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 |
|---|---|---|---|---|---|---|---|
102,748 | Gynecologic Oncology Tissue Processing (10% Formalin Fixation) | 0 | dx.doi.org/10.17504/protocols.io.bp2l62781gqe/v1 | https://www.protocols.io/view/gynecologic-oncology-tissue-processing-10-formalin-dgj43uqw | Mary Mullen M.D., Rachel Abbott | TITLE: Gynecologic Oncology Tissue Processing (10% Formalin Fixation)
AUTHORS: Mary Mullen M.D., Rachel Abbott
[DESCRIPTION]
This is a description of the steps that the Washington University's Gynecologic Oncology Tissue Bank has developed to collect surgical resection biospecimens, for molecular and genomic character... | ["[Specimen Collection & Handling (10% Formalin Fixation)] Tissue should be no bigger than 1x1x0.5 cm.", "[Specimen Collection & Handling (10% Formalin Fixation)] Label cassettes using pencil with Tissue Bank ID, date, and tissue type.", "[Specimen Collection & Handling (10% Formalin Fixation)] Place tissue... |
28,909 | Freezing/Cell Banking | 1 | dx.doi.org/10.17504/protocols.io.8gmhtu6 | https://www.protocols.io/view/freezing-cell-banking-8gmhtu6 | Andrea Argouarch | TITLE: Freezing/Cell Banking
AUTHORS: Andrea Argouarch
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol includes banking dural cells into cryovials for long term storage in liquid nitrogen. </div></div>
[STEPS]
?. [Observations]
At 100% confluency, take pictures of cell morphology, freeze d... | ["[Observations]\nAt 100% confluency, take pictures of cell morphology, freeze down for banking (~0.5 Million per vial), collect remaining cells in flask for gDNA, and seed cells into 1xT25 for karyotyping (~30,000 cells, 60 ul)", "[Preparation]\nTurn off UV lights and clean hood with 70% ethanol", "[Preparation]\nLabe... |
94,116 | Quantification of area and optical density of intracellular neuromelanin with TruAI in H&E stained sections | 1 | dx.doi.org/10.17504/protocols.io.5qpvo36o7v4o/v1 | https://www.protocols.io/view/quantification-of-area-and-optical-density-of-intr-c76czraw | Marta Gonzalez-Sepulveda, Thais Cuadros, Miquel Vila | TITLE: Quantification of area and optical density of intracellular neuromelanin with TruAI in H&E stained sections
AUTHORS: Marta Gonzalez-Sepulveda, Thais Cuadros, Miquel Vila
[DESCRIPTION]
Quantification of area and optical density of intracellular neuromelanin with TruAI in H&E stained sections
[STEPS]
SECTION... | ["[Loading training label function in TruAI Software] Open scanned images with Olympus VS200 Desktop (EVIDENT Technology GmbH, ver. 4.1.1 build 27564).", "[Loading training label function in TruAI Software] Under the ‘Detect’ window, select ‘Training Labels’.", "[Creating training label classes] Create a new training l... |
20,017 | Addition of the adaptor to RNA substrates for 5′ RACE | null | dx.doi.org/10.17504/protocols.io.xsrfnd6 | null | Matus Valach | TITLE: Addition of the adaptor to RNA substrates for 5′ RACE
AUTHORS: Matus Valach
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Simple protocol for mapping 5′-P RNA termini by RT-PCR after the addition of a 5′ adaptor using T4 RNA ligase 1.</div></div>
[STEPS]
?. Mix the following components (10... | ["Mix the following components (10 μL): ABC1ComponentAmount [μL]Final concentration2RNA [1 µg]4100 ng/µL35′ RACE RNA oligo [100 µM]220 µM4RNase-free water (ddH2O)4\nABC1ComponentAmount [μL]Final concentration2RNA [1 µg]4100 ng/µL35′ RACE RNA oligo [100 µM]220 µM4RNase-free water (ddH2O)4", "Denature for 2 min at 70 °C... |
68,145 | Culturing Xanthomonas | 4 | dx.doi.org/10.17504/protocols.io.ewov1nr92gr2/v1 | https://www.protocols.io/view/culturing-xanthomonas-cesrted6 | Murray Grant, Shannon Greer, Joana Vicente | TITLE: Culturing Xanthomonas
AUTHORS: Murray Grant, Shannon Greer, Joana Vicente
[DESCRIPTION]
This is the protocol for culturing strains of Xanthomonas species in preparation for extracting genomic DNA for sequencing.
[STEPS]
1. Streak isolates onto King’s B plates. Incubate at 28°C for ~48 hours.
2. Pick a singl... | ["Streak isolates onto King’s B plates. Incubate at 28°C for ~48 hours.", "Pick a single colony and inoculate to 10ml King’s B liquid media in 30ml universal tubes. Incubate over night at 28°C and 220rpm.", "Pellet 1.8ml of liquid culture in a 2ml Eppendorf tube by centrifuging at 5000g for 10mins. Pour off and discard... |
58,774 | Harvesting Algae | 3 | null | https://www.protocols.io/view/harvesting-algae-b5mwq47e | Jessie Ochs, Bella Oleksy | TITLE: Harvesting Algae
AUTHORS: Jessie Ochs, Bella Oleksy
[DESCRIPTION]
This is a protocol to harvest and maintain algae from a chemostat. In the Duffy Lab, the algae used is Ankistrodesmus falcatus.
[STEPS] | [] |
37,652 | A green micro-algal growth media modified for use as a stringent minimal media for bacteria. | 1 | dx.doi.org/10.17504/protocols.io.bgzujx6w | https://www.protocols.io/view/a-green-micro-algal-growth-media-modified-for-use-bgzujx6w | Mautusi Mitra | TITLE: A green micro-algal growth media modified for use as a stringent minimal media for bacteria.
AUTHORS: Mautusi Mitra
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Introduction: </span></div><div class = "text-block"><span style = "font-style:italic;">Chlamy... | ["[Preparation of TAP stock nutrients]\nMake TAP salts (TAP stock nutrients/FBS solution [Filner’s Beijerinck solution X40]) by dissolving Ammonium chloride (16g), Magnesium sulfate (4g) and Calcium chloride (2.65g). This will give you a final concentration of: Ammonium chloride (7.48 mM ), Magnesium sulfate (16.2 mM) ... |
81,376 | Ionpath MIBI (Multiplexed Ion Beam Imaging) Protocols -- University of Minnesota TMCs | 1 | dx.doi.org/10.17504/protocols.io.5jyl8jyp8g2w/v1 | https://www.protocols.io/view/ionpath-mibi-multiplexed-ion-beam-imaging-protocol-ctp8wmrw | Ionpath Inc. | TITLE: Ionpath MIBI (Multiplexed Ion Beam Imaging) Protocols -- University of Minnesota TMCs
AUTHORS: Ionpath Inc.
[DESCRIPTION]
Link to information regarding Ionpath MIBI as used by the University of Minnesota
[STEPS]
1. Links to company sites:
https://www.ionpath.com/
https://www.ionpath.com/mibiscope/
2. Slides a... | ["Links to company sites:\nhttps://www.ionpath.com/\nhttps://www.ionpath.com/mibiscope/", "Slides and Reagents from Ionpath for MIBI \n Slides (Cat#: 567001): specially formulated, high-purity gold-coated slides \n Reagents\n MIBI 20X TBS-T (Cat#: 567005) \n MIBI 10X PBS (Cat#: 567004)\n ... |
105,684 | USDA LTAR Common Experiment Measurement: Chamber-based fluxes of nitrous oxide (N2O) and methane (CH4) from soil | 0 | dx.doi.org/10.17504/protocols.io.yxmvmemw5g3p/v1 | https://www.protocols.io/view/usda-ltar-common-experiment-measurement-chamber-ba-djfu4jnw | G. Philip Robertson, Michel A. Cavigelli, Harold P. Collins, Curtis Dell, David R. Huggins, Virginia L. Jin, Kevin Kahmark, Mark A. Liebig | TITLE: USDA LTAR Common Experiment Measurement: Chamber-based fluxes of nitrous oxide (N2O) and methane (CH4) from soil
AUTHORS: G. Philip Robertson, Michel A. Cavigelli, Harold P. Collins, Curtis Dell, David R. Huggins, Virginia L. Jin, Kevin Kahmark, Mark A. Liebig
[DESCRIPTION]
Emissions of nitrous oxide (N2O) and ... | ["[Sample Collection] Chamber deployment (minimum of one day before sampling; one week preferred):\n\nPlace chamber bases in representative positions and pound into the soil ~5 cm using a flat board and mallet or other technique. Disturb the soil and surrounding plants as little as possible. As needed, clip plants to b... |
65,202 | Western Blot for IP-TDMS Development | 1 | null | https://www.protocols.io/view/western-blot-for-ip-tdms-development-cbwsspee | Lauren Adams | TITLE: Western Blot for IP-TDMS Development
AUTHORS: Lauren Adams
[DESCRIPTION]
This protocol can be used to determine relative quantities of protein target in IP fractions. Primary antibodies should be selected for the specific protein target.
[STEPS]
1. Take aliquots from IP fractions and add sample loading buffe... | ["Take aliquots from IP fractions and add sample loading buffer to a final concentration of 1X. Boil samples in hot plate at 95ºC for 5-10 min. Briefly, centrifuge samples to ensure sample entire sample is towards bottom of the tube.", "Open gel and place into gel box. Add 1 x MES running buffer, ensuring that there ar... |
82,019 | 8. Taxon Group: Echinodermata | 4 | dx.doi.org/10.17504/protocols.io.4r3l27d63g1y/v1 | https://www.protocols.io/view/8-taxon-group-echinodermata-cucbwssn | Kesella Scott-Somme, Chris Fletcher, Inez Januszczak | TITLE: 8. Taxon Group: Echinodermata
AUTHORS: Kesella Scott-Somme, Chris Fletcher, Inez Januszczak
[DESCRIPTION]
This is part of the collection "DToL Taxon-specific Standard Operating Procedures (SOPs) for Marine Metazoa", lead by the Other Metazoa Working Group. The SOP collection contains guidance on how to process ... | [] |
101,947 | Bone/tooth sampling and cleaning for collagen extraction | 0 | dx.doi.org/10.17504/protocols.io.eq2lyw6mrvx9/v1 | https://www.protocols.io/view/bone-tooth-sampling-and-cleaning-for-collagen-extr-dfs33ngn | Maciej T. Krajcarz, Magdalena Krajcarz, Dorothée G. Drucker, Hervé Bocherens | TITLE: Bone/tooth sampling and cleaning for collagen extraction
AUTHORS: Maciej T. Krajcarz, Magdalena Krajcarz, Dorothée G. Drucker, Hervé Bocherens
[DESCRIPTION]
This protocol presents the procedure of collecting a sample of bone or tooth that is planned for further collagen extraction, prior to stable isotope analy... | ["[Sampling] Prepare the cutting work station. The work must be done under the hood, at a well-ventilated and well-illuminated work station. Respect the health security issues.", "[Sampling] Carefully cut off a fragment of bone or tooth of around 0.12 g to 0.45 g from the selected area of the specimen using a rotary sa... |
null | null | null | dx.doi.org/10.17504/protocols.io.efsbbne | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is a collection of methods from [tentative citation]:<br /><br /><span style="color: #3c3c39;">Jeff Strohm, Robert Hanner, Richard J Heck. (2018) A metabarcoding perspective on soil biodiversity under different tillage treatments. <em>Submitted to</em> Metabarcoding and ... | [] |
96,679 | Lecanosticta acicola isolation protocol | 0 | dx.doi.org/10.17504/protocols.io.q26g7pqe1gwz/v1 | https://www.protocols.io/view/lecanosticta-acicola-isolation-protocol-danf2dbn | Colton Meinecke, Caterina Villari | TITLE: Lecanosticta acicola isolation protocol
AUTHORS: Colton Meinecke, Caterina Villari
[DESCRIPTION]
A guide to the reproduceable isolation of Lecanosticta acicola, the causal agent of brown spot needle blight of pines.
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.j9scr6e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><span lang="EN-US" style="margin: 0px; line-height: 200%; font-family: 'Arial',sans-serif; font-size: 10pt;">Increasing energy expenditure by stimulating thermogenesis through activation of brown adipose tissue (BAT) and/or induction of browning of white adipose tissue (WAT) ... | [] |
26,722 | Protocol for Downscaling Satellite Soil Moisture Estimates using Geomorphometry and Machine Learning | null | dx.doi.org/10.17504/protocols.io.6cahase | null | Mario Guevara, Rodrigo Vargas | TITLE: Protocol for Downscaling Satellite Soil Moisture Estimates using Geomorphometry and Machine Learning
AUTHORS: Mario Guevara, Rodrigo Vargas
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is composed of five steps for downscaling satellite soil moisture estimates using digital t... | ["PREPARE PREDICTION FACTORS: This first stetp is to prepare the prediction factors. Once R is installed and running, please load the library raster and import the DEM terrain parameters. This example is using a geographical coordinate system (lat, long) in degrees ('+proj=longlat +datum=WGS84 +no_defs'). We will consi... |
98,719 | AF & HCM meta-analysis protocol | 0 | null | https://www.protocols.io/view/af-amp-hcm-meta-analysis-protocol-dcm72u9n | Max Aboutorabi | TITLE: AF & HCM meta-analysis protocol
AUTHORS: Max Aboutorabi
[DESCRIPTION]
Background: A systematic review and meta-analysis will be conducted to assess the efficacy and safety of direct oral anticoagulants (DOACs) versus vitamin K antagonists (VKAs) in patients with hypertrophic cardiomyopathy (HCM) and atrial ... | ["[AF & HCM meta-analysis protocol] Identify the question using the PICO framework\nPopulation - patients with concurrent AF and HCM (No constraints were set in terms of type of atrial fibrillation or type of DOAC or VKA the patient was given. Furthermore, there were no constraints in terms of type of hypertrophic ... |
null | null | null | dx.doi.org/10.17504/protocols.io.ebbbain | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is a protocol from: <br /><br />Stedman, K. M., K. Porter, and M. L. Dyall-Smith. 2010. Chapter 6: The isolation of viruses infecting Archaea. Manual of Aquatic Viral Ecology. Waco, TX:American Society of Limnology and Oceanography. doi:10.4319/mave.2010.978-0-9845591-0-7<b... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.c3zyp5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is a technique for isolating phage from agar plates. When working with lytic phage, well-isolated, cleared areas in a lawn of bacteria (called plaques) are removed from the agar (by coring with a sterile pipette) and used to infect fresh bacteria in liquid medium.&nbs... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.k96cz9e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol provides an inexpensive and fast way to cleanse the supernatant of <em>Giardia</em> trophozoites' culture from bovine proteins and any other protein digests present in TYI-S-33. </p>
[BEFORE_START]
<p>Warm non-supplemented DMD+Pen/Strep (1%) and 1xPBS to 37°C. ... | [] |
41,955 | Protocol 2: Know Your BentoLab | 3 | null | https://www.protocols.io/view/protocol-2-know-your-bentolab-bk8bkzsn | TITLE: Protocol 2: Know Your BentoLab
AUTHORS:
[STEPS] | [] | |
28,457 | ChroPack - IMAC | null | dx.doi.org/10.17504/protocols.io.72hhqb6 | null | David Frommholz, Alexandra Raftery, Nadine Stefanczyk | TITLE: ChroPack - IMAC
AUTHORS: David Frommholz, Alexandra Raftery, Nadine Stefanczyk
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Purification Guide for the Isolation of Histidine-tagged Proteins with ChroPack Columns by DALEX Biotech.</span></div><div class = "... | ["How do you want to purify your protein? Do you want to prepare your column for reuse or sanitize it?Please choose below.", "[What do you want to do?]\nHow do you want to purify your protein? Do you want to prepare your column for reuse or sanitize it?Please choose below.", "[Sample Preparation]\nDetermine the weight ... |
78,359 | Interventions (Part 5 of "Effects of Online Exercise Intervention on Physical and Mental Conditions in Young Adults with Chronic Neck Pain") | 1 | dx.doi.org/10.17504/protocols.io.n92ldp6bol5b/v1 | https://www.protocols.io/view/interventions-part-5-of-34-effects-of-online-exerc-cqrxvv7n | Yiting Lin | TITLE: Interventions (Part 5 of "Effects of Online Exercise Intervention on Physical and Mental Conditions in Young Adults with Chronic Neck Pain")
AUTHORS: Yiting Lin
[DESCRIPTION]
This is Part 5 "Effects of Online Exercise Intervention on Physical and Mental Conditions in Young Adults with Chronic Neck Pain"... | [] |
68,125 | Generation of CRISPR constructs | 1 | dx.doi.org/10.17504/protocols.io.j8nlkkzo6l5r/v1 | https://www.protocols.io/view/generation-of-crispr-constructs-cer5td86 | Thanh Ngoc Nguyen | TITLE: Generation of CRISPR constructs
AUTHORS: Thanh Ngoc Nguyen
[DESCRIPTION]
This protocol details the procedure of generation of CRISPR constructs.
[STEPS]
SECTION: Procedure
1. Designing gRNAs using https://chopchop.cbu.uib.no.
SECTION: Procedure
2. Choose the top-ranking gRNA sequences that target the earlie... | ["[Procedure] Designing gRNAs using https://chopchop.cbu.uib.no.", "[Procedure] Choose the top-ranking gRNA sequences that target the earliest exon possible.", "[Procedure] Click on the chosen target sequence, another window with all the information related to this gRNA sequence will appear.", "[Procedure] Copy the tar... |
93,738 | Immunostaining | 1 | dx.doi.org/10.17504/protocols.io.e6nvwd7n7lmk/v1 | https://www.protocols.io/view/immunostaining-c7siznce | Cole S Sitron, Victoria A Trinkaus, F Ulrich Hartl | TITLE: Immunostaining
AUTHORS: Cole S Sitron, Victoria A Trinkaus, F Ulrich Hartl
[DESCRIPTION]
This is a protocol that describes how to use antibody staining to detect cellular epitopes by immunofluorescence microscopy.
[STEPS]
SECTION: Fixation
1. Aspirate media and gently wash each well with 1X PBS.
SECTION: Fix... | ["[Fixation] Aspirate media and gently wash each well with 1X PBS.", "[Fixation] Aspirate PBS and place 500 µL of 4% paraformaldehyde onto each well.", "[Fixation] Fix at Room temperature for 10 min.", "[Fixation] Remove 4% paraformaldehyde and add 1 mL 1X PBS.", "[Immunostaining] Permeabilize 1 mL 0.1% Triton X-100 an... |
65,476 | A cost-effective way of extracting high molecular weight (HMW) DNA from low amounts of fresh or herbarium lichen material | 4 | null | https://www.protocols.io/view/a-cost-effective-way-of-extracting-high-molecular-cb7csriw | Eva Andrea Strasser | TITLE: A cost-effective way of extracting high molecular weight (HMW) DNA from low amounts of fresh or herbarium lichen material
AUTHORS: Eva Andrea Strasser
[DESCRIPTION]
Presented method allows the extraction of high molecular weight (HMW) DNA of all lichen symbionts using low input (5 - 100 mg) lichen material. Ex... | ["[ENZYMATIC DIGESTION - DAY 1] Add 1 mL Buffer 1 to each sample \nMix thoroughly by flipping the tube\nIncubate for 15 minutes at RT\nCentrifuge at 3000 x g for 2 minutes. If necessary repeat at a higher speed (e.g. for crust lichens) until a precipitate forms\nDiscard supernatant\nAdd 500 µL Buffer 2 to each sample \... |
43,729 | PCR (Error-prone PCR) | 1 | dx.doi.org/10.17504/protocols.io.bnxrmfm6 | https://www.protocols.io/view/pcr-error-prone-pcr-bnxrmfm6 | Zhujun Wei | TITLE: PCR (Error-prone PCR)
AUTHORS: Zhujun Wei
[STEPS]
?. Set up a small box with ice, put the tubes of DNA, 2 x Mut Random System, Mut Enhancer and ddH2O into it before loading them into the Bio-rad S1000TM Thermo Cycler.
?. Add the following reagents to a PCR tube (20 μL). AB1IngredientVolume2Template Plasmid(1-1... | ["Set up a small box with ice, put the tubes of DNA, 2 x Mut Random System, Mut Enhancer and ddH2O into it before loading them into the Bio-rad S1000TM Thermo Cycler.", "Add the following reagents to a PCR tube (20 μL). AB1IngredientVolume2Template Plasmid(1-10 ng/µL)0.4 µL32 x Mut Random System10 µL4Forward Primer (1... |
94,244 | Protocol1_Reporter Plasmids Cloning.pdf | 1 | dx.doi.org/10.17504/protocols.io.kqdg3xoyzg25/v1 | https://www.protocols.io/view/protocol1-reporter-plasmids-cloning-pdf-c8aczsaw | angelica.gonzalez | TITLE: Protocol1_Reporter Plasmids Cloning.pdf
AUTHORS: angelica.gonzalez
[DESCRIPTION]
Reporter Plasmids Cloning Outline
[STEPS] | [] |
61,971 | API Synthesis | 6 | dx.doi.org/10.17504/protocols.io.eq2lyne2pvx9/v1 | https://www.protocols.io/view/api-synthesis-b8rtrv6n | BOC Sciences | TITLE: API Synthesis
AUTHORS: BOC Sciences
[DESCRIPTION]
BOC Sciences’ priority is to provide the highest quality APIs to our customers. Our experts have a wealth of experience in the synthesis of APIs with various starting materials and intermediates. The products will be provided with integrated data packages i... | [] |
71,455 | Real time qPCR (Fly Heads) | 4 | dx.doi.org/10.17504/protocols.io.q26g7y4r1gwz/v1 | https://www.protocols.io/view/real-time-qpcr-fly-heads-chz7t79n | Mel Feany | TITLE: Real time qPCR (Fly Heads)
AUTHORS: Mel Feany
[DESCRIPTION]
This Protocol describes how to perform RT qPCR with RNA extracted from fly heads.
[STEPS]
SECTION: RNA Extraction
1. Homogenize 6 heads in 50 µL Qiazol, then add 450 µL Qiazol.
SECTION: RNA Extraction
2. Spin 10 min at 4 °C at 12,000 x g.
SECTION: ... | ["[RNA Extraction] Homogenize 6 heads in 50 µL Qiazol, then add 450 µL Qiazol.", "[RNA Extraction] Spin 10 min at 4 °C at 12,000 x g.", "[RNA Extraction] Incubate supernatant for 5 min at Room temperature .", "[RNA Extraction] Add 100 µL chloroform. Vortex, incubate for 3 min at Room temperature , then spin for 15 ... |
37,070 | Installation instructions for BEAST and BEAGLE on Avell G1550 RTX MUV/A65 RTX MUV | null | dx.doi.org/10.17504/protocols.io.bgfnjtme | https://www.protocols.io/view/installation-instructions-for-beast-and-beagle-on-bgfnjtme | Laise Moraes | TITLE: Installation instructions for BEAST and BEAGLE on Avell G1550 RTX MUV/A65 RTX MUV
AUTHORS: Laise Moraes
[STEPS]
?. [Installing dependency packages]
Open a terminal (Ctrl + Alt + T).Update the package list and install the dependency packages for the BEAST and BEAGLE.
?. [Installing Intel OpenCL implementations]
... | ["[Installing dependency packages]\nOpen a terminal (Ctrl + Alt + T).Update the package list and install the dependency packages for the BEAST and BEAGLE.", "[Installing Intel OpenCL implementations]\nCreate a directory called softwares to your HOME directory, switch to it and then download the Intel OpenCL implementat... |
88,509 | DNA Isolation | 4 | dx.doi.org/10.17504/protocols.io.81wgbxnk3lpk/v1 | https://www.protocols.io/view/dna-isolation-c2n5ydg6 | NUS iGEM | TITLE: DNA Isolation
AUTHORS: NUS iGEM
[DESCRIPTION]
2023 NUS-Singapore iGEM team followed this protocol to isolate the DNA fragments from the agarose gel after the gel electrophoresis.
[STEPS]
1. Prepare and label an Eppondoft tube.
2. Place the agarose gel onto the LED Transilluminator (blue light) to observe the... | ["Prepare and label an Eppondoft tube.", "Place the agarose gel onto the LED Transilluminator (blue light) to observe the DNA band(s).", "Cut out the target DNA band from the agarose gel.", "Put the gel piece into the Eppendorf tube.", "Add 450 µL of into the Eppendorf tube.", "Heat the Eppendorf tube at 55 °C for 20... |
57,799 | In vitro assembling of RNP for nucleofection of hPSCs | 4 | dx.doi.org/10.17504/protocols.io.b4pfqvjn | https://www.protocols.io/view/in-vitro-assembling-of-rnp-for-nucleofection-of-hp-b4pfqvjn | Hanqin Li, Oriol Busquets, Steven Poser, Dirk Hockemeyer, Frank Soldner | TITLE: In vitro assembling of RNP for nucleofection of hPSCs
AUTHORS: Hanqin Li, Oriol Busquets, Steven Poser, Dirk Hockemeyer, Frank Soldner
[DESCRIPTION]
This protocol describes the procedure for the in vitro assembly of ribonucleoprotein (RNP) which can be delivered into human pluripotent stem cells (hPSCs) using ... | ["Thaw Cas9 or PE2 protein on ice . We don’t usually reuse leftover protein, since freezing and thawing compromises protein activity.", "In each nucleofection reaction, prepare 10 µl RNP", "For regular CRISPR/Cas9 editing, use:\n 5 µl, autoclaved H2O\n 2 µl, 40 µM purified Cas9 protein\n 3 µl, 100 µM synthetic... |
74,665 | Decreased risk of Alzheimer disease in bladder cancer patients with intravesical Bacillus Calmette-Guérin therapy: An exploratory meta-analysis | 1 | dx.doi.org/10.17504/protocols.io.3byl4jz12lo5/v1 | https://www.protocols.io/view/decreased-risk-of-alzheimer-disease-in-bladder-can-ck6huzb6 | Junjie Tian, Jianguo Gao, Xiaoyi Chen, Baiye Jin | TITLE: Decreased risk of Alzheimer disease in bladder cancer patients with intravesical Bacillus Calmette-Guérin therapy: An exploratory meta-analysis
AUTHORS: Junjie Tian, Jianguo Gao, Xiaoyi Chen, Baiye Jin
[DESCRIPTION]
Alzheimer disease (AD) is the primary cause of chronic progressive dementia worldwide, accountin... | [] |
72,942 | Discovery of RNA and DNA viruses using next-generation sequencing: Targeted enrichment | 4 | dx.doi.org/10.17504/protocols.io.36wgqj3q3vk5/v1 | https://www.protocols.io/view/discovery-of-rna-and-dna-viruses-using-next-genera-cjgnujve | Lily Tong, Katherine Smollett, Jenna Nichols, Kirsty Kwok, Kyriaki Nomikou, Ma. Jowina Galarion, Daniel Mair, Ana Filipe | TITLE: Discovery of RNA and DNA viruses using next-generation sequencing: Targeted enrichment
AUTHORS: Lily Tong, Katherine Smollett, Jenna Nichols, Kirsty Kwok, Kyriaki Nomikou, Ma. Jowina Galarion, Daniel Mair, Ana Filipe
[DESCRIPTION]
Next-generation sequencing is a powerful tool for viral genomics. Viruses often c... | ["[Hybridisation] Prepare enrichment pools from the pre-prepared Illumina metagenomic sequencing libraries. Each pool should contain 8-16 libraries equal ng of each and a total of 1 μg DNA in a 1.5 mL DNA LoBind tube.", "[Hybridisation] To each pool add the following blocking reagents:", "[Hybridisation] Concentrate th... |
43,413 | Commercial automated scRNA-seq workflow | 1 | dx.doi.org/10.17504/protocols.io.bnmvmc66 | https://www.protocols.io/view/commercial-automated-scrna-seq-workflow-bnmvmc66 | DNA Pipelines R&D, Peter Ellis, Lesley Shirley | TITLE: Commercial automated scRNA-seq workflow
AUTHORS: DNA Pipelines R&D, Peter Ellis, Lesley Shirley
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This SOP describes the procedure for plate based scRNA-seq performed with a commercial available kit from New England BioLabs. Following library cons... | ["[Preparation of lysis buffer plates and FACS]\nImportant! This step must be performed in a designated RNAse free and pre-cDNA amplification area, keeping reagents chilled at all times", "[Preparation of lysis buffer plates and FACS]\nPrepare the cell lysis buffer, which will provide sufficient volume for one 96-well ... |
null | null | null | dx.doi.org/10.17504/protocols.io.dyf7tm | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
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106,809 | Xenograft snRNA-seq Integration and Normalization | 0 | dx.doi.org/10.17504/protocols.io.81wgbzo4ngpk/v1 | https://www.protocols.io/view/xenograft-snrna-seq-integration-and-normalization-dkiz4uf6 | Zac Chatterton, Chiara Pavan, Clare Parish | TITLE: Xenograft snRNA-seq Integration and Normalization
AUTHORS: Zac Chatterton, Chiara Pavan, Clare Parish
[DESCRIPTION]
This protocol describes the integration and normalization of single-nucleus RNA sequencing (snRNA-seq) data obtained from xenograft samples. The process involves loading data from multiple Cell Ra... | ["[Setup and Data Loading:] Set the working directory and specify the path for Cell Ranger outputs.\n\nLoad the necessary R libraries and configure global options.", "[Data Integration] Import multiple Cell Ranger outputs.\n\nCreate Seurat objects for each dataset.", "[Quality Control (QC) and Data Normalization] Filte... |
93,348 | Protocol for Surgical Implications in the Replaced Common Hepatic Artery, a Meta-analysis | 1 | dx.doi.org/10.17504/protocols.io.bp2l6xw4rlqe/v1 | https://www.protocols.io/view/protocol-for-surgical-implications-in-the-replaced-c7eczjaw | Matthew Miller, Chase Schulte, Elizabeth J. Maynes, Benjamin Freedman, Joanna Klansek, Eungjae Kim, Jinbum Dupont, Jae Hwan Choi, Kerrie Lashley, Kyle Carr, Gary Wind, Guinevere Granite, Maria Ximena Leighton | TITLE: Protocol for Surgical Implications in the Replaced Common Hepatic Artery, a Meta-analysis
AUTHORS: Matthew Miller, Chase Schulte, Elizabeth J. Maynes, Benjamin Freedman, Joanna Klansek, Eungjae Kim, Jinbum Dupont, Jae Hwan Choi, Kerrie Lashley, Kyle Carr, Gary Wind, Guinevere Granite, Maria Ximena Leighton
[DES... | ["[Protocol for Surgical Implications in the Replaced Common Hepatic Artery, a Meta-analysis] Background\nThe aim of this literature review is to systematically analyze case reports and series related to the Replaced Common Hepatic Artery (RCHA) identified during preoperative or operative workups. The study will focus ... |
29,923 | Human Pancreas PACT Optical Clearing and High Resolution 3D Microscopy | null | dx.doi.org/10.17504/protocols.io.9gbh3sn | null | Elizabeth Butterworth, Wesley Dickerson, Vindhya Vijay, Kristina Weitzel, Julia Cooper, Eric W. Atkinson, Jason E. Coleman, Kevin Otto, Martha Campbell Thompson | TITLE: Human Pancreas PACT Optical Clearing and High Resolution 3D Microscopy
AUTHORS: Elizabeth Butterworth, Wesley Dickerson, Vindhya Vijay, Kristina Weitzel, Julia Cooper, Eric W. Atkinson, Jason E. Coleman, Kevin Otto, Martha Campbell Thompson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Usin... | ["[Deparaffinization of Formaldehyde-fixed Paraffin Embedded Tissues (If Working with Fresh Tissues, Skip to Step 10)]\nUse a new razor blade or scalpel to cut through the paraffin perpendicular to the surface of the tissue. Cut the paraffin at the edge of the tissue to finish loosening it. Use forceps or a spatula to ... |
109,143 | Explainability of Foundation Models | 0 | dx.doi.org/10.17504/protocols.io.4r3l2qw3pl1y/v1 | https://www.protocols.io/view/explainability-of-foundation-models-dntx5epn | Paola Di Maio | TITLE: Explainability of Foundation Models
AUTHORS: Paola Di Maio
[DESCRIPTION]
A metamodelling approach to support the development of a specifications for explainability in foundation models, adopting a combination of visualization, natural language representation.
[STEPS]
1. Establish Ground Truth
2. Define Alignm... | ["Establish Ground Truth", "Define Alignment", "Select Knowledge Representation", "Visualise KR", "Black box testing", "Define concept, key terms"] |
null | null | null | dx.doi.org/10.17504/protocols.io.puadnse | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Ampicillin solution for E. coli strains transformed with plasmid containing AmpR gene</p>
[STEPS]
?. | [] |
44,167 | V.4 - Direct wastewater RNA capture and purification via the "Sewage, Salt, Silica and SARS-CoV-2 (4S)" method | 4 | dx.doi.org/10.17504/protocols.io.bpdfmi3n | https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-bpdfmi3n | Oscar Whitney, Basem Al-Shayeb, Alex Crits-Cristoph, Mira Chaplin, Vinson Fan, Hannah Greenwald, Adrian Hinkle, Rose Kantor, Lauren Kennedy, Anna Maurer, Robert Tjian, Kara L. Nelson, UC Berkeley Wastewater-based epidemiology consortium | TITLE: V.4 - Direct wastewater RNA capture and purification via the "Sewage, Salt, Silica and SARS-CoV-2 (4S)" method
AUTHORS: Oscar Whitney, Basem Al-Shayeb, Alex Crits-Cristoph, Mira Chaplin, Vinson Fan, Hannah Greenwald, Adrian Hinkle, Rose Kantor, Lauren Kennedy, Anna Maurer, Robert Tjian, Kara L. Nelson, UC Berkel... | ["[Preparing RNA wash buffers]\nPrepareeach of two wash buffers - Wash buffer #1 (4S-WB1) and #2 (4S-WB2), for later use during cleanup of RNA bound to silica columns.\n1 L", "[Preparing RNA wash buffers]\n4S-WB1 composition: ABCD1ReagentOriginal molarity/%Final molarity/%Volume per liter of buffer2NaCl5 M1.5 M300 mL... |
null | null | null | dx.doi.org/10.17504/protocols.io.hnhb5b6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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68,045 | Protocol for In-silico Design, Docking and Molecular Dynamic Simulation of Antisense Oligonucleotides | 5 | dx.doi.org/10.17504/protocols.io.ewov1nr4ogr2/v1 | https://www.protocols.io/view/protocol-for-in-silico-design-docking-and-molecula-cepmtdk6 | Akshay Uttarkar, Mansi Babu, Vidya Niranjan | TITLE: Protocol for In-silico Design, Docking and Molecular Dynamic Simulation of Antisense Oligonucleotides
AUTHORS: Akshay Uttarkar, Mansi Babu, Vidya Niranjan
[DESCRIPTION]
Insilico drug design has been a catalyst in developing novel chemicals, Phyto-actives, nanoparticles, and anti-sense oligonucleotides. A robus... | ["Retrieve the whole mRNA sequence of target gene from GenBank.\n\nURL: http://www.ncbi.nlm.nih.gov/nucleotide/\n \n a.Open the home page and search with keyword i.e. the name of the gene.\n\n\n \n b.After entering the search statement, select the Limits link to limit the search to a particular mo... |
null | null | null | dx.doi.org/10.17504/protocols.io.nu5dey6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The research protocol on the topic:</p>
<p>Study of drug susceptibility of slowly growing nontuberculous mycobacteria (NTM) contains information on sample collection, processing diagnostic material, culture growth, primary differentiation of the isolated culture, and determin... | ["Samples of respiratory material in a volume of 10-25 ml collected in sterile polypropylene 50 ml tubes with a hermetically sealed cap (Corning, USA).", "All samples used in a study were coded and lacked personal information about the patients", "{\"blocks\":[{\"key\":\"e2kkg\",\"text\":\"Diagnostic material processed... |
61,762 | SOP54v1_TGD_GenotypingSubmissionforCollaborators | 4 | dx.doi.org/10.17504/protocols.io.e6nvwk8jzvmk/v1 | https://www.protocols.io/view/sop54v1-tgd-genotypingsubmissionforcollaborators-b8jaruie | Varsha Rajesh | TITLE: SOP54v1_TGD_GenotypingSubmissionforCollaborators
AUTHORS: Varsha Rajesh
[DESCRIPTION]
This is the protocol to submit samples for genotyping for collaborator samples.
[BEFORE_START]
QC Template:
[STEPS]
1. Go to Stanford ilabs: https://stanford.ilabsolutions.com/landing/7
2. Log in with your credentials, ... | ["Go to Stanford ilabs: https://stanford.ilabsolutions.com/landing/7", "Log in with your credentials, then select Core Facilities in the left hand side menu.", "Select Stanford Genomics. Then select Request Services.", "Select \"Whole Genome Genotyping Assay Service Request (Genotyping)\" in their list of services.", "... |
72,739 | Luciferase Assay pH-dependent Fox-activity | 1 | dx.doi.org/10.17504/protocols.io.n2bvj833wgk5/v1 | https://www.protocols.io/view/luciferase-assay-ph-dependent-fox-activity-cjabuian | kyle.kisor | TITLE: Luciferase Assay pH-dependent Fox-activity
AUTHORS: kyle.kisor
[DESCRIPTION]
Working protocol for how to perform luciferase assay. Worked for Fox reporter
[BEFORE_START]
Read entire protocol before starting
[STEPS]
SECTION: Plate Cells
1. 1. Plate 500K cells/well for each conditon
SECTION: Plate Cells
2. Incu... | ["[Plate Cells] 1. Plate 500K cells/well for each conditon", "[Plate Cells] Incubate o/n before transfection", "[Transfection] For each transfection condition create the following tube mixtures. (Volumes are for 1 transfection per condition and can be scaled up)\na. Tube 1: 125uL Optimem + 4uL lipofectamine 3000\nb. Tu... |
38,449 | ORCHARDS Protocol 2017 | 1 | dx.doi.org/10.17504/protocols.io.bhsrj6d6 | https://www.protocols.io/view/orchards-protocol-2017-bhsrj6d6 | Mitchell Arnold, Jonathan L Temte | TITLE: ORCHARDS Protocol 2017
AUTHORS: Mitchell Arnold, Jonathan L Temte
[STEPS] | [] |
86,708 | CAMbank: cfDNA BCT Field Processing v1 | 4 | null | https://www.protocols.io/view/cambank-cfdna-bct-field-processing-v1-cywuxxew | Eliah G Overbey, Krista A Ryon, JangKeun Kim, Christopher E Mason | TITLE: CAMbank: cfDNA BCT Field Processing v1
AUTHORS: Eliah G Overbey, Krista A Ryon, JangKeun Kim, Christopher E Mason
[DESCRIPTION]
Field processing of cfDNA BCTs for the Cornell Aerospace Medicine Biobank (CAMbank).
Instructions for preserving: plasma and RBC Pellets.
[STEPS]
SECTION: Perform Venipuncture
1. Aft... | ["[Perform Venipuncture] After venipuncture, invert the tubes gently 8 to 10 times to fully mix tube anticoagulant with blood sample.\n\nStore the tube upright at room temperature until centrifugation.\n\nNote: The tube stabilizes cell-free DNA for up to 14 days at 6 °C to 37 °C and CTCs for up to 7 days at 15 °C to 30... |
12,927 | ASD FieldSpec3 field measurement protocols | null | dx.doi.org/10.17504/protocols.io.qu7dwzn | null | Margaret Kalacska, J. Pablo Arroyo-Mora, Raymond Soffer, Kathryn Elmer | TITLE: ASD FieldSpec3 field measurement protocols
AUTHORS: Margaret Kalacska, J. Pablo Arroyo-Mora, Raymond Soffer, Kathryn Elmer
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The following protocol describes best practices for collecting field spectrometer measurements with an ASD Fieldspec 3 spe... | ["[Equipment set up]\n1. Connect one of the 12V batteries to the ASD, turn on the instrument and allow it to warm up for at least 30 min. This is important because each of the three detector arrays warm up at different rates. Erroneous spectral features such as spectral steps can occur at the overlap regions between th... |
null | null | null | dx.doi.org/10.17504/protocols.io.j3scqne | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
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88,442 | SMARTerV4 (1x) Amplification for single-cell or single-nuclei RNASeq Protocol | 1 | dx.doi.org/10.17504/protocols.io.261geopdjl47/v2 | https://www.protocols.io/view/smarterv4-1x-amplification-for-single-cell-or-sing-c2k2ycye | Allen Institute | TITLE: SMARTerV4 (1x) Amplification for single-cell or single-nuclei RNASeq Protocol
AUTHORS: Allen Institute
[DESCRIPTION]
Protocol to generate full-length cDNA from single cells, or nuclei, using Takara SMARTer V4.
[STEPS] | [] |
104,333 | OHSU SenNet Senescence-Associated Beta-Galactosidase (SA b-Gal) Staining of Carboxymethyl Cellulose (CMC) Embedded Skin Tissue Sections on Polyethylene Naphthalate (PEN) Coated Slides | 0 | dx.doi.org/10.17504/protocols.io.81wgbzq7ygpk/v1 | https://www.protocols.io/view/ohsu-sennet-senescence-associated-beta-galactosida-dh5m3846 | Julia R Unsworth, Xianmin Luo, Sheila A. Stewart, Megan K. Ruhland | TITLE: OHSU SenNet Senescence-Associated Beta-Galactosidase (SA b-Gal) Staining of Carboxymethyl Cellulose (CMC) Embedded Skin Tissue Sections on Polyethylene Naphthalate (PEN) Coated Slides
AUTHORS: Julia R Unsworth, Xianmin Luo, Sheila A. Stewart, Megan K. Ruhland
[DESCRIPTION]
Senescence-associated beta-galactosida... | ["[TISSUE SECTIONING AND EMBEDDING PROCEDURE] Collecting the Skin", "[TISSUE SECTIONING AND EMBEDDING PROCEDURE] Embedding the Skin in CMC", "[TISSUE SECTIONING AND EMBEDDING PROCEDURE] From the wet lab take petri dishes for each mouse that you are collecting tissue from and place in a bucket of ice", "[TISSUE SECTIONI... |
58,871 | Tissue Homogenization and GELFrEE for Top-Down Proteomics | 6 | dx.doi.org/10.17504/protocols.io.b5qxq5xn | https://www.protocols.io/view/tissue-homogenization-and-gelfree-for-top-down-pro-b5qxq5xn | Bryon Drown, Jeannie Camarillo, Cameron Lloyd-Jones, Neil Kelleher | TITLE: Tissue Homogenization and GELFrEE for Top-Down Proteomics
AUTHORS: Bryon Drown, Jeannie Camarillo, Cameron Lloyd-Jones, Neil Kelleher
[DESCRIPTION]
Solid human tissue is homogenized, protein is extracted, and samples prefractionated and desalted. Protein samples are ready for top-down proteomics.
[GUIDELINE... | ["[Cell lysis, protein precipitation, and lysate quantitation] Cryopulverize tissue sample with Retsch Cryomill", "[Protein fractionation by GELFrEE] Transfer the calculated volume containing 300 µg of protein to a new 1.5-mL Protein LoBind tube. The leftover lysates in 1% (wt/vol) SDS can be stored for several months ... |
40,355 | Processing ddRAD data from raw fastqs to vcf | 5 | dx.doi.org/10.17504/protocols.io.bjnbkman | https://www.protocols.io/view/processing-ddrad-data-from-raw-fastqs-to-vcf-bjnbkman | Thom Nelson, Findley Finseth, Lila Fishman, Colette Sevier Berg | TITLE: Processing ddRAD data from raw fastqs to vcf
AUTHORS: Thom Nelson, Findley Finseth, Lila Fishman, Colette Sevier Berg
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a pipeline that the Fishman lab uses for processing paired-end ddRAD data, from fastq to vcf. These scripts were writte... | ["[Remove PCR duplicates using molecular barcode]\nThis step removes PCR duplicate using the i5 molecular barcode.The resulting files will have the same prefix, but will have the suffix .rmdup.1.fastq (forward reads) and .rmdup.2.fastq (reverse reads)", "[Demultiplex plates using i7 barcode]\nThis step requires 4 fastq... |
61,799 | CBM for propagation of in vitro plantlets | 1 | null | https://www.protocols.io/view/cbm-for-propagation-of-in-vitro-plantlets-b8kfrutn | Lynn Doran, Amanda P. De Souza | TITLE: CBM for propagation of in vitro plantlets
AUTHORS: Lynn Doran, Amanda P. De Souza
[DESCRIPTION]
Media preparation for in vitro propagation of plantlets. Validated for cassava in tissue culture.
[GUIDELINES]
Thoroughly sterilize all materials and work surfaces before pouring media.
Use sterile technique af... | [] |
40,935 | ClearLab Flu+COVID19 Antigen Assay IFU | 4 | dx.doi.org/10.17504/protocols.io.bj8fkrtn | https://www.protocols.io/view/clearlab-flu-covid19-antigen-assay-ifu-bj8fkrtn | petercb3 | TITLE: ClearLab Flu+COVID19 Antigen Assay IFU
AUTHORS: petercb3
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"> Indication: Qualitative detection of the nucleocapsid protein antigen from SARS-CoV-2 in nasopharyngeal aspirate specimens directly or after the aspirate have been added to viral transp... | ["Collect specimen with Clearinse Nasal Wash Aspiration System", "Pipette 100 uL out from specimen chamber (up to first mark of graduated transfer pipette)", "Dispense entire sample from pipette into the assay cassette's extraction well.", "Then, pipette 50uL reagent into the assay cassette's extraction well and let si... |
106,992 | Rapid Bacterial Isolate Whole Genome Sequencing | 0 | dx.doi.org/10.17504/protocols.io.kqdg32ndev25/v1 | https://www.protocols.io/view/rapid-bacterial-isolate-whole-genome-sequencing-dkqq4vvw | Adela Alcolea-Medina, Luke Blagdon Snell, CIDR RESEARCH | TITLE: Rapid Bacterial Isolate Whole Genome Sequencing
AUTHORS: Adela Alcolea-Medina, Luke Blagdon Snell, CIDR RESEARCH
[DESCRIPTION]
Please cite the original publication where this process was described: Charalampous, T., Alcolea-Medina, A., Snell, L.B. et al. Evaluating the potential for respiratory metagenomics to... | ["[Set-up and sample sheet]", "[Set-up and sample sheet] Before beginning:\nEnsure that culture purity plate has been left for 48 hours in the incubator and colonies have \nmatured based on the amount of growth.", "[Isolate DNA extraction (bead-beating and bead wash):] Bead-beating/mechanical lysis of bacterial isolate... |
32,718 | Extracorporeal membrane oxygenation meta-analysis of time-to-event data in respiratory failure in adults | null | dx.doi.org/10.17504/protocols.io.bb7nirme | null | Hyunsuk Frank Roh, Chang-Guk Kim, Soon-Ho Chon, Jung Mogg Kim | TITLE: Extracorporeal membrane oxygenation meta-analysis of time-to-event data in respiratory failure in adults
AUTHORS: Hyunsuk Frank Roh, Chang-Guk Kim, Soon-Ho Chon, Jung Mogg Kim
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Purpose:</span><span>Time-to-event ... | [] |
68,924 | Overall protocol for MicroPOTS LCMS top down proteomics of pancreas tissue sections | 1 | dx.doi.org/10.17504/protocols.io.bp2l61oy5vqe/v1 | https://www.protocols.io/view/overall-protocol-for-micropots-lcms-top-down-prote-cfi4tkgw | Mowei Zhou, James M Fulcher, Yen-Chen Liao, Ljiljana.PasaTolic | TITLE: Overall protocol for MicroPOTS LCMS top down proteomics of pancreas tissue sections
AUTHORS: Mowei Zhou, James M Fulcher, Yen-Chen Liao, Ljiljana.PasaTolic
[DESCRIPTION]
This is the overall workflow for LCMS top down proteomics of pancreas functional units from tissue sections using the MicroPOTS platform. The ... | ["[Tissue collection] The tissue sections were prepared and shipped from Vanderbilt-TMC following the protocol below:", "[Sample preparation] Functional units (islet and acinar) were dissected and collected into the microPOTS platform using the method below:", "[Data Acquisition] The samples were analyzed by LCMS top d... |
73,400 | Procedure to analyze cannabinoids in bovine plasma using solid phase extraction & UPLC MS/MS | 6 | dx.doi.org/10.17504/protocols.io.bp2l6927dlqe/v1 | https://www.protocols.io/view/procedure-to-analyze-cannabinoids-in-bovine-plasma-cjwyupfw | Geraldine Magnin | TITLE: Procedure to analyze cannabinoids in bovine plasma using solid phase extraction & UPLC MS/MS
AUTHORS: Geraldine Magnin
[DESCRIPTION]
This procedure described the quantification of 21 phytocannabinoids in 100uL bovine plasma. 200uL of acetonitrile is added to 100uL plasma extract, cleaned up by centrifugatio... | ["[Preparation of solutions] Standards stock mixture. From the commercially available solutions, a stock solution containing the mixture of analytes at 10 µg/mL in ACN is prepared and stored at -20 °C. In a 4-mL glass vial,", "[Preparation of solutions] add 20 µL of CBC, CBCA, CBD, CBD-7-acid, CBDA, CBDV, CBDVA, CBG, C... |
69,782 | Preparation of single cell suspensions from human intestinal biopsies for single cell genomics applications | 1 | dx.doi.org/10.17504/protocols.io.q26g7bxqklwz/v4 | https://www.protocols.io/view/preparation-of-single-cell-suspensions-from-human-cgdwts7e | Ran RZ Zhou, Oni Basu | TITLE: Preparation of single cell suspensions from human intestinal biopsies for single cell genomics applications
AUTHORS: Ran RZ Zhou, Oni Basu
[DESCRIPTION]
The protocol is adapted from Fujii's and Smillies's reports for single cell transcriptome analysis from human intestines. It provides details on acquirement of... | ["[Pre-Dissociation] Chill wash media and dissociation media on ice. Samples are transfered with Advanced DMEM/F12 based media in 1.7 ml eppendorf tubes on ice. Once received in lab, samples are transfered to 35 mm dish using sharp-end forceps after the media are chilled. Alternatively, tissues can be transferred using... |
83,132 | Ovation RRBS Methyl-seq library prep | 4 | dx.doi.org/10.17504/protocols.io.kxygx3kydg8j/v1 | https://www.protocols.io/view/ovation-rrbs-methyl-seq-library-prep-cve4w3gw | Nelly Olova | TITLE: Ovation RRBS Methyl-seq library prep
AUTHORS: Nelly Olova
[DESCRIPTION]
This protocol describes a library prep procedure for 1 to 96 samples with the Ovation RRBS Methyl-seq System. The original Tecan Ovation protocol describes a low throughput procedure, therefore this protocol is especially targeted for manu... | ["[Calculations] Prepare a list of samples and their concentrations, calculate the required volumes for 100 ng DNA and nuclease-free water for a final reaction volume of 8.5 µL.", "[Calculations] Calculate the volume of a methylation conversion control to spike in each sample. This is usually unmethylated Lambda virus ... |
null | null | null | dx.doi.org/10.17504/protocols.io.qfsdtne | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Objective: To feed individual house flies a specific amount of bacteria in order to
determine bacteria “fate” (persistence, via enumeration; spatiotemporal location, via
microscopy) and house fly immune response (whole fly or tissue-specific, via
downstream mRNA or protein expre... | ["[Preparing House Flies for Bacterial Feeding] {\"blocks\":[{\"key\":\"3g659\",\"text\":\"Collect pupae from colony and surface sanitize for 2 minutes each with gentle swirling in 10% bleach, sterile H2O, 100% ethanol, sterile\\u00a0H2O. \",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[{\"offset\":111,\"len... |
20,837 | UC Davis - Glutathione Peroxidase | null | dx.doi.org/10.17504/protocols.io.ykdfus6 | null | Peter Havel | TITLE: UC Davis - Glutathione Peroxidase
AUTHORS: Peter Havel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">
Glutathione peroxidase (GPx) catalyzes the reduction of hydroperoxides, including hydrogen peroxides, by red... | ["Background or Non-enzymatic Wells - add 120 µl of Assay Buffer and 50 µl of co-substrate mixture to three wells.", "Positive Control Wells (bovine erythrocyte GPx) - add 100 µl of Assay Buffer, 50 µl of Co-Substrate Mixture, and 20 µl of diluted GPx (control) to three wells.", "Sample Wells - add 100 µl of Assay Buff... |
24,037 | Biochemical Measures of Neuropathy - Genotyping | null | dx.doi.org/10.17504/protocols.io.3qdgms6 | null | Eva Feldman | TITLE: Biochemical Measures of Neuropathy - Genotyping
AUTHORS: Eva Feldman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">Oxidative stress is highly correlated with the metabolic changes caused by hyperglycemia. Incre... | ["[PCR Amplification:]\nPrepare a Master Mix containing the following volumes of reagents:", "[PCR Amplification:]\nInto each 0.5mL thin-walled tube, pipette 23.0-μL of Master Mix.", "[PCR Amplification:]\nPipet 2.0 μL of DNA template (200 ng/μL) into thin-walled tube. Mix gently, and spin down.", "[PCR Amplification:]... |
34,454 | Production of Crude AAV Virus Extract | null | dx.doi.org/10.17504/protocols.io.bdvwi67e | null | Allen Institute for Brain Science | TITLE: Production of Crude AAV Virus Extract
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used to produce crude preps of AAV of any serotype.</div><div class = "text-block"><span style = "font-weight:bold;">Note</span><span>: Research re... | [] |
49,664 | Test with subprotocols, version2 | 1 | null | https://www.protocols.io/view/test-with-subprotocols-version2-buq8nvzw | Lenny Teytelman | TITLE: Test with subprotocols, version2
AUTHORS: Lenny Teytelman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a test.</div></div>
[STEPS]
?. [Day 1: Sample Prep]
This section has instructions for sample processing and preparation.
?. [Day 2: Culturing]
valuesvalues * 215=A2*217=A3*219=A4... | ["[Day 1: Sample Prep]\nThis section has instructions for sample processing and preparation.", "[Day 2: Culturing]\nvaluesvalues * 215=A2*217=A3*219=A4*2\nvaluesvalues * 215=A2*217=A3*219=A4*2", "[Day 2: Culturing]"] |
96,797 | REDI-NET FF-1 FILTH FLY FIELD SAMPLING | 0 | dx.doi.org/10.17504/protocols.io.j8nlk8b5wl5r/v1 | https://www.protocols.io/view/redi-net-ff-1-filth-fly-field-sampling-dar52d86 | REDI-NET Consortium | TITLE: REDI-NET FF-1 FILTH FLY FIELD SAMPLING
AUTHORS: REDI-NET Consortium
[DESCRIPTION]
To outline steps for properly collecting filth flies from cattle and environmental locations to evaluate the risk of zoonotic disease transmission by the detection of pathogens from vertebrate DNA (vDNA).
[BEFORE_START]
NOTE: Obe... | ["[SAMPLING TEAM] This SOP assumes that the animals’ owners/handlers/veterinarians are on site to corral cattle, move them through the chute, and operate the chute. If collecting from cattle, animals should be restrained in a chute or squeeze chute or in a head gate. If animals are only restrained in a head gate, be aw... |
65,074 | Live imaging to investigate mitophagy kinetics and NEMO recruitment in HeLa-M cells | 1 | dx.doi.org/10.17504/protocols.io.rm7vzy9w5lx1/v1 | https://www.protocols.io/view/live-imaging-to-investigate-mitophagy-kinetics-and-cbsssnee | OLIVIA HARDING, Erika L.F. Holzbaur | TITLE: Live imaging to investigate mitophagy kinetics and NEMO recruitment in HeLa-M cells
AUTHORS: OLIVIA HARDING, Erika L.F. Holzbaur
[DESCRIPTION]
There is no substitute for live cell imaging in the investigation of the kinetics of subcellular biology. Here, we enumerate a protocol to visualize fluorescently-tagged... | ["[Replace Standard Media with Imaging Media] Wait until imaging chamber is heated to 37 °C.", "[Replace Standard Media with Imaging Media] Aspirate media from sample.", "[Replace Standard Media with Imaging Media] Repeat the following two steps for a total of 2 washes.\nAdd 200 µL Imaging media gently to dish.\nAspira... |
58,387 | Donor Selection Criteria for Inclusion in the UCSD Female Reproductive TMC | 3 | dx.doi.org/10.17504/protocols.io.b49tqz6n | https://www.protocols.io/view/donor-selection-criteria-for-inclusion-in-the-ucsd-b49tqz6n | Valentina Stanley, Mana Parast, Louise Laurent | TITLE: Donor Selection Criteria for Inclusion in the UCSD Female Reproductive TMC
AUTHORS: Valentina Stanley, Mana Parast, Louise Laurent
[DESCRIPTION]
This document outlines the inclusion and exclusion criteria for donors of placenta, fallopian tubes and uterine myometrium in the Human BioMolecular Atlas Program ... | [] |
32,136 | fastGRO | 1 | dx.doi.org/10.17504/protocols.io.bbmgik3w | https://www.protocols.io/view/fastgro-bbmgik3w | Elisa Barbieri, Connor Hill, Alessandro Gardini | TITLE: fastGRO
AUTHORS: Elisa Barbieri, Connor Hill, Alessandro Gardini
[STEPS]
?. [Nuclei isolation]
Harvest cells and wash in cold 1X PBS
?. [Nuclear Run On]
Prepare fresh 2x Nuclear run-on buffer (NRO). (/sample)10 mM Tris-HCl ph8 5 mM MgCl2300 mM KCl1 mM DTT 500 μM ATP500 μM GTP500 μM 4-thio-UTP2 μM CTP200 μ/ml Su... | ["[Nuclei isolation]\nHarvest cells and wash in cold 1X PBS", "[Nuclear Run On]\nPrepare fresh 2x Nuclear run-on buffer (NRO). (/sample)10 mM Tris-HCl ph8 5 mM MgCl2300 mM KCl1 mM DTT 500 μM ATP500 μM GTP500 μM 4-thio-UTP2 μM CTP200 μ/ml Superase-in1% Sarkosyl (N-Laurylsarcosine sodium salt solution)\n100 µl\nPer libra... |
null | null | null | dx.doi.org/10.17504/protocols.io.hakb2cw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Preparation of Vibrio natriegens cell stocks for long-term storage at -80C. Principle is to remove any accumulated metabolic waste from overnight culture and resuspend in 20% glycerol final.</p>
[BEFORE_START]
<p>prepare 60% glycerol stock. </p>
<p>prepare LB3 media (high sa... | [] |
57,779 | Preparing of genomic DNA from in vitro cultured cells | 4 | dx.doi.org/10.17504/protocols.io.b4ntqven | https://www.protocols.io/view/preparing-of-genomic-dna-from-in-vitro-cultured-ce-b4ntqven | Hanqin Li, Yogendra Verma, Dirk Hockemeyer, Frank Soldner | TITLE: Preparing of genomic DNA from in vitro cultured cells
AUTHORS: Hanqin Li, Yogendra Verma, Dirk Hockemeyer, Frank Soldner
[DESCRIPTION]
This protocol describes a standard procedure for preparing crude cell lysate which can be further analyzed by PCR.
Protocol overview:
A. Preparing crude cell lysate directly f... | ["[A.\tPreparing crude cell lysate directly from hPSCs culture] Add 500 µl crude lysis buffer (Proteinase K added) to a fully confluent well of a 6 -well plate (~1.5 million cells)", "[A.\tPreparing crude cell lysate directly from hPSCs culture] Incubate at 37 °C 10 min", "[A.\tPreparing crude cell lysate directly from... |
null | null | null | dx.doi.org/10.17504/protocols.io.q9gdz3w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>A protocol to in vitro transcribe sgRNAs from oligos for S. pyogenes Cas9. </p>
[BEFORE_START]
<p><strong>10X transcription buffer</strong></p>
<ul>
<li>300mM Tris-Cl pH 8.1</li>
<li>250mM MgCl2</li>
<li>0.1% Triton X-100</li>
<li>20mM spermidine</li>
<li>100mM DTT</li>
</ul... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ta8eihw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol can be used to isolate single cells from human fetal thigh from age GA6-GA11.</p>
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.fhubj6w | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?. | [] |
83,163 | Tail suspension test to assess depression/anxiety behavior in parkinsonian mice | 1 | dx.doi.org/10.17504/protocols.io.n2bvj3odxlk5/v1 | https://www.protocols.click/view/tail-suspension-test-to-assess-depression-anxiety-cvf3w3qn | natalia.lopezgonzalezdelrey | TITLE: Tail suspension test to assess depression/anxiety behavior in parkinsonian mice
AUTHORS: natalia.lopezgonzalezdelrey
[DESCRIPTION]
The Tail Suspension Test is a mouse behavioral paradigm measuring behavioral despair or “depression-like” behavior and learned helplessness.
[GUIDELINES]
All mice should be careful... | ["[Tail Suspension Test] The mouse must be suspended using a piece of adhesive tape. The tape should be strong enough to prevent the mouse from falling and should not damage the skin of the tail. Tape length may vary with specific systems) and should only be applied to the very end of the tail (with 2-3 millimeters of ... |
20,608 | ImageJ Fluorescence Image Composition | null | dx.doi.org/10.17504/protocols.io.yc8fszw | null | Kenneth Schackart, Kattika Kaarj | TITLE: ImageJ Fluorescence Image Composition
AUTHORS: Kenneth Schackart, Kattika Kaarj
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details how to use ImageJ software to create a composite image from fluorescence images taken with a microscope.</div></div>
[STEPS]
?. [Get ImageJ ]
... | ["[Get ImageJ ]\nGo to https://imagej.nih.gov/ij/download.html and download the software corresponding to your operating system.", "[Get ImageJ ]\nSometimes ImageJ will be hard to find and not show up within your programs. You may have to manually go into your hard drive and open the software from where you downloaded ... |
74,165 | Light-Seq Cell Barcoding | 4 | dx.doi.org/10.17504/protocols.io.eq2ly77jplx9/v2 | https://www.protocols.io/view/light-seq-cell-barcoding-cknvuve6 | Jocelyn Y. Kishi, Ninning Liu, Emma R. West, Kuanwei Sheng, Jack J. Jordanides, Matthew Serrata, Constance L. Cepko, Sinem K. Saka, Peng Yin | TITLE: Light-Seq Cell Barcoding
AUTHORS: Jocelyn Y. Kishi, Ninning Liu, Emma R. West, Kuanwei Sheng, Jack J. Jordanides, Matthew Serrata, Constance L. Cepko, Sinem K. Saka, Peng Yin
[DESCRIPTION]
We present Light-Seq, an approach for multiplexed spatial indexing of intact biological samples using light-directed DNA ba... | ["[Protocol Overview] This protocol is for selective barcoding of cells seeded onto an Ibidi 18-well µ-slide for our Light-Seq paper. https://www.nature.com/articles/s41592-022-01604-1\n\nA separate protocol can be found for selective barcoding of tissue samples. \nhttps://www.protocols.io/view/light-seq-x54v9jno4g3e/v... |
30,842 | Ki-67 Staining Protocol | null | dx.doi.org/10.17504/protocols.io.bac2iaye | null | Sam Li | TITLE: Ki-67 Staining Protocol
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. Prepare 70% Ethanol and chill to -20°C.Tip: Do not freeze ethanol for long-term storage.
?. Prepare target cells of interest and wash 2X with PBS, centrifuging at 350xg for 5 minutes.
?. Discard supernatant and l... | ["Prepare 70% Ethanol and chill to -20°C.Tip: Do not freeze ethanol for long-term storage.", "Prepare target cells of interest and wash 2X with PBS, centrifuging at 350xg for 5 minutes.", "Discard supernatant and loosen the cell pellet by vortexing.", "Add 3ml cold 70% ethanol drop by drop to the cell pellet while vort... |
64,428 | Rockwerx Male Enhancement Reviews Where To Buy It? | 1 | dx.doi.org/10.17504/protocols.io.5jyl89q76v2w/v1 | https://www.protocols.io/view/rockwerx-male-enhancement-reviews-where-to-buy-it-ca6kshcw | rockwerxmalenhancenteviews | TITLE: Rockwerx Male Enhancement Reviews Where To Buy It?
AUTHORS: rockwerxmalenhancenteviews
[DESCRIPTION]
Rockwerx Male Enhancement Reviews Where To Buy It?
[STEPS]
1. Rockwerx Male Enhancement Reviews Where To Buy It?
For any relationship to be successful, sexual fulfillment is pivotal. While keeping the body h... | ["Rockwerx Male Enhancement Reviews Where To Buy It?\nFor any relationship to be successful, sexual fulfillment is pivotal. While keeping the body healthy is important, numerous people do n’t know what their sexual requirements are. Unfortunately, numerous men do not give themselves the help they need to achieve the co... |
41,678 | ITP-CRISPR detection of SARS-CoV-2 RNA | 4 | dx.doi.org/10.17504/protocols.io.bkxnkxme | https://www.protocols.io/view/itp-crispr-detection-of-sars-cov-2-rna-bkxnkxme | Ashwin Ramachandran, Diego A. Huyke, Eesha Sharma, Malaya K. Sahoo, ChunHong Huang, Niaz Banaei, Benjamin A. Pinsky, Juan G. Santiago | TITLE: ITP-CRISPR detection of SARS-CoV-2 RNA
AUTHORS: Ashwin Ramachandran, Diego A. Huyke, Eesha Sharma, Malaya K. Sahoo, ChunHong Huang, Niaz Banaei, Benjamin A. Pinsky, Juan G. Santiago
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The rapid spread of COVID-19 across the world has revealed majo... | ["[Chip preparation before testing]\nRinse the NS12AZ channel in the following order: Wash solution 1 for 2 min, Wash solution 2 for 2 min, Wash solution 3 for 2 min, Wash solution 2 for 2 min, Wash solution 4 for 2 min, and Wash solution 3 for 2 min. Between each rinse step, dry the channel using vacuum.\nIn the curre... |
null | null | null | dx.doi.org/10.17504/protocols.io.h6hb9b6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?. | [] |
60,024 | Unclear insomnia types in randomized controlled trials and systematic reviews: the protocol for a meta-epidemiological study | 1 | dx.doi.org/10.17504/protocols.io.kxygxz3bkv8j/v3 | https://www.protocols.io/view/unclear-insomnia-types-in-randomized-controlled-tr-b6uyrexw | Masahiro Banno, Yasushi Tsujimoto, Kunihiro Kohmura, Eisuke Dohi, Shunsuke Taito, Hidehiro Someko, Yuki Kataoka | TITLE: Unclear insomnia types in randomized controlled trials and systematic reviews: the protocol for a meta-epidemiological study
AUTHORS: Masahiro Banno, Yasushi Tsujimoto, Kunihiro Kohmura, Eisuke Dohi, Shunsuke Taito, Hidehiro Someko, Yuki Kataoka
[DESCRIPTION]
Objectives. To examine tendencies and charac... | ["[BACKGROUND] Insomnia disorder is diagnosed when both nocturnal insomnia symptoms and daytime dysfunctions continued for at least 1 month in the tenth revision of the International Statistical Classification of Diseases and Related Health Problems (ICD-10), and for at least 3 months in the third edition of the Intern... |
52,637 | Marine Bacteria Plasmid Conjugation | 4 | null | https://www.protocols.io/view/marine-bacteria-plasmid-conjugation-bxm5pk86 | Aalker , Alpher Aspiras, Nicholas Shikuma | TITLE: Marine Bacteria Plasmid Conjugation
AUTHORS: Aalker , Alpher Aspiras, Nicholas Shikuma
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol can be used to mate broad host range plasmids (including pBTK and other plasmids containing RSF1010 origins of replication) into diverse marine... | ["[Day 1]\nStreak out the marine bacteria and E.coli strains containing the plasmids to be mated using the streak plate method.\nBe sure to check the library to determine the location of the strains and which media, antibiotics, and/or media supplements (i.e. Diaminopimelic Acid [DAP]) should be used for each strain/pl... |
null | null | null | dx.doi.org/10.17504/protocols.io.hw5b7g6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes an ELISA assay for measurement of Granzyme B (CTLA-1) in supernatants collected from T cell dependent cytotoxicity (TDCC) cultures after BiTE® treatment.</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
37,332 | Injection of Viral Tracers by Nanoject | null | dx.doi.org/10.17504/protocols.io.bgpujvnw | https://www.protocols.io/view/injection-of-viral-tracers-by-nanoject-bgpujvnw | Allen Institute for Brain Science | TITLE: Injection of Viral Tracers by Nanoject
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the delivery of a neuronal tracer using the Nanoject II. The surgery uses a stereotaxic system to target specific brain coordinates in the ... | [] |
80,701 | FAVIS: Fast and Versatile protocol for metabarcoding of bulk Insect Samples from large-scale diversity monitoring projects | 4 | dx.doi.org/10.17504/protocols.io.kqdg36261g25/v1 | https://www.protocols.io/view/favis-fast-and-versatile-protocol-for-metabarcodin-cs25wgg6 | Elżbieta Iwaszkiewicz-Eggebrecht, Piotr Łukasik, Mateusz Buczek, Junchen Deng, Emily Hartop, Harald Havnås, Monika Prus-Frankowska, Carina R. Ugarph, Paulina Viteri, Anders F. Andresson, Tomas Roslin, Ayco J. M. Tack, Fredrik Ronquist, Andreia Miraldo | TITLE: FAVIS: Fast and Versatile protocol for metabarcoding of bulk Insect Samples from large-scale diversity monitoring projects
AUTHORS: Elżbieta Iwaszkiewicz-Eggebrecht, Piotr Łukasik, Mateusz Buczek, Junchen Deng, Emily Hartop, Harald Havnås, Monika Prus-Frankowska, Carina R. Ugarph, Paulina Viteri, Anders F. Andre... | ["[SECTION 1: Preparation] Set up washing stations", "[SECTION 1: Preparation] Set up a 80 L plastic container with washing liquid and water.", "[SECTION 1: Preparation] Set up a 80 L plastic container with 10% bleach solution by adding nine parts water to one part laboratory bleach (NaOCl - sodium hypochlorite soluti... |
70,969 | Water Extractable Organic Matter (WEOM) | 6 | dx.doi.org/10.17504/protocols.io.ewov1o4oylr2/v1 | https://www.protocols.io/view/water-extractable-organic-matter-weom-chizt4f6 | maggie.bowman | TITLE: Water Extractable Organic Matter (WEOM)
AUTHORS: maggie.bowman
[DESCRIPTION]
The method covers the extraction of water extractable organic matter for soil organic matter characterization using FT-ICR-MS, LCMS, and TOC/TN.
[STEPS]
SECTION: Extraction
1. Weigh out 6 g of air-dried soil in triplicate into a labe... | ["[Extraction] Weigh out 6 g of air-dried soil in triplicate into a labeled 50 mL falcon tube", "[Sample Filtering (LC-MS and TOC/TN)n] Thaw ~20 mLsample prior to filtering", "[Extraction] Add 30 mLof Ultrapure DI (maintaining a 2 g to 10 mL ratio) using large pipette", "[Extraction] Place samples onto orbital shaker f... |
null | null | null | dx.doi.org/10.17504/protocols.io.cvjw4m | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?. | [] |
27,248 | Isolation of single somas from postmortem fresh frozen human brain and immunostaining for AT8 and MAP2 | null | dx.doi.org/10.17504/protocols.io.6uqhevw | null | Marcos Otero-Garcia, Inma Cobos | TITLE: Isolation of single somas from postmortem fresh frozen human brain and immunostaining for AT8 and MAP2
AUTHORS: Marcos Otero-Garcia, Inma Cobos
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">- Protocol optimized to isolate single neuronal somas with cytoplasmic protein aggregates from postmo... | ["Prepare Homogenization Buffer and cool it on ice. ABC1AmountReagentFinal concentration22955 µlIM133 µlDTT 1mM1 µM430 µl50x Protease Inhibitor0.5 x515 µlRNaseIN 40 U/µl0.2 U/µl6No Triton!\nABC1AmountReagentFinal concentration22955 µlIM133 µlDTT 1mM1 µM430 µl50x Protease Inhibitor0.5 x515 µlRNaseIN 40 U/µl0.2 U/µl6No ... |
29,550 | The perfect Crème Brûlée | 1 | null | https://www.protocols.io/view/the-perfect-cr-me-br-l-e-84nhyve | René Bernard | TITLE: The perfect Crème Brûlée
AUTHORS: René Bernard
[DESCRIPTION]
Crème Brûlée has a short ingredient list and does not require specific skills to make, but to get it right, several steps need to be carefully executed to receive the creme, not a pudding that, that is still grainy or liquid. With a caramel crust tha... | ["[Preparation of creme] Take a midsize stainless steel pot and add500 mL of heavy whipping cream and add 100 g sugar.", "[Preparation of creme] Take one Bourbon Vanilla bean and with a small and pointy knife cut it open lengthwise. Remove the sticky vanilla mark with the knife and at it to the cream-sugar-mix. When al... |
41,833 | XPRIZE SHINE - In-tube Fluorescent SARS-CoV-2 NP Test | 4 | dx.doi.org/10.17504/protocols.io.bk4hkyt6 | https://www.protocols.io/view/xprize-shine-in-tube-fluorescent-sars-cov-2-np-tes-bk4hkyt6 | Jon Arizti-Sanz, Catherine A. Freije, Chloe K. Boehm, Sameed M. Siddiqui, Allen M. Goodman, Tinna-Solveig F. Kosoko-Thoroddsen, A'Doriann Y. Bradley, Jeremy Johnson, Pardis C. Sabeti, Cameron Myhrvold | TITLE: XPRIZE SHINE - In-tube Fluorescent SARS-CoV-2 NP Test
AUTHORS: Jon Arizti-Sanz, Catherine A. Freije, Chloe K. Boehm, Sameed M. Siddiqui, Allen M. Goodman, Tinna-Solveig F. Kosoko-Thoroddsen, A'Doriann Y. Bradley, Jeremy Johnson, Pardis C. Sabeti, Cameron Myhrvold
[DESCRIPTION]
<div class = "text-blocks"><div cl... | ["[Sample Collection and Viral Lysis]\nOpen the nasopharyngeal (NP) collection tube and rotate the nasal swab (attached to the NP collection tube cap) 4 times around the inside of each nostril. Return the swab to the collection tube and cap the tube. Nasopharyngeal collection tube contains necessary volume of FastAm... |
22,894 | SPARC C2 Spinal Cord Hemisection Protocol in Rats | null | dx.doi.org/10.17504/protocols.io.2kngcve | null | Elisa Gonzalez-Rothi, Marissa Ciesla, Latoya Allen, Gordon Mitchell | TITLE: SPARC C2 Spinal Cord Hemisection Protocol in Rats
AUTHORS: Elisa Gonzalez-Rothi, Marissa Ciesla, Latoya Allen, Gordon Mitchell
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the procedure for performing a left lateral C2 spinal cord hemisection in rats</div></div>
[S... | ["Rats are anesthetized in a closed chamber (3.5% isoflurane in 100% O2) and transferred to a heated surgical station where anesthesia is maintained via nose cone at 2-2.5% in 100% O2 for the duration of the surgical procedure. Prep injection site for injection using aseptic methods approved by Institutional approval b... |
97,644 | Protocol for Genomic DNA Extraction and Sequencing Library Preparation from Phage Stock | 0 | dx.doi.org/10.17504/protocols.io.kqdg32477v25/v1 | https://www.protocols.io/view/protocol-for-genomic-dna-extraction-and-sequencing-dbkk2kuw | Shuborno Islam, Rathindranath Kabiraj, Al Amin, Sadnane Hussain Pranto, Shantu Dey, Apurba Rajib Malaker, Deb Purna Keya, Arif Mohammad Tanmoy, Samir K Saha, Yogesh Hooda, Senjuti Saha | TITLE: Protocol for Genomic DNA Extraction and Sequencing Library Preparation from Phage Stock
AUTHORS: Shuborno Islam, Rathindranath Kabiraj, Al Amin, Sadnane Hussain Pranto, Shantu Dey, Apurba Rajib Malaker, Deb Purna Keya, Arif Mohammad Tanmoy, Samir K Saha, Yogesh Hooda, Senjuti Saha
[DESCRIPTION]
Whole Genome Seq... | ["[Phage Propagation and Purification] Phage Propagation\nSpotting of phages, co-cultures preparation, and DLA lawning", "[Extraction of Phage genomic DNA] Removal of Bacterial DNA and RNA", "[Extraction of Phage genomic DNA] Digestion of Phage Protein", "[Quantification and Normalization] Normalization before library ... |
93,179 | Library positive controls (LPCs) prepared on the Bravo NGS Workstation | 3 | dx.doi.org/10.17504/protocols.io.q26g7p7j3gwz/v1 | https://www.protocols.io/view/library-positive-controls-lpcs-prepared-on-the-bra-c683zhyn | Anna Schmidt, Sarah Nagel, Matthias Meyer | TITLE: Library positive controls (LPCs) prepared on the Bravo NGS Workstation
AUTHORS: Anna Schmidt, Sarah Nagel, Matthias Meyer
[DESCRIPTION]
Protocol for the preparation of library positive controls (LPCs) in FluidX tubes using the Bravo NGS Workstation. LPCs are used as part of the library preparation workflow of t... | [] |
36,610 | SPARC Cat - Sham Control Chronic Cat 1, Day 0 | 1 | dx.doi.org/10.17504/protocols.io.bfzajp2e | https://www.protocols.io/view/sparc-cat-sham-control-chronic-cat-1-day-0-bfzajp2e | Brett Hanzlicek, Margot Damaser | TITLE: SPARC Cat - Sham Control Chronic Cat 1, Day 0
AUTHORS: Brett Hanzlicek, Margot Damaser
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a procedure for a sham control chronic cat experiment (Day 0) for cystotomy (bladder surgery). The cystotomy is performed without UroMOCA implantatio... | ["[Transport Cat]\nTransport cat from housing site to surgery site.", "[Animal Prep and catheter placement]\nAnimal is anesthetized and abdomen is shaved by the vet team. The cat is then moved into the surgery room and attached to monitors by the vet team.", "[Animal Prep and catheter placement]\nDrape animal and perf... |
61,323 | CODEX® Multiplexed Imaging | Tissue Sectioning | 4 | dx.doi.org/10.17504/protocols.io.eq2lyn8epvx9/v1 | https://www.protocols.io/view/codex-multiplexed-imaging-tissue-sectioning-b75jrq4n | Diane Saunders, Alexander Hopkirk, Conrad Reihsmann, Regina Jenkins, Marcela Brissova, Alvin C. Powers | TITLE: CODEX® Multiplexed Imaging | Tissue Sectioning
AUTHORS: Diane Saunders, Alexander Hopkirk, Conrad Reihsmann, Regina Jenkins, Marcela Brissova, Alvin C. Powers
[DESCRIPTION]
This protocol describes the tissue preparation processes for the CODEX® (now PhenoCycler™) system by Akoya Biosciences. For the comprehens... | ["[Coverslip Preparation] Gather reagents:", "[Coverslip Preparation] Gently place coverslips at the bottom of a 500-mL glass beaker and swirl to spread the coverslips out. Add approximately 20 mL poly-L-lysine solution to the beaker, ensuring coverslips are fully submerged. Rotate the beaker at a 45° angle for 1 min t... |
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