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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47,575 | Obese locomotion on a positive and negative slope at iso-intensity: outcomes related to energetics, mechanics, perceived exertion, and hemodynamics. A study protocol. | 1 | dx.doi.org/10.17504/protocols.io.bspxndpn | https://www.protocols.io/view/obese-locomotion-on-a-positive-and-negative-slope-bspxndpn | Henrique Bianchi Oliveira, Guilherme Droescher de Vargas, Rodrigo Gomes da Rosa, Eduardo Borges Flores, Claudia Gomes Bracht, Bruna Machado Barroso, Leandro Tolfo Franzoni, Ricardo Stein, Luiz Fernando Martins Kruel | TITLE: Obese locomotion on a positive and negative slope at iso-intensity: outcomes related to energetics, mechanics, perceived exertion, and hemodynamics. A study protocol.
AUTHORS: Henrique Bianchi Oliveira, Guilherme Droescher de Vargas, Rodrigo Gomes da Rosa, Eduardo Borges Flores, Claudia Gomes Bracht, Bruna Macha... | ["[Introduction]\nObesity is considered one of the most important public health problems, making both treatment and prevention a priority (Di Cesare et al., 2016; Menéndez et al., 2019). Over 1.9 billion adults are overweight, of these, 650 million are characterized as obese. A concerning factor regarding these numbers... |
57,034 | Staphilococcus Aureus Sampling | 4 | dx.doi.org/10.17504/protocols.io.b3xiqpke | https://www.protocols.io/view/staphilococcus-aureus-sampling-b3xiqpke | Pol Roca Cugat, Olga Sánchez | TITLE: Staphilococcus Aureus Sampling
AUTHORS: Pol Roca Cugat, Olga Sánchez
[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... | ["[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.", "[Preparation] Prepare the area where you are going to work. Disinfect the surfaces with the bleach solution.\nThe subjects should not be... |
null | null | null | dx.doi.org/10.17504/protocols.io.c8wzxd | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
For use in <a href="http://protocols.io/view/Wet-mount-Method-for-Enumeration-of-Aquatic-Viruse-c8pzvm" target="_blank">Wet-Mount Method for Enumeration of Aquatic Viruses</a>
[STEPS]
?. | [] |
87,485 | In vitro LRRK2 kinase activity assay using mass-spectrometry as readout | 4 | dx.doi.org/10.17504/protocols.io.6qpvr385ovmk/v2 | https://www.protocols.io/view/in-vitro-lrrk2-kinase-activity-assay-using-mass-sp-czn5x5g6 | Verena Dederer, Deep Chatterjee, Sebastian Mathea, Stefan Knapp | TITLE: In vitro LRRK2 kinase activity assay using mass-spectrometry as readout
AUTHORS: Verena Dederer, Deep Chatterjee, Sebastian Mathea, Stefan Knapp
[DESCRIPTION]
This protocol can be used in this form or with small adjustments regarding concentration and reaction time to determine in vitro substrate phosphorylatio... | ["Incubate reaction for 3 h at room temperature.\nNote: depeding on kinase this may be shorter or longer.", "[Step-by-Step Protocol] Prepare 50 µL reaction mix I: 50 nM purified LRRK2RCKW and 5 µM Rab8 substrate in buffer containing 20 mM Hepes pH 7.4, 150 mM NaCl, 5% glycerol, 0.5 mM TCEP, 20 µM GDP, 2.5 mM MgCl2.\nAl... |
105,136 | The "IHC and TMA staining, PDO cultivation and dose-resopnse assay" section of the manuscript entitled "The prognostic value of H3K27me3 implies potential therapeutic targets of EZH2 in sinonasal soft tissue sarcoma: evidence gained from an sin | 0 | null | https://www.protocols.io/view/the-34-ihc-and-tma-staining-pdo-cultivation-and-do-diwq4fdw | Chengle Zhou, Jingyi Yang | TITLE: The "IHC and TMA staining, PDO cultivation and dose-resopnse assay" section of the manuscript entitled "The prognostic value of H3K27me3 implies potential therapeutic targets of EZH2 in sinonasal soft tissue sarcoma: evidence gained from an sin
AUTHORS: Chengle Zhou, Jingyi Yang
[DESCRIPTION]
The ma... | ["[1. Construction of Tissue microarrays] Whole slides staining of 27 formalin-fixed, paraffin-embedded (FFPE) tumor samples was firstly conducted utilizing available surgical specimen obtained from the observational trial cohort for primitive discovery. For subsequent validation, remaining FFPE specimens of the previo... |
60,399 | Illumination Power, Stability, and Linearity Measurements for Confocal and Widefield Microscopes | 1 | dx.doi.org/10.17504/protocols.io.5jyl853ndl2w/v2 | https://www.protocols.io/view/illumination-power-stability-and-linearity-measure-b68prhvn | Nathalie Gaudreault, Rizwan Ali, Sergiy V Avilov, Steve Bagley, Rodrigo R Bammann, Fabio Barachati, Laszlo Barna, Valeria Berno, Cristina Bertocchi, Veronika Boczonadi, Ulrike Boehm, Manel Bosch, Craig Brideau, Mariana T Carvalho, Pina Colarusso, Richard Cole, Nasser Darwish-Miranda, Suat Dervish, Ralf Dietzel, Sam Duw... | TITLE: Illumination Power, Stability, and Linearity Measurements for Confocal and Widefield Microscopes
AUTHORS: Nathalie Gaudreault, Rizwan Ali, Sergiy V Avilov, Steve Bagley, Rodrigo R Bammann, Fabio Barachati, Laszlo Barna, Valeria Berno, Cristina Bertocchi, Veronika Boczonadi, Ulrike Boehm, Manel Bosch, Craig Bride... | ["[Illumination power measurement] Warm up the entire system, including the illumination source.", "[Illumination power measurement] Select a low NA, air objective, such as a 10x objective, for this measurement. Ensure it is clean and presents no signs of damage.", "[Illumination power measurement] Place the power met... |
null | null | null | dx.doi.org/10.17504/protocols.io.igacbse | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>To prepare the genomic DNA of microsporidia, 400 ll suspension of purified spores (1010 spores/ml) was mixed with 40 ll KOH (2 mol/l) in a 1.5 ml Eppendorf tube and incubated at 27C for 1 h, TEK buffer (1 mmol/l Tris–HCl, 10 mmol/l EDTA, 0.17 mol/l KCl, pH 8.0) was added and ... | [] |
80,663 | Cost of a Renewable Micro Grid in Moorea | 1 | dx.doi.org/10.17504/protocols.io.n2bvj84o5gk5/v1 | https://www.protocols.io/view/cost-of-a-renewable-micro-grid-in-moorea-cszxwf7n | clairewiegand | TITLE: Cost of a Renewable Micro Grid in Moorea
AUTHORS: clairewiegand
[DESCRIPTION]
Moorea is an island in French Polynesia that depends on imported fossil fuels to meet the community's energy demands, which leads to high costs and high carbon dioxide emissions. The implementation of a renewable energy microgrid may ... | ["[Cost of a Renewable Microgrid in Moorea, French Polynesia] Conduct a comprehensive scientific literature review on microgrids, renewable energy, and their use in island communities. 30240 min .Write high level notes as you read to provide a general overview of the energy landscape in Moorea.", "[Cost of a Renewable... |
35,627 | No Sew Face Mask in 10 Steps | null | dx.doi.org/10.17504/protocols.io.be2jjgcn | null | Julia Borden | TITLE: No Sew Face Mask in 10 Steps
AUTHORS: Julia Borden
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes how to make a face mask out of a t-shirt in 10 easy steps, no sewing required!</div></div>
[STEPS]
?. [Face Mask in 10 Steps]
Lay out a clean t-shirt with a circular col... | ["[Face Mask in 10 Steps]\nLay out a clean t-shirt with a circular collar.", "[Face Mask in 10 Steps]\nCut off the tag, if there is one.", "[Face Mask in 10 Steps]\nFlip over the shirt so the back is facing you. Measure ~6 inches from the center of the collar. This will cover from the top of your nose to your chin, so ... |
58,861 | Liver tissue staining with multiple lanthanides-tagged antibodies | 1 | dx.doi.org/10.17504/protocols.io.b5qmq5u6 | https://www.protocols.io/view/liver-tissue-staining-with-multiple-lanthanides-ta-b5qmq5u6 | Hua Tian | TITLE: Liver tissue staining with multiple lanthanides-tagged antibodies
AUTHORS: Hua Tian
[DESCRIPTION]
Imaging mass spectrometry (IMS) is able to image the multiple lanthanides-tagged antibodies (up to 40) simultaneously at a subcellular resolution on a single tissue section. This protocol is developed for optimiz... | ["Cut the fresh frozen sections at 5µm using a cyromicrotome and mount them on Au-coated silicon slides", "Place the slides at -20 ◦C for 1h and then at 4 ◦C for 30 min for temperature equilibrium", "Fix the tissue slides in 1% PFA for 5 min at 4 ◦C, then in prechilled methanol for 5 min at -20 ◦C", "Wash the slides tw... |
19,647 | Species-specific quantitative PCR (qPCR) protocol developed to identify Haplosporidium pinnae | null | dx.doi.org/10.17504/protocols.io.xe7fjhn | null | Monserrat López-Sanmartín, Gaetano Catanese, Amalia Grau, Jose María Valencia, Jose Rafa García-March, José Ignacio Navas | TITLE: Species-specific quantitative PCR (qPCR) protocol developed to identify Haplosporidium pinnae
AUTHORS: Monserrat López-Sanmartín, Gaetano Catanese, Amalia Grau, Jose María Valencia, Jose Rafa García-March, José Ignacio Navas
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The aim of thi... | ["The qPCR assay for H. pinnae detection and quantification was carried out in duplicate using the species-specific primer pair (HpF3/HpR3) in a Mx3000P Thermocycler (Agilent).", "Amplification reactions were performed in a total volume of 10 µl comprising:", "2 µl of genomic DNA (100 ng),", "5 µl of PowerUpTM SYBRTM G... |
28,893 | Single nick pCrispomyces 2 | null | dx.doi.org/10.17504/protocols.io.8f5htq6 | null | Jaclyn Winter | TITLE: Single nick pCrispomyces 2
AUTHORS: Jaclyn Winter
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.hrhb536 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
89,722 | Dissection of the Carotid Sinus Nerve and Carotid Bifurcation for MicroCT | 1 | dx.doi.org/10.17504/protocols.io.x54v9p341g3e/v1 | https://www.protocols.io/view/dissection-of-the-carotid-sinus-nerve-and-carotid-c3u2ynye | Steven O'Neill | TITLE: Dissection of the Carotid Sinus Nerve and Carotid Bifurcation for MicroCT
AUTHORS: Steven O'Neill
[DESCRIPTION]
Dissection of the carotid sinus nerve begins with the exposure and subsequent removal of the zygomatic arch and angle of the mandible. The region superior to the styloid process and inferior to the ju... | ["[Neck Dissection] Dissection to the carotid sinus nerve (CSN) begins with placing the human cadaver in the supine position and rotating the neck towards the contralateral side from which is intended for dissection.", "[Neck Dissection] Palpate for the sternocleidomastoid (SCM) muscle; follow this muscle from its infe... |
40,651 | HTAPP_Depletion of CD45+ cells from single-cell suspension for single-cell RNA-seq | 1 | dx.doi.org/10.17504/protocols.io.bjxjkpkn | https://www.protocols.io/view/htapp-depletion-of-cd45-cells-from-single-cell-sus-bjxjkpkn | Isaac Wakiro, Sara Napolitano, Sébastien Vigneau, Asaf Rotem, Orit Rozenblatt-Rosen, Bruce Johnson, Aviv Regev | TITLE: HTAPP_Depletion of CD45+ cells from single-cell suspension for single-cell RNA-seq
AUTHORS: Isaac Wakiro, Sara Napolitano, Sébastien Vigneau, Asaf Rotem, Orit Rozenblatt-Rosen, Bruce Johnson, Aviv Regev
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">In some tumor specimens the proportion of ... | ["[Initial Quality Control]\nMix 5 µL of single-cell suspension with 5 µL Trypan blue and load on hemocytometer.", "[Initial Quality Control]\nCount and record the number of viable single-cells, dead single-cells, cell doublets, and whether debris are present, then calculate additional quality control metrics below. Ta... |
19,764 | (-)-α-Bisabolol GC sample preparation | null | null | null | Dennis Dienst, Oliver Mantovani, Pia Lindberg | TITLE: (-)-α-Bisabolol 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 (-)-α-bisabolol samples and external standards in dodecane for GC analysis. This protocol has been es... | ["[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 ... |
88,805 | UPitt TriState SenNet TMC Heart Procurement | 1 | dx.doi.org/10.17504/protocols.io.8epv5xe9jg1b/v1 | https://www.protocols.io/view/upitt-tristate-sennet-tmc-heart-procurement-c2ydyfs6 | John Sembrat, Marta Bueno, Alison Morris, koenigshoffm, Oliver Eickelberg | TITLE: UPitt TriState SenNet TMC Heart Procurement
AUTHORS: John Sembrat, Marta Bueno, Alison Morris, koenigshoffm, Oliver Eickelberg
[DESCRIPTION]
This document outlines the request for specimen procurement before arrival at the TriState SenNet TMC Biospecimen Core at the University of Pittsburgh, as part of the Cell... | ["[Requested processing protocol for Donation following Brain Death Declaration (DBD)] Organ Procurement Organization Recovery Team prepares for organ recovery as consistent with organ transplant protocol with cross clamp and in situ cold flush body cooling with minimal warm ischemic time.", "[Requested processing prot... |
30,184 | RNA isolation of Pinctada fucata martensii | null | dx.doi.org/10.17504/protocols.io.9qgh5tw | null | Xiong Xinwei | TITLE: RNA isolation of Pinctada fucata martensii
AUTHORS: Xiong Xinwei
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol provides details on RNA isolation of the tissue of Pinctada fucata martensii.</div></div>
[STEPS]
?. Incubate for 5 minutes to permit complete dissociation of the nu... | ["Incubate for 5 minutes to permit complete dissociation of the nucleoproteins complex.", "Add a steel ball to each tube and then flacker for 3 min by TissueLayer 2. The frequency is 26 (1/S). Repeat this step one time.", "Centrifuge the lysate for 15 minutes at 12,000 × g at 4 ℃, then transfer the aqueous phase contai... |
65,711 | Condor CBD Gummies – How Does It Help | 1 | dx.doi.org/10.17504/protocols.io.n92ldze3ov5b/v1 | https://www.protocols.io/view/condor-cbd-gummies-how-does-it-help-ccepstdn | ukcondorcbd | TITLE: Condor CBD Gummies – How Does It Help
AUTHORS: ukcondorcbd
[DESCRIPTION]
Condor CBD Gummies- Do you acknowledge Alzheimer's is an extraordinarily inconvenient issue? Do you acknowledge that the issue of joint and body torment that you are rising up to right at this point won't be made due? Could it have the ... | [] |
106,723 | Guidelines for verification of the DDNS method for poliovirus direct detection | 0 | dx.doi.org/10.17504/protocols.io.eq2lyw5jrvx9/v1 | https://www.protocols.io/view/guidelines-for-verification-of-the-ddns-method-for-dkgb4tsn | Joyce Akello, Alex Shaw, Catherine Troman, Erika Bujaki, Manasi Majumdar, Javier Martin, Nick Grassly | TITLE: Guidelines for verification of the DDNS method for poliovirus direct detection
AUTHORS: Joyce Akello, Alex Shaw, Catherine Troman, Erika Bujaki, Manasi Majumdar, Javier Martin, Nick Grassly
[DESCRIPTION]
This document describes a pragmatic approach to conduct in-house verification of the DDNS method for detecti... | ["[Stage 1. Spiking of nuclease free water with positive control dilutions] As the stool matrix to which the DDNS method is applied for is known to occasionally contain inhibitory substances interfering with PCR amplification, nuclease free water should be spiked with the positive\ncontrol dilutions. This will show if ... |
56,280 | Total Starch (as Glucose) Quantification by NZYtech GOD-POD Method | 6 | dx.doi.org/10.17504/protocols.io.b27yqhpw | https://www.protocols.io/view/total-starch-as-glucose-quantification-by-nzytech-b27yqhpw | Lynn Doran, Amanda P. De Souza | TITLE: Total Starch (as Glucose) Quantification by NZYtech GOD-POD Method
AUTHORS: Lynn Doran, Amanda P. De Souza
[DESCRIPTION]
Total starch was previously extracted from plant tissue and enzymatically digested to D-Glucose. This protocol is based on the NZYtech GOD-POD kit's colorimetric determination of D-Gluco... | ["[Prepare Glucose Standards] Prepare glucose standards in microcentrifuge by pipetting the appropriate amounts of 1 mg/mL Glucose standard and distilled water into each labeled tube.\n \n ABC1ug Glucose/50 ul-well (ug)Amount 1 mg/mL Glucose (ul)Amount distilled water (ul)2520180310401604156014052080120625100100", "... |
53,634 | DTI preprocessing, statistical and cluster analysis | 5 | dx.doi.org/10.17504/protocols.io.6qpvrdjozgmk/v1 | https://www.protocols.io/view/dti-preprocessing-statistical-and-cluster-analysis-bymapu2e | Maurizio Bergamino, Jennapher Lingo Vangilder | TITLE: DTI preprocessing, statistical and cluster analysis
AUTHORS: Maurizio Bergamino, Jennapher Lingo Vangilder
[DESCRIPTION]
This protocol outlines preprocessing, statistical and cluster analyses that were applied in 'Using whole-brain diffusion tensor analysis to evaluate white matter structural correlates of del... | ["[Preprocessing data] Double-check if your native and original images are in FLOAT32 and oriented with the MNI.\n-Convert to float-\nfslmaths dwidata.nii.gz dwi.nii.gz -odt float", "[Preprocessing data] DWI Denoising:\ndwidenoise -datatype float32 -noise level_noise.nii.gz [IN] [OUT_denoised]\ndwidenoise -datatype flo... |
54,978 | NAN KB Demo: Appendix for Serum sample preparation and data acquisition | 3 | null | https://www.protocols.io/view/nan-kb-demo-appendix-for-serum-sample-preparation-bzxap7ie | Abby Moore | TITLE: NAN KB Demo: Appendix for Serum sample preparation and data acquisition
AUTHORS: Abby Moore
[DESCRIPTION]
The purpose of this document is to include supporting content for the protocol Serum sample preparation and data acquisition.
[STEPS] | [] |
41,063 | Adverse drug reactions associated with the use of biological agents | 1 | dx.doi.org/10.17504/protocols.io.bkcfkstn | https://www.protocols.io/view/adverse-drug-reactions-associated-with-the-use-of-bkcfkstn | Jorge Machado Alba, Luis Valladales, Yadira Parrado | TITLE: Adverse drug reactions associated with the use of biological agents
AUTHORS: Jorge Machado Alba, Luis Valladales, Yadira Parrado
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify"><span style = "font-style:italic;">Introduction:</span><span> Bi... | [] |
48,395 | Purification of Wild Type eEF2 from pelleted yeast | 1 | null | https://www.protocols.io/view/purification-of-wild-type-eef2-from-pelleted-yeast-bthjnj4n | Clark Fritsch | TITLE: Purification of Wild Type eEF2 from pelleted yeast
AUTHORS: Clark Fritsch
[DESCRIPTION]
The purpose of this protocol is to describe how to purify endogenous eEF2 from Saccharomyces cerevisiae (budding yeast). The protocol can be completed in two days, but three days should be budgeted to complete the protocol.... | ["[Yeast Culture] To begin, you will want to inoculate a single colony of wild-type or modified yeast in 25 mL of YAPD medium and grow for 16 hours at 30 C. By the time that the incubation is complete, the cells should be in stationary phase and be at a high enough cell number to allow you to re-inoculate the yeast int... |
57,803 | MAD4HatTeR | 4 | null | https://www.protocols.io/view/mad4hatter-b4pjqvkn | Andres Aranda-Diaz | TITLE: MAD4HatTeR
AUTHORS: Andres Aranda-Diaz
[DESCRIPTION]
This protocol has been adapted from Paragon Genomics CleanPlex® NGS Panel
[STEPS]
SECTION: mPCR
1. In a PCR Workstation, prepare mPCR reaction mix
Keep Master Mix and thawed primers on ice
on ice Prepare a mPCR mix for your samples using the instructions ... | ["[mPCR] In a PCR Workstation, prepare mPCR reaction mix\n\nKeep Master Mix and thawed primers on ice\n\non ice Prepare a mPCR mix for your samples using the instructions below\nMake fresh dilution of primers each time\n\nVortex reagents before using and spin down to collect liquids \n\n4 µL :\n2 µL \n2 µL. You may dil... |
22,963 | Protein Purification ( Column Cromotography) | null | dx.doi.org/10.17504/protocols.io.2ntgden | null | Sevval Uysalcan, Rengin Yamur Akbiyik | TITLE: Protein Purification ( Column Cromotography)
AUTHORS: Sevval Uysalcan, Rengin Yamur Akbiyik
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"> It is very difficult to purify a desired protein from a cell and tissue in a pure state. If the concentration of this protein is low, it is necessary to... | ["2 ml of resin (Ni-beads) should be put onto columns. Wash column with double distilled water before using resin.\n[Resin]", "1X Binding Buffer should be added until fill the whole column.", "When all Binding Buffer is leaked, samples should be put into columns.", "Wash columns and sample until all residues are gone. ... |
50,388 | Behavioural phenotyping of C. elegans response to Keio single-gene E. coli mutants | 4 | dx.doi.org/10.17504/protocols.io.bvfun3nw | https://www.protocols.io/view/behavioural-phenotyping-of-c-elegans-response-to-k-bvfun3nw | Saul Moore | TITLE: Behavioural phenotyping of C. elegans response to Keio single-gene E. coli mutants
AUTHORS: Saul Moore
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Protocol for screening </span><span style = "font-style:italic;">Caenorhabditis elegans</span><span> behavioural response to </span><sp... | ["[Seeding Petri plates + worm maintenance]\nPrior to each experiment replicate, inoculate 10ml LB broth media with E. coli BW25113 in an Erlenmeyer flask for overnight culture (used as negative control and for raising worms) following the protocol, Inoculating a Liquid Bacterial Culture:(Friday, -11 days)\n{\"blocks\"... |
81,114 | Isolation of sex specific PND 1/2 rat cortical primary astrocytes | 1 | dx.doi.org/10.17504/protocols.io.e6nvwjry7lmk/v1 | https://www.protocols.io/view/isolation-of-sex-specific-pnd-1-2-rat-cortical-pri-ctf2wjqe | Neha Paranjape, Jonathan A. Doorn, Hansjoachim Lehmler, Laura E Dean | TITLE: Isolation of sex specific PND 1/2 rat cortical primary astrocytes
AUTHORS: Neha Paranjape, Jonathan A. Doorn, Hansjoachim Lehmler, Laura E Dean
[DESCRIPTION]
Many xenobiotic metabolizing enzymes, such as P450s, SULTs, UGTs, and sulfatases, are expressed in the brain, including astrocytes, the most abundant cell... | ["[Before you begin] Prepare complete S-MEM", "[Before you begin] Add 5 mL pen/strep solution to the 500 mL S-MEM.", "[Before you begin] Store complete S-MEM medium for up to 2 months at 4ºC", "[Before you begin] Prepare dissociation medium and warm to 37ºC - MUST MAKE FRESH EACH ISOLATION DAY. Prepare 10 mL of dissoci... |
91,346 | GGAssmbler Library Construction | 1 | dx.doi.org/10.17504/protocols.io.81wgbxqkolpk/v2 | https://www.protocols.io/view/ggassmbler-library-construction-c5fsy3ne | Shlomo Yakir Hoch, Ravit Netzer, Lucas Krauss, Karen Hakeny, Sarel J Fleishman | TITLE: GGAssmbler Library Construction
AUTHORS: Shlomo Yakir Hoch, Ravit Netzer, Lucas Krauss, Karen Hakeny, Sarel J Fleishman
[DESCRIPTION]
This protocol describes methods for GGAssembler.
[BEFORE_START]
Please note that protocols with Q5® High-Fidelity DNA Polymerase may differ from protocols with other polymerases... | ["[Amplify constant fragments] Set up the following reaction on ice:", "[Amplify constant fragments] Gently mix the reaction.", "[Amplify constant fragments] Collect all liquid to the bottom of the tube by a quick spin if necessary and overlay the sample with mineral oil if using a PCR machine without a heated lid.", "... |
51,980 | 4D Upper Gastrointestinal Magnetic Resonance Imaging in Healthy Human Subjects and Gastroparetic Patients | 1 | dx.doi.org/10.17504/protocols.io.kxygxpx9dl8j/v1 | https://www.protocols.io/view/4d-upper-gastrointestinal-magnetic-resonance-imagi-bwzkpf4w | Kun-Han Lu, Kristine Mosier, John Wo, Terry Powley | TITLE: 4D Upper Gastrointestinal Magnetic Resonance Imaging in Healthy Human Subjects and Gastroparetic Patients
AUTHORS: Kun-Han Lu, Kristine Mosier, John Wo, Terry Powley
[DESCRIPTION]
This protocol described the steps to acquire and analyze 4D gastric magnetic resonance imaging data under fast and fed states in hea... | ["[Subjects] Twenty healthy subjects (14 females; 6 males) and 15 gastroparetic patients (11 females; 4 males) participated in this study under research protocols approved by the Institutional Review Board at Purdue University and Indiana University School of Medicine. All healthy subjects did not have a prior diagnosi... |
39,945 | 605.2 URMC HTC Human Lung BioSpecimen Ontology framework 081520 | 3 | dx.doi.org/10.17504/protocols.io.bi9hkh36 | https://www.protocols.io/view/605-2-urmc-htc-human-lung-biospecimen-ontology-fra-bi9hkh36 | Gloria Pryhuber, Jennifer Dutra, Jeanne Holden-Wiltse | TITLE: 605.2 URMC HTC Human Lung BioSpecimen Ontology framework 081520
AUTHORS: Gloria Pryhuber, Jennifer Dutra, Jeanne Holden-Wiltse
[STEPS] | [] |
11,411 | Electrocompetent Agrobacterium transformation | null | dx.doi.org/10.17504/protocols.io.pdtdi6n | null | Magdalena Julkowska | TITLE: Electrocompetent Agrobacterium transformation
AUTHORS: Magdalena Julkowska
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Standard protocol for Agrobacterium transformation</div></div>
[STEPS]
?. Add a small amount of plasmid DNA (
?. Pipette Agro cells with DNA into a chilled 0.2 cm electr... | ["Add a small amount of plasmid DNA (", "Pipette Agro cells with DNA into a chilled 0.2 cm electroporation cuvette.Shake cells to bottom of cell", "Pulse cells at 2.5kV.", "Add 1 ml YEP (of LB) media to cuvette, mix, and immediately transfer cells into sterile test tubes.", "Allow cells to shake at 28°C for 2-4 hours."... |
34,702 | Viral Sequencing, from Gunk to Graph (One-Step four-primer PCR alternative) | null | dx.doi.org/10.17504/protocols.io.bd5ni85e | null | David Eccles | TITLE: Viral Sequencing, from Gunk to Graph (One-Step four-primer PCR alternative)
AUTHORS: David Eccles
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a fast "gunk to graph" protocol for analysing viral RNA from nasopharyngeal swabs. The approach involves swab lysis and inactivation at the... | ["[Swab Lysis]\nPrepare a centrifuge tube with heated lysis buffer and a cellulose disc\n1.5 ml", "[Swab Lysis]\nAdd lysis / RNAse inactivation buffer (Twitter reference) to 1.5ml centrifuge tube:OR extraction buffer #2 (see paper):\n500 µl\n[Tris]\n[EDTA]\n[SDS]\n[NaCl]\n500 µl\n[guanidine hydrochloride]\n[Tris [pH ... |
64,193 | Immunofluorescent Staining of phosphoRab10 in cultured cells | 1 | dx.doi.org/10.17504/protocols.io.ewov1nmzkgr2/v1 | https://www.protocols.io/view/immunofluorescent-staining-of-phosphorab10-in-cult-caw9sfh6 | Herschel Dhekne, Suzanne R R Pfeffer | TITLE: Immunofluorescent Staining of phosphoRab10 in cultured cells
AUTHORS: Herschel Dhekne, Suzanne R R Pfeffer
[DESCRIPTION]
This protocol can be used to detect the amount and localization of endogenous phospho-Rab10 by light microscopy. Cells that yield detectable, endogenous phosphorylated Rab10 without the need... | ["[Cell culture] Culture the cells in high glucose DMEM medium with glutamine and sodium pyruvate, 10% fetal bovine serum, with additional non-essential amino acids and Penicillin/Streptomycin.", "[Cell culture] MEFs are generally flat and occupy a relatively large surface area: cell counts per confluent dish are ~5X l... |
50,076 | Immuno-correlative light and electron microscopy (iCLEM) using SEM | 4 | dx.doi.org/10.17504/protocols.io.bu54ny8w | https://www.protocols.io/view/immuno-correlative-light-and-electron-microscopy-i-bu54ny8w | Viola Oorschot, Jillian C Danne, Benjamin Lindsey, Jan Kaslin, Georg Ramm | TITLE: Immuno-correlative light and electron microscopy (iCLEM) using SEM
AUTHORS: Viola Oorschot, Jillian C Danne, Benjamin Lindsey, Jan Kaslin, Georg Ramm
[DESCRIPTION]
Immuno- correlative light and electron microscopy (iCLEM) combines ultrastructural information obtained from high resolution electron microscopy ... | ["[Tissue fixation] Dissect out the tissue of interest (example, forebrain of Tg(proliferating cell nuclear antigen:GFP) transgenic adult zebrafish with olfactory bulbs attached for tissue orientation) on a teflon plate or dental wax sheet using fine forceps and a scalpel blade, at room temperature and place in fixativ... |
50,293 | Objectives (Part 2 of Safety and Efficacy of Imatinib for Preserving Beta-Cell Function in New-onset Type 1 Diabetes Mellitus) | 1 | dx.doi.org/10.17504/protocols.io.bvcvn2w6 | https://www.protocols.io/view/objectives-part-2-of-safety-and-efficacy-of-imatin-bvcvn2w6 | Stephen.Gitelman , Jeffrey A. Bluestone | TITLE: Objectives (Part 2 of Safety and Efficacy of Imatinib for Preserving Beta-Cell Function in New-onset Type 1 Diabetes Mellitus)
AUTHORS: Stephen.Gitelman , Jeffrey A. Bluestone
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is Part 2 of "Safety and Efficacy of Imatinib for Preserving Bet... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.jg4cjyw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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61,890 | Preparation of 1M calcium chloride solution (CaCl2) | 4 | dx.doi.org/10.17504/protocols.io.36wgq7mokvk5/v1 | https://www.protocols.io/view/preparation-of-1m-calcium-chloride-solution-cacl2-b8parvie | Alfonso Pérez Escudero, Alid Al-Asmar, gabrielmadirolas | TITLE: Preparation of 1M calcium chloride solution (CaCl2)
AUTHORS: Alfonso Pérez Escudero, Alid Al-Asmar, gabrielmadirolas
[DESCRIPTION]
Original source of the protocol: WormBook Methods http://www.wormbook.org/chapters/www_strainmaintain/strainmaintain.html
This protocol is for making 1M calcium chloride solutio... | ["Weigh 7.4 g of calcium chloride dihydrate (CaCl2·2H2O).", "Dissolve it in ~40 mL of milliQ water in a 100mL measuring cylinder.", "Fill up to 50 mL.", "Filter-sterilize.", "Store at 4°C. \nWe usually use it without problem for up to at least a year after preparation.", "Add a clean stirring magnet, and leave it on a ... |
62,577 | GeoMX Digital Spatial Profiler Whole Transcriptome Assay for Human Pancreas | 4 | dx.doi.org/10.17504/protocols.io.8epv59bong1b/v1 | https://www.protocols.io/view/geomx-digital-spatial-profiler-whole-transcriptome-b9crr2v6 | Ann Fu, Yanping Zhang, Heather Kates, Jing Chen, Alberto Riva, Clayton E Mathews, Martha Campbell-Thompson | TITLE: GeoMX Digital Spatial Profiler Whole Transcriptome Assay for Human Pancreas
AUTHORS: Ann Fu, Yanping Zhang, Heather Kates, Jing Chen, Alberto Riva, Clayton E Mathews, Martha Campbell-Thompson
[DESCRIPTION]
Purpose:
This protocol details processing fixed paraffin sections from human pancreas for the Nanos... | ["[Slide preparation] Bake slides at 60 °C for 60 min immediately before use.", "[Slide deparaffinization] Dewax and rehydrate sections using slide tray stations or a Leica XL slide autostainer. \nDo not allow tissue sections to dry once rehydrated and avoid touching tissue when drying around edges.", "[Slide deparaff... |
94,349 | Labeling lysosomes in the adult Drosophila brain using LysoTracker | 4 | dx.doi.org/10.17504/protocols.io.j8nlkojjwv5r/v1 | https://www.protocols.io/view/labeling-lysosomes-in-the-adult-drosophila-brain-u-c8dmzs46 | Mel Feany | TITLE: Labeling lysosomes in the adult Drosophila brain using LysoTracker
AUTHORS: Mel Feany
[DESCRIPTION]
This protocol describes the labeling and quantification of Lysosomes in the adult Drosophila brain using the LysoTracker dye
[STEPS]
1. Prepare the working solution, 0.05 μM LysoTracker Green DND26, using 1X PBS... | ["Prepare the working solution, 0.05 μM LysoTracker Green DND26, using 1X PBS", "Brains from 10-day-old animals are dissected in ice-cold 1X PBS", "The dissected brain is transferred to a glass slide, and the excess 1X PBS removed", "The brains are re-incubated with 0.05 μM LysoTracker for 5 min at Room temperature", "... |
null | null | null | dx.doi.org/10.17504/protocols.io.urvev66 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Study Material for Manuscript: Sensitivity for Multimorbidity: The Role of Diagnostic Uncertainty of Physicians when Evaluating Multimorbid Video Case-based Vignettes (English version of study protocols)
[STEPS] | [] |
88,884 | Quick saag paneer/tofu | 1 | dx.doi.org/10.17504/protocols.io.yxmvm3pe5l3p/v1 | https://www.protocols.io/view/quick-saag-paneer-tofu-c22uygew | Lenny Teytelman | TITLE: Quick saag paneer/tofu
AUTHORS: Lenny Teytelman
[DESCRIPTION]
(Based on the NYT recipe https://cooking.nytimes.com/recipes/1021954-saag-paneer)
My kids don't like fried onion, and one of them doesn't like paneer. So this is a very quick saag with onion powder and tofu instead.
[STEPS]
1. Mince the spinach in... | ["Mince the spinach in a food processor. Do not overprocess into a puree.", "Heat ghee on medium-low", "Fry garlic and ginger for 1 min or less", "Add spinach", "Add cup of water", "Raise the heat to medium and add coriander, cumin, onion powder, salt, pepper.", "Cook for 5 min", "Add cubed tofu and cook another 2-3 ... |
null | null | null | dx.doi.org/10.17504/protocols.io.ffzbjp6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Steps to make half strength MS + B5 vitamins solid growth medium (w/ 1% sucrose) for standard Marchantia tissue culture.</p>
[STEPS]
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36,605 | Biston betularia protocols: Assembly trapping | 1 | dx.doi.org/10.17504/protocols.io.8epv51odjl1b/v1 | https://www.protocols.io/view/biston-betularia-protocols-assembly-trapping-bfy5jpy6 | Ivy Whiteford, Carl Yung, Amy Corthine, Ilik Saccheri | TITLE: Biston betularia protocols: Assembly trapping
AUTHORS: Ivy Whiteford, Carl Yung, Amy Corthine, Ilik Saccheri
[DESCRIPTION]
The peppered moth, Biston betularia, is a textbook example of industrial melanism. Here we describe the procedures associated with trapping wild males using laboratory-reared females.
[STE... | ["[In the field] When arriving at a field site for the first time, traps need to be assembled. First a dowel is inserted for rigidity. Second, one of the blue conical vents is placed in the trap. Third, one or two pre-assembled female calling pots are attached to the internal velcro strip. Fourth, the second blue conic... |
52,564 | Isolation of Membrane-enriched fractions from mouse cortical neurons | 1 | dx.doi.org/10.17504/protocols.io.bxjupknw | https://www.protocols.io/view/isolation-of-membrane-enriched-fractions-from-mous-bxjupknw | Odetta Antico, Erica Barini, Miratul M. K. Muqit | TITLE: Isolation of Membrane-enriched fractions from mouse cortical neurons
AUTHORS: Odetta Antico, Erica Barini, Miratul M. K. Muqit
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Upon mitochondrial damage, activation of the PINK1 kinase and Parkin ubiquitin ligase induces ubiquitylation of multip... | ["[Membrane Isolation For Neurons-Mitochondrial depolarisation ◊TIMING 1-9h, day of experiment]\nTo depolarize or uncouple mitochondrial membrane potential in neurons, cultures could be untilto with a combination of Antimycin A and Oligomycin dissolved in DMSO at .", "[Membrane Isolation For Neurons-Mitochondria... |
105,111 | Community-based lifestyle intervention using targeted shared care approach versus usual care on pregnancy outcomes in Nigerian women with gestational diabetes mellitus (ALEVIATE GDM): study protocol for a randomized controlled trial | 0 | dx.doi.org/10.17504/protocols.io.n92ld8j7nv5b/v1 | https://www.protocols.io/view/community-based-lifestyle-intervention-using-targe-divx4e7n | Ifeoma I Ulasi, Ekenechukwu E. Young, Euzebus C Ezugwu, Victor M Oguoma, Akintunde A Adeseye, Timothy C Skinner, Chinwuba K Ijoma, Nneka Iloanusi, Ifeyinwa Nnakenyi, Ikechukwu Obi, Sunday G Mba, Ejiofor V Ugwu, Ezekiel U Nwose | TITLE: Community-based lifestyle intervention using targeted shared care approach versus usual care on pregnancy outcomes in Nigerian women with gestational diabetes mellitus (ALEVIATE GDM): study protocol for a randomized controlled trial
AUTHORS: Ifeoma I Ulasi, Ekenechukwu E. Young, Euzebus C Ezugwu, Victor M Oguoma... | ["[INTRODUCTION] BACKGROUND\nThere have been various studies on the prevalence of gestational diabetes mellitus in Nigeria, albeit using different criteria for diagnosis. Although guidance for management of GDM has been included in the Nigerian guidelines for management of DM [1], it is unclear the proportion of physic... |
62,526 | Limitless Glucose 1 Highly Effective Pills or Fake Report Check Now | 3 | dx.doi.org/10.17504/protocols.io.rm7vzyo1xlx1/v1 | https://www.protocols.io/view/limitless-glucose-1-highly-effective-pills-or-fake-b9a6r2he | LimitlessGlucose | TITLE: Limitless Glucose 1 Highly Effective Pills or Fake Report Check Now
AUTHORS: LimitlessGlucose
[DESCRIPTION]
Official Website - Click Here for OcuPrime Vision Support
Availability Of OcuPrime Vision Support - Online On Website
Main Benefits - Improve EYE Vision Without Any Side Effect
[STEPS] | [] |
33,870 | INterventions for Complex Traumatic Events (INCiTE): systematic review | 1 | dx.doi.org/10.17504/protocols.io.bdbni2me | https://www.protocols.io/view/interventions-for-complex-traumatic-events-incite-bdbni2me | Peter Coventry | TITLE: INterventions for Complex Traumatic Events (INCiTE): systematic review
AUTHORS: Peter Coventry
[STEPS] | [] |
27,240 | j5 Protocols Collection | null | dx.doi.org/10.17504/protocols.io.6ughetw | null | Mike Fero | TITLE: j5 Protocols Collection
AUTHORS: Mike Fero
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A collection of protocols compatible with j5 and referenced in Springer-Verlag book chapter by M. Fero, N. Hillson and J.K. Craft.</div></div>
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.gxcbxiw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>These protocols accompany the following publication:</p>
<p> </p>
<p>David O'Connor, et. al. (2017) The Healthy Brain Network Serial Scanning Initiative. GigaScience...</p>
[STEPS] | [] |
21,609 | Vandy - Modified Roux-en-Y Gastric Bypass in Mice | null | dx.doi.org/10.17504/protocols.io.zchf2t6 | null | Teri Stevenson, Vance L. Albaugh | TITLE: Vandy - Modified Roux-en-Y Gastric Bypass in Mice
AUTHORS: Teri Stevenson, Vance L. Albaugh
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">This is the protocol for the modified gastric bypass in the mouse. In t... | ["Preoperative Care 1. All animals must be singly-housed, given Ensure 12 hours before surgery and have all bedding removed from the cages being used for housing. 2. Preoperative pain medications should be administered: a. Ketoprofen (5 mg/kg) b. Saline is given at the end of surgery and a second dose is given ... |
55,382 | Engineering solutions for biological studies of flow-exposed endothelial cells on orbital shakers | 4 | dx.doi.org/10.17504/protocols.io.b2bwqape | https://www.protocols.io/view/engineering-solutions-for-biological-studies-of-fl-b2bwqape | Andreia Fernandes, Vahid Hosseini, Viola Vogel, Robert Lovchik | TITLE: Engineering solutions for biological studies of flow-exposed endothelial cells on orbital shakers
AUTHORS: Andreia Fernandes, Vahid Hosseini, Viola Vogel, Robert Lovchik
[DESCRIPTION]
Shear stress is extremely important for endothelial cell (EC) function. The popularity of 6-well plates on orbital shakers to i... | ["[PROTOCOL 1:] Coating the center of cell culture wells with non-adherent PEG gel", "[PROTOCOL 1:] Remark:\nTo harvest protein or RNA, a cell scraper can be used, and one should be careful not to collect the PEG-coating as well.", "[PROTOCOL 1:] Draw a cross to locate the center of the well and mark the limits of a vi... |
41,089 | A General Protocol for Pilot-Testing the Screening Stage of a Systematic Review (Manual) | 1 | dx.doi.org/10.17504/protocols.io.bkc9ksz6 | https://www.protocols.io/view/a-general-protocol-for-pilot-testing-the-screening-bkc9ksz6 | Paul Whaley, Ruth Garside, Jacqualyn Eales | TITLE: A General Protocol for Pilot-Testing the Screening Stage of a Systematic Review (Manual)
AUTHORS: Paul Whaley, Ruth Garside, Jacqualyn Eales
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Studies of potential relevance to the objectives of a systematic reviews, as found by the search strate... | ["[Preparing for Training]\nDefine the initial set of eligibility criteria in discussion with topic experts, attempting to be as clear and unambiguous as possible.", "[Preparing for Training]\nIdentify the reviewers who will conduct the screening process.", "[Preparing for Training]\nSelect a random subset of the full ... |
50,518 | Efficacy of follow-up after intensive care unit (ICU) discharge for improving long-term outcomes and mental health in ICU patients and informal caregivers: a systematic review and meta-analysis protocol. | 1 | dx.doi.org/10.17504/protocols.io.bvjwn4pe | https://www.protocols.io/view/efficacy-of-follow-up-after-intensive-care-unit-ic-bvjwn4pe | Shodai Yoshihiro, Shunsuke Taito, Kota Yamauchi, Shunsuke Kina, Takero Terayama, Yusuke Tsutsumi, Yuki Kataoka, Takeshi Unoki | TITLE: Efficacy of follow-up after intensive care unit (ICU) discharge for improving long-term outcomes and mental health in ICU patients and informal caregivers: a systematic review and meta-analysis protocol.
AUTHORS: Shodai Yoshihiro, Shunsuke Taito, Kota Yamauchi, Shunsuke Kina, Takero Terayama, Yusuke Tsutsumi, Yu... | [] |
43,647 | Raffaelea plant inoculation | 3 | dx.doi.org/10.17504/protocols.io.bnu7mezn | https://www.protocols.io/view/raffaelea-plant-inoculation-bnu7mezn | You Li | TITLE: Raffaelea plant inoculation
AUTHORS: You Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The purpose of this protocol is to test pathogenicity of the ambrosia fungi Raffaelea.</div><div class = "text-block"><span>This protocol is part of the Bark Beetle Mycobiome (BBM) Research Coordinatio... | [] |
59,026 | Adaption for small samples - Nuclei isolation from snap-frozen tissue for single nucleus RNA Sequencing | 4 | dx.doi.org/10.17504/protocols.io.rm7vzyx75lx1/v1 | https://www.protocols.io/view/adaption-for-small-samples-nuclei-isolation-from-s-b5vsq66e | Jolet Y Mimpen, Claudia Paul, Tendon Seed Network, Adam Cribbs, Sarah Snelling | TITLE: Adaption for small samples - Nuclei isolation from snap-frozen tissue for single nucleus RNA Sequencing
AUTHORS: Jolet Y Mimpen, Claudia Paul, Tendon Seed Network, Adam Cribbs, Sarah Snelling
[DESCRIPTION]
Previously, we described a robust protocol for the isolation of nuclei from snap frozen fibrous tissue... | ["[Preparation] Prepare and pre-cool all reagents, materials, and equipment:\nGet a box of ice to cool down buffers and tubes\nGet a box of dry ice. Put a Petri dish on the dry ice to allow it to cool. Stick a scalpel and a pair of forceps in the dry ice to allow them to cool. \nLet swinging bucket centrifuge with 15mL... |
58,847 | Response of Disease Model Mutants to Cholinergic Drugs | 1 | dx.doi.org/10.17504/protocols.io.b5p7q5rn | https://www.protocols.io/view/response-of-disease-model-mutants-to-cholinergic-d-b5p7q5rn | Thomas J. O'Brien | TITLE: Response of Disease Model Mutants to Cholinergic Drugs
AUTHORS: Thomas J. O'Brien
[DESCRIPTION]
Protocol for testing if disease model mutant C. elegans strains show increased resistance/sensitivity to the action of cholinergic drugs after 1 and 4 hour exposure times.
[GUIDELINES]
For the 1 hour time point it i... | ["[Pick L4 worms for bleaching (9 days prior to tracking)] Pick 10 x L4 worms onto 4 x 90mm NGM-agar plates pre-seeded with E. coli OP50 for each strain (remember to include a relevant control strain).\n\ne.g. if looking to compare the response of one mutant to N2 reference: you would have 4 x 90 mm plates with strain ... |
97,515 | CODA (part 6): register the nuclear coordinates and construct 3D cell matrix | HuBMAP | JHU-TMC | 0 | dx.doi.org/10.17504/protocols.io.n2bvjnrnxgk5/v1 | https://www.protocols.io/view/coda-part-6-register-the-nuclear-coordinates-and-c-dbgj2jun | Kyu Sang Han, Pei-Hsun Wu, Joel Sunshine, Ashley Kiemen, Sashank Reddy, Denis Wirtz | TITLE: CODA (part 6): register the nuclear coordinates and construct 3D cell matrix | HuBMAP | JHU-TMC
AUTHORS: Kyu Sang Han, Pei-Hsun Wu, Joel Sunshine, Ashley Kiemen, Sashank Reddy, Denis Wirtz
[DESCRIPTION]
Using the registration transformations calculated in low-resolution (as described CODA (part 2): calculate re... | ["[register the nuclear coordinates] As input, this function needs the path to the low-resolution images that were registered in CODA-part2 (pth1x), the path containing the coordinates calculated in CODA-part4 (pthcoords), and the scale factor between these images. For cell detection performed in 10x and registration c... |
54,751 | Live, in vivo, imaging (GCaMP6F), Video Processing, and Analysis | 4 | dx.doi.org/10.17504/protocols.io.bzp7p5rn | https://www.protocols.io/view/live-in-vivo-imaging-gcamp6f-video-processing-and-bzp7p5rn | Bryan Yoo, Jessica Griffiths, Sarkis Mazmanian | TITLE: Live, in vivo, imaging (GCaMP6F), Video Processing, and Analysis
AUTHORS: Bryan Yoo, Jessica Griffiths, Sarkis Mazmanian
[DESCRIPTION]
Protocol for GCaMP6F imaging and analysis in gut neurons used in Yoo et al 2021
[STEPS]
SECTION: Preparation
1. AAV-PHP.S-CAG-GCaMP6F (1012VGs) was delivered systemically to... | ["[Preparation] AAV-PHP.S-CAG-GCaMP6F (1012VGs) was delivered systemically to WT C57.", "[Preparation] 3-4 weeks after infection, mice were anesthetized with 2% isoflurane on a heating pad (Kent Scientific, Torrington, CT-DCT15) with plastic sleeve covers (Kent Scientific, Torrington, CT-DCT1520P).", "[Preparation] The... |
107,180 | A Protocol for Assessing Open Data Practices: Honours Students Can Lead the Way. | 0 | dx.doi.org/10.17504/protocols.io.kxygxyxmdl8j/v1 | https://www.protocols.io/view/a-protocol-for-assessing-open-data-practices-honou-dkwk4xcw | Haya Deeb, tomasz.zielinski, Andrew.Millar | TITLE: A Protocol for Assessing Open Data Practices: Honours Students Can Lead the Way.
AUTHORS: Haya Deeb, tomasz.zielinski, Andrew.Millar
[DESCRIPTION]
Introduction
The culture of scientific research is increasingly recognising the importance of Open Data. Open Data practices involve making research data freely ava... | ["[Sampling Framework and Selection Process] Research groups within the biosciences at the University of Edinburgh were selected for study based on the educational interests of the undergraduate honours student researchers. Articles from each group were retrieved from the University’s public Edinburgh Research Explorer... |
73,533 | Protocol for Cross-species characterization in the reproduction of Spodoptera Sunia (Lepidoptera: Noctuidae) | 4 | dx.doi.org/10.17504/protocols.io.81wgbyzk3vpk/v1 | https://www.protocols.io/view/protocol-for-cross-species-characterization-in-the-cj25uqg6 | Carlos Ivan Real Baca, Carlos Alberto Zuniga Gonzalez | TITLE: Protocol for Cross-species characterization in the reproduction of Spodoptera Sunia (Lepidoptera: Noctuidae)
AUTHORS: Carlos Ivan Real Baca, Carlos Alberto Zuniga Gonzalez
[DESCRIPTION]
The Protocol describes the process for Cross-species Characterization in the reproduction of Spodoptera Sunia(Lepidoptera: Noc... | ["Stage 1: Field tracking\nThe search for Spodoptera sunia was carried out in an onion plantation in Sébaco (12.87845, -86.09147), it was inspected in the upper and lower part of the leaves, larvae of different instars were collected, later they were placed in polyethylene cups of 4 and 16 ounces with the leaves and bu... |
24,057 | Mammalian Cell Culture: Refreshing Media | null | dx.doi.org/10.17504/protocols.io.3qzgmx6 | null | Kenneth Schackart | TITLE: Mammalian Cell Culture: Refreshing Media
AUTHORS: Kenneth Schackart
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol explains how to refresh the media of cultured mammalian cells grown in a tissue culture flask.</div></div>
[STEPS]
?. [Assessing Culture Health]
Assess cell healt... | ["[Assessing Culture Health]\nAssess cell health under light microscope before beginning.", "[Refreshing media]\nUsing a serological pipet, remove old media from flask and transfer to waste beaker.\nTo avoid contamination, avoid touching the pipette tip to anything. Holding the flask such that the lid is pointed up wil... |
56,900 | SARS-CoV-2 NCBI submission protocol: SRA, BioSample, and BioProject | 1 | null | https://www.protocols.io/view/sars-cov-2-ncbi-submission-protocol-sra-biosample-b3tcqniw | Ruth Timme, Emma Griffiths, Duncan MacCannell, Lee Katz, Michael Weigand, Technical Outreach and Assistance for States Team | TITLE: SARS-CoV-2 NCBI submission protocol: SRA, BioSample, and BioProject
AUTHORS: Ruth Timme, Emma Griffiths, Duncan MacCannell, Lee Katz, Michael Weigand, Technical Outreach and Assistance for States Team
[DESCRIPTION]
PURPOSE:
This is a SARS-CoV-2 specific protocol that covers the steps needed to establish ... | ["["Ingredients" to have in place before starting your submissions] Set up a new NCBI submission environment for your lab\n1.1: Create an NCBI user account\n1.2: Set up an NCBI submission user group for your lab\n1.4: Bookmark the link to your Submission Portal\n1.5. Identify or establish new BioProjects (det... |
70,860 | High Performance Liquid Chromatography (HPLC) and sample preparation | 1 | dx.doi.org/10.17504/protocols.io.yxmvm2ko5g3p/v1 | https://www.protocols.io/view/high-performance-liquid-chromatography-hplc-and-sa-chfkt3kw | gurvir.virdi | TITLE: High Performance Liquid Chromatography (HPLC) and sample preparation
AUTHORS: gurvir.virdi
[DESCRIPTION]
HPLC for metabolites in mDA neurons
[STEPS]
SECTION: Pre-sample prep
1. Prior to harvesting mDA neurons, all cells were incubated in phenol-free medium for 24 hours with and without the presence of 80 micro... | ["[Pre-sample prep] Prior to harvesting mDA neurons, all cells were incubated in phenol-free medium for 24 hours with and without the presence of 80 micromolar (µM) L-Dopa (Sigma).", "[Extracellular metabolite sample prep] For extracellular metabolites, media after 24 hours was mixed 1:1 in 0.8 Molarity (M) ice cold pe... |
46,204 | Modelling protocols for derivation of Fe(III) NICA constants and calculations of ambient Fe speciation and apparent Fe(III) solubility in seawater | 5 | dx.doi.org/10.17504/protocols.io.brc4m2yw | https://www.protocols.io/view/modelling-protocols-for-derivation-of-fe-iii-nica-brc4m2yw | Kechen Zhu, Jan E. Groenenberg, Eric P. Achterberg, Martha Gledhill | TITLE: Modelling protocols for derivation of Fe(III) NICA constants and calculations of ambient Fe speciation and apparent Fe(III) solubility in seawater
AUTHORS: Kechen Zhu, Jan E. Groenenberg, Eric P. Achterberg, Martha Gledhill
[DESCRIPTION]
Calculations of iron (Fe) speciation using the NICA-Donnan model can ... | ["[The application of PEST-ORCHESTRA to the estimation of NICA-Donnan parameters in seawater] Install chemical speciation software ORCHESTRA and parameter estimation program PEST", "[The application of PEST-ORCHESTRA to the estimation of NICA-Donnan parameters in seawater] Set up the combination of PEST-ORCHESTRA", "[T... |
46,790 | Cleaning colonial ascidians | 4 | dx.doi.org/10.17504/protocols.io.brxem7je | https://www.protocols.io/view/cleaning-colonial-ascidians-brxem7je | Simon Blanchoud, Marta Wawrzyniak | TITLE: Cleaning colonial ascidians
AUTHORS: Simon Blanchoud, Marta Wawrzyniak
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol has been successfully used with Botrylloides diegensis and Botryllus schlosseri.</div></div>
[STEPS]
?. [Cleaning colonial ascidians]
Select the slides to be ... | ["[Cleaning colonial ascidians]\nSelect the slides to be cleaned.", "[Cleaning colonial ascidians]\nPlace them in the first container in a slide rack.", "[Cleaning colonial ascidians]\nTake one slide.", "[Cleaning colonial ascidians]\nUsing the single-edge razor blade, wipe clean as much surface as possible.", "[Cleani... |
40,777 | ELISA for quantification of IL-18 in human serum. | 6 | dx.doi.org/10.17504/protocols.io.bj3hkqj6 | https://www.protocols.io/view/elisa-for-quantification-of-il-18-in-human-serum-bj3hkqj6 | Angel Justiz-Vaillant | TITLE: ELISA for quantification of IL-18 in human serum.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Interleukins (IL) are a type of cytokine first thought to be expressed by leukocytes alone but have later been found to be produced by many other body cells. T... | ["An anti-human IL-18 coating antibody is adsorbed onto microwells by incubation overnight at 4°C.", "Add 50 µl of human serum. Human IL-18 present in the serum sample binds to antibodies adsorbed to the microwells.", "The microplate is blocked with 3% non-fat milk-PBS buffer and later wash to remove unbound proteins."... |
null | null | null | dx.doi.org/10.17504/protocols.io.rwwd7fe | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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87,501 | JMN-MSMP Muscle Single Cell Isolation | 1 | null | https://www.protocols.io/view/jmn-msmp-muscle-single-cell-isolation-czpmx5k6 | ccherry | TITLE: JMN-MSMP Muscle Single Cell Isolation
AUTHORS: ccherry
[DESCRIPTION]
Single cell isolation from muscle
[STEPS]
SECTION: Single cell isolation
1. Tissue was finely diced in RPMI 1640 (Gibco) with 1.6 Wunsh U/mL Liberase TL (Roche Diagnostics) and 0.2 mgl/mL deoxyribonuclease I (Roche Diagnostics).
SECTION: Sing... | ["[Single cell isolation] Tissue was finely diced in RPMI 1640 (Gibco) with 1.6 Wunsh U/mL Liberase TL (Roche Diagnostics) and 0.2 mgl/mL deoxyribonuclease I (Roche Diagnostics).", "[Single cell isolation] Finely diced tissue was incubated at 37C for 45 minutes.", "[Single cell isolation] Digested tissues were ground s... |
80,261 | Advanced Blast Simulator (ABS) blast model in rat - VandeVord Lab | 1 | dx.doi.org/10.17504/protocols.io.dm6gpjk9jgzp/v1 | https://www.protocols.io/view/advanced-blast-simulator-abs-blast-model-in-rat-va-csmdwc26 | pvord | TITLE: Advanced Blast Simulator (ABS) blast model in rat - VandeVord Lab
AUTHORS: pvord
[DESCRIPTION]
This is a protocol to describe the materials and methods utilized to perform preclinical traumatic brain injury (TBI) using a blast model for rodents. Blast waves are generated using a custom Advanced Blast Simulator ... | ["Prepare membranes for use (See Note 1)", "Connect ABS1 driver to gas tank (See Note 2)", "Connect ABS wall pressure sensors to data acquisition system allowing for the calculation of the static (side-on) pressure within tube. (See Note 3)", "Place membrane between the driver and driven section and seal properly", "Co... |
20,448 | Splitting 96 Well Plates for gDNA Extraction and Continuing Culture | null | dx.doi.org/10.17504/protocols.io.x78frrw | null | Celeste Karch, Rita Martinez, Jacob Marsh | TITLE: Splitting 96 Well Plates for gDNA Extraction and Continuing Culture
AUTHORS: Celeste Karch, Rita Martinez, Jacob Marsh
[STEPS]
?. Coat 96 well plate with Matrigel per well.
50 µl
?. Incubate at for .
?. Prepare plate for expansion by aspirating Matrigel from plate.
?. Add mTesR1 + 10 uM Rock Inhibitor to appr... | ["Coat 96 well plate with Matrigel per well.\n50 µl", "Incubate at for .", "Prepare plate for expansion by aspirating Matrigel from plate.", "Add mTesR1 + 10 uM Rock Inhibitor to appropriate wells.\n50 µl", "Aspirate media from original plate.", "Wash with PBS and aspirate.\n200 µl", "Add of 0.05% Trypsin.\n25 µl",... |
69,292 | Online Survey Among Medical Professionals on Second Opinions in the Indication for Elective Caesarean Sections in Germany: Study Protocol | 1 | dx.doi.org/10.17504/protocols.io.kqdg39e2pg25/v1 | https://www.protocols.io/view/online-survey-among-medical-professionals-on-secon-cfwktpcw | Anke Kaulbert, Barbara Prediger | TITLE: Online Survey Among Medical Professionals on Second Opinions in the Indication for Elective Caesarean Sections in Germany: Study Protocol
AUTHORS: Anke Kaulbert, Barbara Prediger
[DESCRIPTION]
Background:
Caesarean section (CS) rates have been continuously rising worldwide over the last decade without being ac... | [] |
29,276 | meta analysis | null | dx.doi.org/10.17504/protocols.io.8t4hwqw | null | chuandan wan | TITLE: meta analysis
AUTHORS: chuandan wan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A systematic literature search was performed using PubMed, Embase, and WANFANG MED ONLINE databases up to March 18, 2019. All literature was analyzed using Meta Disc 1.4 and STATA 14.0 software. Diagnostic mea... | ["This meta-analysis was conducted following the criteria of Preferred Reporting Items for Systematic Review and Meta Analyses . A literature search was systematically performed using PubMed, Embase, Cochrane Library, and WANFANG medicine online databases for all relevant articles without language or regional limitatio... |
65,027 | HeLa culture, transfection, and labeling of Halo-fusion proteins (Provisional unformatted) | 4 | null | https://www.protocols.io/view/hela-culture-transfection-and-labeling-of-halo-fus-cbrbsm2n | OLIVIA HARDING, holzbaur | TITLE: HeLa culture, transfection, and labeling of Halo-fusion proteins (Provisional unformatted)
AUTHORS: OLIVIA HARDING, holzbaur
[DESCRIPTION]
High-throughput, predictable systems that are easily modulated are ideal for the study of cell biology. Here we developed a protocol to investigate the role of the Nucl... | ["Olivia Harding, Erika L.F. Holzbaur\n Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104\n Abstract\n High-throughput, predictable systems that are easily modulated are ideal for the study of cell biology. Here we developed a protocol to investigate the role of t... |
null | null | null | dx.doi.org/10.17504/protocols.io.icgcatw | null | null | TITLE: No Title
AUTHORS:
[BEFORE_START]
<p>There is the preparation of CTAB solution.</p>
<p> </p>
<p>CTAB Buffer</p>
<p>100ml 1M Tris HCl pH 8.0</p>
<p>280ml 5 M NaCl</p>
<p>40ml of 0.5 M EDTA </p>
<p>20 g of CTAB (cetyltrimethyl ammonium bromide) </p>
<p>Bring total volume to 1 L with ddH<sub>2</sub>O</p>
<p> </p>
... | [] |
96,366 | How to book a sorting slot in PPMS | 0 | null | https://www.protocols.io/view/how-to-book-a-sorting-slot-in-ppms-dacn2ave | Daniel Gimenes | TITLE: How to book a sorting slot in PPMS
AUTHORS: Daniel Gimenes
[DESCRIPTION]
Step by step protocol on how to book a cell sorter at EMBL's Flow Cytometry Core Facility
[STEPS]
SECTION: Access the PPMS calendar
1. Go to https://ppms.embl.de
SECTION: Access the PPMS calendar
2. Click on Flow Cytometry Core Facility
... | ["[Access the PPMS calendar] Go to https://ppms.embl.de", "[Access the PPMS calendar] Click on Flow Cytometry Core Facility", "[Access the PPMS calendar] Login into your account", "[Access the PPMS calendar] On the upper tabs, click on \"BOOK\"", "[Access the PPMS calendar] Select one of the cell sorters that you want ... |
90,331 | Hippocampal Cultures, lentivirus production, vGLUT1-pHluorin imaging and analysis | 1 | dx.doi.org/10.17504/protocols.io.q26g7pdkkgwz/v1 | https://www.protocols.io/view/hippocampal-cultures-lentivirus-production-vglut1-c4f3ytqn | Leonardo A Parra-Rivas | TITLE: Hippocampal Cultures, lentivirus production, vGLUT1-pHluorin imaging and analysis
AUTHORS: Leonardo A Parra-Rivas
[DESCRIPTION]
Hippocampal Cultures, lentivirus production, vGLUT1-pHluorin imaging and analysis
[STEPS]
SECTION: Hippocampal Cultures
1.
Before dissection, add 100 μL of 1 mg/mL Poly-d-Lysine
sol... | ["[Hippocampal Cultures] Before dissection, add 100 μL of 1 mg/mL Poly-d-Lysine\n solution on to the inner well of each Mattek dish. Spread evenly and \nallow the coating to proceed for 2 h at room temperature. After 2 h wash\n the dishes thrice with ddH2O. Dry the dishes thoroughly using an aspirator and let them sit ... |
92,516 | Crop DNA Extraction with Lab-Made Magnetic Nanoparticles | 4 | dx.doi.org/10.17504/protocols.io.e6nvwdqm7lmk/v1 | https://www.protocols.io/view/crop-dna-extraction-with-lab-made-magnetic-nanopar-c6kczcsw | Haichuan Wang, Xueqi Zhao, Li Tan, Junwei Zhu, david.hyten | TITLE: Crop DNA Extraction with Lab-Made Magnetic Nanoparticles
AUTHORS: Haichuan Wang, Xueqi Zhao, Li Tan, Junwei Zhu, david.hyten
[DESCRIPTION]
Molecular breeding methods, such as marker-assisted selection and genomic selection, require high-throughput and cost-effective methods for isolating genomic DNA from plants... | ["[Nanopartcle synthesis, sample collection, DNA preparation, evaluation and PCR] Weigh FeCl2·4H2O (4.34g, 0.0218 mol).", "[Nanopartcle synthesis, sample collection, DNA preparation, evaluation and PCR] Weigh FeCl3·6H2O (10.84 g, 0.04 mol).", "[Nanopartcle synthesis, sample collection, DNA preparation, evaluation and ... |
94,170 | Mouse Water Restriction | 4 | dx.doi.org/10.17504/protocols.io.x54v9pn34g3e/v1 | https://www.protocols.io/view/mouse-water-restriction-c772zrqe | Avalon Amaya, Jackie Swapp | TITLE: Mouse Water Restriction
AUTHORS: Avalon Amaya, Jackie Swapp
[DESCRIPTION]
This protocol describes a semi-customized workflow to perform water restriction with mice designated for future experiments.
Water restriction is a common method used to increase engagement and motivation of mice performing behavioral e... | ["[Maintaining a Mouse on Water Restriction] Open Waterlog and access mouse record by repeating", "[Taking a Mouse off Water Restriction] Repeat section \"Maintaining a Mouse on Water Restriction\". Specifically .", "[Taking a Mouse off Water Restriction] Remove mouse from water restriction in Waterlog.", "[Taking a ... |
71,653 | Discharge of LiPo Batteries Using Saltwater Electrolysis | 1 | dx.doi.org/10.17504/protocols.io.14egn274mg5d/v2 | https://www.protocols.io/view/discharge-of-lipo-batteries-using-saltwater-electr-ch8dt9s6 | marshall.bennett | TITLE: Discharge of LiPo Batteries Using Saltwater Electrolysis
AUTHORS: marshall.bennett
[DESCRIPTION]
Procedure developed using information gathered from the following sources:
How To Dispose Of Lipo Batteries? - Standard Battery (standardbatteryinc.com)
Discharging & Disposing of LiPo Batteries – HeliDirect Supp... | ["Place the battery into a container that is sealable with a vented lid, such as a five gallon bucket.", "Carefully pour the salt/water solution into the container holding the battery so that it is completely submerged and covered in several inches of water.", "Check for activity from the battery and cover the bucket w... |
null | null | null | dx.doi.org/10.17504/protocols.io.kfjctkn | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<p><strong>Virtualization must be enabled for Docker to work.</strong> This is performed through the BIOS. To access the BIOS you must restart the computer and press the appropriate key immediately upon start up. Each computer has it's own key to enter the BIOS so google you spec... | [] |
47,559 | Protocols for "The genome analysis of Tripterygium wilfordii reveals TwCYP712K1 and TwCYP712K2 responsible for oxidation of friedelin in celastrol biosynthesis pathway" | 2 | dx.doi.org/10.17504/protocols.io.bspfndjn | https://www.protocols.io/view/protocols-for-34-the-genome-analysis-of-tripterygi-bspfndjn | Tianlin Pei, Mengxiao Yan, Yu Kong, Hang Fan, Jie Liu, Mengying Cui, Yumin Fang, Binjie Ge, Jun Yang, Qing Zhao | TITLE: Protocols for "The genome analysis of Tripterygium wilfordii reveals TwCYP712K1 and TwCYP712K2 responsible for oxidation of friedelin in celastrol biosynthesis pathway"
AUTHORS: Tianlin Pei, Mengxiao Yan, Yu Kong, Hang Fan, Jie Liu, Mengying Cui, Yumin Fang, Binjie Ge, Jun Yang, Qing Zhao
[DESCRIPTION]
<div cla... | [] |
67,278 | Standards-Compliant General Protocol for Systematic Reviews | 1 | dx.doi.org/10.17504/protocols.io.n92ldydzxl5b/v3 | https://www.protocols.io/view/standards-compliant-general-protocol-for-systemati-cdxns7me | Paul Whaley, Stephen M Wattam | TITLE: Standards-Compliant General Protocol for Systematic Reviews
AUTHORS: Paul Whaley, Stephen M Wattam
[DESCRIPTION]
This general protocol is designed to support the planning of SRs that are concerned with the effects of environmental exposures on human health outcomes, or the prevention or mitigation thereof.
I... | ["[A. Securing capacity, competencies, and tools] [osf_record] Create an Open Science Framework (OSF) record for the project. \nPRISMA-P 1a, 1b / PROSPERO 1\n\nCreate an OSF record for the project (this template may help https://osf.io/zjevp/ - click the fork button, then click \"duplicate template\", and rename the te... |
null | null | null | dx.doi.org/10.17504/protocols.io.hudb6s6 | null | null | TITLE: No Title
AUTHORS:
[STEPS] | [] |
23,199 | Creative Biolabs Offers Scholarship Worth $1,000 to College Students | null | dx.doi.org/10.17504/protocols.io.2v7ge9n | null | Jerry Carter | TITLE: Creative Biolabs Offers Scholarship Worth $1,000 to College Students
AUTHORS: Jerry Carter
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">New York, US–May 15, 2019 </span><span>Creative Biolabs, a company located in New York, recently launched it 2019 Schola... | ["New York, US–May 15, 2019 Creative Biolabs, a company located in New York, recently launched it 2019 Scholarship Program. For students majoring in chemistry or biology at an accredited college or university, 3.0 GPA or more makes them eligible for this opportunity. The Scholarship can be applied until June 15, 2019. ... |
58,213 | Protocols for safety study of nacre powder in an intra-osseous sheep model | 2 | dx.doi.org/10.17504/protocols.io.b44dqys6 | https://www.protocols.io/view/protocols-for-safety-study-of-nacre-powder-in-an-i-b44dqys6 | dota.iandolo | TITLE: Protocols for safety study of nacre powder in an intra-osseous sheep model
AUTHORS: dota.iandolo
[STEPS] | [] |
44,490 | Tissue Clearing Using CLARITY Method | 1 | dx.doi.org/10.17504/protocols.io.bppimmke | https://www.protocols.io/view/tissue-clearing-using-clarity-method-bppimmke | Seth Currlin, Marda Jorgensen, Jerelyn Nick | TITLE: Tissue Clearing Using CLARITY Method
AUTHORS: Seth Currlin, Marda Jorgensen, Jerelyn Nick
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This document covers the CLARITY protocol for volumetric tissue clearing. This method can be applied to many tissue types and is easily modified. </div><di... | ["[Tissue Clearing using CLARITY method]\nCollect samples into cold 4% PFATissue samples are procured and transferred in cold (4°C) 4% paraformaldehyde (PFA) made with sterile saline or phosphate-buffered saline (PBS) (pH 7.4).When tissue is received for clearing immediately start step 2 below.", "[Tissue Clearing usin... |
63,354 | Vagotomy and Tamoxifen treatment | 4 | dx.doi.org/10.17504/protocols.io.261gen9q7g47/v1 | https://www.protocols.io/view/vagotomy-and-tamoxifen-treatment-b942r8ye | arpine.sokratian, andrew.west | TITLE: Vagotomy and Tamoxifen treatment
AUTHORS: arpine.sokratian, andrew.west
[DESCRIPTION]
This protocol provides the methodology of vagotomy procedure and tamoxifen injections in a murine model, investigating the pathological role of alpha-synuclein in the gastrointestinal (GI) system. The mouse model includes feat... | ["[Vagotomy and Tamoxifen treatment] Perform surgical subdiaphragmatic vagotomy in 1-month-old male and female SNCAbow;Vil-CreERT2 mice.", "[Vagotomy and Tamoxifen treatment] Prior to surgery, sterilize all surgical instruments. Use syringe, needles, sutures, and scalpels from sterile packs, open it at the time of the ... |
60,005 | Quantification of the SARS-CoV-2 using electronegative membrane filtration and dPCR | 4 | dx.doi.org/10.17504/protocols.io.bp2l61xwrvqe/v2 | https://www.protocols.io/view/quantification-of-the-sars-cov-2-using-electronega-b6udres6 | Solana Narum, Thibault Stalder, Erik Coats, Eva Top | TITLE: Quantification of the SARS-CoV-2 using electronegative membrane filtration and dPCR
AUTHORS: Solana Narum, Thibault Stalder, Erik Coats, Eva Top
[DESCRIPTION]
This protocol was developed in an effort to serve as a timely and efficient method for the surveillance of the SARS-CoV-2 in primary influent wastewat... | ["[Sample Collection] Composite primary influent samples are collected over 24 hours with several samples taken each hour.", "[Sample Collection] 100 mL sub-samples are collected in 2 x 50 mL sterile conical tubes. The samples are stored at 4 °C until further processing.", "[Concentration of Viral Fraction]", "[Concent... |
73,279 | iPSC Transduction | 4 | dx.doi.org/10.17504/protocols.io.q26g7y1y1gwz/v1 | https://www.protocols.io/view/ipsc-transduction-cjs7unhn | Ali Albalakhi, Ning Xia | TITLE: iPSC Transduction
AUTHORS: Ali Albalakhi, Ning Xia
[DESCRIPTION]
This is the iPSC transduction protocol.
[GUIDELINES]
Note:
Cells will need to be maintained in StemFlex medium to reform healthy iPSCs colony-like morphology (4-5 days)
Given that we don’t know what viral titer will be toxic to the cells during... | ["[Begin transduction with cell line 7026]", "[Day 1:] Split iPS cells into single cells in complete medium with RVC. (500µl per well)", "[Day 1:] Seed cells at 5.0X104 cells in glass-bottom 24-well plates", "[Day 2: Calculations are for 24-well plates. (If using a 6 well plate, then seed at 1x105 cells per well, 850µL... |
18,043 | Purification of total RNA (microRNA and mRNA) from liquid samples | null | dx.doi.org/10.17504/protocols.io.vu3e6yn | null | atsuko mizoguchi | TITLE: Purification of total RNA (microRNA and mRNA) from liquid samples
AUTHORS: atsuko mizoguchi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Total RNA was extracted from cells and the cultured supernatant and exosome which was extracted from the same amount of supernatant using 3D-Gene® RNA ex... | ["For 300ul of cultured supernatant and exosome in 1.7ml centrifuge tube, add 900 μl 3D-Gene RNA extraction (Toray Industries,Inc., Kanagawa, Japan)reagent from a liquid sample kit.", "Homogenize by vortexing for 1min to mix.Place the tube containing the homogenate on the benchtop\n[incubation]", "[incubation]", "Cent... |
89,588 | Soil eDNA Sample Collection Protocol | 4 | null | https://www.protocols.io/view/soil-edna-sample-collection-protocol-c3quymww | Stephen Douglas Russell | TITLE: Soil eDNA Sample Collection Protocol
AUTHORS: Stephen Douglas Russell
[DESCRIPTION]
**This protocol represents an initial working draft for citizen-science-based collecting and processing of soil samples for eventual eDNA analysis. This notice will be removed once the protocol has been tested and revised.**
Th... | ["[Ordering the kit] This protocol requires that you have a Soil eDNA Sample Collection Kit from Mycota Lab. They can be ordered online here:\n\nhttp://www.mycota.com/shop\n\nBefore ordering the kit, be sure your intended sampling location is not within one of the USDA's APHIS Quarantine Areas. We are not able to accep... |
34,758 | Bionano genome mapping from animal tissue | null | dx.doi.org/10.17504/protocols.io.bd7ei9je | null | Graham J Etherington, Darren Heavens, David Baker, Ashleigh Lister, Rose McNelly, Gonzalo Garcia, Bernardo Clavijo, Iain Macaulay, Wilfried Haerty, Federica Di Palma | TITLE: Bionano genome mapping from animal tissue
AUTHORS: Graham J Etherington, Darren Heavens, David Baker, Ashleigh Lister, Rose McNelly, Gonzalo Garcia, Bernardo Clavijo, Iain Macaulay, Wilfried Haerty, Federica Di Palma
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Bionano genome map protocol<... | ["The Bionano genome maps were prepared by taking approximately of DNA (in this case extracted from a polecat) from the sample stored in 100% EtOH.\n10 mg", "The IrysPrep Animal Tissue DNA Isolation from Fibrous Tissue protocol was followed using the IrysPrep Animal Tissue DNA kit (RE-013-10) from Bionano Genomics.", ... |
95,629 | Preparation of JF dye for retro-orbital injection in mice | 1 | dx.doi.org/10.17504/protocols.io.yxmvm7rznv3p/v2 | https://www.protocols.io/view/preparation-of-jf-dye-for-retro-orbital-injection-c9mmz446 | Boaz Mohar | TITLE: Preparation of JF dye for retro-orbital injection in mice
AUTHORS: Boaz Mohar
[DESCRIPTION]
How to prepare JF dyes for retro orbital injection.
[STEPS]
SECTION: Dye preperation
1. Take an aliqote with 100 nmol of dye from -20 °C storage.
SECTION: Dye preperation
2. Add 20 µL DMSO and do ~10 up and down w... | ["[Dye preperation] Take an aliqote with 100 nmol of dye from -20 °C storage.", "[Dye preperation] Add 20 µL DMSO and do ~10 up and down with the pipeter", "[Dye preperation] Add 20ul Pluronic F-127 20% in DMSO ~10 up and down with the pipeter", "[Dye preperation] Add 60ul 1x PBS ~10 up and down with the pipeter", "[... |
null | null | null | dx.doi.org/10.17504/protocols.io.mjmc4k6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong><em>Gene expression</em></strong> - <strong><em>MQRT-PCR</em></strong></p>
<p>Reverse transcriptase reactions were performed using High Capacity cDNA Reverse transcription kit (Applied Biosystems, FosterCity, CA, USA) according to the manufacturer ’ s protocol with 35... | [] |
33,676 | Separation and purification of human PBMC from BUFFY COAT | null | dx.doi.org/10.17504/protocols.io.bc5kiy4w | https://www.protocols.io/view/separation-and-purification-of-human-pbmc-from-buf-bc5kiy4w | Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino | TITLE: Separation and purification of human PBMC from BUFFY COAT
AUTHORS: Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Separation and purificati... | ["Put the needed amount of blood sample from buffy coat into a 50 ml conical tube.", "Add an equal volume of PBS 1X and mix well.\n{\"blocks\":[{\"data\":[],\"depth\":0,\"entityRanges\":[],\"inlineStyleRanges\":[],\"key\":\"7sj4k\",\"text\":\"\",\"type\":\"unstyled\"},{\"data\":[],\"depth\":0,\"entityRanges\":[],\"inli... |
null | null | null | dx.doi.org/10.17504/protocols.io.ufcetiw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
SECTION: Day Prior to Assay
?.
SECTION: Materials to Prepare
?.
SECTION: Procedure
?.
SECTION: Procedure
?.
SECTION: Procedure
?.
SECTION: Procedure
?.
SECTION: Procedure
?.
SECTION: Procedure
?.
SECTION: Procedure
?.
SECTION: Procedure
?.
SECTION: Procedure
?.
SECTION: Pro... | ["[Day Prior to Assay] Turn on XFp analyzer to warm up overnight\n\nHydrate XFp sensor cartridge\n Add 200 μl XF calibration solution (included with FluxPak) to each well. \n Add 400 μl sterile PBS or H2O to each moat. \n Incubate overnight at 37oC in non-CO2 incubator.", "[Materials to Prepare] Seahorse DMEM ... |
84,695 | Human Follicular Fluid Procurement and Processing | 1 | dx.doi.org/10.17504/protocols.io.eq2lyjpzmlx9/v1 | https://www.protocols.click/view/human-follicular-fluid-procurement-and-processing-cwxxxfpn | hannah.anvari, asma.giornazi, shriya.shah, maryellen.pavone, francesca.e.duncan francesca.duncan | TITLE: Human Follicular Fluid Procurement and Processing
AUTHORS: hannah.anvari, asma.giornazi, shriya.shah, maryellen.pavone, francesca.e.duncan francesca.duncan
[DESCRIPTION]
Purpose: This protocol is intended for use in the collection and storage of human follicular fluid in a research setting. The protocol details... | ["[Collection and processing fluids for storage] Follicular fluid is collected from an individual undergoing an egg retrieval procedure in\n50 mL conical tubes at the Fertility and Reproductive Medicine clinic within Northwestern Medicine and stored at 2-4 °C immediately following collection. Research coordinator will... |
24,388 | sci-ATAC-seq HTAN | null | dx.doi.org/10.17504/protocols.io.33cgqiw | null | Andrew Adey, Andrew Fields, Casey Th, Ryan Mulqueen, Sarah Vitak, Eleonora Juarez | TITLE: sci-ATAC-seq HTAN
AUTHORS: Andrew Adey, Andrew Fields, Casey Th, Ryan Mulqueen, Sarah Vitak, Eleonora Juarez
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Single-cell combinatorial indexing ATAC-seq (Sci-ATAC-seq) workflow fro human cells/tissue.</div><div class = "text-block">This protocol... | ["[Prepare Buffers and Pre-chill ]\nNote: NIB keeps for ~1 month at 4C. For most preparations, 15 mL is sufficient.", "[Nuclear Isolation]\nGeneralized nuclear isolation steps:1. Pellet liquid cultured cells incentrifuge at 500 rcf for 2. Aspirate pellet and resuspend in 3. Incubate on ice for3. Pellet liquid culture... |
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