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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40,869 | Sample Informed Consent Form Template (Appendix C of Phase 3 study of Vaccine Candidate for COVID-19) | 1 | dx.doi.org/10.17504/protocols.io.bj6dkra6 | https://www.protocols.io/view/sample-informed-consent-form-template-appendix-c-o-bj6dkra6 | Chris Ockenhouse, Chris Gast, Renee Holt, Jorge Flores | TITLE: Sample Informed Consent Form Template (Appendix C of Phase 3 study of Vaccine Candidate for COVID-19)
AUTHORS: Chris Ockenhouse, Chris Gast, Renee Holt, Jorge Flores
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This is Appendix C of "Phase 3 randomized, double-blinded, placebo-contro... | [] |
60,277 | cDNA Synthesis Using SuperScript III First-Strand Synthesis System for RT-PCR | 4 | null | https://www.protocols.io/view/cdna-synthesis-using-superscript-iii-first-strand-b64vrgw6 | Lynn Doran | TITLE: cDNA Synthesis Using SuperScript III First-Strand Synthesis System for RT-PCR
AUTHORS: Lynn Doran
[DESCRIPTION]
The SuperScript® III First-Strand Synthesis System for RT-PCR is used to synthesize first-strand cDNA from purified total RNA. RNA targets from 100 bp to >12 kb can be detected with this system.
... | ["Allow reagents to thaw completely, mix, and briefly minicentrifuge 10 mM dNTP mix and 50 ng/ul random hexamers before use. Store on ice when not in use.", "Label two PCR tubes per sample, RT and NRT.", "Treat gloves and pipettes with RNase away and sterilize work area with 70% ethanol before pipetting reagents.", "I... |
19,103 | Login to UA HPC web-portal | null | dx.doi.org/10.17504/protocols.io.wv7fe9n | null | Bonnie Hurwitz | TITLE: Login to UA HPC web-portal
AUTHORS: Bonnie Hurwitz
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This describes the steps involved in logging into the UA High-Performance Computing (HPC) web-portal for the UA Biosystems Analytics class. The instructors should have already given you access t... | ["Go to the HPC web-portal: https://ood.hpc.arizona.edu/pun/sys/dashboard and login with your UA net-id", "On the top menu bar select \"clusters\" and \"ocelote shell access\" from the pull-down list.", "A shell terminal will open for you. You can navigate to the class directory using the \"cd\" command, and then creat... |
31,427 | iDISCO Clearing and Staining of Pancreas | null | dx.doi.org/10.17504/protocols.io.baxbifin | null | Maria Jimenez Gonzalez, Sarah Stanley, Rosemary Li | TITLE: iDISCO Clearing and Staining of Pancreas
AUTHORS: Maria Jimenez Gonzalez, Sarah Stanley, Rosemary Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a protocol for iDISCO Clearing and immunostaining of pancreata/intrapancreatic ganglia in mice.</div></div>
[STEPS]
?. [Perfusion]
Pre... | ["[Perfusion]\nPreparation of Buffers- Heparinized PBS: 10 mg/100 ml PBS- Prepare a 4% PFA solution in PBS (Dilution of 1:4 of 16%PFA)", "[Perfusion]\nPlace the solutions (Heparanized PBS and 4% PFA) in a box with ice and prime the tubes of the perfusion pump with HeparInized PBS. Anesthetize the mouse by inducing anes... |
51,798 | The Simulated Random Assignment of Missense Mutations Throughout a Gene of Interest Can Determine Whether Missense Mutations Found in That Gene in a Population of Tumor Genomes Are Non-Randomly Distributed | 3 | dx.doi.org/10.17504/protocols.io.bwtwpepe | https://www.protocols.io/view/the-simulated-random-assignment-of-missense-mutati-bwtwpepe | Richard L Cullum, David J Riese II | TITLE: The Simulated Random Assignment of Missense Mutations Throughout a Gene of Interest Can Determine Whether Missense Mutations Found in That Gene in a Population of Tumor Genomes Are Non-Randomly Distributed
AUTHORS: Richard L Cullum, David J Riese II
[DESCRIPTION]
Human malignancies result from the accumulation ... | [] |
47,059 | Human Pancreas Histopathology Assessment | 1 | dx.doi.org/10.17504/protocols.io.br7tm9nn | https://www.protocols.io/view/human-pancreas-histopathology-assessment-br7tm9nn | Martha Campbell Thompson | TITLE: Human Pancreas Histopathology Assessment
AUTHORS: Martha Campbell Thompson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-style:italic;">DRAFT</span></div><div class = "text-block">Purpose:</div><div class = "text-block">The purpose of this protocol is to outline proper p... | ["Process human pancreas for fixed paraffin samples (dx.doi.org/xxx) and submit to the University of Florida Molecular Pathology Core (https://molecular.pathology.ufl.edu/) or another GLP-compliant histology laboratory for routine paraffin embedding.", "From 1 block of each region, create 4 µm paraffin sections and app... |
90,843 | Evaluating GPNMB ACD mutants by Western Blotting and immunofluorescence. | 4 | dx.doi.org/10.17504/protocols.io.4r3l22yz4l1y/v1 | https://www.protocols.io/view/evaluating-gpnmb-acd-mutants-by-western-blotting-a-c4x3yxqn | Erin Bogacki, Patrick Lewis, sherbst | TITLE: Evaluating GPNMB ACD mutants by Western Blotting and immunofluorescence.
AUTHORS: Erin Bogacki, Patrick Lewis, sherbst
[DESCRIPTION]
This protocol describes the evaluation of cellular processing of GPNMB mutants by Western Blotting and Immunofluorescent imaging in a HEK293 overexpression model.
[STEPS]
SECTIO... | ["[Seed cells] Seed HEK293 cells. \nA) For Western Blotting, we recommend seeding 2.5 x 10^5 cells per well of a 12-well culture plate.\nB) For Immunofluorescence, we recommend seeding 1.2 x 10^5 cells per well of a 24-well culture plate. Seed cells on Poly-D-Lysine coated coverslips. \nNote: we routinely culture HEK29... |
73,620 | General Setup and Takedown Procedures for Rodent Neurosurgery | 4 | dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1 | https://www.protocols.io/view/general-setup-and-takedown-procedures-for-rodent-n-cj5uuq6w | Avalon Amaya, Jackie Swapp, Ali Williford, Robert E Howard | TITLE: General Setup and Takedown Procedures for Rodent Neurosurgery
AUTHORS: Avalon Amaya, Jackie Swapp, Ali Williford, Robert E Howard
[DESCRIPTION]
This protocol describes the pre-operative setup and post-operative take-down procedures utilized for rodent stereotaxic neurosurgical procedures.
[BEFORE_START]
Notice... | ["[Prepare Surgical Station for Surgery (all procedures)] Disinfect the surgical area.", "[Prepare Surgical Station for Surgery (all procedures)] Spray area for the surgical drape with PREempt and let sit for at least 5 min.", "[Prepare Surgical Station for Surgery (all procedures)] Spray all other surfaces - surgical ... |
15,008 | Preparing DNA samples from mixed sand prior to extraction | null | dx.doi.org/10.17504/protocols.io.sv8ee9w | null | null | TITLE: Preparing DNA samples from mixed sand prior to extraction
AUTHORS:
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. Add 20 mL MilliQ water to pot
?. Remove plant, if any. Transfer to square petri dish.
?. Push a 50mL Falcon into the sand up to the 35 mL mark.
?. Tilt pot to a horizontal position and... | ["Add 20 mL MilliQ water to pot", "Remove plant, if any. Transfer to square petri dish.", "Push a 50mL Falcon into the sand up to the 35 mL mark.", "Tilt pot to a horizontal position and remove the falcon tube, retaining as much sand as possible.\nRotating the tube while removing it may help", "Cap and wipe down the tu... |
56,691 | Bogus Data Acquisition Protocol IV | 1 | null | https://www.protocols.io/view/bogus-data-acquisition-protocol-iv-b3ktqkwn | Abby Moore | TITLE: Bogus Data Acquisition Protocol IV
AUTHORS: Abby Moore
[DESCRIPTION]
The purpose of this protocol is to demo protocol development.
[BEFORE_START]
Before you start .....
[GUIDELINES]
Guidelines ....
[STEPS]
1. In this step, I'll refer to the software that you need to use. I used the Software compone... | ["In this step, I'll refer to the software that you need to use. I used the Software component to do this.", "In this step, I'll refer to an image using embed code from Box.", "In this step, I need to direct to to execute one of the following protocols depending on your context. Then you need to return to this protocol... |
63,882 | Attention! Blue Madeira CBD Gummies (Bear Gummy)Reviews: Scam Or Legit! | 3 | dx.doi.org/10.17504/protocols.io.6qpvr62jzvmk/v1 | https://www.protocols.io/view/attention-blue-madeira-cbd-gummies-bear-gummy-revi-camisc4e | Julie Ko | TITLE: Attention! Blue Madeira CBD Gummies (Bear Gummy)Reviews: Scam Or Legit!
AUTHORS: Julie Ko
[DESCRIPTION]
Blue Madeira CBD Gummies is not related to safety concerns because of being naturally extracted. It is made legal by the federal level but still remains under question by various authorities and state la... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.mhdc326 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Analysis scripts of GATK pipeline </p>
[STEPS]
?.
?.
?.
?.
?. | [] |
56,809 | Staphilococcus Aureus Sampling | 4 | null | https://www.protocols.io/view/staphilococcus-aureus-sampling-b3qhqmt6 | Pol Roca Cugat | TITLE: Staphilococcus Aureus Sampling
AUTHORS: Pol Roca Cugat
[DESCRIPTION]
This protocol is intended to study the affectation of Staphilococcus Aureus, including the MRSA variant. It outlines the basic protocol for a multi-subject study.
[GUIDELINES]
This protocol is intended to study the affectation of Staphiloco... | ["[Preparation] Wash your hands with soap. Put on your lab coat, your mask and your goggles or face shield. Make sure your mask is airtight and air cannot escape through the sides.", "[Sampling] Observe the subject. If their nails are longer than 3-6mm (white part that can be accessed). \nBitten-down nails could lead t... |
64,349 | Measuring Rock Velocities | 1 | null | https://www.protocols.io/view/measuring-rock-velocities-ca35sgq6 | Alison E E. Malcolm | TITLE: Measuring Rock Velocities
AUTHORS: Alison E E. Malcolm
[DESCRIPTION]
This protocol describes the measurement of a wave speed using transducers, a function generator, and an oscilloscope.
[BEFORE_START]
Collect your materials, ensure your work area is clean and make sure you've told someone you'll be working in... | ["[Pre-experiment setup] Attach the transducers to the samples with honey and clamps. For S-wave transducers the polarization is aligned with the direction of the coaxial cable plug. (If you are measuring P-wave velocities with S-wave transducers, please see step 9.)", "[Pre-experiment setup] Connect the cables", "[P... |
null | null | null | dx.doi.org/10.17504/protocols.io.ew9bfh6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
These methods accompany the following publication:<br /><br /><em><span style="color: #222222; font-family: arial, sans-serif; font-size: 12.8px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align... | [] |
96,954 | Endosomal, lysosomal, mitochondrial, or Golgi immunoprecipitation for quantitative proteomics | 4 | dx.doi.org/10.17504/protocols.io.261ge5p57g47/v1 | https://www.protocols.io/view/endosomal-lysosomal-mitochondrial-or-golgi-immunop-daw22fge | J. Wade Harper, Louis R R Hollingsworth, Chan Lee | TITLE: Endosomal, lysosomal, mitochondrial, or Golgi immunoprecipitation for quantitative proteomics
AUTHORS: J. Wade Harper, Louis R R Hollingsworth, Chan Lee
[DESCRIPTION]
Previous studies have developed methods for the immunoisolation of lysosomes, mitochondria, EEA1-positive endosomes, Golgi, and other organelles ... | ["[Lysosomal immunoprecipitation (Lyso-IP) for organellar proteomics] Resuspend cell pellets in 1 mL of Lyso-KBPS buffer supplemented with protease and phosphatase inhibitor tablets and lyse with 25-30 strokes with a 2 mL Dounce homogenizer on ice. Collect with a Pasteur pipette. Harvest into low-bind microcentrifuge t... |
78,440 | SDS-PAGE gel electrophoresis | 4 | null | https://www.protocols.io/view/sds-page-gel-electrophoresis-cqugvwtw | Lynn Doran, Steven J Burgess | TITLE: SDS-PAGE gel electrophoresis
AUTHORS: Lynn Doran, Steven J Burgess
[DESCRIPTION]
SDS-PAGE gel electrophoresis protocol for analyzing samples from plant leaf tissue via immunofluorescence. In this protocol no Coomassie blue is added to samples, the reason is that this interferes with the fluorescent signal dur... | ["[Prepare gel tank and buffers] Create a 1X working dilution of Tris/Glycine/SDS buffer (~1 L is required per gel tank) by diluting 10X stock 1:10 with distilled H2O.", "[Prepare gel tank and buffers] Carefully remove the comb from the precast gel and the tape across the bottom.", "[Prepare gel tank and buffers] Ass... |
98,347 | Ultra-deep ATAC-seq for sorted neurons | 0 | dx.doi.org/10.17504/protocols.io.eq2lyw35rvx9/v1 | https://www.protocols.io/view/ultra-deep-atac-seq-for-sorted-neurons-dcaj2scn | Andrea Kriz, Alisa Mo | TITLE: Ultra-deep ATAC-seq for sorted neurons
AUTHORS: Andrea Kriz, Alisa Mo
[DESCRIPTION]
Isolation of neurons from frozen post-mortem human brain tissue and preparation of ATAC-seq libraries for ultra-deep sequencing and somatic mutation detection.
[STEPS]
SECTION: Isolation of Nuclei from Adult Human Brain Tissue ... | ["[Isolation of Nuclei from Adult Human Brain Tissue (modified from Allen Human Brain Tissue PF0291)] Buffer preparation: On the day prior to sorting, prepare the following buffers:\na. Nuclei Isolation Media (NIM): \n\n \n\nFilter through 0.22µM filter and store at 4°C. Can keep for ~1-2 weeks. \n\nb. Blocking buffer... |
31,599 | In vitro transcription of DIG-labelled RNA probe | null | dx.doi.org/10.17504/protocols.io.ba4pigvn | null | Ida Barlow | TITLE: In vitro transcription of DIG-labelled RNA probe
AUTHORS: Ida Barlow
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Protocol for making DIG-labelled RNA probes suitable for </span><span style = "font-style:italic;">in situ</span><span> hybridisation</span></div></div>
[STEPS]
?. Assem... | ["Assemble reaction on ice:make up to 20ul total volume with WATER\n[DTT]\n[10X DIG-NTP mix (5 mM)]\n[RNAse inhibitor]\n[10 X transcription buffer]\n[linearlised template]\n[RNA polymerase]\n[TOTAL volume]\n5mM DIG-NTP mix (10X):", "Mix well by gently flicking and spin down tube contents", "Incubate at for\n37 °C", "A... |
41,440 | RAPID RNA Extraction | 4 | dx.doi.org/10.17504/protocols.io.bkp8kvrw | https://www.protocols.io/view/rapid-rna-extraction-bkp8kvrw | Noah Toppings | TITLE: RAPID RNA Extraction
AUTHORS: Noah Toppings
[STEPS]
?. Add 140 µL saliva to 560 µL lysis buffer.
?. Shake the tubes violently by hand.
?. Incubate at 61 ºC for 5 min.
?. Apply entire 700 µL to spin column.
?. Spin at 8 kRCF for 1 min.
?. Remove flowthrough with a pipette.
?. Add 500 µL wash 1 to the column.
?. ... | ["Add 140 µL saliva to 560 µL lysis buffer.", "Shake the tubes violently by hand.", "Incubate at 61 ºC for 5 min.", "Apply entire 700 µL to spin column.", "Spin at 8 kRCF for 1 min.", "Remove flowthrough with a pipette.", "Add 500 µL wash 1 to the column.", "Spin at 8 kRCF for 1 min.", "Remove flowthrough with a pipett... |
null | null | null | dx.doi.org/10.17504/protocols.io.simecc6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol refers to a study having the aim to identify and test at field artificial structures suitable as collectors for common cuttlefish <em>Sepia officinalis</em> eggs in wild condition.</p>
<p>During the same study, three different protocols were tested and compared.... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.uhaet2e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Importance
Recently, we showed that the elderly are significantly underrepresented in randomized controlled trials (RCT) in rheumatoid arthritis (RA) and osteoarthritis (OA). While this phenomenon has been detected in other fields as well, efforts by various international instit... | ["[INTRODUCTION] The elderly – commonly defined by an age of 65 or more years – are significantly underrepresented in clinical trials as has been shown for a wide variety of diseases and throughout various medical specialties.[1-18] This poses a potentially serious problem as older people differ from younger adults in ... |
12,586 | Density-based removal of bacteria from a culture of the marine heterotrophic flagellate Cafeteria roenbergensis | null | dx.doi.org/10.17504/protocols.io.qiiduce | null | Sarah Duponchel, Monica Berjon-Otero, Matthias Fischer | TITLE: Density-based removal of bacteria from a culture of the marine heterotrophic flagellate Cafeteria roenbergensis
AUTHORS: Sarah Duponchel, Monica Berjon-Otero, Matthias Fischer
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Heterotrophic flagellates require co-culture with bacteria tha... | ["[Preparation of Cafeteria roenbergensis culture]\nDetermine the cell density of aCafeteria roenbergensis culture: stain 10 µL of Cafeteria culture with 1 µL of Lugol’s acid iodine solution and count them on a haemocytometer (Neubauer Chamber)", "[Preparation of Cafeteria roenbergensis culture]\nResuspend the cell pel... |
null | null | null | dx.doi.org/10.17504/protocols.io.e3ubgnw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?. | [] |
50,000 | Endoglycosidase H (Endo H) digestion assay | 1 | dx.doi.org/10.17504/protocols.io.bu3qnymw | https://www.protocols.io/view/endoglycosidase-h-endo-h-digestion-assay-bu3qnymw | Vik Khurana | TITLE: Endoglycosidase H (Endo H) digestion assay
AUTHORS: Vik Khurana
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details the endoglycosidase H (Endo H) digestion assay.</div></div>
[STEPS]
?. [Endoglycosidase H (Endo H) digestion assay]
PREPARE:
?. [Endoglycosidase H (Endo H) di... | ["[Endoglycosidase H (Endo H) digestion assay]\nPREPARE:", "[Endoglycosidase H (Endo H) digestion assay]\nMake sure the lysis buffer (Table 1) is chilled.", "[Endoglycosidase H (Endo H) digestion assay]\nGet samples and keep on dry ice.", "[Endoglycosidase H (Endo H) digestion assay]\nGet a large box and fill to approx... |
80,666 | AMPLIFY: Creation, Testing, and Revision | 1 | dx.doi.org/10.17504/protocols.io.36wgqj895vk5/v1 | https://www.protocols.io/view/amplify-creation-testing-and-revision-csz2wf8e | Juliet Capriola | TITLE: AMPLIFY: Creation, Testing, and Revision
AUTHORS: Juliet Capriola
[DESCRIPTION]
This project seeks to create a video-based scientific data platform called AMPLIFY, with the goal to revolutionize the way we communicate scientific studies and findings to the general public. This platform will be created on the i... | ["[Pre-Creation] Reach out to any community members, scientists, programmers, and other experts I have in mind for the project to be a part of the team.", "[Creation] With software engineers and all other members of the team, create the app/platform as outlined in the research proposal. We will meet 5x week. Everyone w... |
16,328 | immunehistochemistry and transcriptomic analysis of iodine and breast cancer | 1 | dx.doi.org/10.17504/protocols.io.t7gerjw | https://www.protocols.io/view/immunehistochemistry-and-transcriptomic-analysis-o-t7gerjw | Carmen Aceves | TITLE: immunehistochemistry and transcriptomic analysis of iodine and breast cancer
AUTHORS: Carmen Aceves
[DESCRIPTION]
The present work analyzes the antineoplastic effects of molecular iodine alone and in combination with the neoadjuvant therapy FEC/TE (5-fluorouracil/epirubicin/cyclophosphamide or taxotere/epirubi... | [] |
37,098 | ATAC-STARR-seq | 1 | dx.doi.org/10.17504/protocols.io.bggijtue | https://www.protocols.io/view/atac-starr-seq-bggijtue | Tyler Hansen, Emily Hodges | TITLE: ATAC-STARR-seq
AUTHORS: Tyler Hansen, Emily Hodges
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Transcriptional enhancers control cell-type specific gene expression in humans and dysfunction can lead to debilitating diseases, including cancer. Identifying </span><span style = "font-s... | ["[Anneling Oligos]\nDilute oligos to 100 µM in STE buffer.", "[Anneling Oligos]\nMake Adaptor Mixes in 200μL PCR tubes:Mix (Adaptor A) [50µL]: 5µL Tn5MERV oligo (100µM) 5µL Tn5_1 Oligo (100µM) 40µL H2OMix (Adaptor B) [50µL]: 5µL Tn5MERV oligo (100µM) 5µL Tn5_2_ME_Comp Oligo (100µM) 40µL H2O", "[Ann... |
40,567 | 602.2 Donor Acceptance Criteria for URMC HTC HuBMAP and LungMAP Inclusion | 4 | dx.doi.org/10.17504/protocols.io.bjuxknxn | https://www.protocols.io/view/602-2-donor-acceptance-criteria-for-urmc-htc-hubma-bjuxknxn | Gloria Pryhuber | TITLE: 602.2 Donor Acceptance Criteria for URMC HTC HuBMAP and LungMAP Inclusion
AUTHORS: Gloria Pryhuber
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Purpose and Scope of the Procedure</div><div class = "text-block"><ul style = "list-style-type:disc;"><li style = "counter-reset:ol0;list-style-ty... | ["[Review Case: accept or decline based on eligibility]\nTake referral call or BRINDL screening report", "[Review Case: accept or decline based on eligibility]\nReview Eligibility Criteria", "[Review Case: accept or decline based on eligibility]\nStart Case Record in BRINDL Inventory Screening Log", "[Review Case: acce... |
52,456 | T Drops Male Enhancement - Does (T+Drops Male Enhancement) Really Works Or Scam? | 1 | dx.doi.org/10.17504/protocols.io.bxggpjtw | https://www.protocols.io/view/t-drops-male-enhancement-does-t-drops-male-enhance-bxggpjtw | health | TITLE: T Drops Male Enhancement - Does (T+Drops Male Enhancement) Really Works Or Scam?
AUTHORS: health
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><a href="https://www.healthpills24x7.com/order-t-drops-male-enhancement" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style... | ["Product Name: T Drops Male EnhancementOfficial Website: Click Here To Order T Drops In (DE,AT) Like routine requirements of food, clothes, and shelter, one also needs sex. It is considered as a prime requirement of the body when one grows. For males and females, it is a primary need at a certain age, which must ... |
95,962 | Micro-PET CT procedures for brain imaging of rats | 0 | dx.doi.org/10.17504/protocols.io.e6nvwdw2zlmk/v1 | https://www.protocols.io/view/micro-pet-ct-procedures-for-brain-imaging-of-rats-c9x2z7qe | christopher.cawthorne, María Sanchiz Calvo, eduard.bentea | TITLE: Micro-PET CT procedures for brain imaging of rats
AUTHORS: christopher.cawthorne, María Sanchiz Calvo, eduard.bentea
[DESCRIPTION]
Micro-PET CT procedures for brain imaging of rats
[STEPS]
1. A range of PET radiotracers and radioligands (“radiopharmaceuticals”) can be used to
image biochemical flux and rece... | ["A range of PET radiotracers and radioligands (“radiopharmaceuticals”) can be used to\nimage biochemical flux and receptor density in rodents. PET\nradiopharmaceuticals are administered in very low ‘tracer’ doses to avoid\npharmacological effects, the specific activity of the tracer must be carefully\nevaluated to ens... |
44,890 | LooK SPOT Antigen Rapid Test System | 1 | dx.doi.org/10.17504/protocols.io.bp32mqqe | https://www.protocols.io/view/look-spot-antigen-rapid-test-system-bp32mqqe | Diego Lai | TITLE: LooK SPOT Antigen Rapid Test System
AUTHORS: Diego Lai
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">LooK SPOT COVID-19 antigen rapid test </span><span>is a lateral flow immunoassay intended for the qualitative detection of nucleocapsid protein antigen from... | ["Download LooK SPOT app from Google Play Store or Apple Store and install it. Register the app with your information. The minimum requirement for supported smartphone models and OS: iPhone 6 and above, with iOS 13 and above, with 8MP rear camera and above. Android phone with Android OS 7.1 and above, with 8MP rear cam... |
91,568 | Tissue processing and freezing after surgery | 1 | null | https://www.protocols.io/view/tissue-processing-and-freezing-after-surgery-c5nqy5dw | Bettina Ergün | TITLE: Tissue processing and freezing after surgery
AUTHORS: Bettina Ergün
[DESCRIPTION]
The aim of this protocol is to document the processing of fresh tissue after surgery.
The collected tissue must also be documented in the files which are linked down below
The protocol descibes in detail how to process the res... | ["[Sample processing in the lab] Fresh tissue should be processed on the same day if possible, but can be stored at 4°C for a maximum of overnight.\nTo reduce pathogens, the tissue should be incubated for 60 min atRoom temperature", "[Sample processing in the lab]", "[Sample processing in the lab]", "[Sample processing... |
null | null | null | dx.doi.org/10.17504/protocols.io.h4rb8v6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?. | [] |
40,595 | Chicken immunization with Keyhole limpet hemocynin (KLH)-gp120 fragment (254-274) conjugate raises anti-KLH antibodies in egg yolks. | 4 | dx.doi.org/10.17504/protocols.io.bjvtkn6n | https://www.protocols.io/view/chicken-immunization-with-keyhole-limpet-hemocynin-bjvtkn6n | Angel Justiz-Vaillant | TITLE: Chicken immunization with Keyhole limpet hemocynin (KLH)-gp120 fragment (254-274) conjugate raises anti-KLH antibodies in egg yolks.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Chicken immunization with peptides is inefective if only just the peptides are b... | ["Two healthy layer chickens (brown Leghorn), aged approximately 6 months, are injected intramuscularly at multiple sites on the breast with the peptide-keyhole limpet hemocyanin (KLH) conjugate.", "The chickens are immunized on day 0, with 0.2 µmol/ml of the fragment 254-274 of HIV gp120-conjugated to KLH (immunogen) ... |
98,426 | Alternative method to visualize receptor dynamics in cell membranes | 0 | dx.doi.org/10.17504/protocols.io.rm7vzj8z8lx1/v1 | https://www.protocols.io/view/alternative-method-to-visualize-receptor-dynamics-dcc22sye | Ravelli Cosetta, Corsini Michela, Ventura Anna, Domenichini Mattia, Grillo Elisabetta, Mitola Stefania | TITLE: Alternative method to visualize receptor dynamics in cell membranes
AUTHORS: Ravelli Cosetta, Corsini Michela, Ventura Anna, Domenichini Mattia, Grillo Elisabetta, Mitola Stefania
[DESCRIPTION]
This protocol details alternative method to visualize receptor dynamics in cell membranes.
[STEPS]
SECTION: Cell tran... | ["[Cell transfection (day 1 and 2)] The day before transfection, seed 2x104/cm2 of CHO cells in 6 well plate in F12 medium supplemented with 100 IU/mL penicillin and 100 µg/mL streptomycin and 10% FCS (complete medium) and culture under normal conditions at37 °C in 5% CO2. When using different cell lines, ensure a cell... |
30,209 | Salmonella blood culture surveillance: Antibiotic susceptibility testing | null | dx.doi.org/10.17504/protocols.io.9q9h5z6 | null | Sien Ombelet | TITLE: Salmonella blood culture surveillance: Antibiotic susceptibility testing
AUTHORS: Sien Ombelet
[STEPS] | [] |
101,178 | Quantification of SARS-CoV-2 in wastewater | 1 | dx.doi.org/10.17504/protocols.io.81wgbx39ylpk/v2 | https://www.protocols.io/view/quantification-of-sars-cov-2-in-wastewater-de223gge | David Ian Walker, James Lowther, Nick Evens, Jonathan Warren, Jonathan Porter, Kata Farkas, Davey Jones | TITLE: Quantification of SARS-CoV-2 in wastewater
AUTHORS: David Ian Walker, James Lowther, Nick Evens, Jonathan Warren, Jonathan Porter, Kata Farkas, Davey Jones
[DESCRIPTION]
This procedure describes the concentration and quantification of SARS-CoV-2 from wastewater as used by the Environmental Monitoring for Health... | ["[Preparation of daily phi6 process control working suspensions] On each day of testing, a new batch of phi6 process control working suspension should be made.", "[Preparation of daily phi6 process control working suspensions] Remove an aliquot of phi6 stock from the freezer (prepared according to Appendix 1), thaw an... |
20,496 | RNA-Seq Data Analysis (Bowtie-TopHat-Cufflinks) | null | dx.doi.org/10.17504/protocols.io.x9qfr5w | null | Kiichi Hirota | TITLE: RNA-Seq Data Analysis (Bowtie-TopHat-Cufflinks)
AUTHORS: Kiichi Hirota
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Library preparation]
Total RNA was extracted from cells using RNeasy® Mini Kit (Qiagen).
?. [Library preparation]
Poly(A) RNA libraries were constructed using TruSeq® Stranded mRNA... | ["[Library preparation]\nTotal RNA was extracted from cells using RNeasy® Mini Kit (Qiagen).", "[Library preparation]\nPoly(A) RNA libraries were constructed using TruSeq® Stranded mRNA Library Prep Kit (Illumina).", "[Sequencing]\nThe libraries were sequenced at 100 bp paired-ends on an Illumina HiSeq 2500 platform.",... |
20,810 | UC Davis - Genotyping | null | dx.doi.org/10.17504/protocols.io.yjifuke | null | Brandon Willis | TITLE: UC Davis - Genotyping
AUTHORS: Brandon Willis
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Standard PCR conditions for genotyping of mutant mouse DNA extracted from somatic (e.g., tail) tissue.</div></div>
[... | ["I. DNA Extraction using DNEasy kit.Procedure 1. Make a cocktail of ATL with 180uL buffer ATL and 20uL Proteinase K. Add 200uL to each tube. Be sure tail snip is submerged. 2. Incubate at 55°C for 6-12 hours in heat block or water bath. 3. Remove tubes from heat source and vortex. 4. Add 400 ul of AL/Ethanol mixtu... |
28,198 | PCR Using Q5U Hot Start High-Fidelity DNA Polymerase (NEB #M0515) | null | dx.doi.org/10.17504/protocols.io.7sehnbe | https://www.protocols.io/view/pcr-using-q5u-hot-start-high-fidelity-dna-polymera-7sehnbe | New England Biolabs | TITLE: PCR Using Q5U Hot Start High-Fidelity DNA Polymerase (NEB #M0515)
AUTHORS: New England Biolabs
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Please note that protocols with </span><span style = "font-style:italic;">Q5U Hot Start High-Fidelity DNA Polymerase</span><span> may differ fr... | [] |
41,752 | Glass Milk preparation - forked | 4 | null | https://www.protocols.io/view/glass-milk-preparation-forked-bkzykx7w | Martin Codyre | TITLE: Glass Milk preparation - forked
AUTHORS: Martin Codyre
[STEPS]
?. [Glass Milk Preparation]
To prepare glass milk, 325 mesh silicon dioxide (Spectrum Chemicals - SI108) was combined with an excess volume of 10% HCl (~3 N HCl) made from combining 37%and MilliQ water (Millipore) in a fume hood
(dry silica powder s... | ["[Glass Milk Preparation]\nTo prepare glass milk, 325 mesh silicon dioxide (Spectrum Chemicals - SI108) was combined with an excess volume of 10% HCl (~3 N HCl) made from combining 37%and MilliQ water (Millipore) in a fume hood\n(dry silica powder should not be inhaled).", "[Glass Milk Preparation]\nAfter acid washing... |
50,205 | Efficacy and safety of endovascular arteriovenous fistula creation with comparison to surgically created fistulas: a systematic review and meta-analysis protocol | 1 | dx.doi.org/10.17504/protocols.io.bu95nz86 | https://www.protocols.io/view/efficacy-and-safety-of-endovascular-arteriovenous-bu95nz86 | Yoshinosuke Shimamura, Hajime Yamazaki, Takamasa Miyauchi, Hiroshi Ueta, Yasutaka Kuniyoshi, Yasushi Tsujimoto | TITLE: Efficacy and safety of endovascular arteriovenous fistula creation with comparison to surgically created fistulas: a systematic review and meta-analysis protocol
AUTHORS: Yoshinosuke Shimamura, Hajime Yamazaki, Takamasa Miyauchi, Hiroshi Ueta, Yasutaka Kuniyoshi, Yasushi Tsujimoto
[DESCRIPTION]
This systemic... | ["[Introduction] Functional vascular access is the lifeline of hemodialysis patients. The Kidney Disease Outcomes Quality Initiative guideline strongly recommends the creation of arteriovenous fistulas for long-term vascular access. Although arteriovenous fistulas have been created using open surgery, endovascular tech... |
68,919 | Rapid Diagnostic Tests and ELISA for diagnosing Chronic Chagas Disease: Systematic revision and meta-analysis | 1 | dx.doi.org/10.17504/protocols.io.4r3l2oxppv1y/v1 | https://www.protocols.io/view/rapid-diagnostic-tests-and-elisa-for-diagnosing-ch-cfixtkfn | Sandra Helena Suescún-Carrero, Philippe Tadger, Carolina Sandoval Cuellar, lauramirez, Lluis Armadans-Gil | TITLE: Rapid Diagnostic Tests and ELISA for diagnosing Chronic Chagas Disease: Systematic revision and meta-analysis
AUTHORS: Sandra Helena Suescún-Carrero, Philippe Tadger, Carolina Sandoval Cuellar, lauramirez, Lluis Armadans-Gil
[DESCRIPTION]
Objective
To determine the diagnostic validity of the enzyme-linked immun... | ["Protocol and registration", "Eligibility criteria", "Data sources", "Study search and selection", "Data collection process", "Definition for data extraction", "Risk of bias and applicability", "Diagnostic accuracy measures", "Summary of results", "Addinitional analyses"] |
46,785 | Subcloning colonial ascidians | 4 | dx.doi.org/10.17504/protocols.io.brw9m7h6 | https://www.protocols.io/view/subcloning-colonial-ascidians-brw9m7h6 | Laura Bugada, Simon Blanchoud | TITLE: Subcloning colonial ascidians
AUTHORS: Laura Bugada, Simon Blanchoud
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">We have been subcloning colonial ascidians since some time already, till now - with a lot of success. This protocol has been ruinously used by many of our co-workers.</div></di... | ["[Subcloning colonial ascidians]\nPlace the cleaned slides to be subclone in the first tray inside a slide rack.\n{\"blocks\":[{\"key\":\"d1gg0\",\"text\":\"\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[]}],\"entityMap\":[]}", "[Subcloning colonial ascidians]\nTake one sli... |
null | null | null | dx.doi.org/10.17504/protocols.io.eq7bdzn | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<p><strong>Materials:</strong><br /><br />1) SOB medium</p>
<ul>
<li>1.0% Bacto-tryptone</li>
<li>0.5% Bacto-yeast extract</li>
<li>10.0 mM NaCl</li>
<li>2.5 mM KCl</li>
<li>10.0 mM MgCl<sub>2</sub></li>
<li>10.0 mM MgSO<sub>4</sub></li>
<li>Prepare the MgCl<sub>2</sub> and MgSO<... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.fw7bphn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.mcfc2tn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Methods for TransEpithelial Electrical Resistance (TEER) and short circuit current measurement of the effects of soluble mediator on intestinal epithelial cells. </p>
[BEFORE_START]
<p>Prepare Forskolin (10µM), UTP (100µM), Amiloride (10µM), DIDS (100µM) and GlyH-101 (50 µM)... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.cgvtw5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol is for dephosphorylation of 5´-ends of DNA using rSAP in restriction enzyme reaction (M0371)
[STEPS]
?.
?.
?.
?.
?. | [] |
54,758 | Metagenome Preparations and Analysis | 4 | dx.doi.org/10.17504/protocols.io.bzqep5te | https://www.protocols.io/view/metagenome-preparations-and-analysis-bzqep5te | Bryan Yoo, Jessica Griffiths, Sarkis Mazmanian | TITLE: Metagenome Preparations and Analysis
AUTHORS: Bryan Yoo, Jessica Griffiths, Sarkis Mazmanian
[DESCRIPTION]
Protocol for metagenome preparation and analysis used in Yoo et al 2021
[STEPS]
SECTION: Fecal Collection
1. AAV-PHP.S:hSYN1-hM3Dq-mRuby2 (1012VGs) was delivered systemically to TH-Cre and ChAT-Cre mic... | ["[Fecal Collection] AAV-PHP.S:hSYN1-hM3Dq-mRuby2 (1012VGs) was delivered systemically to TH-Cre and ChAT-Cre mice. 3-4 week after infection, C21 (3mg/kg) was administered daily for 10 consecutive days. Fecal pellets were collected in sterile containers one day before initial C21 dose, and between doses thereafter.", "... |
null | null | null | dx.doi.org/10.17504/protocols.io.dq45yv | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is a modified protocol from the original NEB splitting the 50uL aliquot into two separate tubes for dual reactions from a single tube.
[GUIDELINES]
<strong>Transformation Protocol Variables</strong><br /><br /><strong>Thawing</strong>: Cells are best thawed on ice and DNA ... | [] |
59,815 | DNA metabarcoding protocol for siphonophore gut contents | 1 | dx.doi.org/10.17504/protocols.io.5qpvo57o7l4o/v2 | https://www.protocols.io/view/dna-metabarcoding-protocol-for-siphonophore-gut-co-b6nfrdbn | Alejandro Damian Serrano | TITLE: DNA metabarcoding protocol for siphonophore gut contents
AUTHORS: Alejandro Damian Serrano
[DESCRIPTION]
Protocol for the SiphWeb DNA metabarcoding of siphonophore gut content.
Starting with DNA extractions from pooled frozen gastrozooids, this protocol takes the user through the steps of PCR amplification, P... | ["[DNA Extractionion] Mainly identical to:\nhttp://www.bea.ki.se/documents/EN-DNeasy%20handbook.pdf\nWith the following modifications:\n\n-Digestion at 56 °C \n-Elution using 2 rounds of incubation and centrifuge with 50 µL QIAgen DNeasy Blood & Tissue kit, cultured cells , incubating 10 min at 56 °C , to a total of 10... |
null | null | null | dx.doi.org/10.17504/protocols.io.j2wcqfe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Seawater is collected and preserved to be analyzed in lab using an InFlux Flow Cytometer with the Spigot software package. The populations targeted for enumeration are <em>Prochlorococcus</em>, <em>Synechococcus</em>, unclassied pico-eukaryotes (cells sized around 1μm), and h... | [] |
43,236 | Introduction to Equipment and Supplies | 3 | null | https://www.protocols.io/view/introduction-to-equipment-and-supplies-bngcmbsw | , Alyssa Ayala | TITLE: Introduction to Equipment and Supplies
AUTHORS: , Alyssa Ayala
[STEPS] | [] |
41,738 | CoVIDScandx | 1 | dx.doi.org/10.17504/protocols.io.bkzikx4e | https://www.protocols.io/view/covidscandx-bkzikx4e | Muhammad Munir | TITLE: CoVIDScandx
AUTHORS: Muhammad Munir
[STEPS]
?. Add smart lysis buffer with 1:1 ratio in the VTM sample
?. Heat for 68C for 8 minutes and then 95C for 10 minutes
?. Cool and take 3 ul to colorimetric LAMP master mix (NB: M1800)
?. Vortex reaction mix and centrifuge to collect material
?. Pipet 24 μl per reaction... | ["Add smart lysis buffer with 1:1 ratio in the VTM sample", "Heat for 68C for 8 minutes and then 95C for 10 minutes", "Cool and take 3 ul to colorimetric LAMP master mix (NB: M1800)", "Vortex reaction mix and centrifuge to collect material", "Pipet 24 μl per reaction into desired reaction vessels and add 1 µl of sample... |
82,801 | Generation of membrane tubules pulled from giant unilamellar vesicles (GUVs) | 4 | dx.doi.org/10.17504/protocols.io.j8nlkw7p5l5r/v1 | https://www.protocols.io/view/generation-of-membrane-tubules-pulled-from-giant-u-cu4rwyv6 | Javier Espadas, Aurelien Roux | TITLE: Generation of membrane tubules pulled from giant unilamellar vesicles (GUVs)
AUTHORS: Javier Espadas, Aurelien Roux
[DESCRIPTION]
This protocol explains the methodology to generate lipid nanotubes pulled from giant unilamellar vesicles for fluorescence microscopy experiments.
[STEPS]
SECTION: Protocol
1. Mix D... | ["[Protocol] Mix DOPC, DOPS and Atto 647N DOPE at 59.9:40:0.1 mol% respectively in a final volume of 200 µL with chloroform and 0.5 g/L lipid final concentration in a glass vial.", "[Protocol] Dry the lipid mixture in the glass vials for 120 min in a vacuum chamber forming the dried lipid films on the bottom of the gla... |
22,160 | RNA isolation for tissue | null | dx.doi.org/10.17504/protocols.io.zvqf65w | null | Chin Yee Tan | TITLE: RNA isolation for tissue
AUTHORS: Chin Yee Tan
[STEPS]
?. Homogenization in TriZolAdd 1mlper and homogenize using handheld homogenizer.
[Trizol]
[tissue]
?. Incubate at RT for to allow nucleoprotein complexes to dissociate.
?. Spin down at max speed in a chilled centrifuge for .
?. Carefully remove the top aque... | ["Homogenization in TriZolAdd 1mlper and homogenize using handheld homogenizer.\n[Trizol]\n[tissue]", "Incubate at RT for to allow nucleoprotein complexes to dissociate.", "Spin down at max speed in a chilled centrifuge for .", "Carefully remove the top aqueous phase and transfer to a new Eppendorf tube. The interphase... |
67,041 | Bjerrum Schafer-Nielsen buffer, modified by DING LAB, v1.0 | 4 | dx.doi.org/10.17504/protocols.io.3byl4bnzzvo5/v1 | https://www.protocols.io/view/bjerrum-schafer-nielsen-buffer-modified-by-ding-la-cdp9s5r6 | Pingtao Ding | TITLE: Bjerrum Schafer-Nielsen buffer, modified by DING LAB, v1.0
AUTHORS: Pingtao Ding
[DESCRIPTION]
This is a modified transfer buffer recipe for a semi-dry Western blot.
[STEPS]
SECTION: proportion guide
1. 48 millimolar (mM)
39 millimolar (mM)
15 % volume
pH 9.2
This recipe is modified from the original T... | ["[proportion guide] 48 millimolar (mM) \n39 millimolar (mM) \n15 % volume \npH 9.2\n\nThis recipe is modified from the original Towbin (1979) buffer, with increased Tris base but reduced glycine.\nThis recipe is suitable for semi-dry transfer, and ideal for SDS-PAGE and 2-D PAGE.\n\nReferences:\n\nGarfin DE and Ber... |
97,034 | Immunofluorescence for confocal imaging after slice recording | 4 | dx.doi.org/10.17504/protocols.io.6qpvr8xmolmk/v1 | https://www.protocols.io/view/immunofluorescence-for-confocal-imaging-after-slic-dazi2f4e | Cecilia Tubert, DeNard V Simmons | TITLE: Immunofluorescence for confocal imaging after slice recording
AUTHORS: Cecilia Tubert, DeNard V Simmons
[DESCRIPTION]
This protocol describes the steps for immunostaining and confocal imaging of ex vivo slices following an electrophysiological experiment.
[STEPS]
SECTION: Immunofluorescence - Before the proc... | ["[Immunofluorescence - Before the procedure:] Prepare PBS", "[Immunofluorescence - Before the procedure:] If needed, prepare aliquots of NGS. Store at -20C and thaw immediately before use.", "[Immunofluorescence - Before the procedure:] If needed, reconstitute/aliquot antibodies and store them according to manufacture... |
47,955 | Sample preparation protocol for total proteomic analysis of mouse tissues including brain | 4 | dx.doi.org/10.17504/protocols.io.bs3tngnn | https://www.protocols.io/view/sample-preparation-protocol-for-total-proteomic-an-bs3tngnn | Raja S. Nirujogi, Houjiang Zhou, Dario R Alessi | TITLE: Sample preparation protocol for total proteomic analysis of mouse tissues including brain
AUTHORS: Raja S. Nirujogi, Houjiang Zhou, Dario R Alessi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Mass spectrometry-based proteomics has emerged as fundamental technique to study functional chan... | ["[Sample preparation and S-Trap Assisted Digestion]\nSnap freeze mouse tissue immediately after isolation in liquid nitrogen and store at .\n-80 °C", "[Sample preparation and S-Trap Assisted Digestion]\nPulverize frozen tissue in liquid nitrogen to a fine powder and snap freeze immediately in 2 ml tubes. This is done ... |
99,287 | WATER PRODUCTION FOR AWARE (Mesophilic Bacteria in PCA (Plate Count Agar)) | 0 | dx.doi.org/10.17504/protocols.io.4r3l22xxxl1y/v3 | https://www.protocols.io/view/water-production-for-aware-mesophilic-bacteria-in-dc7x2zpn | Celia Manaia | TITLE: WATER PRODUCTION FOR AWARE (Mesophilic Bacteria in PCA (Plate Count Agar))
AUTHORS: Celia Manaia
[DESCRIPTION]
The protocol summarises the procedures used for analytical control. The protocol describes the
Standard Operating Procedure (SOP) for the optimization of advanced tertiary treatment of water, based on ... | ["[Methods: The section below summarises the procedures used for analytical control – detailed protocols are annexed to this protocol.] Mesophilic Bacteria in PCA (Plate Count Agar):", "[Methods: The section below summarises the procedures used for analytical control – detailed protocols are annexed to this protocol.] ... |
63,165 | PDI Project Workflow 2 | 1 | null | https://www.protocols.click/view/pdi-project-workflow-2-b9w5r7g6 | timothy.propst, tim.propst | TITLE: PDI Project Workflow 2
AUTHORS: timothy.propst, tim.propst
[DESCRIPTION]
This the new (Summer 2022) PDI workflow. Note that “project” and “sub-project” will now be referred to as “job” and “task,” respectively. Also, in time there will be a new position created, the PDI Operations Manager (OM). Until that t... | ["[Phase 1: Job conceptualization.] Customer reaches out to the PDI team.", "[Phase 1: Job conceptualization.] All customer requests are forwarded to the Director of Operations (DO). This includes expansions, extensions, and revisions from previous PDI jobs as well as new jobs.", "[Phase 1: Job conceptualization.] DO a... |
77,626 | Fluid Percussion Model in rats - Lyeth Lab | 4 | dx.doi.org/10.17504/protocols.io.rm7vzb2r5vx1/v1 | https://www.protocols.io/view/fluid-percussion-model-in-rats-lyeth-lab-cp22vqge | Bruce G. Lyeth Ph. D. | TITLE: Fluid Percussion Model in rats - Lyeth Lab
AUTHORS: Bruce G. Lyeth Ph. D.
[DESCRIPTION]
This is a protocol to describe the materials and methods utilized to perform preclinical traumatic brain injury (TBI) using the fluid percussion model in rats.
The posting of this protocol is part of the mission of the PRE... | ["Check that the fluid percussion device has been cleaned and calibrated according to the maintenance schedule (see Note 1).", "Examine the fluid percussion device for proper alignment of pendulum striker with the cylinder's piston.", "Perform multiple pendulum drops with outlet closed to detect the presence of any air... |
94,937 | Analysis of sugars, small organic acids, and alcohols by HPLC-RID | 6 | dx.doi.org/10.17504/protocols.io.5qpvob7y9l4o/v2 | https://www.protocols.io/view/analysis-of-sugars-small-organic-acids-and-alcohol-c8xzzxp6 | Hannah M. Alt, Alexander F. Benson, Stefan J. Haugen, Morgan A. Ingraham, William E. Michener, Sean P. Woodworth, Kelsey J. Ramirez, Gregg T. Beckham | TITLE: Analysis of sugars, small organic acids, and alcohols by HPLC-RID
AUTHORS: Hannah M. Alt, Alexander F. Benson, Stefan J. Haugen, Morgan A. Ingraham, William E. Michener, Sean P. Woodworth, Kelsey J. Ramirez, Gregg T. Beckham
[DESCRIPTION]
An analytical method was developed using high performance liquid chromato... | ["[Preparation of standards] Standards\n\nAllow standard level ampules (listed in 'Materials' section) to come to room temperature, vortex, and transfer contents of ampules into 2 mL amber HPLC vials.\nTo create lower concentration calibration levels than provided in the kit, dilute the lowest concentration ampule to y... |
20,777 | UC Davis - Endoplasmic reticulum stress | null | dx.doi.org/10.17504/protocols.io.yihfub6 | null | Fawaz G. Haj | TITLE: UC Davis - Endoplasmic reticulum stress
AUTHORS: Fawaz G. Haj
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">This test is designated to determine if rodents exhibit signs of endoplasmic reticulum stress, throu... | ["Unless otherwise requested by the PI or stated in the protocol, mice will be euthanized using cervical dislocation.", "Collect maximum blood from portal vein and isolate plasma according to standard protocols or as desired by the P.I.", "Quickly collect tissues designated by the P.I. Each tissue should be divided int... |
91,814 | Sinai SCENT TMC - 10X Xenium | 4 | dx.doi.org/10.17504/protocols.io.e6nvwdqe2lmk/v1 | https://www.protocols.io/view/sinai-scent-tmc-10x-xenium-c5wey7be | Sojin Kim, Ksenija Sabic | TITLE: Sinai SCENT TMC - 10X Xenium
AUTHORS: Sojin Kim, Ksenija Sabic
[DESCRIPTION]
Imagine obtaining histological insights into disease biology and gaining a molecular perspective on the subcellular spatial gene expression of 100s to 1,000s of RNA targets in the same tissue section?
With high-plex Xenium In Situ, y... | ["[Overview and Intro] Xenium In Situ measures gene expression in tissue sections derived from either formalin fixed and paraffin embedded (FFPE) or fresh frozen (FF) tissue samples placed on Xenium Slides. This Protocol Planner provides an overview of the workflow along with the Xenium Analyzer overview. To enable eff... |
80,145 | Human neuroblastoma cell line SH-SY5Y culturing | 1 | dx.doi.org/10.17504/protocols.io.ewov1ow42lr2/v1 | https://www.protocols.io/view/human-neuroblastoma-cell-line-sh-sy5y-culturing-cshrwb56 | Qing Wang | TITLE: Human neuroblastoma cell line SH-SY5Y culturing
AUTHORS: Qing Wang
[DESCRIPTION]
This is the brief protocol for seeding and culturing human neuroblastoma SH-SY5Y cells.
[STEPS]
1. 1. SH-SY5Y cells (ATCC, Manassas, VA, USA, Cat# CRL-2266, RRID:CVCL_0019) were seeded at 70-80% density.
2. 2. Change medium to DME... | ["1. SH-SY5Y cells (ATCC, Manassas, VA, USA, Cat# CRL-2266, RRID:CVCL_0019) were seeded at 70-80% density.", "2. Change medium to DMEM/F12 supplemented with 15% FBS, 1% penicillin-streptomycin and 10μM retinoic acid (11320-033, Gibco) for differentiation for four days"] |
96,519 | Macroalgae Analysis | 0 | dx.doi.org/10.17504/protocols.io.4r3l22xypl1y/v1 | https://www.protocols.io/view/macroalgae-analysis-dahf2b3n | Nohea Rodriguez, Kai Bloom, Mistie Tran | TITLE: Macroalgae Analysis
AUTHORS: Nohea Rodriguez, Kai Bloom, Mistie Tran
[DESCRIPTION]
Determine the abundance and biomass of the invasive macroalgae species, Turbinaria and Sargassum. Then, identify marine species located on random samples of each species. Turbinaria decreases fish abundance and biodiversity, comp... | ["[Algae Transect Survey] Split into five groups of four people.", "[Algae Transect Survey] Swim to the group's transect location, approximately 5 meters apart.", "[Algae Transect Survey] Begin 30 meter transect along reef crest, parallel to the shore.", "Swim along transect tape and record the presence of rock, coral,... |
80,853 | Methodology for Frontier Model of the Environmental Inefficiency effects on Livestock Bioeconomy | 1 | dx.doi.org/10.17504/protocols.io.8epv5j824l1b/v1 | https://www.protocols.io/view/methodology-for-frontier-model-of-the-environmenta-cs7vwhn6 | C A Zuniga-Gonzalez | TITLE: Methodology for Frontier Model of the Environmental Inefficiency effects on Livestock Bioeconomy
AUTHORS: C A Zuniga-Gonzalez
[DESCRIPTION]
This protocol considers the methodology used for Stochastic Frontier Analysis on the Livestocks Bioeconomic model. The applied methodology measured the eco-efficiency of Me... | ["[Stochatics Frontier Analysis] Collecting Data. The study was carried out in 102 cattle farms for milk production in six municipalities of the state of Tlaxcala Mexico, in 2020. The production units were randomly selected, and dividing them among the four regions of importance in dairy production in the state of Tlax... |
42,332 | 15-minute DNA extraction from beetle legs for PCR barcoding | 4 | dx.doi.org/10.17504/protocols.io.bmj4k4qw | https://www.protocols.io/view/15-minute-dna-extraction-from-beetle-legs-for-pcr-bmj4k4qw | Chase Mayers | TITLE: 15-minute DNA extraction from beetle legs for PCR barcoding
AUTHORS: Chase Mayers
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This method allows for quick extraction of DNA from beetle specimens for routine PCR amplification of barcoding genes such as COI (cytochrome oxidase subunit 1) f... | ["Use a pipette to transfer of PrepMan Ultra Sample Preparation Reagent into a small microcentrifuge tube. Label the tube appropriately.If possible, this should be done in a sterile environment and away from PCR equiptment to avoid contaminating the PrepMan reagent with unwanted DNA.\n50 µl", "Using sterile forceps, r... |
74,354 | Transglutaminase-induced corneal collagen cross-linking on the central cornea thickness and intraocular pressure in vivo | 1 | dx.doi.org/10.17504/protocols.io.261ge3eool47/v1 | https://www.protocols.io/view/transglutaminase-induced-corneal-collagen-cross-li-ckusuwwe | Puspita Hapsari Sitorasmi, Yuniar Sarah Ningtiyas, Indri Wahyuni, Yulia Primitasari | TITLE: Transglutaminase-induced corneal collagen cross-linking on the central cornea thickness and intraocular pressure in vivo
AUTHORS: Puspita Hapsari Sitorasmi, Yuniar Sarah Ningtiyas, Indri Wahyuni, Yulia Primitasari
[DESCRIPTION]
Background: Corneal collagen crosslinking (CXL) is a procedure for making bonds that... | ["[Subject and measures] Ethical approval was obtained from the Animal Care and Use Committee (ACUC) Faculty of Veterinary Medicine, Universitas Airlangga (No. 2.KEH.071.07.2022). All procedures were performed to ethical standards.", "[Cross-linking procedure] Anesthesia was induced via intramuscular injection of 0.1 m... |
19,765 | (-)-patchoulol GC sample preparation | null | dx.doi.org/10.17504/protocols.io.xivfke6 | null | Dennis Dienst, Oliver Mantovani, Pia Lindberg | TITLE: (-)-patchoulol GC sample preparation
AUTHORS: Dennis Dienst, Oliver Mantovani, Pia Lindberg
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This is a quick guide for the preparation of (-)--patchoulol samples and external standards in dodecane for GC analysis. This protocol has been est... | ["[Preparation of BCP (β-caryophyllene) internal standard (IS) stocks]\nABCD1 BCP Standard 2Stock A1: 10 Dilution\nfrom Original BCP Stock\n(⇒ 89 mg *mL-1)\n 3 ⇓ 4Stock B ... |
65,596 | Functionality test (OpenVent polymerase, PCR Master Mixes) | 4 | null | https://www.protocols.io/view/functionality-test-openvent-polymerase-pcr-master-cca4ssgw | Nadine Mowoh, Stephane Fadanka | TITLE: Functionality test (OpenVent polymerase, PCR Master Mixes)
AUTHORS: Nadine Mowoh, Stephane Fadanka
[DESCRIPTION]
After production, we typically subject our products to a batch of quality control assays to ascertain their functionality, efficacy and ability to meet their intended purpose.
Strict quality cont... | ["[Functionality test] DNA polymerase Enzyme and PCR Master mix\n\n \n\nPipetting:\n\nThaw all reagents on ice in a bowl\nLabel reaction tubes (PCR tubes) according to the number of samples, and including controls in each run (negative and positive controls) as needed.\n\nPolymerase enzyme type:\n\nIf using a 10x cellu... |
86,551 | Lentivirus Production, Lentivirus Transduction, and Sorting Protocol | 1 | dx.doi.org/10.17504/protocols.io.14egn3336l5d/v1 | https://www.protocols.io/view/lentivirus-production-lentivirus-transduction-and-cyrxxv7n | Ning Xia | TITLE: Lentivirus Production, Lentivirus Transduction, and Sorting Protocol
AUTHORS: Ning Xia
[DESCRIPTION]
Lentivirus Production, Lentivirus Transduction, and Sorting Protocol for making the transduced iPSCs and SH-SY5Ys
[STEPS]
SECTION: Transfection
1. Seed HEK293FT cells into 6-well dishes, 1.1e6, 2 ml/well.
: 80%... | ["[Transfection] Seed HEK293FT cells into 6-well dishes, 1.1e6, 2 ml/well.\n: 80% confluence after 20 h.", "[Transfection] After 20 h, transfect HEK293FT cells using Lipo3000.\n\na. Tube A: Dilute 7 ul Lipo3000 in 250 ul OPTI-MEM/well, vortex 3s.\n\nb. Tube B: Dilute below in 250 ul OPTI-MEM/well.\n1 ug Packaging... |
75,902 | Carotenoid Pigment Analysis in Leaf Extracts by HPLC - UNFINISHED | 4 | null | https://www.protocols.io/view/carotenoid-pigment-analysis-in-leaf-extracts-by-hp-cnc6vaze | Laurie Leonelli, Lynn Doran | TITLE: Carotenoid Pigment Analysis in Leaf Extracts by HPLC - UNFINISHED
AUTHORS: Laurie Leonelli, Lynn Doran
[DESCRIPTION]
Pigment extraction and carotenoid analysis by high performance liquid chromatography (HPLC) from leaf tissue.
Additional References:
García‐Plazaola, J. I., & Becerril, J. M. (1999). A rapid ... | ["[Prepare HPLC] Contact IGB GEGC Lab Manager to ensure the instrument is up to date on maintenance status, out of storage status, and in analysis mode."] |
34,840 | Staining of fish Red Blood Cells | null | dx.doi.org/10.17504/protocols.io.bd9yi97w | null | Robson Andrade Rodrigues, Mayara Schueroff Siqueira, Brenda Oliveira Martins, Carlos Eurico Fernandes, Lilian Franco-Belussi, Diogo Provete | TITLE: Staining of fish Red Blood Cells
AUTHORS: Robson Andrade Rodrigues, Mayara Schueroff Siqueira, Brenda Oliveira Martins, Carlos Eurico Fernandes, Lilian Franco-Belussi, Diogo Provete
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This is a technique to extract blood and prepare blood fi... | ["[Preparing blood film]\nLet the slide dry", "[Staining]\nWait for", "[Staining]\nTake about of the MGGW stain solution and drop it on the slide so all the slide is covered.\n300 µl\nThe stock solution of the May-Grünwald-Giemsa-Wright (MGGW) stain is made with of eosin methyl blue of May-Grünwald, of eosin methy... |
36,836 | 14CO2-based assay for measuring Rubisco activity & activation state | 1 | dx.doi.org/10.17504/protocols.io.bf8cjrsw | https://www.protocols.io/view/14co2-based-assay-for-measuring-rubisco-activity-a-bf8cjrsw | Cristina Rodrigues Gabriel Sales, Anabela Silva, Elizabete Carmo-Silva | TITLE: 14CO2-based assay for measuring Rubisco activity & activation state
AUTHORS: Cristina Rodrigues Gabriel Sales, Anabela Silva, Elizabete Carmo-Silva
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The Rubisco activity </span><span style = "vertical-align:super;">14</span><span>CO</span>... | ["[REAGENTS & SOLUTIONS]\nREAGENTS & SOLUTIONS TO PREPARE BEFOREHAND", "[REAGENTS & SOLUTIONS]\nBasic extraction buffer (1x) Bicine-NaOH MgCl2.6H2O EDTA Benzamidine ε-Aminocaproic acidDissolve in ultrapure H2O; adjust pH to 8.2 with NaOH; degas the solution bubbling with nitrogen (5 min/100 mL), then add: 2-Merca... |
34,383 | A do-it-yourself low-cost agarose gel documentation and DNA quantification system | 1 | dx.doi.org/10.17504/protocols.io.bdtpi6mn | https://www.protocols.io/view/a-do-it-yourself-low-cost-agarose-gel-documentatio-bdtpi6mn | Rachel Howard-Till, Claudia Osorio, Marcos Olivos, Bradley Till | TITLE: A do-it-yourself low-cost agarose gel documentation and DNA quantification system
AUTHORS: Rachel Howard-Till, Claudia Osorio, Marcos Olivos, Bradley Till
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes how to build your own agarose gel documentation system to create ... | ["[DNA electrophoresis]\nLoad 5 μl of your genomic DNA sample on a 1% agarose gel. Also run 5 μl aliquots of lambda DNA standards of 2, 4, 8, 16, and 32 μg/ml (ng/μl). This will allow you to create a standard curve to compare your sample to. Run gel approximately 20 minutes at 100 V. The DNA should be migrated into the... |
null | null | null | dx.doi.org/10.17504/protocols.io.mcqc2vw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The third report of the National Cholesterol Education Program guidelines recommend calculating the 10-year morbidity of atherosclerotic cardiovascular disease using risk calculators when treating high blood cholesterol in adults. We analyzed the changes in cardiovascular ris... | [] |
97,494 | Rating scale for parkinsonian motor signs in macaques and other non‐human primates | 0 | dx.doi.org/10.17504/protocols.io.x54v928ppl3e/v1 | https://www.protocols.io/view/rating-scale-for-parkinsonian-motor-signs-in-macaq-dbfw2jpe | Adriana Galvan, Thomas Wichmann | TITLE: Rating scale for parkinsonian motor signs in macaques and other non‐human primates
AUTHORS: Adriana Galvan, Thomas Wichmann
[DESCRIPTION]
This protocol details rating scale for parkinsonian motor signs in macaques and other non‐human primates.
[GUIDELINES]
Appendix 1: Description of individual score criteria
... | ["[Description of rating scale] Parkinsonian motor signs in macaques closely resemble findings in humans. To quantify the degree of parkinsonism in our animals, we use the rating scale reproduced on the next two pages. There are a variety of such scales available, each differing slightly by areas of emphasis.1‐3", "[D... |
null | null | null | dx.doi.org/10.17504/protocols.io.krscv6e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>RME is one of the liquid-liquid extraction method using a surfactant and organic solvent to extract cold-adapted lipase AMS8. </p>
[STEPS] | [] |
89,754 | Using Amira to manually segment organelles in vEM for machine learning | 1 | dx.doi.org/10.17504/protocols.io.bp2l61rb5vqe/v3 | https://www.protocols.io/view/using-amira-to-manually-segment-organelles-in-vem-c3v2yn8e | Grace Park, Nora Forknall, Larissa Heinrich, Henrique Ludwig, Ruchi Parekh, Alyson Petruncio, Jacquelyn Price, Diana Ramirez, rymert, Stephan Saalfeld, Alia Suleiman, Rebecca Vorimo, Aubrey Weigel | TITLE: Using Amira to manually segment organelles in vEM for machine learning
AUTHORS: Grace Park, Nora Forknall, Larissa Heinrich, Henrique Ludwig, Ruchi Parekh, Alyson Petruncio, Jacquelyn Price, Diana Ramirez, rymert, Stephan Saalfeld, Alia Suleiman, Rebecca Vorimo, Aubrey Weigel
[DESCRIPTION]
In this protocol we d... | ["[Protocol Introduction] The purpose of this protocol is to document the unique annotation method and style used by CellMap Project Team to annotate organelles using Amira-Avizo (Thermo Fisher Scientific). We defined 37 organelle subclasses to annotate within cell and tissue data and classified them. The definitions u... |
42,211 | Immunohistochemical staining of heparan sulfate (HS) and collagen type XVIII (col18) core proteins in islet beta cells of formalin-fixed human pancreas and isolated human islets | 1 | dx.doi.org/10.17504/protocols.io.bmgbk3sn | https://www.protocols.io/view/immunohistochemical-staining-of-heparan-sulfate-hs-bmgbk3sn | Lora Starrs, Debra Brown, Sarah Popp, Andrew Ziolkowski, Charmaine Simeonovic | TITLE: Immunohistochemical staining of heparan sulfate (HS) and collagen type XVIII (col18) core proteins in islet beta cells of formalin-fixed human pancreas and isolated human islets
AUTHORS: Lora Starrs, Debra Brown, Sarah Popp, Andrew Ziolkowski, Charmaine Simeonovic
[DESCRIPTION]
<div class = "text-blocks"><div c... | ["See Guidelines, \"Before starting\".", "Deparaffinize slides in each xylene for 1 min. rehydrate slides in graded alcohols beginning in absolute ethanol (10 dips)/ container of absolute ethanol), followed by 90% ethanol (10 dips) and 70% ethanol (10 dips). Wash well in running tap water for 5 min.", "Blot around sect... |
20,383 | Tomato Transformation | null | dx.doi.org/10.17504/protocols.io.x57fq9n | null | Alex Rajewski, Joyce van Eck | TITLE: Tomato Transformation
AUTHORS: Alex Rajewski, Joyce van Eck
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is slightly modified from the citatation below. All credit for this protocol should be directed toward those authors.</div><div class = "text-block">This protocol details ... | ["[Sterilize and Sow Seeds]\nSurface sterilize seeds with chlorine gas according to the following protocol\n{\"blocks\":[{\"key\":\"el7tu\",\"text\":\"This protocol details how to surface sterilize plant seeds for tissue culture regeneration/transformation or for other techniques requiring sterile seeds.\",\"type\":\"u... |
92,921 | Heparin and Tocilizumab in Patients with Severe COVID-19: The HEPMAB Randomized Clinical Trial | 4 | dx.doi.org/10.17504/protocols.io.ewov1qk9kgr2/v1 | https://www.protocols.io/view/heparin-and-tocilizumab-in-patients-with-severe-co-c6yzzfx6 | Lucas Trindade Cantú Ribeiro, Giovanni Landoni, vinicius.quintao, Roberto Kalil Filho, Ludhmila Abrahão Hajjar | TITLE: Heparin and Tocilizumab in Patients with Severe COVID-19: The HEPMAB Randomized Clinical Trial
AUTHORS: Lucas Trindade Cantú Ribeiro, Giovanni Landoni, vinicius.quintao, Roberto Kalil Filho, Ludhmila Abrahão Hajjar
[DESCRIPTION]
Clinical presentation of severe Coronavirus disease 2019 (COVID-19) is associated t... | ["[HEPMAB Study Protocol] INTRODUCTION \n \nCoronavirus 2019 related Severe Acute Respiratory Syndrome (COVID-19) quickly evolved from an epidemic outbreak in Wuhan, China, to a pandemic affecting more than 2 million individuals worldwide. Although COVID-19 infection primarily manifests as a respiratory tract infection... |
86,057 | Fixation of Breast Tissue from Komen Tissue Bank into FFPE or PFPE blocks | 4 | dx.doi.org/10.17504/protocols.io.81wgbxynolpk/v1 | https://www.protocols.io/view/fixation-of-breast-tissue-from-komen-tissue-bank-i-cyahxsb6 | kschneider | TITLE: Fixation of Breast Tissue from Komen Tissue Bank into FFPE or PFPE blocks
AUTHORS: kschneider
[DESCRIPTION]
FFPE blocks were created as in protocol 005v8.0 and PFPE blocks were created as in protocol 005v5.0 from the Komen Tissue Bank.
[STEPS] | [] |
50,936 | Electrophysiological characterizations of pancreatic islet cells | 4 | dx.doi.org/10.17504/protocols.io.bvyyn7xw | https://www.protocols.io/view/electrophysiological-characterizations-of-pancreat-bvyyn7xw | Toshinori Hoshi Laboratory | TITLE: Electrophysiological characterizations of pancreatic islet cells
AUTHORS: Toshinori Hoshi Laboratory
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Hormone release from pancreatic cells, for example glucagon from α-cells and insulin from β-cells, is controll... | ["[Procedure]\nSonicate 8 μM escin diluted with the internal solution in the bath sonicator for > 10 min 4 μM escin is sometimes sufficient", "[Procedure]\nStart the perfusion of the recording chamber so that the chamber solution is at ; the perfusion is continuous\n35 °C", "[Procedure]\nTake a culture ... |
93,382 | Materials and assembly for a portable soil greenhouse gas flux collection case | 1 | dx.doi.org/10.17504/protocols.io.dm6gp3mkpvzp/v2 | https://www.protocols.io/view/materials-and-assembly-for-a-portable-soil-greenho-c7fezjje | Rachel E. Clarkson, David Walla, Robert Harrison, Myron Coleman, Marty Schmer, VIRGINIA.JIN | TITLE: Materials and assembly for a portable soil greenhouse gas flux collection case
AUTHORS: Rachel E. Clarkson, David Walla, Robert Harrison, Myron Coleman, Marty Schmer, VIRGINIA.JIN
[DESCRIPTION]
The collection of soil nitrous oxide, carbon dioxide, and methane greenhouse gas (GHG) flux measurements utilizing sta... | ["[Plumbing the Flux Case] Flip orientation of solenoid valves", "[Plumbing the Flux Case] Insert and tighten the plastic plug in all five of the solenoid valves", "Cut the Teflon tape lengthwise to create two thin strips.", "[Plumbing the Flux Case] Remove the top screw from the solenoid valve using a medium Philips s... |
36,419 | Purification of RNA from a DNA/RNA Extract | null | dx.doi.org/10.17504/protocols.io.bftbjnin | https://www.protocols.io/view/purification-of-rna-from-a-dna-rna-extract-bftbjnin | Roey Angel, Eva Petrova | TITLE: Purification of RNA from a DNA/RNA Extract
AUTHORS: Roey Angel, Eva Petrova
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The following protocol is intended as a downstream application for our </span><a href="https://protocols.io/view/total-nucleic-acids-extraction-from-soil-yw9fxh6" ... | ["[DNA digestion]\nPrepare the following mixture in a 1.5 ml tube: to of TNA extract ( to of DNA). per up to Complete to with RNase-free water\n10 µl\n42 µl\n1 µg\n3 µg\n[TURBO DNase buffer 10x]\n[RNaseOUT]\n[0,1M DTT]\n[Turbo DNase]\n[DNA]\n50 µl", "[DNA digestion]\nIncubate at for .\n37 °C", "[RNA purification... |
21,975 | Selection of a “housekeeping” miRNA to normalize qRT-PCR data | null | dx.doi.org/10.17504/protocols.io.zpxf5pn | null | Barbara Rizzacasa, Elena Morini, Ruggiero Mango, Chiara Vancheri, Simone Budassi, Gianluca Massaro, Sara Maletta, Massimiliano Macrini, Silvio D’Annibale, Francesco Romeo, Giuseppe Novelli, Francesca Amati | TITLE: Selection of a “housekeeping” miRNA to normalize qRT-PCR data
AUTHORS: Barbara Rizzacasa, Elena Morini, Ruggiero Mango, Chiara Vancheri, Simone Budassi, Gianluca Massaro, Sara Maletta, Massimiliano Macrini, Silvio D’Annibale, Francesco Romeo, Giuseppe Novelli, Francesca Amati
[DESCRIPTION]
<div class = "text-bl... | ["Identifcation of a \"housekeeping\" microRNA among the 84 circulating of the Human Serum & Plasma miScript miRNA PCR Array (MIHS-106ZA, QIAGEN):", "[Selection criteria:]\n•\ta Ct range", "[Selection criteria:]\n•\ta 0.5FC1.5 (GeneGlobe Data Analysis Center)", "[Selection criteria:]\n•\tevaluation of expression leve... |
null | null | null | dx.doi.org/10.17504/protocols.io.d7q9mv | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<span style="color: #333333; font-family: helvetica, sans-serif; font-size: 14px; line-height: 21px;"><strong>Motivation: </strong>An important step of "metagenomics" analysis is the assembly of multiple genomes from mixed sequence reads of multiple species in a microbial commun... | [] |
84,455 | Isolation of EVs by ultracentrifugation | 4 | dx.doi.org/10.17504/protocols.io.q26g7pb6qgwz/v1 | https://www.protocols.click/view/isolation-of-evs-by-ultracentrifugation-cwqfxdtn | Chloe.Rodgers | TITLE: Isolation of EVs by ultracentrifugation
AUTHORS: Chloe.Rodgers
[DESCRIPTION]
How to isolate EVs from culture media using differential centrifugation.
[STEPS]
1. Preparation of cells
Notes: Cell cultures must be grown to approximately 90% confluency and EVs need to be isolated from a minimum of 200mL media to ... | ["Preparation of cells\n\nNotes: Cell cultures must be grown to approximately 90% confluency and EVs need to be isolated from a minimum of 200mL media to get a high enough\nEV yield. As FBS contains natural EVs, EV depleted FBS should be used in the media incubated with cells for 48 hrs prior to isolation. This media i... |
null | null | null | dx.doi.org/10.17504/protocols.io.ksgcwbw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><em>Amrasca biguttula biguttula </em>(Ishida) commonly known as cotton leafhopper is a serious pest of cotton and okra. Nutritional requirements or growth physiology for this insect has not been much known till date. We developed artificial membrane feeding method for leafhop... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.kjfcujn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>fafs</p>
[STEPS] | [] |
99,988 | Liquid Growth Medium - Yeast | 0 | dx.doi.org/10.17504/protocols.io.5qpvokr2bl4o/v1 | https://www.protocols.io/view/liquid-growth-medium-yeast-ddvu266w | Mathias Hammer, Ammeret Rossouw, Azra Lari, Ben Montpetit, David Grunwald | TITLE: Liquid Growth Medium - Yeast
AUTHORS: Mathias Hammer, Ammeret Rossouw, Azra Lari, Ben Montpetit, David Grunwald
[DESCRIPTION]
This protocol describes the steps to prepare liquid culture medium for Saccharomyces cerevisiae.
[BEFORE_START]
Have the following solutions premixed:
Glucose 20% 500 ml solution:
Con... | ["[Preparation of 500ml liquid yeast growth medium] Compound medium for autoclave", "[Preparation of 500ml liquid yeast growth medium] Fill a 500 ml flask with 450 mLddH2O. \nAdd a magnetic stirring bar and place the flask on a stirring hot plate.", "[Preparation of 500ml liquid yeast growth medium] Add 3.36 g Yeast Ni... |
51,744 | High-molecular weight DNA extraction from challenging fungi using CTAB for lysis and precipitation | 1 | dx.doi.org/10.17504/protocols.io.bwr8pd9w | https://www.protocols.io/view/high-molecular-weight-dna-extraction-from-challeng-bwr8pd9w | Ashley Jones, Benjamin Schwessinger | TITLE: High-molecular weight DNA extraction from challenging fungi using CTAB for lysis and precipitation
AUTHORS: Ashley Jones, Benjamin Schwessinger
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left"><span>Extracting pure high-molecular weight DNA from... | ["[PREPARATION]\nGrow fungus and collect ~500 mg of sample (spores for rust fungi). Keep frozen at -80°C or liquid nitrogen until ready.\nIdeal for fungi that have a small genome, approximately 50 Mb.Take into consideration cell density and genome size; low cell density and/or smaller genomes may need to be prepped twi... |
64,266 | Radiographic evaluation | 1 | dx.doi.org/10.17504/protocols.io.36wgq7qekvk5/v1 | https://www.protocols.io/view/radiographic-evaluation-cazisf4e | geoffrey.pages | TITLE: Radiographic evaluation
AUTHORS: geoffrey.pages
[DESCRIPTION]
This radiographic evaluation protocol was used perioperatively to manage dogs treated by TPLO for cranial cruciate ligament disease.
[BEFORE_START]
Two experienced observers (1 Dipl. ECVS and 1 ECVS resident, with more than 3 years in TPA measurem... | ["[Tibial Plateau Angle measurement] Tibial Plateau Angle was measured following previously described landmarks (Dismukes 2008).\n\nMechanical axis:\nThe landmarks used to determine the mechanical axis were the midpoint between the apices of the 2 tibial intercondylar eminences and the center of the circle created by t... |
102,703 | CPTAC FFPE Sample Processing | 0 | dx.doi.org/10.17504/protocols.io.14egn6w66l5d/v1 | https://www.protocols.io/view/cptac-ffpe-sample-processing-dgip3udn | Jingxian Liu | TITLE: CPTAC FFPE Sample Processing
AUTHORS: Jingxian Liu
[DESCRIPTION]
This is a description of the steps that Clinical Proteomic Tumor Analysis Consortium (CPTAC) has developed to collect surgical resection biospecimens. There are multiple protocols with various preservation methods and targeted assays. Here only t... | ["[Sample Processing for CPTAC Renal Cell Carcinoma] The CPTAC Biospecimen Core Resource (BCR) at the Pathology and Biorepository Core of the Van Andel Research Institute in Grand Rapids, Michigan manufactured and distributed biospecimen kits to the Tissue Source Sites (TSS) located in the US, Europe, and Asia. Each ki... |
69,836 | Simple Panzanella Salad | 1 | dx.doi.org/10.17504/protocols.io.yxmvm2726g3p/v1 | https://www.protocols.io/view/simple-panzanella-salad-cgfkttkw | Lenny Teytelman | TITLE: Simple Panzanella Salad
AUTHORS: Lenny Teytelman
[DESCRIPTION]
(This recipe is based on the "Panzanella With Mozzarella and Herbs" by Melissa Clark in the New York Times.)
This Tuscan salad is like an Italian version of Gazpacho. Perfect when tomatoes are in season and you have some stale white bread.
This v... | ["Cut up the bread in 1-inch cubes and toast at 425 degrees for ~10 minutes. Let them cool.", "Place cut up tomatoes in a large salad bowl.", "Add cut/torn mozzarella, sliced red onion, minced garlic.", "Add:\n 2 tablespoon red wine vinegar\n oregano or thyme\n1/2 teaspoon of salt\n6 tablespoons of extra virgin olive o... |
29,458 | In vitro testing of guide RNA efficiency for CRISPR-mediated genome editing | null | dx.doi.org/10.17504/protocols.io.8zshx6e | null | Srinidhi Holalu, Angela Fang, Benjamin Blackman | TITLE: In vitro testing of guide RNA efficiency for CRISPR-mediated genome editing
AUTHORS: Srinidhi Holalu, Angela Fang, Benjamin Blackman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>In CRISPR-mediated genome editing, guide RNAs (gRNAs) serve to target the Cas9 nuclease to an intended tar... | ["[Cloning a template fragment from genomic DNA]\nPerform DNA extraction using CTAB method or any other methods that you may use routinely for your plant species.", "[Cloning a template fragment from genomic DNA]\nDesign primers flanking your target PAM sites (NGG). PCR to amplify around 500-600 bp of genomic/gene frag... |
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