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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48,841 | The efficacy and safety of preoperative glucocorticoid in herniorrhaphy: A systematic review and meta-analysis (protocol) | 1 | dx.doi.org/10.17504/protocols.io.btxhnpj6 | https://www.protocols.io/view/the-efficacy-and-safety-of-preoperative-glucocorti-btxhnpj6 | Jun Watanabe, Kazuma Rifu, Takehiro Kagaya, Kazuhiko Kotani, Naohiro Sata | TITLE: The efficacy and safety of preoperative glucocorticoid in herniorrhaphy: A systematic review and meta-analysis (protocol)
AUTHORS: Jun Watanabe, Kazuma Rifu, Takehiro Kagaya, Kazuhiko Kotani, Naohiro Sata
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Introd... | [] |
32,720 | Bioflux Analyses | null | dx.doi.org/10.17504/protocols.io.bb7qirmw | null | Tobias Weise, Bettina Boettcher, Slavena Vylkova | TITLE: Bioflux Analyses
AUTHORS: Tobias Weise, Bettina Boettcher, Slavena Vylkova
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Biofilm formation under shear flow conditions was monitored using the Bioflux1000 device (Fluxion Biosciences, Inc.). In short, Candida albicans overnight cultures were w... | [] |
46,929 | Cost-conscious generation of multiplexed short-read DNA libraries for whole-genome sequencing | 1 | dx.doi.org/10.17504/protocols.io.14egnx27zl5d/v2 | https://www.protocols.io/view/cost-conscious-generation-of-multiplexed-short-rea-br3rm8m6 | Ashley Jones, David Stanley, Scott Ferguson, Benjamin Schwessinger, Justin Borevitz, Norman Warthmann | TITLE: Cost-conscious generation of multiplexed short-read DNA libraries for whole-genome sequencing
AUTHORS: Ashley Jones, David Stanley, Scott Ferguson, Benjamin Schwessinger, Justin Borevitz, Norman Warthmann
[DESCRIPTION]
Massively parallel, second-generation short-read DNA sequencing has become an integral t... | ["[DNA quantification] To measure a 96-well microplate of DNA samples with a dsDNA quantification high sensitivity kit (for microplate reader) (BioDynami or Thermo Fisher Scientific), ensure concentrations are ≤ 33 ng/µL. For instance, first quantify a few samples on a Qubit Fluorometer. Highly concentrated microplates... |
54,593 | Enzymatic Ethanol Assay | 4 | dx.doi.org/10.17504/protocols.io.bp2l6b8n5gqe/v2 | https://www.protocols.io/view/enzymatic-ethanol-assay-bzi9p4h6 | Sarah Hammer, Dev Kapadia, Shuen Hon, Marybeth Maloney, Daniel Olson, Lee Lynd | TITLE: Enzymatic Ethanol Assay
AUTHORS: Sarah Hammer, Dev Kapadia, Shuen Hon, Marybeth Maloney, Daniel Olson, Lee Lynd
[DESCRIPTION]
This protocol describes a 96-well-plate-based, enzymatic assay for reliably estimating ethanol concentrations in experimental samples in one hour. In the presence of excess NAD+, alcoho... | ["[Preparation] Create a microplate spectrophotometer program to read absorbance at 340 nm of each well in a 96-well plate. \nThe program should take absorbance readings at 340 nm every 20 - 30 seconds (or at minimum interval), shaking for 10 seconds immediately before each reading. \nThe program should be set to run f... |
44,409 | Adrenal Chromaffin Cell Cultures | 4 | dx.doi.org/10.17504/protocols.io.bpkzmkx6 | https://www.protocols.io/view/adrenal-chromaffin-cell-cultures-bpkzmkx6 | Ellen Kantar, David Sulzer | TITLE: Adrenal Chromaffin Cell Cultures
AUTHORS: Ellen Kantar, David Sulzer
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is about culturing of adrenal chromaffin cells from rats.</div><div class = "text-block">For rat-derived cultures, adrenal glands from 7- to 12-day-old Sprague Da... | ["Animals are decapitated (anaesthetize the animals with Ketaset® KETAMINE, FORT DODGE® #NDC-0856-2013-01 if decapitation is not an approved protocol).", "Decapitate and pin the body belly-down. Spray with .\n[ethanol]", "Cut the skin along the spinal column (it’s easier starting from the neck) and pull it out to both ... |
97,806 | Fear Conditioning | 0 | dx.doi.org/10.17504/protocols.io.261ge56bdg47/v1 | https://www.protocols.io/view/fear-conditioning-dbrn2m5e | Sabina Marciano, Roberta Marongiu | TITLE: Fear Conditioning
AUTHORS: Sabina Marciano, Roberta Marongiu
[DESCRIPTION]
Behavioral assay to measure fear learning and memory in mice.
[STEPS]
SECTION: Fear Acquisition
1. Habituate mice to the room. Set up fear conditioning chambers as well as protocols (listed below) in VideoFreeze software.
2. Place indiv... | ["[Fear Acquisition] Habituate mice to the room. Set up fear conditioning chambers as well as protocols (listed below) in VideoFreeze software.", "Place individual mice in a lit fear conditioning apparatus scented with peppermint spray.", "Protocol:\n2 min baseline followed by 5 tone-shock pairings where the shock foll... |
84,424 | Donor case selection protocol | 4 | dx.doi.org/10.17504/protocols.io.bp2l6xnmzlqe/v1 | https://www.protocols.click/view/donor-case-selection-protocol-cwpgxdjw | kyu sang han, Sashank Reddy, peihsun.wu, Denis Wirtz | TITLE: Donor case selection protocol
AUTHORS: kyu sang han, Sashank Reddy, peihsun.wu, Denis Wirtz
[DESCRIPTION]
Inclusion
Age 18-35 or 50 and over
English Speaking
Able to provide consent
Undergoing reconstructive or aesthetic procedures necessitating skin excision at the scalp or abdomen
Exclusion
Known collagen... | ["[Sample collection guideline] Patient samples will be obtained from skin that is to be discarded from patients presenting for reconstructive or aesthetic procedures necessitating skin excision. No other procedures or follow-up is needed for research purposes.", "[Sample collection guideline] Inclusion/Exclusion Crite... |
37,088 | How to set up a protocol hackathon for your team | null | dx.doi.org/10.17504/protocols.io.bgf8jtrw | https://www.protocols.io/view/how-to-set-up-a-protocol-hackathon-for-your-team-bgf8jtrw | Anita Bröllochs, protocols.io Ambassadors | TITLE: How to set up a protocol hackathon for your team
AUTHORS: Anita Bröllochs, protocols.io Ambassadors
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Communicate and collaborate effectively with </span><a href="http://protocols.io" style = "text-decoration:underline;color:blue;cursor:poin... | ["[Preparations ]\nDecide on a time for your protocol entry session (hackathon).\nThis can really be however long you'd like it to be. If you're only planning to get a few of your protocols up on protocols.io, you can plan for this to be or if you are planning to get a lot done, it can last up to a half a day or day.... |
73,948 | A lateral flow-based at-home test for detection of SARS-CoV-2 | 1 | dx.doi.org/10.17504/protocols.io.14egnzmezg5d/v2 | https://www.protocols.io/view/a-lateral-flow-based-at-home-test-for-detection-of-ckf4utqw | Peng Xu, Venice Servellita, Krzysztof Langer, Dan Weisgerber, Gordon Murtaugh, Adam R Abate, Charles Chiu | TITLE: A lateral flow-based at-home test for detection of SARS-CoV-2
AUTHORS: Peng Xu, Venice Servellita, Krzysztof Langer, Dan Weisgerber, Gordon Murtaugh, Adam R Abate, Charles Chiu
[DESCRIPTION]
***This protocol was a finalist in the XPRIZE Global Rapid Covid Testing competition***
We have developed a highly sens... | ["[SPECIMEN REQUIREMENTS] 1. Nasopharyngeal (NP) or nasopharyngeal/oropharyngeal (NP/OP) swab samples are collected with flocked swabs in universal transport media (UTM) or viral transport media (VTM).\n a. Specimens may be stored at 4˚C for up to 72 hours post-collection.\n b. Specimens should be stored ... |
null | null | null | dx.doi.org/10.17504/protocols.io.gg3btyn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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null | null | null | dx.doi.org/10.17504/protocols.io.ci3ugm | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
How to make a IPTG – 1 M (100 x) Stock Solution
[GUIDELINES]
Make a <a href="http://store.p212121.com/IPTG/" target="_blank">IPTG</a> – 1 M (100 x) Stock Solution
[STEPS]
?.
?.
?.
?. | [] |
48,419 | The association between echo intensity and muscle strength or physical performance in the older population: a scoping review | 3 | dx.doi.org/10.17504/protocols.io.btibnkan | https://www.protocols.io/view/the-association-between-echo-intensity-and-muscle-btibnkan | Takashi Kitagawa, Masatoshi Nakamura, Yoshihiro Fukumoto | TITLE: The association between echo intensity and muscle strength or physical performance in the older population: a scoping review
AUTHORS: Takashi Kitagawa, Masatoshi Nakamura, Yoshihiro Fukumoto
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Objective: </span><s... | [] |
63,906 | K1 Keto Reviews Is K1 Keto Life Pills Scam Or Legit? | 1 | dx.doi.org/10.17504/protocols.io.261genjy7g47/v1 | https://www.protocols.io/view/k1-keto-reviews-is-k1-keto-life-pills-scam-or-legi-canasdae | ketoreviewsketopillsas | TITLE: K1 Keto Reviews Is K1 Keto Life Pills Scam Or Legit?
AUTHORS: ketoreviewsketopillsas
[DESCRIPTION]
K1 Keto Reviews Is K1 Keto Life Pills Scam Or Legit?
[STEPS]
1. K1 Keto Reviews Is K1 Keto Life Pills Scam Or Legit?
One of the most significant enterprises facing developed countries moment is the frequence o... | ["K1 Keto Reviews Is K1 Keto Life Pills Scam Or Legit?\nOne of the most significant enterprises facing developed countries moment is the frequence of fat and rotundity. Development countries are not far behind the advanced bones. When a person weighs further than what's allowed normal for their height, that existent is... |
44,913 | Isolation of RNA form Enterococcus faecalis | 4 | null | https://www.protocols.io/view/isolation-of-rna-form-enterococcus-faecalis-bp4rmqv6 | Elizabeth Fozo | TITLE: Isolation of RNA form Enterococcus faecalis
AUTHORS: Elizabeth Fozo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Isolation of RNA form Enterococcus faecalis</div></div>
[STEPS]
?. [Steps]
E. faecalis is stored at -80. Please see the appropriate personnel (i.e., Dr. Fozo) to pull the cult... | ["[Steps]\nE. faecalis is stored at -80. Please see the appropriate personnel (i.e., Dr. Fozo) to pull the culture from frozen.", "[Steps]\nBegin a 10 ml liquid broth overnight (ON) of E. faecalis; grow without aeration in 37°Cincubator.", "[Steps]\nThe following morning, dilute culture to be 0.01in fresh media. Note... |
41,644 | Preparation of single-cell suspensions for scMEP mass cytometry analysis | 4 | dx.doi.org/10.17504/protocols.io.bkwkkxcw | https://www.protocols.io/view/preparation-of-single-cell-suspensions-for-scmep-bkwkkxcw | Felix Hartmann | TITLE: Preparation of single-cell suspensions for scMEP mass cytometry analysis
AUTHORS: Felix Hartmann
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Preparation of single cell suspensions to be analyzed for metabolic and phenotypic features by scMEP mass cytometry analysis. This protocols spans... | ["[Obtain single-cell suspension]\nPrepare single-cell suspension with your established method of choice.Be aware: cell aggregates clog the small tubing of the CyTOF and prevent acquisition.Use of digestive enzymes might be necessary but can lead to epitope loss.Cell numbers depend on the experimental question but prep... |
72,454 | Freely moving recording: Chronic recoverable Neuropixels in mice | 1 | null | https://www.protocols.io/view/freely-moving-recording-chronic-recoverable-neurop-cizeuf3e | Emily A Aery Jones | TITLE: Freely moving recording: Chronic recoverable Neuropixels in mice
AUTHORS: Emily A Aery Jones
[DESCRIPTION]
This protocol collection explains how to build a low-cost, lightweight system to implant Neuropixels 1.0 probes into mice, record during freely moving behavior, then recover the probe for future use. This ... | ["[Design the enclosure] Consider what acrylic to use (e.g. 1/4\" P95 matte black acrylic).\nUse black if you're planning to track LEDs in the dark or white if you're planning to track a Black6 mouse based on center of mass.\nUse matte finish to reduce reflections from LEDs and overhead lights.\nThicker material makes ... |
59,144 | Tuning the expression levels of native genes | 4 | dx.doi.org/10.17504/protocols.io.kqdg3px1ql25/v1 | https://www.protocols.io/view/tuning-the-expression-levels-of-native-genes-b5zgq73w | Carolyn N Bayer, Ana Gabriela Veiga Sepulchro, Maja Rennig, Morten Norholm | TITLE: Tuning the expression levels of native genes
AUTHORS: Carolyn N Bayer, Ana Gabriela Veiga Sepulchro, Maja Rennig, Morten Norholm
[DESCRIPTION]
This protocol collection describes how to use our optimised tetAOPT dual selection marker in E. coli K12 and Nissle. This dual selection marker can be used for positive ... | ["[Ordering of oligonucleotides] order the following oligonucleotides:", "[Ordering of oligonucleotides] 2 primers annealing in the tetA cassette. These two primers have to each include 50 bp overhangs. The primer annealing upstream of tetA should contain homology to the 50 first basepairs of the gene of interest. The ... |
null | null | null | dx.doi.org/10.17504/protocols.io.mejc3cn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Measurement of DNA can be done using two broad methods (Spectrophotometric or Fluorometric).</p>
<p> </p>
<p>Qubit is a fluorometric method and uses a double stranded DNA specific dye. Therefore the sensitivity is higher and impurities like RNA or nucleotides in the sample wi... | [] |
68,147 | Anthoceros agrestis Oxford (hornwort) transformation v02 | 1 | dx.doi.org/10.17504/protocols.io.eq2lynowevx9/v1 | https://www.protocols.io/view/anthoceros-agrestis-oxford-hornwort-transformation-cestteen | Eftychis Frangedakis, Manuel Waller | TITLE: Anthoceros agrestis Oxford (hornwort) transformation v02
AUTHORS: Eftychis Frangedakis, Manuel Waller
[DESCRIPTION]
Anthoceros agrestis Oxford (hornwort) transformation v02
[BEFORE_START]
Pray (not needed anymore)
[STEPS]
6. Tissue preparation:
Collect approximately 1 g of thallus tissue grown for 4-6 ... | ["Tissue preparation: \n\nCollect approximately 1 g of thallus tissue grown for 4-6 weeks under low light intensity (approximately 0.1 g of tissue per petri dish - 10 petri dishes in total). Figure1 and Figure 4.1\n\nTransfer the tissue into an empty petri dish, add sterile water until the tissue is covered and fragme... |
69,378 | Top Down Proteomics Data Collection for Microdissected Pancreas Tissue Functional Units | 1 | dx.doi.org/10.17504/protocols.io.261ge3pw7l47/v1 | https://www.protocols.io/view/top-down-proteomics-data-collection-for-microdisse-cfzatp2e | James M Fulcher, Isaac Kwame Attah, Mowei Zhou, Ljiljana.PasaTolic | TITLE: Top Down Proteomics Data Collection for Microdissected Pancreas Tissue Functional Units
AUTHORS: James M Fulcher, Isaac Kwame Attah, Mowei Zhou, Ljiljana.PasaTolic
[DESCRIPTION]
The protocol describes how to use laser capture microdissection (LCM) to cut small regions of interest (~200-300 μm) from tissue secti... | ["[Liquid chromatography (LC) method setup] Set up reversed-phase LC system with online trapping for desalting.\n\nDual pump configuration\nMobile phase A (MPA): 0.2% formic acid in water (LCMS grade)\nMobile phase B (MPB): 0.2% formic acid in acetonitrile (LCMS grade)", "[Mass spectrometer (MS) method setup] Calibrate... |
54,238 | Titan ONT SARS-CoV-2 Strain Characterization Workflow for the Terra Platform | 5 | null | https://www.protocols.io/view/titan-ont-sars-cov-2-strain-characterization-workf-by76pzre | Jill V Hagey, Frank J Ambrosio, Kevin Libuit, Technical Outreach and Assistance for States Team | TITLE: Titan ONT SARS-CoV-2 Strain Characterization Workflow for the Terra Platform
AUTHORS: Jill V Hagey, Frank J Ambrosio, Kevin Libuit, Technical Outreach and Assistance for States Team
[DESCRIPTION]
The Titan_ONT workflow is a part of the Public Health Viral Genomics Titan series for SARS-CoV-2 genomic character... | ["[Setup Terra and Google Cloud Accounts]", "[Import Titan ONT workflow from Dockstore] Importing the Titan Workflow from Dockstore to the User Workspace\n\nThe Titan_ONT workflow is hosted in the Theiagen Dockstore (https://dockstore.org/) repository and has to be imported into the user's Terra Workspace. Begin by cli... |
39,939 | Coral tissue and skeleton DNA extraction | 4 | dx.doi.org/10.17504/protocols.io.bi9bkh2n | https://www.protocols.io/view/coral-tissue-and-skeleton-dna-extraction-bi9bkh2n | Molly Moynihan | TITLE: Coral tissue and skeleton DNA extraction
AUTHORS: Molly Moynihan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This extraction protocol is based on the Qiagen DNeasy PowerBiofilm kit with modifications from Sunagawa et al. 2010.</div><div class = "text-block">Sunagawa, S., Woodley, C. M. & ... | ["[Preparation]\nIf needed, prepare lysozyme by dissolving of lysozyme powder (≥ 40,000 units/mg) per of nuclease free water. Multiple aliquots can be prepared and stored at .\n12.5 mg\n1 mL\n-20 °C", "[Preparation]\nThaw samples and lysozyme (if frozen).", "[Preparation]\nClean surfaces and pipettes with 10% bleach... |
94,862 | Nest Building Test | 4 | null | https://www.protocols.io/view/nest-building-test-c8vnzw5e | Valina L. Dawson, Ted Dawson, Hanseok Ko | TITLE: Nest Building Test
AUTHORS: Valina L. Dawson, Ted Dawson, Hanseok Ko
[DESCRIPTION]
Used to assess nigrostriatal sensorimotor function in mice. Based on the Deacon 2006 protocol.
[STEPS]
1. Place 2.5 g nestlet into feeder of each cage.
2. Individually house mice must then pull the cotton nestlet from the feeder... | ["Place 2.5 g nestlet into feeder of each cage.", "Individually house mice must then pull the cotton nestlet from the feeder by rearing and useing complext fine motor skills.", "Scores based on the amount of unused nestlet material were determined 16 hours after the nestlet was placed. Further details on scoring can be... |
null | null | null | dx.doi.org/10.17504/protocols.io.ubieske | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
The present study forms part of an ongoing longitudinal project examining risks and resilience for schizophrenia-spectrum disorders in a non-clinical ascertained sample of college students. The main objective of the study was examine the validity of psychometrically assessed pos... | [] |
66,209 | Extraction of bacterial DNA using ChargeSwitch gDNA Mini Bacteria kit on KingFisher Flex robot | 1 | dx.doi.org/10.17504/protocols.io.6qpvrdzezgmk/v2 | https://www.protocols.io/view/extraction-of-bacterial-dna-using-chargeswitch-gdn-ccv9sw96 | Leyi Wang, Carol Maddox, Melanie Prarat, Yan Zhang, Lifang Yan, Akhilesh Ramachandran, Sai Sankara Narayanan, Girish Patil | TITLE: Extraction of bacterial DNA using ChargeSwitch gDNA Mini Bacteria kit on KingFisher Flex robot
AUTHORS: Leyi Wang, Carol Maddox, Melanie Prarat, Yan Zhang, Lifang Yan, Akhilesh Ramachandran, Sai Sankara Narayanan, Girish Patil
[DESCRIPTION]
This procedure is used to extract genome DNA of bacteria isolates us... | ["Sample processing", "Bacterial Broth Culture\n\nIf using broth, pick single colony and grow in 5 ml Trypticase Soy Broth (TSB), overnight grow at 37 degree without shaking. Use 0.4 ml of the bacterial culture and centrifuge for 4min at 8000 rpm, discard supernatant and resuspend the cell pellet in 100 μL of Resuspens... |
83,276 | Sectioning of Mouse Brain by Cryostat | 1 | dx.doi.org/10.17504/protocols.io.5jyl8prw7g2w/v1 | https://www.protocols.click/view/sectioning-of-mouse-brain-by-cryostat-cvjkw4kw | Maryana Nissan | TITLE: Sectioning of Mouse Brain by Cryostat
AUTHORS: Maryana Nissan
[DESCRIPTION]
This protocol describes how to use the cryostat to prepare and slice mouse brain sections for Immunohistochemistry
[STEPS]
SECTION: Preparation Methods
1. After removing the brain from -80C storage, leave the brain on dry ice for 15-2... | ["[Preparation Methods] After removing the brain from -80C storage, leave the brain on dry ice for 15-20 minutes. This will ensure there is not a big temperature difference when it is placed in the chamber of the cryostat. The cryostat my lab uses is Leica, model CM-30505.", "[Preparation Methods] Label microscope slid... |
24,501 | Post-Fixation Heavy Metal Staining and Resin Embedding for Electron Microscopy (EM) | null | dx.doi.org/10.17504/protocols.io.36vgre6 | null | Jessica Riesterer, Erin Stempinski, Claudia Lopez | TITLE: Post-Fixation Heavy Metal Staining and Resin Embedding for Electron Microscopy (EM)
AUTHORS: Jessica Riesterer, Erin Stempinski, Claudia Lopez
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Tissues, cell monolayers, organoids and xenografts all image differently depending on the sample prepa... | ["[Day 1]\nOnce the fixed samples are received, they are post fixed in 2% (v/v) OsO4 prepared in 0.1M Na Cacodylate (pH 7.4) for 1.5 hours at room temperature. All these steps are performed using aluminum foil protected 2 ml centrifuge tubes. The three incubations done at room temperature are completed using a rotating... |
30,946 | Library Prep for CUT&RUN with NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7645) | 1 | dx.doi.org/10.17504/protocols.io.bagaibse | https://www.protocols.io/view/library-prep-for-cut-amp-run-with-nebnext-ultra-ii-bagaibse | Nan Liu | TITLE: Library Prep for CUT&RUN with NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7645)
AUTHORS: Nan Liu
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = ":UNDERLINE;">Choose your protocol:</span></div><div class = "text-block"><div class = "justify" style = "text-align:left"... | ["[NEBNext End Prep]\nImportant Note: Please use manufacturer protocol if you are making histone modification CUT&RUN library. Do not use this one, which is optimized for small fragments.Mix componentsAdd the following components to a sterile nuclease-free tube: AB1ReagentVolume2CUT&RUN DNA (6ng)25 μl3(green) NEBNext ... |
85,006 | Sample preparation for TMT-based total and phospho-proteomic analysis of cells and tissues | 4 | dx.doi.org/10.17504/protocols.io.261ged49yv47/v1 | https://www.protocols.click/view/sample-preparation-for-tmt-based-total-and-phospho-cw9nxh5e | Ilham Seffouh, Tran Le Cong Huyen Bao Phan, Toan K. Phung, Dario R Alessi, Raja S. Nirujogi | TITLE: Sample preparation for TMT-based total and phospho-proteomic analysis of cells and tissues
AUTHORS: Ilham Seffouh, Tran Le Cong Huyen Bao Phan, Toan K. Phung, Dario R Alessi, Raja S. Nirujogi
[DESCRIPTION]
Mass spectrometry-based proteomics and phosphoproteomics are highly sensitive and un-biased techniques to ... | ["[Lysate preparation: For cells] Prepare cells at a suitable confluency ~70 to 80% in a 15 cm dish. Ensure to have sufficient replicates, preferably 4 replicates per condition.", "[Lysate preparation: For cells] Wash cells with 5 mL plain DMEM medium and wash with 5 mL PBS.", "[Lysate preparation: For cells] Add 700 ... |
null | null | null | dx.doi.org/10.17504/protocols.io.s8iehue | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol explores how to run USEARCH (v11.0.667) (<a href="https://academic.oup.com/bioinformatics/article/26/19/2460/230188" target="_blank" rel="noopener noreferrer">Edgar, 2010</a>) on a 16s RNA dataset.</p>
<p> </p>
<p>USEARCH is a sequence analysis tool that offers ... | [] |
33,093 | Tunnel Slide Preparation for Motor Speed Recordings | 1 | dx.doi.org/10.17504/protocols.io.bcjdiui6 | https://www.protocols.io/view/tunnel-slide-preparation-for-motor-speed-recording-bcjdiui6 | Uriel Barboza Perez, Ekaterina Krasnopeeva, Jerko Rosko, Teuta Pilizota | TITLE: Tunnel Slide Preparation for Motor Speed Recordings
AUTHORS: Uriel Barboza Perez, Ekaterina Krasnopeeva, Jerko Rosko, Teuta Pilizota
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Preparation of our standard tunnel-slide, used for BFM speed measurements and experiments involving rapid med... | ["[Tunnel Slide Making]\nTake out 22x40 mm coverslips and standard microscope slides.", "[Tunnel Slide Making]\nCut 2 pieces of Scotch sticky tape and tape them perpendicularly on the microscope slide.\nThe separation between the tapes should be approximately 3-4mm apart from each other.", "[Tunnel Slide Making]\nCut ... |
92,684 | User Guide for CytoFLEX S Analyzer | 1 | dx.doi.org/10.17504/protocols.io.yxmvm3br6l3p/v1 | https://www.protocols.io/view/user-guide-for-cytoflex-s-analyzer-c6rkzd4w | Jamie C Tijerina | TITLE: User Guide for CytoFLEX S Analyzer
AUTHORS: Jamie C Tijerina
[DESCRIPTION]
This is the Caltech Flow Cytometry Facility's User Guide for the CytoFLEX S Analyzer. This guide is given to all investigators who are trained to run the CytoFLEX S in the facility. A copy is kept in a binder next to the instrument at al... | ["Download the full user guide here."] |
40,769 | ELISA for quantification of IL-9 in human serum. | 6 | dx.doi.org/10.17504/protocols.io.bj29kqh6 | https://www.protocols.io/view/elisa-for-quantification-of-il-9-in-human-serum-bj29kqh6 | Angel Justiz-Vaillant | TITLE: ELISA for quantification of IL-9 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. They... | ["An anti-human IL-9 coating antibody is adsorbed onto microwells by incubation overnight at 4°C.", "Add 50 µl of human serum. Human IL-9 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.",... |
66,013 | Functionality test (TBE electrophoresis buffer) | 4 | null | https://www.protocols.io/view/functionality-test-tbe-electrophoresis-buffer-ccp5svq6 | Cordellia Cordellia Fulai, Nadine Mowoh, Stephane Fadanka | TITLE: Functionality test (TBE electrophoresis buffer)
AUTHORS: Cordellia Cordellia Fulai, Nadine Mowoh, Stephane Fadanka
[DESCRIPTION]
This protocol describes the comparative analysis of resolution of bands and band patterns after electrophoresis with the BenBio TBE buffer formulation as compared with a commerci... | ["[PCR amplification] In order to have the PCR amplicons to use for this experiment we typically amplify the 0.5 and/or 1kb regions of the Lambda DNA in a PCR reaction as follow:\n\nPreparing for PCR amplification of 0.5 and 1kb Lambda DNA\n\nCrush some ice and put in a clean bowl\nRemove and thaw all PCR reagents on i... |
103,371 | BAF_S05_Plate Reader SpectraMax iD3 | 0 | dx.doi.org/10.17504/protocols.io.eq2lyweepvx9/v1 | https://www.protocols.io/view/baf-s05-plate-reader-spectramax-id3-dg7j3zkn | Nicholas Sherman | TITLE: BAF_S05_Plate Reader SpectraMax iD3
AUTHORS: Nicholas Sherman
[DESCRIPTION]
Standard operation of the SpectraMax iD3 plate reader.
[STEPS]
SECTION: General:
1. The instrument can measure in 3 distinct modes: Absorbance, Luminescence or Fluorescence.
--> Fluorescence wavelength range: EX 250-830nm, EM 270-850nm... | ["[General:] The instrument can measure in 3 distinct modes: Absorbance, Luminescence or Fluorescence.\n--> Fluorescence wavelength range: EX 250-830nm, EM 270-850nm. Plate sizes: 96 or 384 wells.\n--> Luminescence wavelength range: 300-850nm or 300 - 650 nm for \"All Wavelengths\" setting. Plate sizes: 96 or 384 wells... |
null | null | null | dx.doi.org/10.17504/protocols.io.q3ydypw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The biGBac system presented by Weissmann <em>et al. </em>(Weissmann <em>et al, </em>2016 and Weissmann <em>et al, </em>2018) is a modular insect cell expression system designed for expression of multi-subunit complexes. The system is very powerful, allowing up to 25 genes to ... | [] |
24,106 | RNA re-precipitation protocol | null | dx.doi.org/10.17504/protocols.io.3signce | null | Cristian Riccio | TITLE: RNA re-precipitation protocol
AUTHORS: Cristian Riccio
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">If the RNA you have extracted is not pure and contains some residual contamination, as shown by poor Nanodrop ratios, you can reprecipitate the RNA, wash it and re-dissolve it to purify it.<... | ["Add 10% volume 3M sodium acetate pH 5.2 and 250% volume ethanol. So if your RNA solution is 100 ul, add 10 ul NaAc solution and 250 ul ethanol.", "Mix well and put on dry ice for 30 min or -20 overnight", "Centrifuge max speed 30 min at 4 C, remove supernatant", "3 washes with 75% ethanol kept on dry ice. For example... |
null | null | null | dx.doi.org/10.17504/protocols.io.n83dhyn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Modified from Lippmeier et al. 2009</p>
[STEPS]
?.
?.
?.
?.
?.
?. | [] |
62,446 | 10Xv3.1 Genomics Sample Processing | 1 | dx.doi.org/10.17504/protocols.io.dm6gpwd8jlzp/v2 | https://www.protocols.io/view/10xv3-1-genomics-sample-processing-b88nrzve | Allen Institute for Brain Science | TITLE: 10Xv3.1 Genomics Sample Processing
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
This protocol is used for the rapid generation of 3’ transcriptomic-NGS-ready- single-cell-libraries from pools of cells.
Note: Research reported in this publication was supported by the National Institute Of Mental Hea... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.kdics4e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>El ensayo de herida o ruptura <em>in vitro</em>, es un método fácil, de bajo costo y bien desarrollado para medir migración celular <em>in vitro</em>. Los pasos básicos implican la creación de una “herida” en una monocapa celular, capturando las imágenes al principio y en in... | [] |
24,415 | Cultivation of Seminavis robusta | null | dx.doi.org/10.17504/protocols.io.337gqrn | null | Lev Tsypin, Aaron Turkewitz | TITLE: Cultivation of Seminavis robusta
AUTHORS: Lev Tsypin, Aaron Turkewitz
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describes how we grew </span><span style = "font-style:italic;">S. robusta</span><span> and stored cultures at 4 C. Under these condtiions, the cells grow ... | ["[Growth]\nSet up an incubator for 12 hr day-night cycling at 18 C.", "[Growth]\nInoculate 100 mL F/2 in 175 cm2 flask with ~500,000 cells", "[Cold storage]\nScrape a growing 175 cm2 flask", "[Cold storage]\nMix 5 mL of scraped culture with 5 mL fresh F/2 medium in a 15 mL falcon tube", "[Cold storage]\nWrap with foil... |
19,147 | Insulin Tolerance Test in Mouse | null | dx.doi.org/10.17504/protocols.io.wxjffkn | https://www.protocols.io/view/insulin-tolerance-test-in-mouse-wxjffkn | Nancy Smith, Mourad Ferdaoussi, Haopeng Lin, Patrick Macdonald | TITLE: Insulin Tolerance Test in Mouse
AUTHORS: Nancy Smith, Mourad Ferdaoussi, Haopeng Lin, Patrick Macdonald
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details the insulin tolerance test in mice. This is performed on C57Bl6, transgenic SENP1 KO and ZMIZ1 KO mouse models. Typic... | ["[Fasting]\nFasting begins first thing in the morning (around 9am). Fast mice for 4-6 hours before ITT begins. Transfer mice to clean cage and wire top. Keep water bottles during the fasting period.\nIf using High Fat diet (HFD), save food to give back at the end of the ITT.Mark tails with a sharpie for easier iden... |
50,978 | Spectral Flow Phenotyping of CD226 KO CD127- Tregs During Expansion | 4 | null | https://www.protocols.io/view/spectral-flow-phenotyping-of-cd226-ko-cd127-tregs-bv2an8ae | Matthew Brown, Brusko Laboratory | TITLE: Spectral Flow Phenotyping of CD226 KO CD127- Tregs During Expansion
AUTHORS: Matthew Brown, Brusko Laboratory
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This Standard Operating Procedure provides instructions for staining surface and intracellular markers on primary cells to be use... | ["[Preparing Falcon Tubes and Cells for Staining]\nTransfer 100,000 Unelectroporated CD127- Tregs into the \"CD127- Tregs\" tube.", "[Preparing Falcon Tubes and Cells for Staining]\nObtain the appropriate number of 5 mL Falcon Tubes based on the cell subsets and timepoints being analyzed.", "[Preparing Falcon Tubes an... |
81,838 | Therapeutic applications and effects of Lupinus angustifolius (Blue lupin) and its components. A systematic review with meta-analysis. | 4 | dx.doi.org/10.17504/protocols.io.e6nvwjw6wlmk/v1 | https://www.protocols.io/view/therapeutic-applications-and-effects-of-lupinus-an-ct6nwrde | Rafael Fernández Castillo | TITLE: Therapeutic applications and effects of Lupinus angustifolius (Blue lupin) and its components. A systematic review with meta-analysis.
AUTHORS: Rafael Fernández Castillo
[DESCRIPTION]
Reviews have focused on the blue lupin (Lupinus angustifolius) diet based on the reduction of analytical and anthropometric ... | ["[Therapeutic application and effects of Lupinus Angustifolius (Blue lupin) and its components. A systematic reviews with Mata-analysis] Therapeutic applications and effects of Lupinus angustifolius (Blue lupin) and its components. A systematic review with meta-analysis. ... |
67,560 | https://www.facebook.com/ViaKetoAppleGummiesinUnitedKingdom/ | 3 | dx.doi.org/10.17504/protocols.io.yxmvmnreog3p/v1 | https://www.protocols.io/view/https-www-facebook-com-viaketoapplegummiesinunited-cd8gs9tw | fdaaffa | TITLE: https://www.facebook.com/ViaKetoAppleGummiesinUnitedKingdom/
AUTHORS: fdaaffa
[DESCRIPTION]
https://www.facebook.com/ViaKetoAppleGummiesinUnitedKingdom/
[STEPS] | [] |
69,682 | Midbrain organoid generation from mfNPC | 4 | dx.doi.org/10.17504/protocols.io.6qpvr4x1pgmk/v1 | https://www.protocols.io/view/midbrain-organoid-generation-from-mfnpc-cgastsee | Rachel Bates | TITLE: Midbrain organoid generation from mfNPC
AUTHORS: Rachel Bates
[DESCRIPTION]
This protocol describes our method for the differentiation of human floor plate neural progenitor cells into human midbrain-like organoids (hMLOs). This protocol has been developed using a combination of several published protocols.
Ad... | ["[Day 0] Human floor plate neuronal progenitor cells (mfNPC) were derived using Smits 2019 protocol. They were maintained for a minimum of 5 passages before being used to generate organoids in maintenance medium.", "[Day 0] mfNPCs were detached using accutase at 37 °C for 3 min .", "[Day 0] Re-suspend cells in d0 indu... |
17,656 | ZitR purification | null | dx.doi.org/10.17504/protocols.io.vgye3xw | null | PALOMA VARELA | TITLE: ZitR purification
AUTHORS: PALOMA VARELA
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. | [] |
54,331 | Paraoxonase 1 and chronic obstructive pulmonary disease: A meta-analysis (protocol) | 1 | dx.doi.org/10.17504/protocols.io.bza3p2gn | https://www.protocols.io/view/paraoxonase-1-and-chronic-obstructive-pulmonary-di-bza3p2gn | Jun Watanabe, Kazuhiko Kotani, Alejandro Gugliucci | TITLE: Paraoxonase 1 and chronic obstructive pulmonary disease: A meta-analysis (protocol)
AUTHORS: Jun Watanabe, Kazuhiko Kotani, Alejandro Gugliucci
[DESCRIPTION]
Introduction:Oxidative stress is a driving factor in the pathophysiology of chronic obstructive pulmonary disease (COPD). While paraoxonase 1 (PON1) is a... | [] |
62,431 | OcuPrime Vision Support Reviews: Shocking Side Effects & Customer Complaints | 3 | dx.doi.org/10.17504/protocols.io.q26g74d51gwz/v1 | https://www.protocols.io/view/ocuprime-vision-support-reviews-shocking-side-effe-b877rzrn | ocuprimevision | TITLE: OcuPrime Vision Support Reviews: Shocking Side Effects & Customer Complaints
AUTHORS: ocuprimevision
[DESCRIPTION]
Official Website - Click Here forOcuPrime Vision Support
Availability Of OcuPrime Vision Support - Online On Website
Main Benefits - Improve EYE Vision Without Any Side Effect
VISIT THE OFF... | [] |
34,449 | Whitefly DNA extraction, partial mtCO1 gene amplification and gel electrophoresis | null | dx.doi.org/10.17504/protocols.io.bdvri656 | https://www.protocols.io/view/whitefly-dna-extraction-partial-mtco1-gene-amplifi-bdvri656 | Joachim Nwezeobi, Onyeyirichi Onyegbule, Chukwuemeka Nkere, Joseph Onyeka, Sharon van Brunschot, Susan Seal, John Colvin | TITLE: Whitefly DNA extraction, partial mtCO1 gene amplification and gel electrophoresis
AUTHORS: Joachim Nwezeobi, Onyeyirichi Onyegbule, Chukwuemeka Nkere, Joseph Onyeka, Sharon van Brunschot, Susan Seal, John Colvin
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. Single whitefly adults were randomly cho... | ["Single whitefly adults were randomly chosen from each of the 1.5 ml Eppendorf tubes containing 70% ethanol, using a sterilized entomological pin.", "Each whitefly was transferred to a clean 1.5 ml Eppendorf tube.", "To extract insect DNA, 50 µl of 10% Chelex was added to the tube and the whitefly was crushed using a ... |
23,624 | Pyrosequencing | null | dx.doi.org/10.17504/protocols.io.3bggijw | null | Bing Yang | TITLE: Pyrosequencing
AUTHORS: Bing Yang
[STEPS] | [] |
53,103 | Geometric morphometrics nesomyinae rodent skulls | 2 | dx.doi.org/10.17504/protocols.io.bx4ppqvn | https://www.protocols.io/view/geometric-morphometrics-nesomyinae-rodent-skulls-bx4ppqvn | Lea Terray, Christiane Denys, Steven Goodman, Voahangy Soarimalala, Aude Lalis, Raphaël Cornette, christiane.denys | TITLE: Geometric morphometrics nesomyinae rodent skulls
AUTHORS: Lea Terray, Christiane Denys, Steven Goodman, Voahangy Soarimalala, Aude Lalis, Raphaël Cornette, christiane.denys
[DESCRIPTION]
Here we aim to define how skull morphology in an endemic and monophyletic clade of rodents (subfamily Nesomyinae), which ... | [] |
22,435 | A rat model of contrast-induced acute kidney injury following intra-arterial contrast administration | null | dx.doi.org/10.17504/protocols.io.z6bf9an | null | Zhiqing Wang | TITLE: A rat model of contrast-induced acute kidney injury following intra-arterial contrast administration
AUTHORS: Zhiqing Wang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Contrast-induced acute kidney injury (CI-AKI) is an iatrogenic complication frequently developed after cardiac cathe... | ["[Surgical Procedure]\nRats were deprived of water for 48 hours。", "Body weight of each rat was measure.", "Deeply anaesthetized was conducted by pentobarbital sodium (40 mg/kg, i.p.).", "The right femoral vein and carotid artery were both cannulated by short peripheral catheters which were widely used in the nursing ... |
86,388 | In situ immunoglobulin M (IgM) detection in formalin-fixed, paraffin-embedded (FFPE) pig tissues | 4 | dx.doi.org/10.17504/protocols.io.5qpvo3rj7v4o/v1 | https://www.protocols.io/view/in-situ-immunoglobulin-m-igm-detection-in-formalin-cykuxuww | Jayne E Wiarda, Crystal Loving | TITLE: In situ immunoglobulin M (IgM) detection in formalin-fixed, paraffin-embedded (FFPE) pig tissues
AUTHORS: Jayne E Wiarda, Crystal Loving
[DESCRIPTION]
An immunohistochemistry (IHC) staining protocol for in situ identification of IgM in pig tissue.
[BEFORE_START]
Starting specimens:
Starting samples = FFPE tis... | ["[Baking] Before starting the assay: \nPreheat a dry oven to 60℃ \nLoad slides for assay into vertical slide rack\n\nBaking\nBake slides 20 min 60℃\n\nWhile slides bake:\nPrepare 0.05% PBS-T (can store at RT up to 1 month)", "[Deparaffinizing & Rehydrating] Immediately before deparaffinizing:\nAdd ~200 mL xylenes ... |
19,919 | WarmStart LAMP® | null | dx.doi.org/10.17504/protocols.io.xppfmmn | null | Kenneth Schackart | TITLE: WarmStart LAMP®
AUTHORS: Kenneth Schackart
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">How to run nucleic acid amplification using the Warm-Start LAMP kit.</div><div class = "text-block">Each reaction produces 25 μL.</div><div class = "text-block"><span>For the original protocol, look at:... | ["[Prepare Work Area]\nSpray entire work area with 70% EtOH including pipettes, tip holder used for holding PCR tubes, and work surface. Wipe with a paper towel.", "[Prepare Work Area]\nSpray entire work area with RNAway.", "[ Gather Materials]\nTake styrofoam container to Marley 527 (directly across from Marley 509) a... |
null | null | null | dx.doi.org/10.17504/protocols.io.nafdabn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol provides an useful technique for detecting allele frequencies in the cDNA sample</p>
[STEPS]
?.
?.
?.
?.
?.
?. | [] |
85,537 | Targets of sympathetic nerves in myenteric plexus of human colon | 1 | dx.doi.org/10.17504/protocols.io.dm6gp3bx8vzp/v1 | https://www.protocols.io/view/targets-of-sympathetic-nerves-in-myenteric-plexus-cxr9xm96 | Dominic R Parker, Lukasz. Wiklendt, Adam G Humenick, Bao Nan Chen, Sia C Tiong, David A Wattchow, Phil G Dinning, Simon Brookes | TITLE: Targets of sympathetic nerves in myenteric plexus of human colon
AUTHORS: Dominic R Parker, Lukasz. Wiklendt, Adam G Humenick, Bao Nan Chen, Sia C Tiong, David A Wattchow, Phil G Dinning, Simon Brookes
[DESCRIPTION]
This protocol outlines basic methods to measure distributions of axonal varicosities (comparing ... | ["All handling of un-fixed human tissue is exclusively done by staff trained in occupational health and safety requirements for handling hazardous material, wearing appropriate PPE (gloves, gowns and masks) and working in areas designated for human tissue. Users of this protocol should check local requirements with th... |
55,926 | Skim Milk Flocculation and RNA Extraction for SARS-CoV-2 Viral Capture | 4 | dx.doi.org/10.17504/protocols.io.b2uwqexe | https://www.protocols.io/view/skim-milk-flocculation-and-rna-extraction-for-sars-b2uwqexe | Jillian Dunbar, Stephen P Hilton, Jamie VanTassell, Julia Raymond, Marlene K Wolfe, Pengbo Liu, Christine Moe | TITLE: Skim Milk Flocculation and RNA Extraction for SARS-CoV-2 Viral Capture
AUTHORS: Jillian Dunbar, Stephen P Hilton, Jamie VanTassell, Julia Raymond, Marlene K Wolfe, Pengbo Liu, Christine Moe
[DESCRIPTION]
This protocols describes the use of Skim Milk Flocculation to concentrate and extract SARS-CoV-2 from ... | ["[Preparing Solutions for Procedure] Prepare the NaPP stock by dissolving 1 g of NaPP in 100 mL of . This should be prepared once a month, and should be autoclaved before use.", "[Day 2 - Process Moore Swab] Autoclave 10 mL of NaPP stock, 10 mL of Tween 80 stock, and 1 mL of Antifoam A stock.", "[Moore Swab Processin... |
49,234 | space_publications_versions protocol 1 | 1 | null | https://www.protocols.io/view/space-publications-versions-protocol-1-bubsnsne | Maria Guliakina | TITLE: space_publications_versions protocol 1
AUTHORS: Maria Guliakina
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">test</div></div>
[STEPS]
?. test
?. est 2
?. | ["test", "est 2"] |
null | null | null | dx.doi.org/10.17504/protocols.io.fs7bnhn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?. | [] |
96,962 | mxIF protocol | 0 | dx.doi.org/10.17504/protocols.io.e6nvw1pb9lmk/v1 | https://www.protocols.io/view/mxif-protocol-daxa2fie | Fan Wu | TITLE: mxIF protocol
AUTHORS: Fan Wu
[DESCRIPTION]
This protocol is developed by SenNet JHU TMC group
[STEPS]
SECTION: Dewaxing and rehydration
1. Tissue slides are baking 1 hour before dewaxing
SECTION: Dewaxing and rehydration
3. Tissue slides are then dipped in water several times to finish rehydration
SECTION: De... | ["[Dewaxing and rehydration] Tissue slides are baking 1 hour before dewaxing", "[Dewaxing and rehydration] Tissue slides are then dipped in water several times to finish rehydration", "[Dewaxing and rehydration] Tissue dewaxing is performed with 5 minutes sequential wash in 3 times 100% xylene, 3\ntimes 100% EtOH, foll... |
48,631 | Paper Microfluidic Chip Fabrication via Wax Printing | 1 | dx.doi.org/10.17504/protocols.io.btqxnmxn | https://www.protocols.io/view/paper-microfluidic-chip-fabrication-via-wax-printi-btqxnmxn | Kattika Kaarj | TITLE: Paper Microfluidic Chip Fabrication via Wax Printing
AUTHORS: Kattika Kaarj
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol will guide you through the process of paper microfluidic chip preparation via wax printing technique. This protocol does not include instruction on how to ... | ["[Paper chip preparation]\nPrint the chip designs from the file on a ~3 x 8 inches NC membrane via wax printer.\nWithin the printing command window, select the advanced setting and change a paper type to \"Japanese envelope chou#4\" which size matches our NC membrane. Select the scale with 100% to maintain the correc... |
93,870 | Histone extraction HLB protocol | 1 | dx.doi.org/10.17504/protocols.io.x54v9p49pg3e/v1 | https://www.protocols.io/view/histone-extraction-hlb-protocol-c7wnzpde | Sigrid Verhelst | TITLE: Histone extraction HLB protocol
AUTHORS: Sigrid Verhelst
[DESCRIPTION]
Protocol to extract histone proteins using a hypotonic lysis buffer for isolation of nuclei prior to acid extraction of histones that is easily amenable to label-free MS owing to the lack of detergents in the lysis buffer.
[STEPS]
SECTION: ... | ["[Isolate nuclei] Start from a dry (snap-frozen) cell pellet", "[Isolate nuclei] Add hypotonic lysis buffer (HLB) to cell pellet: 200 µL for 1x106 cells and resuspend softly", "[Isolate nuclei] Rotate for 30 min at 4°C to promote lysis of cell membrane (mechanical shear)", "[Isolate nuclei] Pellet the nuclei by centri... |
50,496 | How to import OAI-PMH identifiers in OpenRefine | 1 | dx.doi.org/10.17504/protocols.io.bvi8n4hw | https://www.protocols.io/view/how-to-import-oai-pmh-identifiers-in-openrefine-bvi8n4hw | Andrea Marchitelli, Alessandra Moi, Carlo Bianchini | TITLE: How to import OAI-PMH identifiers in OpenRefine
AUTHORS: Andrea Marchitelli, Alessandra Moi, Carlo Bianchini
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocollo per importare in OpenRefine una lista di identificatori OAI-PMH per successive elaborazioni.</div></div>
[STEPS]
?. Open O... | ["Open OpenRefine and choose \"Create project\".", "Select \"Web Addresses (URLs)\" as the data source for the new project and click \"Next\". Enter the OAI-PMH baseurl of the identified target, choose the ListIdentifiers verb and the appropriate metadataPrefix.E.g. http://www.bibliotecheoggi.it/trends/oai?verb=ListIde... |
45,672 | Protocol for Preparing SOC | 6 | null | https://www.protocols.io/view/protocol-for-preparing-soc-bqugmwtw | Prince Samoh | TITLE: Protocol for Preparing SOC
AUTHORS: Prince Samoh
[STEPS]
?. Total Volume = 100ml
?. Weigh 2g of Tryptone into a 150 ml beakerAdd 0.5g of Yeast ExtractAdd 0.058g of NaCl [10mM]Add 0.019g KCl [2.5mM]Add 1mL 2M MgCl2 [10mM]Add 0.12g MgSO4 [10mM]Top up with distilled water to reach the 100ml mark
?. Autoclave solut... | ["Total Volume = 100ml", "Weigh 2g of Tryptone into a 150 ml beakerAdd 0.5g of Yeast ExtractAdd 0.058g of NaCl [10mM]Add 0.019g KCl [2.5mM]Add 1mL 2M MgCl2 [10mM]Add 0.12g MgSO4 [10mM]Top up with distilled water to reach the 100ml mark", "Autoclave solution at 121oC, 0.1MPa for 15 -20 minutes", "Allow the solution to c... |
14,830 | T cell isolation from mouse tissues | 1 | dx.doi.org/10.17504/protocols.io.sqnedve | https://www.protocols.io/view/t-cell-isolation-from-mouse-tissues-sqnedve | Kristin Anderson | TITLE: T cell isolation from mouse tissues
AUTHORS: Kristin Anderson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines the steps for isolating murine T cells from mouse blood, ascites, spleen, and ID8 tumors.</div><div class = "text-block"><span>In brief: Spleens were disrupted ... | ["[Spleen digestion]\n1. Harvest cells by smashing spleen through a 70um filter.2. Spin down cells at 369xg for 4-5 minutes at 4C.3. Remove supernatant and lyse red blood cells with 2 mL ACK lysis buffer for 2 minutes at room temperature.4. Quench lysis using 10mL T cell media.5. Spin down cells at 369xg for 4-5 minute... |
null | null | null | dx.doi.org/10.17504/protocols.io.hcib2ue | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes the quantification of luciferase activity in Ostreococcus and Bathycoccus cells that have been transformed with a firefly luciferase coding sequence upstream of the OTTH595 high affinity transporter promoter. Using this methods we were able to show th... | [] |
77,373 | Preparation of 1L of Foraging Buffer | 4 | dx.doi.org/10.17504/protocols.io.j8nlkw28xl5r/v1 | https://www.protocols.io/view/preparation-of-1l-of-foraging-buffer-cps5vng6 | Alfonso Pérez Escudero, Alid Al-Asmar, gabrielmadirolas | TITLE: Preparation of 1L of Foraging Buffer
AUTHORS: Alfonso Pérez Escudero, Alid Al-Asmar, gabrielmadirolas
[DESCRIPTION]
Protocol is mainly inspired from: WormBook Methods http://www.wormbook.org/chapters/www_strainmaintain/strainmaintain.html.
We use this protocol for our foraging experiments with the worm Caenorh... | ["In order to perform this protocol, you will need the following solutions:\npH=6 phosphate buffer (as prepared in: https://www.protocols.io/view/preparation-of-0-5l-of-phosphate-buffer-ph-6-0-n2bvj8r7bgk5/v1)\n1 M magnesium sulfate (as prepared in: https://www.protocols.io/view/preparation-of-1m-magnesium-sulfate-solu... |
78,008 | Neuropathological work up and whole slide image analysis of human brain tissue | 1 | null | https://www.protocols.io/view/neuropathological-work-up-and-whole-slide-image-an-cqeyvtfw | Caitlin S. Latimer, Amanda Keen, Jeanelle Ariza-Torres, emelief, C. Dirk Keene | TITLE: Neuropathological work up and whole slide image analysis of human brain tissue
AUTHORS: Caitlin S. Latimer, Amanda Keen, Jeanelle Ariza-Torres, emelief, C. Dirk Keene
[DESCRIPTION]
The National Institute of Aging – Alzheimer's Association (NIA-AA) have established criteria for the neuropathological assessment a... | ["[Neuropathological work up] Cut 5-µm-thick sections fromparaffin-embedded tissue blocks using a microtome.", "[Neuropathological work up] Form a ribbon of tissue using the microtome and a blade to cut the tissue.", "[Neuropathological work up] Transfer ribbon to a 2-7℃ water bath", "[Neuropathological work up] Pick u... |
null | null | null | dx.doi.org/10.17504/protocols.io.gaibsce | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>These methods accompany:</p>
<p> </p>
<p>Huang Zhihai, Xu Jiang, Xiao Shuiming, Liao Baosheng, Gao Yuan, Zhai Chaochao, Qiu Xiaohui, Xu Wen, Chen Shilin</p>
<p> (2016): Supporting data for 'Comparative optical genome analysis of two Pangolin species Manis pentadactyla and Man... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.hehb3b6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><span style="color: #000339; font-family: Raleway, sans-serif; font-size: 14px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; w... | [] |
107,928 | H_QTof_PL_v2 | 0 | dx.doi.org/10.17504/protocols.io.n92ld8xr8v5b/v2 | https://www.protocols.io/view/h-qtof-pl-v2-dmmy447w | Fang Bian | TITLE: H_QTof_PL_v2
AUTHORS: Fang Bian
[DESCRIPTION]
To extract plasma lipids for LCMS analysis.
[BEFORE_START]
Use LCMS grade water and solvents.
[GUIDELINES]
Use glassware throughout this protocol.
[STEPS]
SECTION: To extract plasma lipids for LCMS study
1. Transfer plasma 50 ul (regular pipette tips) into a 3 ... | ["[To extract plasma lipids for LCMS study] Transfer plasma 50 ul (regular pipette tips) into a 3 ml glass tube", "[To extract plasma lipids for LCMS study] Add 200 ul of LCMS grade-chloroform/methanol (2:1)", "[To extract plasma lipids for LCMS study] Stand for 5 min at room temperature.", "[To extract plasma lipids f... |
96,801 | Short-Term Freezing of Anopheles stephensi (Mosquito) Larvae | 0 | dx.doi.org/10.17504/protocols.io.j8nlk8b5dl5r/v1 | https://www.protocols.io/view/short-term-freezing-of-anopheles-stephensi-mosquit-dar92d96 | Michael C. Young1, Jackson Watkins, Gabriela Ramirez, Emily N. Gallichotte, MaKala Herndon, Elisha Xiao-Kim, Madison Stoltz, Maria Alexandra Marquez, Gaukhar Iskakova, Jennifer Barfield, Karen M. Dobos, Gregory D. Ebel | TITLE: Short-Term Freezing of Anopheles stephensi (Mosquito) Larvae
AUTHORS: Michael C. Young1, Jackson Watkins, Gabriela Ramirez, Emily N. Gallichotte, MaKala Herndon, Elisha Xiao-Kim, Madison Stoltz, Maria Alexandra Marquez, Gaukhar Iskakova, Jennifer Barfield, Karen M. Dobos, Gregory D. Ebel
[DESCRIPTION]
Mosquito ... | ["[Phase I: Establish and maintain mosquito colony] Phenotypic Analysis of developing mosquitoes (Figure 1)\n\nLarvae develop from eggs to first instar larvae (L1) around 2-3 days after transferring egg paper.\nL1 develop into L2/L3 over the next 4 days (approximately). During that time, they show the\nability to hatc... |
28,108 | Preparation of 1000X Antibiotic Stock Solution | null | dx.doi.org/10.17504/protocols.io.7pkhmkw | null | NUS iGEM | TITLE: Preparation of 1000X Antibiotic Stock Solution
AUTHORS: NUS iGEM
[STEPS]
?. Weigh x grams of antibiotic-of-interest.
?. Dilute in pure 100% ethanol for chloramphenicol or sterile deionized water for kanamycin and ampicillin.
?. Syringe filter water-based antibiotic solution using a 0.22-μm filter | ["Weigh x grams of antibiotic-of-interest.", "Dilute in pure 100% ethanol for chloramphenicol or sterile deionized water for kanamycin and ampicillin.", "Syringe filter water-based antibiotic solution using a 0.22-μm filter"] |
78,439 | Fluorescent Western Protocol | 4 | null | https://www.protocols.io/view/fluorescent-western-protocol-cqufvwtn | Lynn Doran, Steven J Burgess | TITLE: Fluorescent Western Protocol
AUTHORS: Lynn Doran, Steven J Burgess
[DESCRIPTION]
Analysis of proteins using fluorescent immunoblot.
Note:
- The choice of secondary antibody depends on the choice of primary antibody, whether it is derived from a mouse (monoclonal) or a rabbit (polyclonal).
- It is advis... | ["Keep membranes in the black Western Blot incubation box for all steps, this is important after adding the secondary antibody because the signal is light-sensitive and will become bleached if exposed to light for a long enough period.", "Wet with 1x PBS for 2 min min", "Rinse membrane with dH2O", "Discard PBS and incu... |
null | null | null | dx.doi.org/10.17504/protocols.io.dzq75v | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol outlines and evaluates the filtration steps needed for the preparation of samples (viral concentrates) containing a density of viral particles concentrated from large volumes of natural water samples. (<a href="http://www.aslo.org/books/mave/MAVE_110.pdf" target="_... | [] |
57,474 | Collection – Staining– Analysis of vaginal smears | 4 | dx.doi.org/10.17504/protocols.io.rm7vzy3rrlx1/v1 | https://www.protocols.io/view/collection-staining-analysis-of-vaginal-smears-b4daqs2e | Roberta Marongiu | TITLE: Collection – Staining– Analysis of vaginal smears
AUTHORS: Roberta Marongiu
[DESCRIPTION]
The 4 stages of the rodent’s female cycle are:
Metestrous – M
Diestrous -D
Proestrous -P
Estrous – E
Transitional stages, i.e. showing characteristics of two consecutive stages e.g. M-D or D-P, are not uncommon, parti... | ["[Sample collection] Pre-label slides with study number, animal numbers, date and time of collection, using a permanent marker, and place them on a suitable tray. Slides can be set up on a date basis, with one set of slides for all females each day.", "[Sample collection] Hold the mouse by the base of the tail, liftin... |
null | null | null | dx.doi.org/10.17504/protocols.io.hu7b6zn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Please contact Dr. Steven Wilhelm (wilhelm@utk.edu) for additional information regarding this protocol.</p>
[GUIDELINES]
<div title="Page 7">
<div>
<div>
<p>Mutations and off-target effects<br /> The method has various safeguards against the effects of mutations and off-targ... | [] |
40,350 | COVID Blood Processing for scRNAseq | 1 | dx.doi.org/10.17504/protocols.io.bjm6kk9e | https://www.protocols.io/view/covid-blood-processing-for-scrnaseq-bjm6kk9e | Peter Szabo, Steven Wells, Peter A. Sims, Donna Farber | TITLE: COVID Blood Processing for scRNAseq
AUTHORS: Peter Szabo, Steven Wells, Peter A. Sims, Donna Farber
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the isolation of lymphocytes and pan-mononuclear cells from human whole blood for scRNAseq analysis.</div></div>
[STEPS]... | ["[Preparing Buffer]\nCreate the following DPBS Solution-EDTA in a bottle of DPBS by using the table below: ABCD1ComponentVolume (mL)Starting Conc.Final Conc.2DPBS474-3FBS25100%5%4EDTA10.5 M1 mM\nABCD1ComponentVolume (mL)Starting Conc.Final Conc.2DPBS474-3FBS25100%5%4EDTA10.5 M1 mM", "[Preparation of Blood]\nPlace sam... |
92,490 | TaME-seq2 | 1 | dx.doi.org/10.17504/protocols.io.dm6gpjxy5gzp/v2 | https://www.protocols.io/view/tame-seq2-c6jizcke | jean-marc, Milan Stosic, Alexander Hesselberg, trinro | TITLE: TaME-seq2
AUTHORS: jean-marc, Milan Stosic, Alexander Hesselberg, trinro
[DESCRIPTION]
Tagmentation-assisted multiplex PCR enrichment sequencing for viral genomic profiling (TaME-seq2). Viral genome and integration enrichment library preparation protocol.
Manuscript:
TaME-seq2: Tagmentation-assisted multiplex... | ["[Sample preparation] Prepare and normalize DNA/cDNA samples by measuring sample concentration and diluting in nuclease-free water if necessary. \n\nSample volume should be 15 µL \n\n50 ng input is recommended, but the protocol works with less and performance is more dependent on viral load.", "[Tagmentation] Prepare... |
49,841 | p1 11/5 | 1 | null | https://www.protocols.io/view/p1-11-5-buwrnxd6 | Maria Guliakina | TITLE: p1 11/5
AUTHORS: Maria Guliakina
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">test</div></div>
[STEPS]
?. test
?. {"blocks":[{"key":"ccqb3","text":"","type":"unstyled","depth":0,"inlineStyleRanges":[],"entityRanges":[],"data":[]}],"entityMap":[]} | ["test", "{\"blocks\":[{\"key\":\"ccqb3\",\"text\":\"\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[]}],\"entityMap\":[]}"] |
54,048 | Minimum inhibitory concentration of butanol for E. coli KJK01 | 4 | dx.doi.org/10.17504/protocols.io.byz8px9w | https://www.protocols.io/view/minimum-inhibitory-concentration-of-butanol-for-e-byz8px9w | Arshshaikh | TITLE: Minimum inhibitory concentration of butanol for E. coli KJK01
AUTHORS: Arshshaikh
[DESCRIPTION]
This protocol helps you determine the minimum inhibitory concentration (MIC) of butanol for E. coli KJK01. However, this technique can be extended to determine the MIC of any metabolite for any strain by making adj... | ["Take a 96 welled plate.", "[Media condition preparation] Calculate the amount of butanol that you require in the starting well. Wilbanks 2017 paper suggests that butanol shows strong toxic effects below 10 g/L and entirely inhibits growth at 15 g/L. We should expect our MIC to fall in this range. Hence, we can start ... |
98,058 | Protocol_Psychosocial Support and Care for Children with Special Health Care Needs and Their Families: A Scoping Review for Enhancing the Care System | 0 | dx.doi.org/10.17504/protocols.io.6qpvr8o4zlmk/v1 | https://www.protocols.io/view/protocol-psychosocial-support-and-care-for-childre-dbzi2p4e | Tomo Nonoyama | TITLE: Protocol_Psychosocial Support and Care for Children with Special Health Care Needs and Their Families: A Scoping Review for Enhancing the Care System
AUTHORS: Tomo Nonoyama
[DESCRIPTION]
Introduction: The increasing number of children with special health care needs (CSHCN) due to advancements
in medical technol... | ["[Review Protocol] Review Protocol\n \n((cshcn[tiab]) OR (\"children with\nspecial needs\"[tiab] OR \"children with special health care\nneeds\"[tiab] OR \"children with special healthcare needs\"[tiab])\nOR (\"children with special needs\"[tiab] OR \"children with\nspecial health care needs\"[tiab]) AND (care[tiab] O... |
38,659 | anemia, iron defficency anemia and amaranth trial in Ethiopia | 3 | dx.doi.org/10.17504/protocols.io.bhzbj72n | https://www.protocols.io/view/anemia-iron-defficency-anemia-and-amaranth-trial-i-bhzbj72n | Alemselam Orsango | TITLE: anemia, iron defficency anemia and amaranth trial in Ethiopia
AUTHORS: Alemselam Orsango
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><h1><a href="" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">Summary</span></a></h1></div><div class = "text-block"><spa... | [] |
70,181 | E. coli growth trend measurement (culture with silver ion) | 4 | dx.doi.org/10.17504/protocols.io.81wgby1byvpk/v1 | https://www.protocols.io/view/e-coli-growth-trend-measurement-culture-with-silve-cgsdtwa6 | Weizhuo.Chen, An.Huang | TITLE: E. coli growth trend measurement (culture with silver ion)
AUTHORS: Weizhuo.Chen, An.Huang
[DESCRIPTION]
This protocol helps obtain growth curve of E. coli cultured with concentration gradient of silver ion.
[STEPS]
SECTION: IPTG induction
1. Grow Escherichia coli overnight and dilute the culture using LB to ... | ["[IPTG induction] Grow Escherichia coli overnight and dilute the culture using LB to OD600=0.4-0.6.", "[IPTG induction] Add IPTG to cell culture (final concentration 1mM), and incubate the culture 3h at 171 rpm, 37℃ in orbital shaking incubator.", "[Sample addition to microplate wells] Cells cultures, LB broth and sil... |
26,335 | Nile Red Staining of Drosophila Larval Tissues | null | dx.doi.org/10.17504/protocols.io.5x7g7rn | null | Elizabeth Allen | TITLE: Nile Red Staining of Drosophila Larval Tissues
AUTHORS: Elizabeth Allen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is used to stain late larval </span><span style = "font-style:italic;">Drosophila</span><span> lipid droplets in fat bodies and intestines with Nile Red,... | ["Dissect tissues in ice cold PBS, keeping samples on ice until required sample size is obtained.", "Fix tissues in 4% PFA for 20 minutes.", "Wash tissues 3x in PBS.", "Stain samples in Nile Red at 0.5 ug/mL diluted in PBS for 1 hour.\n{\"blocks\":[{\"key\":\"5sif3\",\"text\":\"Nile Red is prepared in acetone to make a... |
null | null | null | dx.doi.org/10.17504/protocols.io.hgfb3tn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes the knock-down of specific tRNA(s) in mammalian cells using short hairpin RNA (shRNA)-based RNA interference (RNAi). We have used this method successfully to silence specific tRNAs in in HeLa<sup>1</sup> and N2a cells<sup>2</sup>.</p>
<p> </p>
<p>Refer... | [] |
102,392 | LYSOSOMAL ISOLATION PROTOCOL | 0 | dx.doi.org/10.17504/protocols.io.kqdg32kdqv25/v1 | https://www.protocols.io/view/lysosomal-isolation-protocol-df8y3rxw | Scott Vermilyea | TITLE: LYSOSOMAL ISOLATION PROTOCOL
AUTHORS: Scott Vermilyea
[DESCRIPTION]
This protocol details the isolation of lysosomes.
[STEPS]
SECTION: Subcellular Lysosome Isolation Protocol
1. In Vitro Harvest
SECTION: Subcellular Lysosome Isolation Protocol
1.1. Following designated treatment, wash cells three times with DM... | ["[Subcellular Lysosome Isolation Protocol] In Vitro Harvest", "[Subcellular Lysosome Isolation Protocol] Following designated treatment, wash cells three times with DMEM followed by the application of 0.5 mL of homogenization buffer supplemented with proteinase and phosphatase buffer.\n\n Homogenisation Buffer:", "[Su... |
37,081 | SPARC bilateral phrenic neurophysiology preparation with phrenic afferent stimulation - spinal intact study | 1 | dx.doi.org/10.17504/protocols.io.bgfzjtp6 | https://www.protocols.io/view/sparc-bilateral-phrenic-neurophysiology-preparatio-bgfzjtp6 | Kristi Streeter, Michael sunshine, David Fuller | TITLE: SPARC bilateral phrenic neurophysiology preparation with phrenic afferent stimulation - spinal intact study
AUTHORS: Kristi Streeter, Michael sunshine, David Fuller
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for conducting bilateral phrenic neurograms in anesthetized, paralyzed,... | ["Isoflurane induction: 2.5-3% in 100% O2 in a closed chamber for 3-5 minutes", "Transfer to nose cone and maintain at 3% in 100% 02.", "Place intravenous line into tail vein for delivery of drugs/anesthesia/fluids (flush with heparinized saline). Reduce isoflurane anesthesia to 1%. Begin urethane infusion (1.8g/kg in ... |
91,172 | OT-2 Protocol to transfer volume from several plates to a single plate | 5 | dx.doi.org/10.17504/protocols.io.6qpvr4o62gmk/v2 | https://www.protocols.io/view/ot-2-protocol-to-transfer-volume-from-several-plat-c5acy2aw | Ana Mariya Anhel, Lorea Alejaldre, Ángel Goñi-Moreno | TITLE: OT-2 Protocol to transfer volume from several plates to a single plate
AUTHORS: Ana Mariya Anhel, Lorea Alejaldre, Ángel Goñi-Moreno
[DESCRIPTION]
This protocol is meant to transfer samples from different plates to a single or fewer final plates than the source number, in other words, merge samples of differe... | ["[Files Preparation] Preparing Customized Template\n\nPreparing the template (a .xlsx) with the specific variables for each experiment.\n\nAttached there is a template of the variable file with several sheets and a PDF file explaining each variable:\nGeneralVariables: variables related to the labware to be used\nPipet... |
89,090 | Tissue Protein Extraction: Tissue Homogenization using Urea-based Buffer and Bead Mill Homogenizers | 4 | dx.doi.org/10.17504/protocols.io.36wgq3op5lk5/v1 | https://www.protocols.io/view/tissue-protein-extraction-tissue-homogenization-us-c29ayh2e | J Bons, J P Rose, M A Watson, B Schilling | TITLE: Tissue Protein Extraction: Tissue Homogenization using Urea-based Buffer and Bead Mill Homogenizers
AUTHORS: J Bons, J P Rose, M A Watson, B Schilling
[DESCRIPTION]
Tissue homogenization to isolate protein in preparation for downstream proteomic profiling.
[STEPS]
9. Transfer the supernatant (clear lysate con... | ["Transfer the supernatant (clear lysate containing the soluble proteins) to a clean\n1.5-mL microcentrifuge tube, carefully avoiding any liquid fat layer on top and\ndebris at the bottom of the tube.", "Chill the adaptor sets of the bead mill homogenizer at -20°C.", "Freshly prepare the lysis buffer as described in Ta... |
52,264 | Use of drugs associated with QT interval prolongation at the hospital level during the start of the COVID-19 pandemic in Colombia | 1 | dx.doi.org/10.17504/protocols.io.bxagpibw | https://www.protocols.io/view/use-of-drugs-associated-with-qt-interval-prolongat-bxagpibw | Jorge Machado Alba, Andrés Gaviria-Mendoza, Manuel Enrique Machado-Duque, Luis Fernando Valladales-Restrepo | TITLE: Use of drugs associated with QT interval prolongation at the hospital level during the start of the COVID-19 pandemic in Colombia
AUTHORS: Jorge Machado Alba, Andrés Gaviria-Mendoza, Manuel Enrique Machado-Duque, Luis Fernando Valladales-Restrepo
[DESCRIPTION]
Background: Many of the therapeutic proposal... | [] |
88,662 | Using high throughput amplicon sequencing to determine the diet of two generalist stink bugs (Hemiptera) in agricultural and urban landscapes. | 1 | dx.doi.org/10.17504/protocols.io.e6nvwdewdlmk/v1 | https://www.protocols.io/view/using-high-throughput-amplicon-sequencing-to-deter-c2twyepe | Olivier Berteloot | TITLE: Using high throughput amplicon sequencing to determine the diet of two generalist stink bugs (Hemiptera) in agricultural and urban landscapes.
AUTHORS: Olivier Berteloot
[DESCRIPTION]
The use of DNA metabarcoding has become an increasingly popular technique to infer
feeding interactions in herbivores and genera... | ["[Sample collection] From 2019-2022, H. halys and P. rufipes were collected in commercial organic orchards (apple, pear and mixed crops), private orchards and urban gardens. 25 locations were sampled throughout the northern parts of Belgium. P. rufipes specimens were hand-caught by scanning trees, shrubs and wildflowe... |
null | null | null | dx.doi.org/10.17504/protocols.io.q2edybe | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
45,104 | QIAamp DNA FFPE Tissue Kit protocol | 4 | null | https://www.protocols.io/view/qiaamp-dna-ffpe-tissue-kit-protocol-bqaqmsdw | SANTIAGO SEPULVEDA | TITLE: QIAamp DNA FFPE Tissue Kit protocol
AUTHORS: SANTIAGO SEPULVEDA
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The QIAamp DNA FFPE Tissue Kit is optimized for purification of DNA from FFPE tissue</div><div class = "text-block">sections. It uses well-established QIAamp DNA Micro technology fo... | ["[Long incubations]\nIncubate at for (or until the sample has been completely lysed)\n56 °C", "[Long incubations]\nIncubate at for\n90 °C\nIncubation at 90°C in Buffer ATL partially reverses formaldehyde modification of nucleic acids. Longer incubation times or higher incubation temperatures may result in more frag... |
96,705 | Bioinformatics manual for population epigenomics combining whole-genome and target genome sequencing | 0 | dx.doi.org/10.17504/protocols.io.8epv5xw4ng1b/v1 | https://www.protocols.io/view/bioinformatics-manual-for-population-epigenomics-c-dan92dh6 | Odile Rogier, Isabelle Lesur Kupin, Mamadou Dia Sow, Christophe Boury, Alexandre Duplan, Abel Garnier, Abdeljalil Senhaji rachik, Peter Civan, Josquin Daron, Alain Delaunay, Ludovic Duvaux, Vanina Benoit, Erwan Guichoux, Gregoire Le Provost, Edmond Sanou, Christophe Ambroise, Christophe Plomion, Jérôme Salse, Vincent S... | TITLE: Bioinformatics manual for population epigenomics combining whole-genome and target genome sequencing
AUTHORS: Odile Rogier, Isabelle Lesur Kupin, Mamadou Dia Sow, Christophe Boury, Alexandre Duplan, Abel Garnier, Abdeljalil Senhaji rachik, Peter Civan, Josquin Daron, Alain Delaunay, Ludovic Duvaux, Vanina Benoit... | ["[Whole Genome Sequencing - Removing false C/T mutations] Trimming\n \nPublication: Bolger et al., 2014\nVersion: 0.38\nGithub: https://github.com/usadellab/Trimmomatic", "[Whole Genome Sequencing - Removing false C/T mutations] A preliminary Whole Genome Sequencing (WGS) step was considered for filtering purposes, to... |
38,035 | The combination of LMWH (Low-Molecular-Weight Heparin) and Aspirin as a prophylaxis treatment for pre-eclampsia and SGA (Small-for-Gestational Age) neonates in medium- and high-risk women: protocol for a Systematic Review and Meta-Analysis. | 3 | dx.doi.org/10.17504/protocols.io.bhdtj26n | https://www.protocols.io/view/the-combination-of-lmwh-low-molecular-weight-hepar-bhdtj26n | Christos-Georgios Kontovazainitis, Georgios Mitsiakos, Dimitra Gialamprinou | TITLE: The combination of LMWH (Low-Molecular-Weight Heparin) and Aspirin as a prophylaxis treatment for pre-eclampsia and SGA (Small-for-Gestational Age) neonates in medium- and high-risk women: protocol for a Systematic Review and Meta-Analysis.
AUTHORS: Christos-Georgios Kontovazainitis, Georgios Mitsiakos, Dimitra ... | [] |
106,137 | Methods for human brainstem tissue processing and capture for spatial transcriptomics using 10x-Genomics Visium Spatial platform. | 0 | dx.doi.org/10.17504/protocols.io.dm6gpzm3dlzp/v1 | https://www.protocols.io/view/methods-for-human-brainstem-tissue-processing-and-djvz4n76 | Sandy S. Pineda, Hongyun Li, Zhixiang Wu, Amy Burke, Ping Wu, YuHong Fu, Glenda Halliday | TITLE: Methods for human brainstem tissue processing and capture for spatial transcriptomics using 10x-Genomics Visium Spatial platform.
AUTHORS: Sandy S. Pineda, Hongyun Li, Zhixiang Wu, Amy Burke, Ping Wu, YuHong Fu, Glenda Halliday
[DESCRIPTION]
This protocol details the process of preparing formalin fixed human ti... | ["[Tissue preparation] Selected formalin fixed & paraffin embedded (FFPE) blocks of human post-mortem, midbrains\nand pons were cut in a rotary microtome at 6 µm thickness.\nTwo or three tissue sections were cut and placed on each poly-prep slides. Slides were dried in an oven for 180 min at 42 °C and placed in desicca... |
33,151 | HCR of patched/recorded Cerebellar Molecular Layer Interneurons | null | dx.doi.org/10.17504/protocols.io.bck7iuzn | null | Carly Martin, Naeem Nadaf, Tomas Osorno, Stephanie Rudolph, Chuck Vanderburg, Wade Regehr, Evan Macosko | TITLE: HCR of patched/recorded Cerebellar Molecular Layer Interneurons
AUTHORS: Carly Martin, Naeem Nadaf, Tomas Osorno, Stephanie Rudolph, Chuck Vanderburg, Wade Regehr, Evan Macosko
[STEPS]
?. Imaging and analysis
?. Neurons were filled with 100 μM Alexa-594 via patch pipette to visualize their morphology using 2-ph... | ["Imaging and analysis", "Neurons were filled with 100 μM Alexa-594 via patch pipette to visualize their morphology using 2-photon imaging. After completion of the electrophysiological recordings the patch electrode was retracted and the cell resealed. We used a custom 2-photon laser-scanning microscope with a 40x, 0.8... |
80,356 | Cell culture and Western blot | 4 | null | https://www.protocols.io/view/cell-culture-and-western-blot-csqcwdsw | Andrea Dickey, rabrisch | TITLE: Cell culture and Western blot
AUTHORS: Andrea Dickey, rabrisch
[DESCRIPTION]
Protocol for detecting Rab7a phosphorylation at S72 by LRRK1 and LRRK1 mutants in HEK 293T cells.
[STEPS]
SECTION: Cell culture and transfection
1. Day - 1
Split 293T cells in 6-well dishes 1440 min before transfection at 200K/wel... | ["[Cell culture and transfection] Day - 1 \n\nSplit 293T cells in 6-well dishes 1440 min before transfection at 200K/well in 2 mL DMEM (with FBS and with P/S)", "[Cell culture and transfection] Day - 2 \n\nTransfection", "[Cell culture and transfection] Warm PEI and Opti-MEM at RT for 15 min \nLabel a tube for each wel... |
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