Hirano, Masahiro Banno
[STEPS] | [] |
41,589 | Testing safety mechanism | 1 | dx.doi.org/10.17504/protocols.io.bkuvkww6 | https://www.protocols.io/view/testing-safety-mechanism-bkuvkww6 | Andreea S | TITLE: Testing safety mechanism
AUTHORS: Andreea S
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">In order to test the efficiency of the kill switch mechanism, we plan on performing the following experiments:</div><div class = "text-block"><span style = "font-weight:bold;">Test amino acid autotrop... | ["[Test safety mechanisms in the lab]\nPlate mutants on minimal media supplemented with the auxotrophy amino acid or solanine.", "[Test safety mechanisms in the lab]\nPick one colony and inoculate . Grow B. mycoides\n5 mL\n30 33", "[Test safety mechanisms in the lab]\nThe next day inoculate a working culture ( media +... |
84,242 | Dual coloMOCA implantation protocol | 4 | dx.doi.org/10.17504/protocols.io.36wgq3535lk5/v1 | https://www.protocols.io/view/dual-colomoca-implantation-protocol-cwhsxb6e | Brett Hanzlicek, Dennis Bourbeau | TITLE: Dual coloMOCA implantation protocol
AUTHORS: Brett Hanzlicek, Dennis Bourbeau
[DESCRIPTION]
This protocol describes the implantation of two bowel devices (ColoMOCA) in pigs.
[STEPS]
SECTION: Anesthesia
1. Anesthetize/prep the animal for surgery.
Aseptic procedures by trained personnel are utilized du... | ["[Anesthesia] Anesthetize/prep the animal for surgery.\n\n Aseptic procedures by trained personnel are utilized during the surgery. All tools are sterilized prior to insertion. Drapes will be used and personnel performing surgery will wear clean surgical scrubs, and sterile gowns/gloves and masks.", "[La... |
28,833 | Massively parallel long-read sequencing of single cell RNA isoforms | null | dx.doi.org/10.17504/protocols.io.8d9hs96 | null | Jafar S Jabbari, Luyi Tian | TITLE: Massively parallel long-read sequencing of single cell RNA isoforms
AUTHORS: Jafar S Jabbari, Luyi Tian
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the subsampling of 10x Chromium generated single cell GEMs after reverse transcription for cDNA amplification. The pr... | ["[GEM Generation & Barcoding]", "[GEM Generation & Barcoding]\nFollow the 10x Genomics user guide for Single Cell Gene Expression (v3) or Single Cell Immune Profiling (v1 Chemistry) kits for GEM Generation and Barcoding for the required number of cells.NOTE: This protocol is also compatible with Next Gem single cell ... |
15,131 | PCR S11 - Red Sea medium | null | dx.doi.org/10.17504/protocols.io.sz3ef8n | null | Roscoff Culture Collection | TITLE: PCR S11 - Red Sea medium
AUTHORS: Roscoff Culture Collection
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Medium to grow cyanobacteria, in particular </span><span style = "font-style:italic;">Prochlorococcus </span><span>and </span><span style = "font-style:italic;">Synechococcus</sp... | ["[Prepare medium]\nWe generally prepare two or three 10L carboys at a timeTo 1 L of H2O, add 33.33g of Red Sea Salt Dissolve by shaking (20 min on agitator)Heat seawater during 20min at 100°CTo 1 L of H2O, add 33.33g of Red Sea SaltDissolve by shaking (20 min on agitator)Heat seawater during 20min at 100°C", "Add to s... |
95,667 | Mime-seq 2.0: a method to sequence microRNAs from specific mouse cell types | 4 | dx.doi.org/10.17504/protocols.io.rm7vzxzzxgx1/v1 | https://www.protocols.io/view/mime-seq-2-0-a-method-to-sequence-micrornas-from-s-c9ntz5en | Ariane Mandlbauer, Qiong Sun, Niko Popitsch, Tanja Schwickert, Miroslava Spanova, Jingkui Wang, Stefan Ameres, Meinrad Busslinger, Luisa Cochella | TITLE: Mime-seq 2.0: a method to sequence microRNAs from specific mouse cell types
AUTHORS: Ariane Mandlbauer, Qiong Sun, Niko Popitsch, Tanja Schwickert, Miroslava Spanova, Jingkui Wang, Stefan Ameres, Meinrad Busslinger, Luisa Cochella
[DESCRIPTION]
The description of precise miRNA expression patterns is crucial to ... | ["[Total RNA isolation] Measure concentration (Qubit BR RNA kit); ideally, at least 3.3 μg of total RNA are used for small RNA library preparation per sample (will be split in ox/unox).", "[Total RNA isolation] Extract total RNA from frozen cells or tissue using TRIzol, depending on sample type follow manufacturer’s in... |
null | null | null | dx.doi.org/10.17504/protocols.io.qhydt7w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>This is a short tutorial on how to get started analyzing FASTA files via the command line.</strong></p>
<p> </p>
<p>Code is intended for use on an Ubuntu 16.04 LTS OS, but it may work on other Unix or Unix-like systems.</p>
<p> </p>
<p>Here we will use the ETE3 toolki... | [] |
66,218 | Quick DNA Extraction for Fungal Barcoding (X-Amp) | 4 | dx.doi.org/10.17504/protocols.io.4r3l2oy2pv1y/v2 | https://www.protocols.io/view/quick-dna-extraction-for-fungal-barcoding-x-amp-ccwisxce | Stephen Douglas Russell | TITLE: Quick DNA Extraction for Fungal Barcoding (X-Amp)
AUTHORS: Stephen Douglas Russell
[DESCRIPTION]
Below you will find a simple and fast two-step DNA extraction protocol that works well with many different groups of fungi. This protocol can be utilized in preparation for DNA barcoding of fungi utilizing Oxf... | ["[X-Amp Extractions] Place 15 µL to 25 µL of into each cell that contains tissue. I typically use 20 µL. Using less solution means the overall cost basis per sample will be lower. This process is easiest with a multichannel pipette. One option is to keep a PCR Rack dedicated to an 8-strip of X-Amp for pipetting.",... |
74,181 | UPitt TriState SenNet TMC Lung Procurement | 4 | dx.doi.org/10.17504/protocols.io.81wgbyr83vpk/v1 | https://www.protocols.io/view/upitt-tristate-sennet-tmc-lung-procurement-ckpduvi6 | John Sembrat, Alison Morris, koenigshoffm, Oliver Eickelberg | TITLE: UPitt TriState SenNet TMC Lung Procurement
AUTHORS: John Sembrat, Alison Morris, koenigshoffm, Oliver Eickelberg
[DESCRIPTION]
This document outlines the request for specimen procurement before arrival at the TriState SenNet TMC Biospecimen Core at the University of Pittsburgh, as part of the Cellular Senescenc... | ["[Requested processing protocol for Donation following Brain Death Declaration (DBD)] Organ Procurement Organization Recovery Team prepares for organ recovery as consistent with organ transplant protocol with cross clamp and in situ cold flush body cooling with minimal warm ischemic time.\n\nIncludes flush with Perfad... |
49,723 | Human Islet Quantification and Purity Assessment | 1 | dx.doi.org/10.17504/protocols.io.bus3nwgn | https://www.protocols.io/view/human-islet-quantification-and-purity-assessment-bus3nwgn | James Lyon, Aliya Spigelman, Jocelyn Manning Fox, Patrick Macdonald | TITLE: Human Islet Quantification and Purity Assessment
AUTHORS: James Lyon, Aliya Spigelman, Jocelyn Manning Fox, Patrick Macdonald
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the Quantification and Purity of Assessment of human islets, as performed by the Alberta Diabet... | ["[Preparation and use of Dithizone stain in Human Islet Preparations]\nPreparation of DMSO-dithizone (DTZ)Weigh out 0.2g of dithizone powder into a 50ml conical tube. Add 6mls of DMSO and mix until the powder is in solution. Bring the resulting dithizone solution to 40ml total volume with HBSS and mix. Transfer the di... |
49,890 | Purification of the CARD8-DPP9 Complex from Expi293F Cells | 1 | dx.doi.org/10.17504/protocols.io.buyanxse | https://www.protocols.io/view/purification-of-the-card8-dpp9-complex-from-expi29-buyanxse | Louis R Hollingsworth | TITLE: Purification of the CARD8-DPP9 Complex from Expi293F Cells
AUTHORS: Louis R Hollingsworth
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol associated with "DPP9 sequesters the NLRP1 C-terminus to repress inflammasome activation" by Sharif*, Hollingsworth*, Griswold*, et al., Bachovchi... | ["[Protein Expression]\nGrow Expi293F cells (ThermoFisher, A14527) in Expi293™ Expression Medium (ThermoFisher, A1435101) to 2-3 million cells/mL at the desired culture volume, such as 1L. Choose the appropriate flask for the desired volume of cell culture to ensure appropriate gas exchange--I use a 2L Fernbach flask f... |
44,159 | Laboratory protocol for bacteriological and physico-chemical technique in water sample analysis | 1 | dx.doi.org/10.17504/protocols.io.bpc7mizn | https://www.protocols.io/view/laboratory-protocol-for-bacteriological-and-physic-bpc7mizn | Shibabaw Tadesse Mr Gemeda; , shibabaw Tadesse Gemeda, Solomon Melake Mr Birhan; , Hailu Tolasa Mr Bedane | TITLE: Laboratory protocol for bacteriological and physico-chemical technique in water sample analysis
AUTHORS: Shibabaw Tadesse Mr Gemeda; , shibabaw Tadesse Gemeda, Solomon Melake Mr Birhan; , Hailu Tolasa Mr Bedane
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "... | ["[V1]"] |
93,558 | Spatial N-glycomics with MALDI-MSI for human lung tissue | 1 | dx.doi.org/10.17504/protocols.io.5jyl8p876g2w/v2 | https://www.protocols.io/view/spatial-n-glycomics-with-maldi-msi-for-human-lung-c7kwzkxe | Dusan Velickovic, Chris Anderton | TITLE: Spatial N-glycomics with MALDI-MSI for human lung tissue
AUTHORS: Dusan Velickovic, Chris Anderton
[DESCRIPTION]
This protocol describes the procedure to obtain high quality MALDI mass spectrometry images of N-linked glycans from formalin-fixed paraffin embedded tissue. This protocol is optimized for human lun... | ["[Scope] This protocol describes the procedure to obtain high quality matrix-assisted laser desorption/ionization (MALDI) mass spectrometry images of N-linked glycans from formalin-fixed paraffin embedded tissue.", "[Health and Safety] Wear nitrile gloves and safety glasses. Follow standard laboratory safety procedure... |
109,194 | Sinai SCENT TMC - 5x5 Project Bulk RNAseq | 0 | dx.doi.org/10.17504/protocols.io.x54v926w4l3e/v1 | https://www.protocols.io/view/sinai-scent-tmc-5x5-project-bulk-rnaseq-dnvi5e4e | HIMC at Mount Sinai | TITLE: Sinai SCENT TMC - 5x5 Project Bulk RNAseq
AUTHORS: HIMC at Mount Sinai
[DESCRIPTION]
Bulk RNA sequencing protocol
[STEPS]
SECTION: Protocols
1. Dissect the snap-frozen or -80'C stored tissues.
SECTION: Protocols
2. Dissected tissues are placed directly into a labeled 1.5 mL RNAlater (Qiagen) collection tube an... | ["[Protocols] Dissect the snap-frozen or -80'C stored tissues.", "[Protocols] Dissected tissues are placed directly into a labeled 1.5 mL RNAlater (Qiagen) collection tube and stored at 4°C for up to 24 hours to allow the RNAlater to penetrate the tissue fully before being transferred to -20°C or lower until use.", "[P... |
null | null | null | dx.doi.org/10.17504/protocols.io.g7tbznn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This week we're going to take a closer look at the taxonomy of your datasets using mothur. We'll classify taxonomy and diversity using the metagenomic reads that mapped to 16S ribosomal RNA. The Tara Oceans folks have already pulled out the reads that match 16S ribosomal RNA,... | [] |
49,852 | Citric Acid Water Restriction | 4 | dx.doi.org/10.17504/protocols.io.buw4nxgw | https://www.protocols.io/view/citric-acid-water-restriction-buw4nxgw | Thomas R Clarke | TITLE: Citric Acid Water Restriction
AUTHORS: Thomas R Clarke
[DESCRIPTION]
How to prepare and carry out citric acid water restriction for motivating mice to engage in behaviour.
[STEPS]
SECTION: Baseline Weights
1. Handle animals and weigh for 3-5 days to establish a mean baseline weight prior to introduction of the... | ["[Baseline Weights] Handle animals and weigh for 3-5 days to establish a mean baseline weight prior to introduction of the CA water", "[Preparing 2% CA Water] Prepare the following:\n\n2 bottles\nCitric acid crystals\nSterile Gloves or weighing boats\nScales", "[Preparing 2% CA Water] Empty one of the water bottles, p... |
58,555 | Sample Site Questionnaire | 3 | null | https://www.protocols.io/view/sample-site-questionnaire-b5e3q3gn | Dilip Abraham, Nicola Elviss, Nicholas Feasey, Nick Grassly, Jacob John, Gagandeep Kang, John Scott Meschke, Venkata Raghava Mohan, Satheesh Nair, Jonathan Rigby, Rajan Srinivasan, Catherine Troman, Christopher Uzzell | TITLE: Sample Site Questionnaire
AUTHORS: Dilip Abraham, Nicola Elviss, Nicholas Feasey, Nick Grassly, Jacob John, Gagandeep Kang, John Scott Meschke, Venkata Raghava Mohan, Satheesh Nair, Jonathan Rigby, Rajan Srinivasan, Catherine Troman, Christopher Uzzell
[DESCRIPTION]
The following document is a questionna... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.hfbb3in | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>A protocol to create a genomic library (2-5 kb insert size) to screen for genomic regions functioning as centromeres. Uses the NEBNext Illumina library prep kit from NEB to add adapters to fragments and then the fragments can be efficiently assembled into a vector containing ... | [] |
105,946 | SOP for Endoscopy Collection | 1 | dx.doi.org/10.17504/protocols.io.x54v92oq1l3e/v1 | https://www.protocols.io/view/sop-for-endoscopy-collection-djp24mqe | Joanna Bi | TITLE: SOP for Endoscopy Collection
AUTHORS: Joanna Bi
[DESCRIPTION]
SOP for Endoscopy Collection
[STEPS]
SECTION: Purpose
1. Due to the time and temperature sensitive nature of tissue collection, we must be fully prepared with all supplies for the procedure and that all persons involved in the collection process are... | ["[Purpose] Due to the time and temperature sensitive nature of tissue collection, we must be fully prepared with all supplies for the procedure and that all persons involved in the collection process are assigned a particular role. Here, we have provided detailed guidelines on exactly how to navigate through a endosco... |
101,562 | OSU TriState SenNet Processing and Storing of Explanted IPF Lungs | 1 | dx.doi.org/10.17504/protocols.io.e6nvw1b17lmk/v1 | https://www.protocols.io/view/osu-tristate-sennet-processing-and-storing-of-expl-dfe23jge | Sean D. Stacey, Brenda F. Reader, Lorena Rosas, Victor Peters, Ana L Mora, Mauricio Rojas | TITLE: OSU TriState SenNet Processing and Storing of Explanted IPF Lungs
AUTHORS: Sean D. Stacey, Brenda F. Reader, Lorena Rosas, Victor Peters, Ana L Mora, Mauricio Rojas
[DESCRIPTION]
This protocol describes the processing and storing of explanted idiopathic pulmonary fibrosis (IPF) lungs by the Comprehensive Transp... | ["[Objective] To preserve lung tissue for further downstream cellular, protein, RNA, or DNA analyses.", "[Preparation] Use appropriate PPE that includes nitrile gloves and disposable gown or washable lab coat.", "[Preparation] Place three underpads and all needed equipment, including biohazard, receptacles, surgical ki... |
46,945 | What to include in the PDF of your protocol | 1 | dx.doi.org/10.17504/protocols.io.br39m8r6 | https://www.protocols.io/view/what-to-include-in-the-pdf-of-your-protocol-br39m8r6 | Emma Ganley, Anita Broellochs, Lenny Teytelman | TITLE: What to include in the PDF of your protocol
AUTHORS: Emma Ganley, Anita Broellochs, Lenny Teytelman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A list to advise on the different elements that are possible to include as part of your protocol in protocols.io. If possible, please include the... | ["KeywordsPlease include a list of any keywords that are relevant to your protocol. This will increase discoverability of your protocol as the protocols.io search tool searches title and keywords.\nThe protocols.io search checks against title and keyword - this is important for discoverability of your protocol both if ... |
97,817 | Two-action sequence reinforcement | 1 | dx.doi.org/10.17504/protocols.io.3byl49248go5/v1 | https://www.protocols.io/view/two-action-sequence-reinforcement-dbrz2m76 | Jonathan Tang | TITLE: Two-action sequence reinforcement
AUTHORS: Jonathan Tang
[DESCRIPTION]
Two-action sequence reinforcement protocol for mouse studies from Tang et al 2023.
[GUIDELINES]
Individual mice were subjected to a single session of protocol each day, with sessions following each other on consecutive days.
[STEPS]
SEC... | ["[First reinforcement session+ Baseline] Mice were placed in a grey open-field behaviour recording for this protocol. \nTo acquire baseline behavior, individual mice were allowed to behave freely inside the box for 30 minutes when the laser stimulation was not available for reinforcement.", "After initial behavior acq... |
22,570 | Euplotes crassus transfection using Lipofectamine 2000 as vehicle (provisional) | null | dx.doi.org/10.17504/protocols.io.2aigace | null | RACHELE CESARONI, Rachele Cesaroni | TITLE: Euplotes crassus transfection using Lipofectamine 2000 as vehicle (provisional)
AUTHORS: RACHELE CESARONI, Rachele Cesaroni
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. Collect 4 x 104 well-fed Euplotes crassus cells (we used E.coli as the only food source) by centrifugation at 400 rcf for 3 minu... | ["Collect 4 x 104 well-fed Euplotes crassus cells (we used E.coli as the only food source) by centrifugation at 400 rcf for 3 minutes.", "Wash the cells twice with artificial sea water (see attachment for the recipe) and once with 500 mM sorbitol, 0.5 mM Tris-HCl, pH 7.0 (400 rcf for 3 minutes each time). Then resuspen... |
103,957 | Protein structure prediction with AlphaFold-Multimer | 0 | dx.doi.org/10.17504/protocols.io.81wgbz25qgpk/v1 | https://www.protocols.io/view/protein-structure-prediction-with-alphafold-multim-dhrv3566 | Elias Adriaenssens | TITLE: Protein structure prediction with AlphaFold-Multimer
AUTHORS: Elias Adriaenssens
[DESCRIPTION]
This protocol describes the protein structure prediction with AlphaFold-Multimer.
[STEPS]
1. Protein sequences were downloaded from the Uniprot server.
2. A locally installed version of AlphaFold-Multimer was used... | ["Protein sequences were downloaded from the Uniprot server.", "A locally installed version of AlphaFold-Multimer was used for structure prediction with 5 models per prediction followed by Amber relaxation.", "Interaction scores (ipDT) and diagnostic plots (PAE plot and pLDDT plot) as well as the generated structures w... |
null | null | null | dx.doi.org/10.17504/protocols.io.mqdc5s6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?. | [] |
69,908 | ONT Post-PCR Pooling & Purification for Fungal Barcoding | 4 | dx.doi.org/10.17504/protocols.io.kxygxz1yzv8j/v3 | https://www.protocols.io/view/ont-post-pcr-pooling-amp-purification-for-fungal-b-cghutt6w | Stephen Douglas Russell, Stephen Douglas Russell | TITLE: ONT Post-PCR Pooling & Purification for Fungal Barcoding
AUTHORS: Stephen Douglas Russell, Stephen Douglas Russell
[DESCRIPTION]
Overview: The goals of this protocol are to pool your PCR product into a single 1.5 mL tube and to purify that product using magnetic beads.
Time required: ~45 minutes ... | ["[Preparation] Bring magnetic beads to room temp. (Should be stored in the fridge)", "[Preparation] Heat a 1.5uL tube of molecular water to 55 °C in the heat block. ~1000uL should be sufficient in the tube. This step is optional but is helpful if a heat block is available.", "[Preparation] Create a fresh batch of 80% ... |
19,201 | Chromatographic profile of aqueous extract by HPLC | null | dx.doi.org/10.17504/protocols.io.wy9ffz6 | null | Luis Wiliunfo Torres Tapia | TITLE: Chromatographic profile of aqueous extract by HPLC
AUTHORS: Luis Wiliunfo Torres Tapia
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This chromatographic detection method was developed in order to solve the most compounds from aqueous extracts leaves of dune and mangrove plant by HPLC.</div... | ["[Sample preparation]\nEach aqueou extract was added a 10% MeOH to improve solubility, and next it was filtered through 0.2 μm filter disc.", "[Movil phase]\nMovil phase consist:- Movil phase A contaned ultrapure type 1 water ( Simplicity® Water Purification System, Millipore) adjusted to pH 2.5 with trifluoroacetic ... |
29,043 | Poly-Lysine Coverslip Preparation | null | dx.doi.org/10.17504/protocols.io.8kthuwn | null | Franchesca Farris, Marda Jorgensen | TITLE: Poly-Lysine Coverslip Preparation
AUTHORS: Franchesca Farris, Marda Jorgensen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Poly-Lysine Coverslip Preparation </div><div class = "text-block">This section describes the process of creating Poly-lysine-coated coverslips that are used for the ti... | ["Remove the coverslips from box.", "Gently place coverslips at the bottom of the glass beaker", "Slowly swirl the beaker to spread the stacks of coverslips.", "Add ca. 7 mL of poly-lysine solution above the coverslips to ensure that all coverslips are fully covered.", "Cover the beaker with plastic wrap and seal with ... |
50,131 | Crystallization of WIPI2d10-364delta263-295 | 4 | dx.doi.org/10.17504/protocols.io.bu7tnznn | https://www.protocols.io/view/crystallization-of-wipi2d10-364delta263-295-bu7tnznn | lmstrong | TITLE: Crystallization of WIPI2d10-364delta263-295
AUTHORS: lmstrong
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Setting crystal trays</div></div>
[STEPS]
?. Mix 1uL of reservoir and 1uL of protein solution on coverslip. Add 0.3uL of seed stock to drop.
?. Quickly invert coverslip onto pre-gre... | ["Mix 1uL of reservoir and 1uL of protein solution on coverslip. Add 0.3uL of seed stock to drop.", "Quickly invert coverslip onto pre-greased 24well plate (Hampton). Gently press on edges of the coverslip to create a good seal", "Repeat for every well in the plate", "Let plate sit at 19C. Checking ever 12-24 hours for... |
104,650 | USDA LTAR Common Experiment measurement: Channelized surface flow discharge | 0 | dx.doi.org/10.17504/protocols.io.rm7vzj195lx1/v1 | https://www.protocols.io/view/usda-ltar-common-experiment-measurement-channelize-difi4bke | Stephen K. Hamilton, Daniel N. Moriasi, Claire Baffaut | TITLE: USDA LTAR Common Experiment measurement: Channelized surface flow discharge
AUTHORS: Stephen K. Hamilton, Daniel N. Moriasi, Claire Baffaut
[DESCRIPTION]
Measurement of surface flow rate (discharge) is often needed for agroecological studies, whether to understand the movement of water itself or to estimate wha... | ["[Protocol steps] Instantaneous discharge measurements pose challenges in headwater and ephemeral stream channels because discharge often changes considerably during and shortly after rain or snowmelt events, resulting in a “flashy” hydrograph, and much or most of the movement of water and materials may occur during h... |
85,738 | Broccoli and Chicken Stir Fry | 1 | dx.doi.org/10.17504/protocols.io.e6nvwdkrzlmk/v1 | https://www.protocols.io/view/broccoli-and-chicken-stir-fry-cxyixpue | Andy Ouyang | TITLE: Broccoli and Chicken Stir Fry
AUTHORS: Andy Ouyang
[DESCRIPTION]
A simple broccoli and chicken stir fry to create as college students with limited cooking experience and ingredients
[STEPS]
SECTION: Prepping Stage
1.
In this step, you will have to gather your ingredients:
2 heads of broccoli
3 defrosted chi... | ["[Prepping Stage] In this step, you will have to gather your ingredients:\n2 heads of broccoli\n3 defrosted chicken breasts\n2/3 cup of soy sauce\n1/3 cup of oyster sauce\nhoney (as much as desired)\n2 tablespoons water\n2 tablespoons cornstarch\n2 teaspoons vegetable oil", "Stir soy sauce and oyster sauce together in... |
90,330 | Free-floating Mouse Brain Immunohistochemistry | 4 | dx.doi.org/10.17504/protocols.io.261ged3j7v47/v2 | https://www.protocols.io/view/free-floating-mouse-brain-immunohistochemistry-c4f2ytqe | Jonathan Breiter | TITLE: Free-floating Mouse Brain Immunohistochemistry
AUTHORS: Jonathan Breiter
[DESCRIPTION]
This protocol enables immunohistochemical staining of murine tissue with superior penetration of the tissue by the reagents due to the free-floating approach.
In this new version, the last step contains a supplemental video ... | ["[Tissue Preparation] Remove PFA-fixed tissue from storage solution and add to mesh bottom netwell insert inside of 12 well plate that is filled with 0.22 μm filtered 1x PBS.", "[Buffer Preparation] Per well of tissue make a minimum of 3.5 mL of blocking solution, consider this is needed for blocking, primary and seco... |
41,046 | DNA extraction - mouse tails - phenol-chloroform | 1 | null | https://www.protocols.io/view/dna-extraction-mouse-tails-phenol-chloroform-bkbwkspe | Wayne Crismani | TITLE: DNA extraction - mouse tails - phenol-chloroform
AUTHORS: Wayne Crismani
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is taken from the URL indicated below from the Jackson Laboratories</div><div class = "text-block">This protocol yields a highly purified DNA preparation fro... | ["Remove 0.5 mm of tail into polypropylene microfuge tube (do not mince). (The tubes must have tight-fitting caps, so that there are no leaks in steps 3 and 7 below.)", "Add 0.5 ml DNA digestion buffer with proteinase K added to 0.5 mg/ml final concentration. (0.5 mg/ml is a high concentration and can probably be reduc... |
41,260 | 18S-V4 rRNA amplification from total genomic DNA for NGS Illumina sequencing | 4 | dx.doi.org/10.17504/protocols.io.yxmvmxdmnl3p/v1 | https://www.protocols.io/view/18s-v4-rrna-amplification-from-total-genomic-dna-f-bkikkucw | Estelle Bigeard, Adriana Lopes Dos Santos, Catherine Ribeiro | TITLE: 18S-V4 rRNA amplification from total genomic DNA for NGS Illumina sequencing
AUTHORS: Estelle Bigeard, Adriana Lopes Dos Santos, Catherine Ribeiro
[DESCRIPTION]
For metabarcoding purpose, the first step involves the amplification by PCR of a given gene region (for example V4 or V9 region of 18S rRNA gene) or... | ["[Preparation of libraries for Illumina sequencing (metabarcoding)] Send to the sequencing platform pictures of gel to check they are conform (purity, degradation, bands intensity, etc) and follow its protocol.\n\nOnce PCR products are correct, they are organized in appropriated PCR plates to send (dryice) to the sequ... |
58,615 | DNA extraction from insect gut-dwelling fungi | 1 | dx.doi.org/10.17504/protocols.io.n2bvj68mnlk5/v1 | https://www.protocols.io/view/dna-extraction-from-insect-gut-dwelling-fungi-b5gxq3xn | Yan Wang | TITLE: DNA extraction from insect gut-dwelling fungi
AUTHORS: Yan Wang
[DESCRIPTION]
This protocol is good for DNA extraction from microbial fungi isolated from aquatic insect guts. It works for small input tissues (starting from one fungal thallus). The product can be used for PCR and Sanger sequencing directly, whic... | ["Suspend fungal thalli and spores in a 1.5 mL centrifuge tube with 2x CTAB buffer (200 µL).", "Freeze and thaw the sample three times by submerging the tube into liquid nitrogen and incubating it at 65 °Cusing a heat block.", "After the final thaw, crush the fungal tissues using a disposable pellet pestle (for 1.5 mL ... |
79,184 | iPhone LiDAR tutorial | 1 | null | https://www.protocols.io/view/iphone-lidar-tutorial-crjqv4mw | Gregor Luetzenburg | TITLE: iPhone LiDAR tutorial
AUTHORS: Gregor Luetzenburg
[DESCRIPTION]
Recording, exporting and analyzing iPhone LiDAR data
The aim of this tutorial is to provide a guide on how to create models of the earth surface on a small to medium scale with the LiDAR sensor built in the Apple iPhones, edit and export those mo... | ["[Recording data] 3d Scanner App basic functionality\n\nTo record data with the iPhone LiDAR scanner, unlock the iPhone and open the 3d Scanner App. Make sure nothing obstructs the LiDAR scanner at the back of the iPhone. By default, the app opens the ‘camera interface’ which is used for scanning 3D models. While scan... |
null | null | null | dx.doi.org/10.17504/protocols.io.vbse2ne | null | null | TITLE: No Title
AUTHORS:
[BEFORE_START]
If you are collecting flies from a field site to begin your house fly colony, be sure to keep field-collected adult flies away from any existing fly colonies or colony supplies. Field flies are likely to carry several fungal and bacterial pathogens that can infect your existin... | [] |
66,809 | Synthetic Procedure of 2-(1-(4-hydroxy-3-methoxyphenyl)propan-2-yl)-6-methoxy-4-propylphenol | 6 | dx.doi.org/10.17504/protocols.io.81wgb6emolpk/v1 | https://www.protocols.io/view/synthetic-procedure-of-2-1-4-hydroxy-3-methoxyphen-cdgzs3x6 | Lisa.Stanley, Rui Katahira, Gregg T. Beckham | TITLE: Synthetic Procedure of 2-(1-(4-hydroxy-3-methoxyphenyl)propan-2-yl)-6-methoxy-4-propylphenol
AUTHORS: Lisa.Stanley, Rui Katahira, Gregg T. Beckham
[DESCRIPTION]
A direct understanding of the degradation reaction pathways of lignin polymers in biomass is difficult due to the complexity of lignin’s structure. To ... | ["[Synthetic Procedure]", "[Synthetic Procedure] A solution of 1480 mL citrate-phosphate buffer (20 mM, pH 3.5) [see Note 1] was heated to 38 °C in a silicone oil bath. A solution of isoeugenol (5.00 mL , 0.0328 mol) in methanol (164 mL ) was added in portions with vigorous stirring to the buffer solution. 20 mg horser... |
61,865 | Liposomes | 6 | dx.doi.org/10.17504/protocols.io.3byl4b3z8vo5/v1 | https://www.protocols.io/view/liposomes-b8nhrvb6 | BOC Sciences | TITLE: Liposomes
AUTHORS: BOC Sciences
[DESCRIPTION]
Liposomes are spherical vesicles with internal cavities and composed of one or more phospholipid bilayers. Their structural components are phospholipids or synthetic amphiphilic combined with cholesterol and other sterols, which can affect membrane permeability... | [] |
85,034 | Multi-Site Optic Fiber Implants | 4 | dx.doi.org/10.17504/protocols.io.6qpvr3dqovmk/v1 | https://www.protocols.io/view/multi-site-optic-fiber-implants-cxaixice | Avalon Amaya, Kenta M. Hagihara, Benjamin Ouellette, Conor Grasso | TITLE: Multi-Site Optic Fiber Implants
AUTHORS: Avalon Amaya, Kenta M. Hagihara, Benjamin Ouellette, Conor Grasso
[DESCRIPTION]
This protocol describes the surgical procedure, instrumentation, and reagents necessary for implanting optic fiber probes involving injection(s) and headpost into an adult mouse brain for in-... | ["[Expose and Prepare the Skull Surface for Fiber Implants] After hair removal and disinfection, create a midline incision with a scalpel blade from approximately behind the eyes to the front of the ears.", "[Align the Skull] Locate Bregma and Lambda landmarks with Dovetail Clamp and Bregma Stylus, and use them to leve... |
75,778 | P3B.-PROCEDIMIENTO DE VALORACIÓN DE PREINSCRIPCIONES Y RESOLUCIÓN DE ADMISIÓN DE ALUMNOS INTERNACIONALES | 1 | dx.doi.org/10.17504/protocols.io.eq2ly7eprlx9/v2 | https://www.protocols.io/view/p3b-procedimiento-de-valoraci-n-de-preinscripcione-cm9au92e | cgarcia | TITLE: P3B.-PROCEDIMIENTO DE VALORACIÓN DE PREINSCRIPCIONES Y RESOLUCIÓN DE ADMISIÓN DE ALUMNOS INTERNACIONALES
AUTHORS: cgarcia
[DESCRIPTION]
Las solicitudes de admisión a los programas de doctorado de la EIDUCAM realizadas por candidatos internacionales serán admitidas a trámite a través de la plataforma LAUREA ACAD... | ["[P3b.-PROCEDIMIENTO DE VALORACIÓN DE PREINSCRIPCIONES Y RESOLUCIÓN DE ADMISIÓN DE ALIMNOS INTERNACIONALES] El Servicio de Admisiones Internacionales valorará administrativamente cada solicitud, y establecerá contacto con los candidatos cuando las solicitudes no cumplan con las exigencias documentales establecidas, es... |
71,015 | Pipetting | 1 | null | https://www.protocols.io/view/pipetting-chkft4tn | Carlos Goller, Carly Sjogren | TITLE: Pipetting
AUTHORS: Carlos Goller, Carly Sjogren
[DESCRIPTION]
Overview and Goals
Lab micropipettes allow us to accurately transfer small volumes of liquids. Units to measure small volumes with micropipettes are: microliter (uL) and milliliter (mL). There are 1000 uL in 1 mL). Effectively using lab micropipette... | ["[Using a pipette] To draw up liquid", "[Using a pipette] Set volume using the volume adjustment wheel", "[Using a pipette] Press a new tip onto the shaft", "[Using a pipette] Press plunger TO the FIRST STOP", "[Using a pipette] Dip tip into liquid", "[Using a pipette] Slowly release the plunger to collect liquid into... |
58,392 | Immunofluorescence on Formalin-Fixed Paraffin-Embedded Tissue Sections | 1 | dx.doi.org/10.17504/protocols.io.b49yqz7w | https://www.protocols.io/view/immunofluorescence-on-formalin-fixed-paraffin-embe-b49yqz7w | Katarzyna Dobaczewska, Zbigniew Mikulski | TITLE: Immunofluorescence on Formalin-Fixed Paraffin-Embedded Tissue Sections
AUTHORS: Katarzyna Dobaczewska, Zbigniew Mikulski
[DESCRIPTION]
Fluorescence staining of FFPE tissues that leads to consistent and quality results.
[GUIDELINES]
Make sure all reagents used in the Freequenza rack are at room temperatur... | ["[Deparaffinization/ Rehydration] a. Bake slides for 1 hour at 60 °C \nb. Dip slides in Propar 20 times then let sit for 10 min. Repeat step 3x, each time with fresh Propar.\nc. Dip slides in 100% reagent alcohol 20 times then let sit for 1 min 30 sec. Repeat step with fresh alcohol.\nd. Dip slides in 90% reagent alco... |
null | null | null | dx.doi.org/10.17504/protocols.io.hxgb7jw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is a 0.05M Tris-Cl (pH 8.0), 0.01M EDTA resuspension buffer containing RNase A
[GUIDELINES]
Storage condition - 4°C after adding RNase A.<br /><strong>Note</strong>: Buffer compositions are given per liter of solution. Buffer calculations are based on Tris Base adjusted to... | [] |
54,689 | Intracardiac perfusion with buffer for anatomical studies | 1 | dx.doi.org/10.17504/protocols.io.3byl4kpp8vo5/v1 | https://www.protocols.io/view/intracardiac-perfusion-with-buffer-for-anatomical-bzm9p496 | Janet R Keast, Peregrine B Osborne, Nicole Wiedmann | TITLE: Intracardiac perfusion with buffer for anatomical studies
AUTHORS: Janet R Keast, Peregrine B Osborne, Nicole Wiedmann
[DESCRIPTION]
This protocol is suitable for preserving tissues for anatomical studies of organs and major pelvic ganglia in adult rats. The protocol is performed under anesthesia and should inc... | ["[Preparation for perfusion] Make up the following solutions:\n\nPerfusion prewash solution: To 300 ml 0.9% sodium chloride (w/v) add 3.75 ml 1% sodium nitrite (w/v) and 0.11 ml heparin (5000 IU/ml). This is made up immediately prior to use.\n\nFixative: 4% paraformaldehyde in 0.1M phosphate buffer, pH 7.4. This is ma... |
54,430 | Infrared PAR-CLIP | 1 | null | https://www.protocols.io/view/infrared-par-clip-bzd6p29e | svetlana.lebedeva | TITLE: Infrared PAR-CLIP
AUTHORS: svetlana.lebedeva
[DESCRIPTION]
Crosslinking and immunoprecipitation (CLIP) protocol based on 4-thiouridine incorporation and sequencing to determine binding sites of RNA-binding proteins (RBPs).
This protocol has been used for the manuscript "Control of immediate early gene express... | ["[Infrared dye labeling of the adapter oligos] Order the following oligos from IDT:\n\n3’ adapter:\n/5rApp/NN NNT GGA ATT CTC GGG TGC CAA GGA AAA AAA AAA AA/iAzideN/ AAA AAA AAA AAA /3Bio/\n\n5’ adapter: \n/5AzideN/GTTCAGAGTTCTACAGTCCGACGATC[CTGATC]rNrNrNrNrNrNrN\n\nChoose the smallest possible scale, and add RNAse fr... |
39,512 | anti-SARS-CoV-2 spike RBD antibody discovery from phage display library | 4 | dx.doi.org/10.17504/protocols.io.bitykepw | https://www.protocols.io/view/anti-sars-cov-2-spike-rbd-antibody-discovery-from-bitykepw | Eve Ngoh, Bei Wang, Cheng-I Wang | TITLE: anti-SARS-CoV-2 spike RBD antibody discovery from phage display library
AUTHORS: Eve Ngoh, Bei Wang, Cheng-I Wang
[STEPS]
?. [Bio-panning Round 1]
Day 1: 1st round bio-panning
?. [Bio-panning Round 1]
Add 2 µM mouse IgG1 (as mouse Fc blocker) to theHX02 human Fab phage library (Humanyx Pte Ltd) and incubate at ... | ["[Bio-panning Round 1]\nDay 1: 1st round bio-panning", "[Bio-panning Round 1]\nAdd 2 µM mouse IgG1 (as mouse Fc blocker) to theHX02 human Fab phage library (Humanyx Pte Ltd) and incubate at RT, 30min.", "[Bio-panning Round 1]\nWash 60 µl of DynaBeads M-280 Streptavidin (Invitrogen #11205D) with 1 ml PBS twice.", "[Bio... |
23,045 | An improved deep learning method for predicting DNA-binding proteins based on contextual features in amino acid sequences | null | dx.doi.org/10.17504/protocols.io.2rdgd26 | null | Ruixiong Ma | TITLE: An improved deep learning method for predicting DNA-binding proteins based on contextual features in amino acid sequences
AUTHORS: Ruixiong Ma
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><a href="" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">With the ... | ["Prepare the dataset:In the process of extracting protein data from UniProt,we removed those sequences with length less than 50 or greater than 1,280 amino acids, resulting in 17,651 DNA-binding protein sequences are selected as positive samples. At the same time, we got 50,500 non-DNA-binding protein sequences as neg... |
null | null | null | dx.doi.org/10.17504/protocols.io.pmndk5e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The provided data are example raw data acquired with simultaneous multislice imaging (SMS) in a preclinical MRI experiment.</p>
<p>zip includes:</p>
<p> </p>
<p>- Matlab code (Main.m) and needed functions</p>
<p>- data arrays</p>
<p> </p>
<p>Password needed to unzip: smsrecon... | [] |
93,785 | Ubiquitin immunoprecipitation using an anti-ubiquitin nanobody | 1 | dx.doi.org/10.17504/protocols.io.dm6gp36k1vzp/v1 | https://www.protocols.io/view/ubiquitin-immunoprecipitation-using-an-anti-ubiqui-c7tzznp6 | Cole S Sitron, Victoria A Trinkaus, F Ulrich Hartl | TITLE: Ubiquitin immunoprecipitation using an anti-ubiquitin nanobody
AUTHORS: Cole S Sitron, Victoria A Trinkaus, F Ulrich Hartl
[DESCRIPTION]
This protocol describes a method to detect ubiquitination on a protein of interest. This technique relies on immunoprecipitation (IP) of ubiquitinated proteins from a cell lys... | ["[Cell collection and lysis] Remove the medium from the wells and trypsinize with 500 µL TrypLE Express.", "[Cell collection and lysis] Quench the TrypLE Express with 500 µL 10% FBS and move the cells into a centrifuge tube.", "[Cell collection and lysis] Pellet cells at 1500 x g for 3 min at 4 °C.", "[Cell collection... |
89,570 | Improving genome-wide mapping of nucleosomes in Trypanosome cruzi. | 4 | dx.doi.org/10.17504/protocols.io.6qpvr4w83gmk/v2 | https://www.protocols.io/view/improving-genome-wide-mapping-of-nucleosomes-in-tr-c3qaymse | Paula Beati, Milena Massimino Stepñicka, Salomé C. Vilchez Larrea, Pablo Smircich, Guillermo Daniel Alonso, Josefina Ocampo | TITLE: Improving genome-wide mapping of nucleosomes in Trypanosome cruzi.
AUTHORS: Paula Beati, Milena Massimino Stepñicka, Salomé C. Vilchez Larrea, Pablo Smircich, Guillermo Daniel Alonso, Josefina Ocampo
[DESCRIPTION]
InTrypanosoma cruzi DNA is packaged into chromatin by octamers of histone proteins that form n... | ["[MNase digestion of T. cruzi epimastigote chromatin] Pellet 10e8 late exponentially growing epimastigotes per reaction (normally 7) by centrifugation at 1700 xg for 5 minutes at Room temperature. Wash the cells with 10 ml Incomplete Lysis Solution (1 mM L-glutamine, 250 mM sucrose, 2.5 mM CaCl2, 1 mM phenylmethylsulf... |
48,931 | publication 1 7.4 w/o doi | 1 | null | https://www.protocols.io/view/publication-1-7-4-w-o-doi-bt2bnqan | Mariia Guliakina, Monica Hassan | TITLE: publication 1 7.4 w/o doi
AUTHORS: Mariia Guliakina, Monica Hassan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Sudden she seeing garret far regard. By hardly it direct if pretty up regret. Ability thought enquire settled prudent you sir. Or easy knew sold on well come year. Something cons... | ["test", "est 2"] |
47,369 | Gold nanoparticle synthesis | 1 | dx.doi.org/10.17504/protocols.io.bshhnb36 | https://www.protocols.io/view/gold-nanoparticle-synthesis-bshhnb36 | Phuong H P Nguyen, Zhonglei He, Furong Tian, James Curtin, Julie Rose Mae Mondala | TITLE: Gold nanoparticle synthesis
AUTHORS: Phuong H P Nguyen, Zhonglei He, Furong Tian, James Curtin, Julie Rose Mae Mondala
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a protocol for citrate reduction methods to synthesize gold nanoparticles. Gold nanoparticles (GNP or AuNP) are sub-mi... | ["[Synthesis of AuNP by Citrate Reduction]\nDissolve (HAuCl4 ) in into a clean Duran bottle\n[of Chloroauric acid]\n[Distilled water]\nHAuCl4 is corrosive so using glass to avoid contacting with metal", "[Synthesis of AuNP by Citrate Reduction]\nHeat with magnetic stirring and bring it to boiling. Keep the lid on l... |
97,492 | CODA: 3D tissue reconstruction pipeline | HuBMAP | JHU-TMC | 0 | dx.doi.org/10.17504/protocols.io.kqdg324xpv25/v1 | https://www.protocols.io/view/coda-3d-tissue-reconstruction-pipeline-hubmap-jhu-dbfu2jnw | Kyu Sang Han, Pei-Hsun Wu, Joel Sunshine, Ashley Kiemen, Sashank Reddy, Denis Wirtz | TITLE: CODA: 3D tissue reconstruction pipeline | HuBMAP | JHU-TMC
AUTHORS: Kyu Sang Han, Pei-Hsun Wu, Joel Sunshine, Ashley Kiemen, Sashank Reddy, Denis Wirtz
[DESCRIPTION]
CODA pipeline with 6 parts
[STEPS]
SECTION: Setting up CODA environment and preparing sample dataset
1. dx.doi.org/10.17504/protocols.io.q26g71rp... | ["[Setting up CODA environment and preparing sample dataset] dx.doi.org/10.17504/protocols.io.q26g71rpkgwz/v1", "[Calculate registration on low-resolution tissue images] dx.doi.org/10.17504/protocols.io.kxygxym3dl8j/v1", "[Deep learning multi-labelling of tissue structures using training on manual annotations] dx.doi.o... |
26,292 | TRANSFECTION OF i3NEURONS (Support Protocol 3) | null | dx.doi.org/10.17504/protocols.io.5wug7ew | null | Michael S. Fernandopulle, Ryan Prestil, Christopher Grunseich, Chao Wang, Li Gan, Michael E. Ward | TITLE: TRANSFECTION OF i3NEURONS (Support Protocol 3)
AUTHORS: Michael S. Fernandopulle, Ryan Prestil, Christopher Grunseich, Chao Wang, Li Gan, Michael E. Ward
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Transient protein expression can easily be studied in i</span><span style = "vertica... | [] |
74,847 | Tissue Sectioning Guidelines - CODEX/PhenoCycler | 4 | null | https://www.protocols.io/view/tissue-sectioning-guidelines-codex-phenocycler-cmb7u2rn | Santhosh Sivajothi | TITLE: Tissue Sectioning Guidelines - CODEX/PhenoCycler
AUTHORS: Santhosh Sivajothi
[DESCRIPTION]
The purpose of this SOP is to provide general guidelines for preparing tissue sections suitable for PhenoCycler/CODEX
[STEPS]
SECTION: Tissue Sectioning Guidelines for CODEX/PhenoCycler
1. Cut FFPE sections on a microtom... | ["[Tissue Sectioning Guidelines for CODEX/PhenoCycler] Cut FFPE sections on a microtome at a thickness of 5 microns. Section thickness should not exceed 10 microns.", "[Tissue Sectioning Guidelines for CODEX/PhenoCycler] For best results, the tissue should be completely adhered to the slide with minimal tears or folds.... |
null | null | null | dx.doi.org/10.17504/protocols.io.nfgdbjw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The authors describe the skin thickness measurement, based on the analysis of images, obtained using a handheld DermaLab® USB Series ultrasound from Cortex Technology. Epidermis and dermis layers of newborns are obtained by ultrasound scanning. The procedures of the mean thic... | [] |
97,898 | Transportmedium | 0 | null | https://www.protocols.io/view/transportmedium-dbui2nue | Bettina Ergün | TITLE: Transportmedium
AUTHORS: Bettina Ergün
[DESCRIPTION]
Transportmedium für Gewebe aus dem OP bzw. Schnellschnitt.
Das Transportmedium enthält eine erhöhte Konzentration an Zellshield zur Keimreduzierung im Ausgangsmaterial der Zellisolierung.
Das Gewebe wird 1 h bei RT in Transportmedium inkubiert (alternativ: ü.... | ["[Transportmedium]"] |
37,020 | Installation instructions for phylogenetic analysis using a conda environment | null | dx.doi.org/10.17504/protocols.io.bgd4js8w | https://www.protocols.io/view/installation-instructions-for-phylogenetic-analysi-bgd4js8w | Laise Moraes | TITLE: Installation instructions for phylogenetic analysis using a conda environment
AUTHORS: Laise Moraes
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The purpose of this protocol is to define and provide instructions for creating a conda environment for phylogenetic analysis</div></div>
[STEPS... | ["[Installing Miniconda]\nCreate a directory called softwares to your HOME directory, switch to it and then download the 64-bit Python 3 Miniconda installer.Install Miniconda quietly, accepting defaults.After installation, remove the Miniconda installer from directory.Set the Miniconda permanent PATH and update conda p... |
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