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 |
|---|---|---|---|---|---|---|---|
63,944 | How to Earn Passive Income through NFTs and DeFi | 3 | dx.doi.org/10.17504/protocols.io.kqdg3pweql25/v1 | https://www.protocols.io/view/how-to-earn-passive-income-through-nfts-and-defi-capgsdjw | Karan Arora | TITLE: How to Earn Passive Income through NFTs and DeFi
AUTHORS: Karan Arora
[DESCRIPTION]
Earning cash with NFTs on BSC and with the aid of using staking AIRT with juicy APYs on AirNFTs may be very worthwhile.
[STEPS] | [] |
70,668 | Control light cycle and measure temperature/humidity in animal housing using Raspberry Pi and Python | 1 | null | https://www.protocols.io/view/control-light-cycle-and-measure-temperature-humidi-cg9ktz4w | Matias Andina | TITLE: Control light cycle and measure temperature/humidity in animal housing using Raspberry Pi and Python
AUTHORS: Matias Andina
[DESCRIPTION]
Python Code and Protocol for controlling animal housing lights, and measure temperature and humidity, using a Raspberry Pi, and ANAVI-light HAT.
[STEPS]
SECTION: Order part... | ["[Order parts] Order ANAVI LIGHT PHAT Advanced Kit (https://www.cro wdsupply.com/anavi-technology/light-phat) and Raspberry Pi (compatible raspberry pi include RPi Zero W and RPi 3B+). This protocol has been tried using a Raspberry Pi 4.", "[Order parts] Measure the length where you want to put your lights.", "[Insta... |
45,219 | Tooth Sampling from the inner pulp chamber for ancient DNA Extraction | 1 | dx.doi.org/10.17504/protocols.io.bqebmtan | https://www.protocols.io/view/tooth-sampling-from-the-inner-pulp-chamber-for-anc-bqebmtan | Gunnar Neumann, Aida Andrades Valtuena, James Fellows Yates, Raphaela Stahl, Guido Brandt | TITLE: Tooth Sampling from the inner pulp chamber for ancient DNA Extraction
AUTHORS: Gunnar Neumann, Aida Andrades Valtuena, James Fellows Yates, Raphaela Stahl, Guido Brandt
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes how to obtain powder from the inner pulp chamber of ... | ["[Workstation preparation]\nPlace a sheet of aluminium foil under the hood.Place weighing paper and drill bits on a sheet of aluminum foil on an easily accessible clean surface outside of the hood. Alternatively, you may place drill bits and weighing paper within hood but be sure to cover them with aluminum foil or a ... |
null | null | null | dx.doi.org/10.17504/protocols.io.kvtcw6n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The appropriate use of clinically accurate diagnostic tests is essential for the detection of pertussis, a poorly controlled vaccine-preventable disease. The purpose of this study was to estimate the sensitivity and specificity of different diagnostic criteria including cultu... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.f25bqg6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p> </p>
<p><em>Collect and preserve samples for flow cytometry analysis. This protocol can be used for lab culture experiments or field samples. </em></p>
<p> </p>
<p> </p>
[STEPS]
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.kpwcvpe | null | null | TITLE: No Title
AUTHORS:
[BEFORE_START]
<p>Prepare CTAB buffer and use within 1-2 weeks</p>
<p> </p>
<p style="margin: 0in; font-family: Calibri; font-size: 12.0pt;"><span style="font-weight: bold;">CTAB buffer (50 ml)</span></p>
<p style="margin-top: 7pt; margin-bottom: 0pt; font-family: Arial; font-size: 10.5pt; co... | [] |
70,816 | P1 private - redesign - collection | 1 | null | https://www.protocols.io/view/p1-private-redesign-collection-chd8t29w | Maria Gul | TITLE: P1 private - redesign - collection
AUTHORS: Maria Gul
[DESCRIPTION]
Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Integer in sapien. Praesent id justo in neque elementum ultrices. Cras elementum. Sed ac dolor sit amet purus malesuada congue. Nunc auctor. Quis autem vel eum iure reprehenderit qui in ... | ["Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Integer in sapien. Praesent id justo in neque elementum ultrices. Cras elementum. Sed ac dolor sit amet purus malesuada congue. Nunc auctor. Quis autem vel eum iure reprehenderit qui in ea voluptate velit esse quam nihil molestiae consequatur, vel illum qui do... |
null | null | null | dx.doi.org/10.17504/protocols.io.qgzdtx6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Ocular images play an essential role in ophthalmology. Current research mainly focus on computer-aided diagnosis using slit-lamp images, however few studies have been done to predict the progression of ophthalmic disease. Therefore by exploring an effective approach of predic... | [] |
92,580 | Visium CytAssist FFPE v4 -- University of Minnesota TMCs | 1 | dx.doi.org/10.17504/protocols.io.n92ldmn99l5b/v4 | https://www.protocols.io/view/visium-cytassist-ffpe-v4-university-of-minnesota-t-c6nczdaw | Laura J Niedernhofer, David A Bernlohr | TITLE: Visium CytAssist FFPE v4 -- University of Minnesota TMCs
AUTHORS: Laura J Niedernhofer, David A Bernlohr
[DESCRIPTION]
The Visium CytAssist Spatial Gene Expression for FFPE assay is designed to analyze mRNA in
tissue sections derived from formalin fixed & paraffin embedded (FFPE) tissue samples. The Visium
CytA... | ["[Deparaffinization, H&E Staining, Imaging & Decrosslinking]", "[Library Preparation & Sequencing]", "[FASTQ Generation] BCL data from Illumina sequencer is demultiplexed and converted into FASTQ format using bcl2fastq software version 2.20.0"] |
106,282 | Analysis of ethylene glycol and 1,4-butanediol by HPLC-RID | 6 | dx.doi.org/10.17504/protocols.io.6qpvr8wrplmk/v1 | https://www.protocols.io/view/analysis-of-ethylene-glycol-and-1-4-butanediol-by-dj2i4qce | 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 ethylene glycol and 1,4-butanediol 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 chromatography ... | ["[Preparation of standards] Standards\n\nPrepare a 10 mg/mL ethylene glycol stock standard by weighing 50 mg of the ethylene glycol raw material into a 20 mL amber vial. Record the weight of the raw material to the nearest 0.1 mg. Add 5 mL of UPW to amber vial and vortex thoroughly until raw material is dissolved.\n... |
63,342 | Lean Start Keto Reviews & Shark Tank 2022 | 1 | dx.doi.org/10.17504/protocols.io.36wgq7e23vk5/v1 | https://www.protocols.io/view/lean-start-keto-reviews-amp-shark-tank-2022-b94nr8ve | leanstartketoreviewsas | TITLE: Lean Start Keto Reviews & Shark Tank 2022
AUTHORS: leanstartketoreviewsas
[DESCRIPTION]
Lean Start Keto Reviews & Shark Tank 2022
[STEPS]
1. Before we dive into spare launch keto reviews proper, it's intriguing how numerous people want to lose weight but unfortunately not all actually know the secret to... | ["Before we dive into spare launch keto reviews proper, it's intriguing how numerous people want to lose weight but unfortunately not all actually know the secret to lose weight and this is why you see it's only a many people that achieve the thing of losing weight. The question you should ask yourself is what's the se... |
null | null | null | dx.doi.org/10.17504/protocols.io.mfdc3i6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Background</strong></p>
<p>Advances in bronchoscopy and CT-guided lung biopsy have improved the evaluation of small pulmonary lesions (PLs), leading to an increase in preoperative histological diagnosis.</p>
<p>We aimed to evaluate the efficacy and safety of transbron... | [] |
67,659 | Designing Knockout Oligonucleotides (Instructor Protocol) | 1 | null | https://www.protocols.io/view/designing-knockout-oligonucleotides-instructor-pro-cebjtakn | Brian P Teague | TITLE: Designing Knockout Oligonucleotides (Instructor Protocol)
AUTHORS: Brian P Teague
[DESCRIPTION]
This is the instructor protocol for Designing Knockout Oligonucleotides, linked below.
[STEPS]
SECTION: Lab Setup
1. This is a "dry" lab - no pipetting involved. Each group of students will need a computer or a ... | ["[Lab Setup] This is a \"dry\" lab - no pipetting involved. Each group of students will need a computer or a laptop.", "[Lab Setup] If there are any genes that students should not choose, prepare this list in advance. In our case, students cannot pick any genes that have already been successfully knocked out. (Because... |
60,215 | Homemade Tn5 transposome assembly and activity evaluation | 4 | dx.doi.org/10.17504/protocols.io.n2bvj69z5lk5/v1 | https://www.protocols.io/view/homemade-tn5-transposome-assembly-and-activity-eva-b62xrgfn | Wei Xu | TITLE: Homemade Tn5 transposome assembly and activity evaluation
AUTHORS: Wei Xu
[DESCRIPTION]
Tn5 Transposome Assembly and Activity Assessment.
[BEFORE_START]
This protocol is basically for homemade Tn5 assembly and activity evaluation in ISSAAC-seq. Tn5 activity is determined by bulk ATAC-seq experiments, which mim... | ["[Reagent setup] Mix 25ul ME_A (100μM) with 25ul ME_Bottom (100μM) in a PCR tube → 50ul Annealed ME_A (50μM) Mix 25ul ME_B (100μM) with 25ul ME_Bottom (100μM) in a PCR tube → 50ul Annealed ME_B (50μM)", "[Reagent setup] Annealing: by denaturing the oligos at 98oC first, and then slowly lowering the temperature from ... |
60,048 | Static insulin secretion analysis of isolated islets | 4 | dx.doi.org/10.17504/protocols.io.bp2l61dxkvqe/v1 | https://www.protocols.io/view/static-insulin-secretion-analysis-of-isolated-isle-b6vqre5w | Julien Ghislain, Vincent Poitout, Caroline CT Tremblay, Marine Croze | TITLE: Static insulin secretion analysis of isolated islets
AUTHORS: Julien Ghislain, Vincent Poitout, Caroline CT Tremblay, Marine Croze
[DESCRIPTION]
This protocol describes the steps to measure insulin secretion in a static, 1-hour assay from isolated pancreatic islets. It is suitable for islets isolated from b... | ["[Preparation of KRB solution and plates] Prepare KRB stocks\nKRB stock I: weigh 27.7 g NaCl bring to 1 L with milliQ water\nKRB stock II: weigh 1.494 g CaCl2•2H2O and bring to 1 L with milliQ water\nKRB stock III: weigh 0.648 g KH2PO4 and bring to 1 L with milliQ water\nKRB stock IV: weigh 1.415 g KCl, 1.17 g MgSO4•7... |
36,854 | child 2 document | null | dx.doi.org/10.17504/protocols.io.bf8wjrxe | https://www.protocols.io/view/child-2-document-bf8wjrxe | Mariia Guliakina, test masha | TITLE: child 2 document
AUTHORS: Mariia Guliakina, test masha
[STEPS] | [] |
98,085 | Assaying NLRP3-mediated LDH and IL-1β release | 0 | dx.doi.org/10.17504/protocols.io.dm6gpzr3plzp/v1 | https://www.protocols.io/view/assaying-nlrp3-mediated-ldh-and-il-1-release-db2d2qa6 | Harper JW, Louis R R Hollingsworth | TITLE: Assaying NLRP3-mediated LDH and IL-1β release
AUTHORS: Harper JW, Louis R R Hollingsworth
[DESCRIPTION]
A general protocol for assaying NLRP3 activation through the downstream release of LDH and IL-1β from cells. Included are protocol for iBMDMs and THP-1 macrophages.
[STEPS]
SECTION: Overview
1. Optimize thes... | ["[Overview] Optimize these protocol for your particular cells lines, treatment regimens, assay kits, etc. on the smaller scale with wild-type (and control NLRP3-KO, if on hand) cells prior to proceeding with large scale experiments. The sensitivity of the particular plate readers you have available is an important fac... |
91,804 | BIT 577 QIIME2 Tutorial | 1 | dx.doi.org/10.17504/protocols.io.5jyl8pqe9g2w/v1 | https://www.protocols.io/view/bit-577-qiime2-tutorial-c5v4y68w | Isabella Livingston | TITLE: BIT 577 QIIME2 Tutorial
AUTHORS: Isabella Livingston
[DESCRIPTION]
Command line scripts for processing and analyzing 16S amplicon data using QIIME2.
[STEPS]
1. Download conda through the QIIME2 website or miniconda website. After installation, download and install QIIME2
2. Activate Qiime environment:
conda ... | ["Download conda through the QIIME2 website or miniconda website. After installation, download and install QIIME2", "Activate Qiime environment:\n\nconda activate qiime2-amplicon-2023.9 \n\n# change out to whatever version has been downloaded", "Import data \n\nqiime tools import \\\n --type 'SampleData[SequencesWithQ... |
45,317 | 3.3 Lentivirus Production and Transduction | 1 | dx.doi.org/10.17504/protocols.io.bqhdmt26 | https://www.protocols.io/view/3-3-lentivirus-production-and-transduction-bqhdmt26 | Evelyn J. Sauter, Lisa K. Kutsche, Simon D. Klapper, Volker Busskamp | TITLE: 3.3 Lentivirus Production and Transduction
AUTHORS: Evelyn J. Sauter, Lisa K. Kutsche, Simon D. Klapper, Volker Busskamp
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This is part 3.3 of the "</span><a href="https://www.protocols.io/private/C65DB81838BC11EBA61A0A58A9FEAC2A/protocols" ... | ["[3.3 Lentivirus Production and Transduction]\nFor the production and transduction of lentiviruses, titration and copy number determination, we follow the protocol from the Trono lab [8].", "[3.3 Lentivirus Production and Transduction]\nOne day prior to transfection, seed 8,000,000 293T/17 cells in a 10 cm culture dis... |
50,346 | Ethical Considerations and Compliance with Good Clinical Practice (Part 12 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.bvein3ce | https://www.protocols.io/view/ethical-considerations-and-compliance-with-good-cl-bvein3ce | Stephen.Gitelman , Jeffrey A. Bluestone | TITLE: Ethical Considerations and Compliance with Good Clinical Practice (Part 12 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 ... | [] |
21,765 | Determination of florfenicol and florfenicol amine in fish plasma (Salmo salar) through HPLC MS/MS | null | dx.doi.org/10.17504/protocols.io.zhdf326 | null | Betty San Martín, Lisette Lapierre, Marcela Fresno, Javiera Cornejo | TITLE: Determination of florfenicol and florfenicol amine in fish plasma (Salmo salar) through HPLC MS/MS
AUTHORS: Betty San Martín, Lisette Lapierre, Marcela Fresno, Javiera Cornejo
[STEPS]
?. [Sample preparation]
of each plasma sample were placed in Falcon tubes and and were added.
250 µl
15 ml
500 µl
2 ml
?. [Samp... | ["[Sample preparation]\nof each plasma sample were placed in Falcon tubes and and were added.\n250 µl\n15 ml\n500 µl\n2 ml", "[Sample preparation]\nExtraction was carried out according to the method described by Li et al. (2006), with modifications.", "[Sample preparation]\nThe tubes were shaken for , sonicated for a... |
51,281 | Conexão do actígrafo no computador - ActTrust | 5 | dx.doi.org/10.17504/protocols.io.bwbrpam6 | https://www.protocols.io/view/conex-o-do-act-grafo-no-computador-acttrust-bwbrpam6 | Daniel Vartanian | TITLE: Conexão do actígrafo no computador - ActTrust
AUTHORS: Daniel Vartanian
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Este protocolo faz parte do processo de coleta de dados actigráficos do Grupo Interdisciplinar de Pesquisa em Sono (GIPSO). Ele foi desenhado para os actígrafos prove... | ["Abra o software ActStudio\nCaso apareça algum pop-up solicitando a configuração da latitude e longitude, clique em Não. Para este procedimento essa configuração não é necessária.", "Acesse a tela Controle\nNa parte superior do ActStudio você verá um botão chamado Controle. Clique sobre ele e depois selecione a aba CO... |
null | null | null | dx.doi.org/10.17504/protocols.io.iarcad6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?. | [] |
94,433 | Immunofluorescence on human brain FFPE sections to identify neuromelanin in A6, A9, and A10 | 4 | dx.doi.org/10.17504/protocols.io.81wgbxejolpk/v1 | https://www.protocols.io/view/immunofluorescence-on-human-brain-ffpe-sections-to-c8f9ztr6 | Hongyun Li, YuHong Fu | TITLE: Immunofluorescence on human brain FFPE sections to identify neuromelanin in A6, A9, and A10
AUTHORS: Hongyun Li, YuHong Fu
[DESCRIPTION]
This is the protocol to scan brain neuromelanin with reduced impact of the chemicals on their original colour and intensity. The immunofluorescence staining protocol is design... | ["[Preparation] Select sections, label the staining method on slides, and load slides to slide racks.", "[Preparation] Check the medium and reagents ready for use.", "[Deparaffin and rehydration] Bake the slides in a 60 °C oven for one hour.", "[Deparaffin and rehydration] Dip slides in HistoChoice for 2 x 7 minutes."... |
null | null | null | dx.doi.org/10.17504/protocols.io.k97cz9n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Giardia is a protozoan parasite of public health relevance that causes gastroenteritis in a wide range of hosts. Two genetically distinct lineages (assemblages A and B) are responsible for the human disease. Although it is clear that differences in virulence occur, pathogenes... | [] |
60,667 | An X-HTDC method for estimating particulate phosphorus from microalgae | 6 | null | https://www.protocols.io/view/an-x-htdc-method-for-estimating-particulate-phosph-b7g3rjyn | Yingyu Hu, Zoe V. Finkel | TITLE: An X-HTDC method for estimating particulate phosphorus from microalgae
AUTHORS: Yingyu Hu, Zoe V. Finkel
[DESCRIPTION]
Here we describe a protocol to estimate particulate phosphorus associated with microalgae using an extra-high temperature dry combustion method (X-HTDC). An 800°C-combustion can completely dec... | ["[Sampling] Sampling microalgae for total particulate phosphorus (i.e. intracellular phosphorus and adsorbed phosphorus)", "[Sampling] Filter microalgae in liquid media onto polycarbonate filters, using gentle vacuum pressure (5 inches Hg).", "[Sampling] Rinse samples with filtered seawater", "[Sampling] Place sample ... |
64,303 | High Molecular Weight Total DNA Extraction from plant tissues for Long Read Sequencing | 4 | dx.doi.org/10.17504/protocols.io.14egn7yy6v5d/v1 | https://www.protocols.io/view/high-molecular-weight-total-dna-extraction-from-pl-ca2psgdn | Subash Rai | TITLE: High Molecular Weight Total DNA Extraction from plant tissues for Long Read Sequencing
AUTHORS: Subash Rai
[DESCRIPTION]
This protocol was developed as a research within GIH collaborative projects for a sample where a species of Neptunia leaves sample was problematic in our previously developed protocol. At st... | ["[Tissues preparation and lysis] Take 10 mL lysis buffer and warm it at 60 °C for 15-20 min.", "[Tissues preparation and lysis] Take ~1 L of liquid nitrogen (LN2) in Dewar Flask that requires for chilling mortar and pestle and grinding the tissues.", "[Tissues preparation and lysis] Take dry ice in an esky/insulated c... |
69,714 | 城市微生物菌相調查計畫 — 採集土壤教學 | 1 | dx.doi.org/10.17504/protocols.io.e6nvwj6p7lmk/v1 | https://www.protocols.io/view/protocol-cgbstsne | Hsin-Mao Wu | TITLE: 城市微生物菌相調查計畫 — 採集土壤教學
AUTHORS: Hsin-Mao Wu
[DESCRIPTION]
城市微生物菌相調查計畫 — 採集土壤教學
[STEPS]
SECTION: 如何加入專案
1. 開啟Line app，將頁面切換成「聊天」，並按下頂部的掃描圖示(紅框處)
SECTION: 如何加入專案
2. 掃描以下QR code或點選此連結微生物公民科學
SECTION: 如何加入專案
3. 加入成功後會顯示以下畫面
SECTION: 如何加入專案
4. 接著等待採集工具包寄送即可開始採集！
SECTION: 採土
5. 移除表土，取距離土表5~7公分之處的土，裝入塑膠夾鏈袋... | ["[如何加入專案] 開啟Line app，將頁面切換成「聊天」，並按下頂部的掃描圖示(紅框處)", "[如何加入專案] 掃描以下QR code或點選此連結微生物公民科學", "[如何加入專案] 加入成功後會顯示以下畫面", "[如何加入專案] 接著等待採集工具包寄送即可開始採集！", "[採土] 移除表土，取距離土表5~7公分之處的土，裝入塑膠夾鏈袋中\n[示意圖片待補]", "[採土] 將塑膠袋中的土均勻混合，倒入採集罐之中", "[採土] 在採集紀錄紙上勾選採樣地點、採樣種類，以及填寫日期、城市、鄉鎮、地點、採集者等資訊", "[採土] 最後拍兩張照片", "[採土] 打開iNaturalist app，上傳剛剛拍攝的兩張照片... |
null | null | null | dx.doi.org/10.17504/protocols.io.imhcc36 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Test cropora for evaluation of drNER, together with the obtained results for each documment, separetly.</p>
[GUIDELINES]
<p>drNER is a rule-based Named-entity recognition method for knowledge extraction of evidence-based dietary recommendations.</p>
<p> </p>
<p>The files are... | [] |
62,943 | ONT DNA Extraction for Fungal Barcoding | 4 | null | https://www.protocols.io/view/ont-dna-extraction-for-fungal-barcoding-b9p7r5rn | Stephen Douglas Russell | TITLE: ONT DNA Extraction for Fungal Barcoding
AUTHORS: Stephen Douglas Russell
[DESCRIPTION]
Below you will find a simple and fast two-step DNA extraction protocol that works well with many different groups of fungi. This protocol can be utilzed in preparation for DNA barcoding of fungi utilizing Oxford Nanopor... | ["[X-Amp Extractions] Place 15 µL to 25 µL of into each cell of 8-well PCR strip. I typically use 20 µL. Using less solution means the overall cost basis per sample will be lower. \n\n96 well plates could also be used for this extraction protocol. Even though it costs more, I prefer to use 8-strips as they are easie... |
67,713 | Human myocardium decellularization | 4 | dx.doi.org/10.17504/protocols.io.4r3l2o22xv1y/v2 | https://www.protocols.io/view/human-myocardium-decellularization-cec9taz6 | Immacolata Belviso, Anna Maria Sacco, Domenico Cozzolino, Daria Nurzynska, Franca Di Meglio, clotilde.castaldo, Veronica Romano | TITLE: Human myocardium decellularization
AUTHORS: Immacolata Belviso, Anna Maria Sacco, Domenico Cozzolino, Daria Nurzynska, Franca Di Meglio, clotilde.castaldo, Veronica Romano
[DESCRIPTION]
The protocol represents a step-by-step method to obtain a decellularized cardiac matrix through the combination of sodium dode... | ["[Preparation of decellularizing solution] Preparation of 600 mL of decellularizing solution", "[Preparation of decellularizing solution] Prepare 300 mL of 2% Triton X-100 solution by measuring 294 mL of double-distilled water in a graduated cylinder and transferring it to a 500 mL beaker.", "[Preparation of decellula... |
74,703 | Protocol for vagus nerve stimulation in awake pigs (subject-4) | 1 | dx.doi.org/10.17504/protocols.io.14egn24ryg5d/v1 | https://www.protocols.io/view/protocol-for-vagus-nerve-stimulation-in-awake-pigs-ck7puzmn | Oliver Armitage | TITLE: Protocol for vagus nerve stimulation in awake pigs (subject-4)
AUTHORS: Oliver Armitage
[DESCRIPTION]
The Vagus nerve innervates a number of thoracic and visceral organs. Exogenous nervous signal, for example, Vagus nerve stimulation (VNS) provides a route to modulating their function for therapeutic purposes. ... | ["[Subjects] Female swine of adult age and weight between 35—55 kg for the experimental design were used.", "[Surgery] Position pig prone and mark neck where the skin implant is to be placed along with the incisions on the neck. Mark where the ECG leads will go on the backside of the subject.", "[Surgery] Cut out circl... |
70,881 | Collection, Broadcast, Packaging and Shipping of Non-Islet Biomaterials | 4 | dx.doi.org/10.17504/protocols.io.81wgby71nvpk/v1 | https://www.protocols.click/view/collection-broadcast-packaging-and-shipping-of-non-chf9t3r6 | Integrated Islet Distribution Program | TITLE: Collection, Broadcast, Packaging and Shipping of Non-Islet Biomaterials
AUTHORS: Integrated Islet Distribution Program
[DESCRIPTION]
This SOP defines a standardized method for processing, broadcasting, packaging and shipping preparation of research quality non-islet biomaterials SOP. These tissues may be mat... | ["[Collection of Acinar/NIPT for Distribution (Fresh and Frozen)] The NIPT (the tissue remaining in the COBE purification bag) should be transferred under sterile conditions, into two 250 mL conical tubes, as soon as feasible during the islet isolation process. Top with HBSS, cap, invert to mix and dilute Ficoll, and... |
71,516 | Novel Object Recognition test for rats, AJA, 10/18/22 | 1 | null | https://www.protocols.io/view/novel-object-recognition-test-for-rats-aja-10-18-2-ch34t8qw | Alicia Avelar | TITLE: Novel Object Recognition test for rats, AJA, 10/18/22
AUTHORS: Alicia Avelar
[DESCRIPTION]
Purpose: to study animal memory using recognition of a familiar object vs. a novel object
[BEFORE_START]
Need to establish that protocol fully works with naive animals. Potentially accounting for side of chamber and obj... | ["[3D printing] Objects were printed on Prusa 3D printers using ultimaker cura software at the UCSD digital media lab in the Geisel library.", "[3D printing] The object sizes were standardized as much as possible depending on the objects shape.", "[3D printing] 2 of the object shapes were from Inayat et al., 2021 publ... |
null | null | null | dx.doi.org/10.17504/protocols.io.htmb6k6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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null | null | null | dx.doi.org/10.17504/protocols.io.fdnbi5e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is used to stain late larval <em>Drosophila</em> lipid droplets in fat bodies and intestines with Nile Red, which emits fluorescence in the 552/636 nm range. </p>
[BEFORE_START]
<p>1. Prepare Nile Red (Sigma-Aldrich) in acetone (1000 ug/mL).</p>
<p>2. Dissect t... | [] |
54,752 | Illumination Power and illumination stability | 1 | dx.doi.org/10.17504/protocols.io.bzp8p5rw | https://www.protocols.io/view/illumination-power-and-illumination-stability-bzp8p5rw | Nathalie Gaudreault, Steve Bagley, Rodrigo R Bammann, Fabio Barachati, Laszlo Barna, Veronika Boczonadi, Ulrike Boehm, Manel Bosch, Craig Brideau, Mariana T Carvalho, Pina Colarusso, Richard Cole, Nasser Darwish-Miranda, Sam Duwé, Frank Eismann, Orestis Faklaris, Andreas Felscher, Manfred Gonnert, David... | TITLE: Illumination Power and illumination stability
AUTHORS: Nathalie Gaudreault, Steve Bagley, Rodrigo R Bammann, Fabio Barachati, Laszlo Barna, Veronika Boczonadi, Ulrike Boehm, Manel Bosch, Craig Brideau, Mariana T Carvalho, Pina Colarusso, Richard Cole, Nasser Darwish-Miranda, Sam Duwé, Frank Eismann,... | ["[Illumination power measurement] Warm up the entire system, including the illumination source (i.e.lasers).", "[Illumination stability measurement] Proceed with the power measurement and measure illumination power in mW over time for each wavelength (excitation wavelength, Figure 3A) as follows: for short-term stabil... |
64,444 | Tyler Perry CBD Gummies Benefits,Ingredients,side effects and Is it legitor Does it Really Work Shark TankReviews [HOAX OR SCAM]{Update 2022}-, What To Know Before Using It?? | 1 | dx.doi.org/10.17504/protocols.io.kqdg3pwjpl25/v1 | https://www.protocols.io/view/tyler-perry-cbd-gummies-benefits-ingredients-side-ca64shgw | diljaan | TITLE: Tyler Perry CBD Gummies Benefits,Ingredients,side effects and Is it legitor Does it Really Work Shark TankReviews [HOAX OR SCAM]{Update 2022}-, What To Know Before Using It??
AUTHORS: diljaan
[DESCRIPTION]
You plan to recuperate just as truly feel over and above anyone's expectations previously! However when ... | ["Tyler Perry CBD Gummies\nProduct Review: —Tyler Perry CBD GummiesUsed For: — 🔶Pain Relief🔶Health Benefits\n🔶Burn excess fat\n🔶Better gut health & promote digestion\n🔶Improves heart health\n🔶Control your appetite\n➢ Where to Buy - 🔶Click Here to Rush Your Order from the Official Website\n➤ Price (for Sale) Buy... |
57,940 | Processing Stack-of-Stars DCE Data | 1 | dx.doi.org/10.17504/protocols.io.5qpvobb2bl4o/v1 | https://www.protocols.io/view/processing-stack-of-stars-dce-data-b4tuqwnw | Rong Zhou | TITLE: Processing Stack-of-Stars DCE Data
AUTHORS: Rong Zhou
[DESCRIPTION]
Step-wise protocol for reconstruction of Stack-of-stars acquired DCE series, T1 and B1 maps and PK (pharmacokinetic) modeling of DCE data using a reference region model is provided.
[STEPS]
SECTION: Reconstruction of Stack-of Stars (SoS) radi... | ["[Reconstruction of Stack-of Stars (SoS) radial k-space sampled DCE data] Image reconstruction", "VFA and AFI images\n\nThe same reconstruction procedure is used for images acquired by the variable flip angle (VFA) and actual flip angle (AFI) stack-of-stars (SoS) pulse sequences. \n\nApply a Fourier transform in the s... |
87,654 | Polymerase Chain Reaction (PCR) | 1 | dx.doi.org/10.17504/protocols.io.261gedrndv47/v1 | https://www.protocols.io/view/polymerase-chain-reaction-pcr-czuex6te | NUS iGEM | TITLE: Polymerase Chain Reaction (PCR)
AUTHORS: NUS iGEM
[DESCRIPTION]
This is the common Polymerase Chain Reaction (PCR) protocol followed by the 2023 NUS-Singapore iGEM team.
[STEPS]
4. Vortex the PCR tubes to mix well.
3. For a 50μL PCR sample, add the following into a PCR tube (follow the sequence):
5. Place... | ["Vortex the PCR tubes to mix well.", "For a 50μL PCR sample, add the following into a PCR tube (follow the sequence):", "Place the PCR tube into the Thermal Cycler with the following conditions:\n\n**Lid Temperature: 105°C; Volume: 50μL", "Upon finishing, cancel the current protocol and take out the PCR sample from th... |
104,299 | Ex vivo imaging of ovulation in mouse ovarian follicles | 0 | dx.doi.org/10.17504/protocols.io.14egn6nxql5d/v1 | https://www.protocols.io/view/ex-vivo-imaging-of-ovulation-in-mouse-ovarian-foll-dh4j38un | Christopher Thomas, Tabea-Lilian Marx, Sarah Mae Penir, Melina Schuh | TITLE: Ex vivo imaging of ovulation in mouse ovarian follicles
AUTHORS: Christopher Thomas, Tabea-Lilian Marx, Sarah Mae Penir, Melina Schuh
[DESCRIPTION]
Understanding ovarian function requires a clear and detailed picture of biological processes that take place deep inside the body, within a narrow window of time. E... | ["[Isolation, culture and imaging of mouse ovarian follicles for the study of ovulation] Prepare 10 ml of isolation medium and 10 ml of culture medium: \n\nIsolation medium\n9.4 ml Alpha-MEM (1X) + GlutaMAX + HEPES (Thermo Fisher, 42360032)\n100 µl 100 IU/ml Penicillin-Streptomycin (Gibco, 15140122)\n500 µl FBS (Gibco... |
106,465 | Washington University SenNet Case Collection Protocol | 1 | dx.doi.org/10.17504/protocols.io.bp2l699rdlqe/v2 | https://www.protocols.io/view/washington-university-sennet-case-collection-proto-dj794rr6 | Daniel Rapp, Matthew Wyczalkowski | TITLE: Washington University SenNet Case Collection Protocol
AUTHORS: Daniel Rapp, Matthew Wyczalkowski
[DESCRIPTION]
This document outlines inclusion and exclusion criteria for healthy participants for the WUSTL Senescence Network (SenNet) by the Tissue Mapping Center (TMC) at Washington University.
[STEPS]
1. Stud... | ["Study coordinator will receive surgeon schedules at the beginning of each week. All surgeons should be IRB approved for the study.", "Study coordinator will evaluate patient for eligibility using criteria detailed in following sections.", "Study coordinator will call potential study participants over phone using IRB ... |
80,765 | Sargassum Island Sustainability | 4 | dx.doi.org/10.17504/protocols.io.3byl4jnjjlo5/v1 | https://www.protocols.io/view/sargassum-island-sustainability-cs45wgy6 | jfermelia | TITLE: Sargassum Island Sustainability
AUTHORS: jfermelia
[DESCRIPTION]
The purpose of this research proposal is to analyze the of sargassum harvesting and implementation for agricultural use on Moorea. Sargassum is increasingly growing in abundance and has been noted to have beneficial effects on the growth and yield... | ["[Pre- Establishment Monitoring] Sections of the bay will need to be identified. Sights should be independently selected from one another. Data will be primarily observed site specifically and thus similarities between all sites is not required. Selecting slightly different sites between areas can also increase the sc... |
69,161 | Git workflow | 5 | dx.doi.org/10.17504/protocols.io.dm6gpje81gzp/v1 | https://www.protocols.io/view/git-workflow-cfshtnb6 | Naeem.Muhammad | TITLE: Git workflow
AUTHORS: Naeem.Muhammad
[DESCRIPTION]
Git workflow for research group Numa
[STEPS]
SECTION: Numa_Git_Workflow
1. Create feature branch
SECTION: Numa_Git_Workflow
2. Make required changes
SECTION: Numa_Git_Workflow
4. Push feature branch to remote
SECTION: Numa_Git_Workflow
5. Create a merg... | ["[Numa_Git_Workflow] Create feature branch", "[Numa_Git_Workflow] Make required changes", "[Numa_Git_Workflow] Push feature branch to remote", "[Numa_Git_Workflow] Create a merge request", "[Numa_Git_Workflow] Commit changes"] |
null | null | null | dx.doi.org/10.17504/protocols.io.gepbtdn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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103,191 | Generating pPB-CAG-mCherry-CAAX Plasmid | 0 | dx.doi.org/10.17504/protocols.io.4r3l2q34pl1y/v1 | https://www.protocols.io/view/generating-ppb-cag-mcherry-caax-plasmid-dgzx3x7n | Shiyi Wang | TITLE: Generating pPB-CAG-mCherry-CAAX Plasmid
AUTHORS: Shiyi Wang
[DESCRIPTION]
Generating pPB-CAG-mCherry-CAAX Plasmid
[STEPS]
1. **Obtain Plasmids** - Obtain pPB-CAG-EGFP and pGLAST-PBase plasmids from Dr. Joseph Loturco.
2. **Insert mCherry-CAAX into pPB-CAG-EGFP** - Insert mCherry-CAAX between XmaI and NotI rest... | ["**Obtain Plasmids** - Obtain pPB-CAG-EGFP and pGLAST-PBase plasmids from Dr. Joseph Loturco.", "**Insert mCherry-CAAX into pPB-CAG-EGFP** - Insert mCherry-CAAX between XmaI and NotI restriction sites in pPB-CAG-EGFP to replace EGFP.", "**Insert hU6 Promoter and shRNA into pPB-CAG-mCherry-CAAX** - Amplify a DNA fragme... |
51,667 | Identification of differentially expressed long noncoding RNAs and pathways in liver tissues from rats with hepatic fibrosis | 1 | dx.doi.org/10.17504/protocols.io.bwptpdnn | https://www.protocols.io/view/identification-of-differentially-expressed-long-no-bwptpdnn | Xiong Xiao, Yan Wang, Xiaozhong Wang | TITLE: Identification of differentially expressed long noncoding RNAs and pathways in liver tissues from rats with hepatic fibrosis
AUTHORS: Xiong Xiao, Yan Wang, Xiaozhong Wang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">To identify long non-coding RNAs (lncRNAs) and their potential roles in he... | ["RNA-Seq Raw Data Clean and Alignment", "Raw reads containing more than 2-N bases were first discarded.", "Then adaptors and low-quality bases were trimmed from raw sequencing reads using FASTX-Toolkit (Version 0.0.13). The short reads less than 16nt were also dropped.", "After that, clean reads were aligned to the GR... |
52,460 | Xoth Cbd gummmies Reviews | 1 | dx.doi.org/10.17504/protocols.io.bxgkpjuw | https://www.protocols.io/view/xoth-cbd-gummmies-reviews-bxgkpjuw | health | TITLE: Xoth Cbd gummmies Reviews
AUTHORS: health
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Xoth Cbd Gummies >> >> >> HURRY UP LImite Stockl Left {Big Sale Only For Today} As Low As Before price</div></div>
[STEPS]
?. Product Name: Xoth cbd Gummies Only Available On Official Website: www.X... | ["Product Name: Xoth cbd Gummies Only Available On Official Website: www.Xothcbdgummies.comXoth CBD Gummies are one of the top-selling CBD edibles used to treat chronic pain & inflammation, muscle recovery, and anxiety. Made with the highest quality Nutrition CBD, Xoth Cbd Gummies can improve virtually every aspec... |
98,117 | IRIS Software Protocol | 0 | dx.doi.org/10.17504/protocols.io.3byl497wjgo5/v1 | https://www.protocols.io/view/iris-software-protocol-db3d2qi6 | Leonardo Zilli, Erica Andreose, Salvatore Di Marzo | TITLE: IRIS Software Protocol
AUTHORS: Leonardo Zilli, Erica Andreose, Salvatore Di Marzo
[DESCRIPTION]
This project aims to investigates the discoverability of University of Bologna's scholarly output within OpenCitations Meta, a platform that stores and delivers bibliographic metadata for alle the publications invol... | ["[IRIS Dataset Preparation] After downloading the IRIS dataset, the contents appear divided into 7 different csv files, descriptive as the following:\n- \"ODS_L1_IR_ITEM_CON_PERSON.csv\": information about the people involved in the publications (authors, editors, etc.)\n- \"ODS_L1_IR_ITEM_DESCRIPTION.csv\": the strin... |
null | null | null | dx.doi.org/10.17504/protocols.io.tihekb6 | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<table cellspacing="0" cellpadding="0" align="center">
<tbody>
<tr>
<td align="left" bgcolor="#FFFFFF" width="450">
<ul>
<li>Cell Staining Buffer (BioLegend Cat. No. <a href="https://www.biolegend.com/cell-staining-buffer-1494.html" target="_blank" rel="noopener noreferrer">42020... | ["[Harvest Tissue or Cells] {\"blocks\":[{\"key\":\"85vo7\",\"text\":\"Obtain desired tissue (e.g. spleen, lymph node, thymus, bone marrow) and prepare a single cell suspension in Cell Staining Buffer (BioLegend Cat. No. 420201). If using in vitro stimulated cells, simply resuspend previously activated cultures in Cell... |
44,357 | Collecting Bark and Ambrosia Beetles | 3 | dx.doi.org/10.17504/protocols.io.bpjdmki6 | https://www.protocols.io/view/collecting-bark-and-ambrosia-beetles-bpjdmki6 | Jiri Hulcr, Andrew J. Johnson, Demian F Gomez | TITLE: Collecting Bark and Ambrosia Beetles
AUTHORS: Jiri Hulcr, Andrew J. Johnson, Demian F Gomez
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the different methods to collect and preserve bark ambrosia beetles. </div><div class = "text-block"><span>This protocol is part ... | [] |
22,232 | Hybridization-capture for nanopore sequencing | null | dx.doi.org/10.17504/protocols.io.zxyf7pw | null | Isac Lee, Rachael Workman, Josh Zhiyong Wang, Winston Timp | TITLE: Hybridization-capture for nanopore sequencing
AUTHORS: Isac Lee, Rachael Workman, Josh Zhiyong Wang, Winston Timp
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Large-scale genomic anomalies – structural variations (SVs) – are pervasive in cancer. Due to the scale of the SVs and the repetiti... | ["[Post adapter-ligation PCR]\nSplit 40 ul eluate to 2 x 20 μL", "[Shearing with Bioruptor Pico]\nShear 3-5 μg DNA in 100 μL to ~2kb using the following settings on Diagenode bioruptor pico : 5 cycles, 4 sec on / 30 sec off", "[End repair and dA-tailing]\nSplit into two reactions to maximize the efficacy of the reactio... |
76,849 | Recovering Plasmid DNA from Bacterial Culture | 1 | dx.doi.org/10.17504/protocols.io.j8nlkw635l5r/v1 | https://www.protocols.io/view/recovering-plasmid-dna-from-bacterial-culture-cparvid6 | Addgene The Nonprofit Plasmid Repository, Alexandru Salceanu | TITLE: Recovering Plasmid DNA from Bacterial Culture
AUTHORS: Addgene The Nonprofit Plasmid Repository, Alexandru Salceanu
[DESCRIPTION]
This protocol is for recovering plasmid DNA from Bacterial Culture. To see the full abstract and other resources, visit https://www.addgene.org/protocols/purify-plasmid-dna/.
[GUIDE... | ["[Generalized DNA Purification] Grow an overnight culture of bacteria.", "[Generalized DNA Purification] Centrifuge the culture to pellet the bacteria before proceeding with DNA preparation.", "[Generalized DNA Purification] Remove the supernatant and resuspend the bacteria in buffer.", "[Generalized DNA Purification]... |
null | null | null | dx.doi.org/10.17504/protocols.io.i36cgre | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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49,053 | Isolation of Human Pancreatic Islets of Langerhans for Research | 1 | dx.doi.org/10.17504/protocols.io.bt55nq86 | https://www.protocols.io/view/isolation-of-human-pancreatic-islets-of-langerhans-bt55nq86 | James Lyon, Aliya Spigelman, Austin Bautista, Nancy Smith, Doug O'Gorman, Jocelyn E Manning Fox, Tatsuya Kin, Patrick Macdonald | TITLE: Isolation of Human Pancreatic Islets of Langerhans for Research
AUTHORS: James Lyon, Aliya Spigelman, Austin Bautista, Nancy Smith, Doug O'Gorman, Jocelyn E Manning Fox, Tatsuya Kin, Patrick Macdonald
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol, and the five linked protocols... | ["[Media and Equipment preparation]\nPrepare all media as described in Human Islet Isolation Media Preparation protocol.Set up equipment as described in IsletCore Equipment Setup for Human Islet Isolation protocol.Set up COBE as described in Human Islet Purification - COBE Setup protocol.", "[Record Identifier Rxxx]\nA... |
97,529 | Heptane preparation of Annonaceae pollen | 0 | dx.doi.org/10.17504/protocols.io.8epv5r6r5g1b/v1 | https://www.protocols.io/view/heptane-preparation-of-annonaceae-pollen-dbgz2jx6 | Couvreur LP Thomas, Tanawat Chaowasku, Raymond W. J. M. van der Ham | TITLE: Heptane preparation of Annonaceae pollen
AUTHORS: Couvreur LP Thomas, Tanawat Chaowasku, Raymond W. J. M. van der Ham
[DESCRIPTION]
The protocol used to study Annonaceae pollen taken from herbarium dried specimens or in field alcohol conserved material. The protocol deviates from previous versions by using Hept... | ["[Sample material] Use a stereo microscope to collect anthers at anthesis of flowers from herbarium specimen or conserved in alcohol (spirit material). Depending on the size of the anthers take 3-10. Place the anthers in a glass vial.", "[Sample material] Crush the anthers with a glass rod. Make sure to clean the rod ... |
41,204 | Serapure Bead production | 4 | dx.doi.org/10.17504/protocols.io.bkguktww | https://www.protocols.io/view/serapure-bead-production-bkguktww | Eric Pederson | TITLE: Serapure Bead production
AUTHORS: Eric Pederson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Production of DNA size separation magnetic beads.</div></div>
[STEPS]
?. [Serapure bead production]
In a 50 mL conical using sterile stock solutions, prepare TE (10 mM Tris-‐HCl and 1 mM EDTA);-... | ["[Serapure bead production]\nIn a 50 mL conical using sterile stock solutions, prepare TE (10 mM Tris-‐HCl and 1 mM EDTA);- 500 μL 1 M Tris pH8 - 100 μL 0.5 M EDTAFill conical to 50 mL mark with dH20.", "[Serapure bead production]\nTo a to a new 50 mL, sterile conical add;- 9 g PEG-‐8000- 10 mL 5 M NaCL (or 2.92 g)... |
100,173 | MagMAX™ CORE Nucleic Acid Purification Kit | 0 | null | https://www.protocols.io/view/magmax-core-nucleic-acid-purification-kit-dd3m28k6 | Karen Keegan | TITLE: MagMAX™ CORE Nucleic Acid Purification Kit
AUTHORS: Karen Keegan
[DESCRIPTION]
MagMAX‱ CORE Nucleic Acid Purification Kit
[STEPS]
1.
For step 3 in box above, follow bacterial DNA purification centrifuge step.
2.
For step 2 in box above, add 200 μl of supernatant from step 1 to the Lysis solution
3. Selec... | ["For step 3 in box above, follow bacterial DNA purification centrifuge step.", "For step 2 in box above, add 200 μl of supernatant from step 1 to the Lysis solution", "Select\nthe programme ‘MagMAXCORE_KF96_kf2 on the MagMAX machine (I used MagMAX express 96 particle processor machine)", "As per the table above, first... |
25,214 | RNA Isolation from Plant Tissue Protocol 14: Ambion Trizol RNA Extraction in Microcentrifuge Tubes with Turbo DNAfree Digestion | null | dx.doi.org/10.17504/protocols.io.4u6gwze | null | null | TITLE: RNA Isolation from Plant Tissue Protocol 14: Ambion Trizol RNA Extraction in Microcentrifuge Tubes with Turbo DNAfree Digestion
AUTHORS:
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Implemented by: Ingrid Jordon-Thaden and Nicholas Miles (Soltis Labs)</div><div class = "text-block">This p... | ["Clean all surfaces and equipment with 20 % bleach, 95 % ethanol, and RNase Zap, and place supplies in hood.", "Prepare sample tubes with labels.", "Fill microcentrifuge tubes with 5 zirconia beads (if they have not been done before tissue collection).", "Prepare aliquots of the following solutions into 50mL Falcon tu... |
80,556 | Human myocardium decellularization | 4 | dx.doi.org/10.17504/protocols.io.4r3l2o22xv1y/v3 | https://www.protocols.io/view/human-myocardium-decellularization-cswkwfcw | Immacolata Belviso, Anna Maria Sacco, Domenico Cozzolino, Daria Nurzynska, Franca Di Meglio, clotilde.castaldo, Veronica Romano | TITLE: Human myocardium decellularization
AUTHORS: Immacolata Belviso, Anna Maria Sacco, Domenico Cozzolino, Daria Nurzynska, Franca Di Meglio, clotilde.castaldo, Veronica Romano
[DESCRIPTION]
The protocol represents a step-by-step method to obtain a decellularized cardiac matrix through the combination of sodium dode... | ["[Preparation of decellularizing solution] Preparation of 600 mL of decellularizing solution", "[Preparation of decellularizing solution] Prepare 300 mL of 2% Triton X-100 solution by measuring 294 mL of double-distilled water in a graduated cylinder and transferring it to a 500 mL beaker.", "[Preparation of decellula... |
43,191 | Homogenate of A. cervicornis | 4 | dx.doi.org/10.17504/protocols.io.4r3l248xpg1y/v1 | https://www.protocols.io/view/homogenate-of-a-cervicornis-bnexmbfn | Stephanie Rosales, Ana M Palacio-Castro | TITLE: Homogenate of A. cervicornis
AUTHORS: Stephanie Rosales, Ana M Palacio-Castro
[DESCRIPTION]
This protocol is to study disease in Acropora cervicornis by using a disease homogenate method. These methods are adapted from methods presented in Muller 2018 https://elifesciences.org/articles/35066.
[BEFORE_START]
Pr... | ["Clean -up", "Bleach tweezers, clippers, slates, airgun, surfaces", "Dose experimental corals with the placebo and disease homogenates", "Obtain healthy and diseased Acropora cervicornis fragments. These fragments are preferably collected from the same area and with similar disease progression.", "Prepare placebo and ... |
101,626 | Extraction of microbial cells from methane-seep carbonate rocks for single-cell analyses (e.g. BONCAT-FISH) using “combination buffer” and percoll density centrifugation | 0 | null | https://www.protocols.io/view/extraction-of-microbial-cells-from-methane-seep-ca-dfg23jye | Magdalena J Mayr, Victoria J. Orphan | TITLE: Extraction of microbial cells from methane-seep carbonate rocks for single-cell analyses (e.g. BONCAT-FISH) using “combination buffer” and percoll density centrifugation
AUTHORS: Magdalena J Mayr, Victoria J. Orphan
[DESCRIPTION]
Protocol to separate cells from carbonate rock to be able to image cells on a filt... | ["[Carbonate fixation] Fix small piece or crushed rock with 2% PFA in 3xPBS (marine samples) over night at 4 °C. \n(PFA is toxic dispose properly and use PPE accordingly).", "[Carbonate cleaning and crushing] Take out sample from freezer and place on ice.", "[Carbonate cleaning and crushing] Wash rocks - to remove cont... |
72,303 | The efficacy of anti-stigma initiatives in reducing dementia stigma in young people: A systematic review protocol | 1 | dx.doi.org/10.17504/protocols.io.14egn22eyg5d/v1 | https://www.protocols.io/view/the-efficacy-of-anti-stigma-initiatives-in-reducin-ciupuevn | Mahfuza Ali, Esra Hassan, Nicolas Farina | TITLE: The efficacy of anti-stigma initiatives in reducing dementia stigma in young people: A systematic review protocol
AUTHORS: Mahfuza Ali, Esra Hassan, Nicolas Farina
[DESCRIPTION]
The aim of this study is to identify and describe the available published research on anti-stigma initiatives aimed at young people th... | [] |
34,267 | End-preparation of amplicon pools | null | dx.doi.org/10.17504/protocols.io.bdp3i5qn | null | Josh Quick | TITLE: End-preparation of amplicon pools
AUTHORS: Josh Quick
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a subprotocol for generating a library from a single amplicon pool</div></div>
[STEPS]
?. Set up the following reaction for each sample:Component ... | ["Set up the following reaction for each sample:Component VolumeDNA amplicons (5ng/ul) Nuclease-free water Ultra II End Prep Reaction Buffer Ultra II End Prep Enzyme Mix Total\n10 µl\n2.5 µl\n1.75 µl\n0.75 µl\n15 µl", "I... |
47,022 | Look for Cell Invasion Experiment? How About Following Information? | 4 | null | https://www.protocols.io/view/look-for-cell-invasion-experiment-how-about-follow-br6nm9de | 181830691 | TITLE: Look for Cell Invasion Experiment? How About Following Information?
AUTHORS: 181830691
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The cell transwell is put into the culture plate, the chamber was called the upper chamber, the culture plate was called the lower chamber, the upper chamber... | [] |
96,771 | Derivation of Spinal Cord Organoids as a quantitative approach to study the mammalian Hedgehog Signalling | 0 | dx.doi.org/10.17504/protocols.io.kxygx3r6og8j/v2 | https://www.protocols.io/view/derivation-of-spinal-cord-organoids-as-a-quantitat-darb2d2n | Markus Holzner, Anton Wutz, Giulio Di Minin | TITLE: Derivation of Spinal Cord Organoids as a quantitative approach to study the mammalian Hedgehog Signalling
AUTHORS: Markus Holzner, Anton Wutz, Giulio Di Minin
[DESCRIPTION]
The Hedgehog (HH) pathway is crucial for embryonic development, and adult homeostasis. Its dysregulation is implicated in multiple diseases... | ["[mESC maintenance] Note: the procedure describes the necessary amounts for the expansion of mouse ESCs in a 3 cm dish. This dimension will provide enough cells to derive SCOs. Volumes can, however, easily be adapted according to the user’s needs.\n \n Pre-coat the necessary number of wells of a 3 cm dish with 1 mL of... |
null | null | null | dx.doi.org/10.17504/protocols.io.feibjce | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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24,557 | Illumina GAII Library Construction and Sequencing for RNA Seq | null | dx.doi.org/10.17504/protocols.io.38mgru6 | null | Eric J. Carpenter, Naim Matasci, Shuangxiu Wu, Jing Sun, Jun Yu, Fabio Rocha Jimenez Vieira, Chris Bowler, Richard G. Dorrell, Matt Gitzendanner, Ling Li, Wensi Du, Kristian Ullrich, Michael S. Barker, James H. Leebens-Mack, Gane Ka-Shu Wong | TITLE: Illumina GAII Library Construction and Sequencing for RNA Seq
AUTHORS: Eric J. Carpenter, Naim Matasci, Shuangxiu Wu, Jing Sun, Jun Yu, Fabio Rocha Jimenez Vieira, Chris Bowler, Richard G. Dorrell, Matt Gitzendanner, Ling Li, Wensi Du, Kristian Ullrich, Michael S. Barker, James H. Leebens-Mack, Gane Ka-Shu Wong
... | ["Isolate polyA RNA from of total RNA treated by using .It is best to use up to 50 µg as the use of a lower mass (typically 20 µg) has been insufficient for successful library construction. This can be assessed by running final PCR products on an agarose gel; the library construction is considered to have failed when... |
40,494 | Binding properties of Staphylococcal protein A (SpA) to purified immunoglobulins tested by double immunodiffusion (Ouchterlony) technique. | 4 | dx.doi.org/10.17504/protocols.io.bjsnknde | https://www.protocols.io/view/binding-properties-of-staphylococcal-protein-a-spa-bjsnknde | Angel Justiz-Vaillant | TITLE: Binding properties of Staphylococcal protein A (SpA) to purified immunoglobulins tested by double immunodiffusion (Ouchterlony) technique.
AUTHORS: Angel Justiz-Vaillant
[STEPS]
?. The binding of SpA to purified IgG are investigated by double immunodiffusion.
?. Briefly, 1% agarose gels are prepared and wells ... | ["The binding of SpA to purified IgG are investigated by double immunodiffusion.", "Briefly, 1% agarose gels are prepared and wells cut into the gel using a template.", "Initially, aliquots of 25 µl each of SpA diluted 1:5 are applied to the centre well.", "The peripheral wells are filled with 25 µl each of purified Ig... |
25,134 | Reverse transcription using SuperSript IV | null | dx.doi.org/10.17504/protocols.io.4sngwde | null | Amin Mahpour | TITLE: Reverse transcription using SuperSript IV
AUTHORS: Amin Mahpour
[STEPS]
?. Mix the following reagents from the kit. Please scale up if more RT reaction is desired. AB1ReagentAmount (uL)2Primer (Random or dT)0.53dNTP (10mM)14RNA11
AB1ReagentAmount (uL)2Primer (Random or dT)0.53dNTP (10mM)14RNA11
?. Incubate the... | ["Mix the following reagents from the kit. Please scale up if more RT reaction is desired. AB1ReagentAmount (uL)2Primer (Random or dT)0.53dNTP (10mM)14RNA11\nAB1ReagentAmount (uL)2Primer (Random or dT)0.53dNTP (10mM)14RNA11", "Incubate the mixture at for . Then, incubate samples on ice for few minutes.\n72 °C\nThis ... |
25,176 | Mixotrophic batch growth of Spirulina platensis | null | dx.doi.org/10.17504/protocols.io.4tygwpw | null | Bruna Emerenciano, Maria Izabel Pereira Batista, Adriano H N Rangel | TITLE: Mixotrophic batch growth of Spirulina platensis
AUTHORS: Bruna Emerenciano, Maria Izabel Pereira Batista, Adriano H N Rangel
[STEPS]
?. 1. Prepare the batch culture in 6 L plastic bottles.
?. Introduce 10 % of inoculum into 3,6 L of Zarrouk medium as control cultivationTo mixotrophic cultivation introduce 10 % ... | ["1. Prepare the batch culture in 6 L plastic bottles.", "Introduce 10 % of inoculum into 3,6 L of Zarrouk medium as control cultivationTo mixotrophic cultivation introduce 10 % of inoculum into 4L of Zarrouk medium supplemented with 2.5%, 5.0% and 10% clarified buffalo mozzarella cheese whey. The initial S. platensis ... |
96,523 | Plastics Study and Protocol | 0 | dx.doi.org/10.17504/protocols.io.eq2lyjm1rlx9/v1 | https://www.protocols.io/view/plastics-study-and-protocol-dahj2b4n | Matthew Kang, Jayden Manalese | TITLE: Plastics Study and Protocol
AUTHORS: Matthew Kang, Jayden Manalese
[DESCRIPTION]
Plastic waste washed upon shores have anthropogenically impacted communities and wildlife. However, the information related to the scale and urgency of this concern is not well quantitatively defined. The procedure uses case studie... | ["[Plastic Collection and Coastal Pollution Evaluation] Allocate a defined fraction of coastline in Mo’orea that is representative of the average.", "[Plastic Collection and Coastal Pollution Evaluation] Measure/Calculate the surface area covered by the studied area using google Earth", "[Plastic Collection and Coastal... |
26,314 | Streaking bacteria on an agar plate from a glycerol stock | null | dx.doi.org/10.17504/protocols.io.5xig7ke | null | Cristian Riccio | TITLE: Streaking bacteria on an agar plate from a glycerol stock
AUTHORS: Cristian Riccio
[STEPS]
?. Transfer the glycerol stock onto dry ice next to a flame.
?. Rub the loop in the glycerol stock.
?. Streak the bacteri in zigzag over half the agar plate.
?. Sterilise the loop in the flame.
?. Sterilise the loop.
?. Z... | ["Transfer the glycerol stock onto dry ice next to a flame.", "Rub the loop in the glycerol stock.", "Streak the bacteri in zigzag over half the agar plate.", "Sterilise the loop in the flame.", "Sterilise the loop.", "Zigzag over half the plate which overlaps with the first half by a quarter of a plate.", "Sterilise t... |
null | null | null | dx.doi.org/10.17504/protocols.io.ebabaie | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This collection is part of the VERVE holiday drive to collect exotic off-the-shelf laboratory recipes. More details <a href="https://www.protocols.io/g/verve-net/news/call-for-recipes" target="_blank">here</a>.<br /><a href="https://twitter.com/whiskeyboy/status/6772760407340892... | [] |
45,725 | Continuous positive airway pressure to reduce the risk of early peripheral oxygen desaturation following apnoea onset in children: Randomised double-blind controlled trial | 1 | dx.doi.org/10.17504/protocols.io.bqv5mw86 | https://www.protocols.io/view/continuous-positive-airway-pressure-to-reduce-the-bqv5mw86 | Jayme Marques | TITLE: Continuous positive airway pressure to reduce the risk of early peripheral oxygen desaturation following apnoea onset in children: Randomised double-blind controlled trial
AUTHORS: Jayme Marques
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>It was a randomised double-blind parallel co... | ["[Continuous positive airway pressure to reduce the risk of early peripheral oxygen desaturation following apnoea onset in children: Randomised double-blind controlled trial]\nContinuous positive airway pressure to reduce the risk of early peripheral oxygen desaturation following apnoea onset in children: Randomised d... |
90,074 | Cold dispase digestion of murine lungs improves recovery and culture of airway epithelial cells | 4 | dx.doi.org/10.17504/protocols.io.rm7vzxo68gx1/v1 | https://www.protocols.io/view/cold-dispase-digestion-of-murine-lungs-improves-re-c372yrqe | piotr.janas, Caroline Chauché, Patrick Shearer, Georgia Perona-Wright, Henry J McSorley, Jürgen Schwarze | TITLE: Cold dispase digestion of murine lungs improves recovery and culture of airway epithelial cells
AUTHORS: piotr.janas, Caroline Chauché, Patrick Shearer, Georgia Perona-Wright, Henry J McSorley, Jürgen Schwarze
[DESCRIPTION]
Airway epithelial cells (AECs) play a key role in maintaining lung homeostasis, epithel... | ["[Cold dispase digestion of murine lungs improves recovery and culture of airway epithelial cells] Euthanise a mouse according to local protocols and regulations (excluding carbon dioxide).", "[Cold dispase digestion of murine lungs improves recovery and culture of airway epithelial cells] Using scissors, cut the sk... |
23,028 | Measles Vaccine Virus Taqman-MGB | null | dx.doi.org/10.17504/protocols.io.2qugdww | null | Mitchell Finger, Michael Lyon, Judy Northill, Ian Mackay | TITLE: Measles Vaccine Virus Taqman-MGB
AUTHORS: Mitchell Finger, Michael Lyon, Judy Northill, Ian Mackay
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This previously unpublished protocol aims to amplify genotype A measles virus (MeV) strains but not non-mealses viruses.</div><div class = "text-b... | ["[Oligonucleotide sequences]\nAB1NameSequence 5'-3'2Measles F 4729 VacAAACCCCCAGCAATTGGAA3Measles R 4795 VacGGTCACCTCGGTCGCTTGT\n4Measles Probe 4757FAM - CCCTCTTCCTCAACACA - MGBNFQ\nAB1NameSequence 5'-3'2Measles F 4729 VacAAACCCCCAGCAATTGGAA3Measles R 4795 VacGGTCACCTCGGTCGCTTGT\n4Measles Probe 4757FAM - CCCTCTTCCTCAA... |
83,162 | Isolation and Processing of Embryonic and Postnatal Brains | 1 | dx.doi.org/10.17504/protocols.io.e6nvwdpe9lmk/v1 | https://www.protocols.click/view/isolation-and-processing-of-embryonic-and-postnata-cvf2w3qe | Maryana Nissan, divya.darwinarulseeli | TITLE: Isolation and Processing of Embryonic and Postnatal Brains
AUTHORS: Maryana Nissan, divya.darwinarulseeli
[DESCRIPTION]
This protocol describes:
-Harvesting embryos from females from embryonic day 10 [e10] to embryonic day 18 [e18]
-Brain isolation of embryonic (e10-e18) and postnatal brains (p0-p30)
-Process... | ["[Harvest embryos from female mouse from embryonic day 10 (e10) to embryonic day 18 (e18)] Place pregnant female in an anesthetic chamber for 2 minutes", "[Harvest embryos from female mouse from embryonic day 10 (e10) to embryonic day 18 (e18)] Euthanize female using cervical dislocation", "[Harvest embryos from femal... |
44,765 | Thiol-Redox Proteomics to Study Reversible Protein Thiol Oxidations in Bacteria | 4 | dx.doi.org/10.17504/protocols.io.bpx5mpq6 | https://www.protocols.io/view/thiol-redox-proteomics-to-study-reversible-protein-bpx5mpq6 | Martina Rossius, Falko Hochgräfe, Haike Antelmann | TITLE: Thiol-Redox Proteomics to Study Reversible Protein Thiol Oxidations in Bacteria
AUTHORS: Martina Rossius, Falko Hochgräfe, Haike Antelmann
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Thiol-redox proteomics methods are rapidly developing tools in redox biology. These are applied to i... | ["[3.1 Fluorescent-Label Thiol-Redox Proteomics: Growth, Harvesting of Cells, and Blocking of Reduced Thiols by IAM]\nInoculate an culture of bacterial cells into two flasks each containing to an optical density at 500 nm (OD500) of 0.05.\n[defined minimal medium]", "[3.1 Fluorescent-Label Thiol-Redox Proteomics: Gro... |
102,530 | Mutant generation in Streptococcus oralis strain S.mitis/oralis 351 | 0 | dx.doi.org/10.17504/protocols.io.261ge5wpog47/v1 | https://www.protocols.io/view/mutant-generation-in-streptococcus-oralis-strain-s-dgda3s2e | Samantha King | TITLE: Mutant generation in Streptococcus oralis strain S.mitis/oralis 351
AUTHORS: Samantha King
[DESCRIPTION]
This protocol is the methodology that we have successfully employed to generate and confirm insertion deletion mutants in Streptococcus oralis strain S.mitis/oralis 351. Attached to the protocol is a file th... | ["[Mutant generation in Streptococcus oralis strain S.mitis/oralis 351] Creation of a plasmid construct", "[Mutant generation in Streptococcus oralis strain S.mitis/oralis 351] The regions upstream and downstream of the region to be deleted were amplified\nusing primers 1 and 2, and 3 and 4, respectively. These primers... |
52,314 | A Protocol for a Scoping Review of The Use of Mental Simulation and Full-Scale Simulation in Practising Healthcare Decision-making Skills of Undergraduate Nursing Students. | 1 | dx.doi.org/10.17504/protocols.io.e6nvw57y7vmk/v1 | https://www.protocols.io/view/a-protocol-for-a-scoping-review-of-the-use-of-ment-bxb2piqe | Burcu DOGAN, Natalie Pattison, Rebecca Scott, Guillaume Alinier | TITLE: A Protocol for a Scoping Review of The Use of Mental Simulation and Full-Scale Simulation in Practising Healthcare Decision-making Skills of Undergraduate Nursing Students.
AUTHORS: Burcu DOGAN, Natalie Pattison, Rebecca Scott, Guillaume Alinier
[DESCRIPTION]
Abstract
Introduction
Full-scale simulation (FSS) ha... | ["[Abstract] Method \nThe methodological framework for scoping review will be followed for this scoping review. Scopus, EBSCOhost the Cumulative Index to Nursing and Allied Health Literature (CINAHL), MEDLINE and for the grey literature ERIC and BASE will be searched for related studies. The search will be limited to J... |
68,648 | DNA Extraction from Yeast | 4 | null | https://www.protocols.io/view/dna-extraction-from-yeast-cfagtibw | Brian Teague | TITLE: DNA Extraction from Yeast
AUTHORS: Brian Teague
[DESCRIPTION]
This is a "quick and dirty" way to get some genomic DNA out of yeast cells. Not pure enough for many things, but should be fine for a PCR template.
This protocol is adapted from
who in turn adapted it from
[GUIDELINES]
The centrifugation ... | ["Make 100 µL of yeast lysis solution by mixing the following in a 1.7 ml microcentrifuge tube:\n70 µL H2O\n20 µL solution, 1 Molarity (M)\n10 µL solution, 10 Mass / % volume", "Choose a yeast colony to analyze and circle it on the bottom of the petri dish. A large one is best.", "Using a micropipette tip, scrape s... |
19,507 | Document 1 | null | dx.doi.org/10.17504/protocols.io.xatfien | null | vittorio scaravilli | TITLE: Document 1
AUTHORS: vittorio scaravilli
[STEPS]
?. | [] |
21,183 | UC Davis - Y-Maze | null | dx.doi.org/10.17504/protocols.io.yw7fxhn | null | Mari Golub | TITLE: UC Davis - Y-Maze
AUTHORS: Mari Golub
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span><span style = "font-weight:bold;"> </span></div><div class = "text-block">The y-maze is a modification of the T- maze which evaluates memory and special learn... | ["Study design:\nTime of day: For any experiment, testing should take place during the same 3-4 hour period on each day. Afternoon testing at least one hour prior to dark cycle onset is best. Testing after “lights out” in the vivarium is not appropriate.\nMixed sex test groups: Males and females should be tested in dif... |
null | null | null | dx.doi.org/10.17504/protocols.io.pnbdman | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Malt extract - yeast extract - peptone - glucose rich medium for yeast growth and maintenance.</p>
[GUIDELINES]
<p>Dissolve all components in deionized water. Autoclave for 15 min @ 120 °C (1.2 atm).</p>
[STEPS]
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.r9xd97n | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?. | ["The mtDNA was extracted using a DNeasy kit (Qiagen).", "Sequencing was performed using PacBio RSII Chemistry P6-C4, 10kb template preparation and sequencing with 3.24 ug input DNA at the Ramaciotti Center at University of New South Wales (UNSW).", "PacBio long-read sequencing of the Alstonville and Japan mtDNA produc... |
null | null | null | dx.doi.org/10.17504/protocols.io.hv8b69w | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<p><strong>Materials and Buffers</strong></p>
<p>1. Chamber slides or cover slips</p>
<p>2. Fixation solution: 4% Paraformaldehyde, in PBS</p>
<p>3. Permeablization solution: 0.5% Triton X-100 in PBS</p>
<p>4. Antibody dilution solution: 5%FBS in PBS</p>
[STEPS]
?.
?.
?.
?.
... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ke7cthn | null | null | TITLE: No Title
AUTHORS:
[STEPS] | [] |
22,834 | Budding yeast ChEC | null | dx.doi.org/10.17504/protocols.io.2isgcee | null | Gabe Zentner | TITLE: Budding yeast ChEC
AUTHORS: Gabe Zentner
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Genome-wide mapping of protein-DNA interactions is critical for understanding gene regulation, chromatin remodeling, and other chromatin-resident processes. Formaldehyde crosslinking followed by chromatin... | ["[Yeast culture and harvest]\nThe day before the experiment, inoculate 3 mL YPD or SC medium with a single colony. Grow overnight at 30°C.", "[Yeast culture and harvest]\nIn the morning, dilute the overnight culture to OD600 = 0.2-0.3 in 50 mL YPD or SC medium in a 300 mL flask. Grow 50 mL culture at 30°C until OD600 ... |
null | null | null | dx.doi.org/10.17504/protocols.io.t89erz6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Protocol for PCR Cloning with Blue/White Selection and Easy Insert Excision using pGEM®-T Easy Vector Systems.
(For use with A3600, A3610, A1360, or A1380.)
[GUIDELINES]
<p><strong>1. Introduction</strong></p>
<p> </p>
<p><strong>1.A. Vector Features</strong></p>
<p> </p>
<... | ["[Ligation] {\"blocks\":[{\"key\":\"d8srh\",\"text\":\"Briefly, centrifuge the pGEM\\u00ae-T or pGEM\\u00ae-T Easy Vector and Control Insert DNA tubes to collect the contents at the bottom of the tubes.\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[]},{\"key\":\"2ga3t\",\"t... |
103,091 | Purification of FUNDC1-GFP | 0 | dx.doi.org/10.17504/protocols.io.4r3l2qnx3l1y/v1 | https://www.protocols.io/view/purification-of-fundc1-gfp-dgwt3xen | Elias Adriaenssens | TITLE: Purification of FUNDC1-GFP
AUTHORS: Elias Adriaenssens
[DESCRIPTION]
This protocol details the purification of FUNDC1-GFP.
[STEPS]
SECTION: Purification - FUNDC1-GFP
1. To purify GFP-tagged
FUNDC1-GFP (available from Addgene) or FUNDC1(Y18A/L21A)-GFP (ΔLIR) (available from Addgene),
fuse the cytosol-expose... | ["[Purification - FUNDC1-GFP] To purify GFP-tagged \n\nFUNDC1-GFP (available from Addgene) or FUNDC1(Y18A/L21A)-GFP (ΔLIR) (available from Addgene), \n\nfuse the cytosol-exposed domain of FUNDC1 (1-50aa) to a C-terminal GFP-tag through cloning into a pET-DUET1 vector (available on Addgene).", "[Purification - FUNDC1-GF... |
58,491 | Immunofluorescence Staining of Brain Slices | 1 | dx.doi.org/10.17504/protocols.io.4r3l2o7y4v1y/v1 | https://www.protocols.io/view/immunofluorescence-staining-of-brain-slices-b5c3q2yn | tomdeerinck | TITLE: Immunofluorescence Staining of Brain Slices
AUTHORS: tomdeerinck
[DESCRIPTION]
Primary antibody labeling to a specific protein using a fluorescence secondary anitbody to label it.
[STEPS]
1. Rinse tissues with ice cold 1x PBS
3x @ 10 min
2. Make up blocking buffer
1x PBS, containing
3% norm... | ["Rinse tissues with ice cold 1x PBS\n 3x @ 10 min", "Make up blocking buffer\n 1x PBS, containing\n 3% normal donkey serum\n 1% bovine serum albumin\n 1% Gelatin from cold water fish skin (G7765 Sigma-Aldrich)\n 0.1% Triton X-100", "Block tissues in blocking buffer 1hr on ice", "Rinse tis... |
43,661 | Nuclei isolation from human lung using grinding for snATAC-seq | 4 | dx.doi.org/10.17504/protocols.io.bnvmme46 | https://www.protocols.io/view/nuclei-isolation-from-human-lung-using-grinding-fo-bnvmme46 | Center for Epigenomics UCSD | TITLE: Nuclei isolation from human lung using grinding for snATAC-seq
AUTHORS: Center for Epigenomics UCSD
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol describing nuclei isolation from frozen tissue including lung using grinding for single nucleus ATAC-seq.</div></div>
[STEPS] | [] |
20,466 | iPSC Restriction Digest: For Screening Edited Clones | null | dx.doi.org/10.17504/protocols.io.x8sfrwe | null | Celeste Karch, Rita Martinez, Jacob Marsh | TITLE: iPSC Restriction Digest: For Screening Edited Clones
AUTHORS: Celeste Karch, Rita Martinez, Jacob Marsh
[STEPS]
?. Prepare the following reagents in a strip cap tube with the previously identified enzyme. ABC1Restriction Digest Protocol2ReagentVolume# of rxns3Buffer (Cut Smart/ NEB)2 µl4DNA from PCR17.75 µl5En... | ["Prepare the following reagents in a strip cap tube with the previously identified enzyme. ABC1Restriction Digest Protocol2ReagentVolume# of rxns3Buffer (Cut Smart/ NEB)2 µl4DNA from PCR17.75 µl5Enzyme (specific)0.25 µl6Total20 µl\nABC1Restriction Digest Protocol2ReagentVolume# of rxns3Buffer (Cut Smart/ NEB)2 µl4DNA... |
54,692 | TIMSTOFPro Crosslinking Optimized for PhoX | 1 | null | https://www.protocols.io/view/timstofpro-crosslinking-optimized-for-phox-bzncp5aw | Johannes Hevler | TITLE: TIMSTOFPro Crosslinking Optimized for PhoX
AUTHORS: Johannes Hevler
[DESCRIPTION]
crosslinking.m:
Method to run cross-linking samples on TimsTof pro instrument. Method and energies are specifically
optimized for PhoX cross-linker reagent (by Richard Scheltema and Markus Lubeck (Brucker))
Standard_DDA_PASEF_1.... | [] |
18,287 | SYSB 3036 W10: Read mapping | null | dx.doi.org/10.17504/protocols.io.v4pe8vn | null | Frank Aylward | TITLE: SYSB 3036 W10: Read mapping
AUTHORS: Frank Aylward
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is an example of a simple short read mapping analysis that could be used as part of a transcriptomics or RNA-seq workflow. </div><div class = "text-block">Code is intended for use on an Ub... | ["[Download the reference genome and index a database with bowtie2]\nThe datasets we will be using here are part of the Dedrick et al BMC Microbiology paper (more details in the Description for this tutorial), which describes some very cool transcriptomic experiments of Mycobacterium smegmatis while is infected with va... |
30,296 | Respiratory picornavirus genotyping conventional nested RT-PCR ("Wisdom VP42 assay") | null | dx.doi.org/10.17504/protocols.io.9tyh6pw | null | Ian Mackay, Judy Northill | TITLE: Respiratory picornavirus genotyping conventional nested RT-PCR ("Wisdom VP42 assay")
AUTHORS: Ian Mackay, Judy Northill
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is my preferred, previously published [Ref 1], rhinovirus (RV) and enterovirus (EV) genotyping assay when seeking to ide... | ["[Oligonucleotide sequences...]\nABC1 NameSequence (5'-3')2RT-PCR(Round 1)HRV_HEV VP42 OSCCGGCCCCTGAATGYGGCTAA3HRV_HEV VP42 OASACATRTTYTSNCCAAANAYDCCCAT4PCR(Round 1)HRV_HEV VP42 IS\nACCRACTACTTTGGGTGTCCGTG5HRV_HEV VP42 IAS\nTCWGGHARYTTCCAMCACCANCC\nABC1 NameSequence (5'-3')2RT-PCR(Round 1)HRV_HEV VP42 OSCCGG... |
60,200 | Single-cell sequencing and analysis | 4 | dx.doi.org/10.17504/protocols.io.bp2l61drdvqe/v1 | https://www.protocols.io/view/single-cell-sequencing-and-analysis-b62grgbw | Daniele Neri, Lori Zeltser | TITLE: Single-cell sequencing and analysis
AUTHORS: Daniele Neri, Lori Zeltser
[DESCRIPTION]
This protocol describes single-cell sequencing and analysis.
[STEPS]
SECTION: Sequencing
1. We performed plate-based single-cell sequencing as described in Snyder et al., 2019 (https://doi.org/10.1126/sciimmunol.aav5581)
SE... | ["[Sequencing] We performed plate-based single-cell sequencing as described in Snyder et al., 2019 (https://doi.org/10.1126/sciimmunol.aav5581)", "[Sequencing] Pooled 3’-end sequencing libraries were sequenced on an Illumina NextSeq 500/550 platform", "[Alignment and count matrix generation] The reads were aligned to m... |
null | null | null | dx.doi.org/10.17504/protocols.io.n2tdgen | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol described the procedures of analyzing RNA-Seq data for the expression of long non-coding RNAs (lncRNAs) as well as protein-coding genes (PCGs), as well as identifying the genomic location of lncRNAs and lncRNA-PCG pairs. As an example, we used an existing RNA-Se... | [] |
101,156 | Supplementary protocols for 'A simple and fast optical clearing method for whole-mount fluorescence in situ hybridization (FISH) imaging' | 0 | null | https://www.protocols.io/view/supplementary-protocols-for-39-a-simple-and-fast-o-de2c3gaw | Junwoo Suh, Yehe liu, Jordan Smith, Michiko Michiko Watanabe, Andrew Rollins, Michael W. Jenkins | TITLE: Supplementary protocols for 'A simple and fast optical clearing method for whole-mount fluorescence in situ hybridization (FISH) imaging'
AUTHORS: Junwoo Suh, Yehe liu, Jordan Smith, Michiko Michiko Watanabe, Andrew Rollins, Michael W. Jenkins
[DESCRIPTION]
We report a single-step optical clearing metho... | ["[Synthesis of H2O LIMPID] Place a 500 ml glass beaker on a large weight balance and tare.", "[Synthesis of H2O LIMPID] Weigh out the same weight (200 g) of powder and gently transfer the urea powder to the glass beaker. This will make a roughly 50 Mass Percent urea solution, which will clear the sample (Supplementa... |
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