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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22,025 | Insulin-secreting human alpha-cells might be a cure for diabetes | null | dx.doi.org/10.17504/protocols.io.zrhf536 | null | Cathy Miller | TITLE: Insulin-secreting human alpha-cells might be a cure for diabetes
AUTHORS: Cathy Miller
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">From one hormone to another, it’s usually a long-term change. To explore whether human cells have this ability to adapt, the Herrera team uses islets from dia... | [] |
42,617 | Isolation of green algal symbionts from freshwater sponges and subsequent reinfection of sponge tissues | 4 | dx.doi.org/10.17504/protocols.io.bmuzk6x6 | https://www.protocols.io/view/isolation-of-green-algal-symbionts-from-freshwater-bmuzk6x6 | April Hill, Ivy Nguyen, Malcolm Hill | TITLE: Isolation of green algal symbionts from freshwater sponges and subsequent reinfection of sponge tissues
AUTHORS: April Hill, Ivy Nguyen, Malcolm Hill
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>A variety of green algal species form intracellular symbioses with freshwater sponges. T... | ["[Algal cell isolation]\nIdentify algal-bearing sponges in the field.", "[Algal cell isolation]\nWash the tissue or gemmules in 1% H2O2 by shaking gently for several seconds at room temperature followed by at least 5 washes in sterile distilled water, M-medium, or Strekal’s medium.", "[Algal cell isolation]\nPlace tis... |
43,389 | Identifying Genetic Dependencies in Cancer by Analyzing siRNA Screens in Tumor Cell Line Panels | 4 | dx.doi.org/10.17504/protocols.io.bnk5mcy6 | https://www.protocols.io/view/identifying-genetic-dependencies-in-cancer-by-anal-bnk5mcy6 | James Campbell, Colm Ryan, Christopher J. Lord | TITLE: Identifying Genetic Dependencies in Cancer by Analyzing siRNA Screens in Tumor Cell Line Panels
AUTHORS: James Campbell, Colm Ryan, Christopher J. Lord
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Loss-of-function screening using RNA interference or CRISPR approaches can be used to identi... | ["[3.1 Processing siRNA Screen Data Using CellHTS2]\nTypically, siRNA screens are conducted in multiwell tissue culture plates. The process of transfecting a cancer cell line with siRNAs is optimized prior to screening and once optimal conditions have been selected (described in [17]), cells are dispensed into multiwel... |
60,673 | Metsch farms protocol | 3 | null | https://www.protocols.io/view/metsch-farms-protocol-b7g9rjz6 | Meghan Duffy, Katherine Hunsberger, Rebecca Bilich | TITLE: Metsch farms protocol
AUTHORS: Meghan Duffy, Katherine Hunsberger, Rebecca Bilich
[DESCRIPTION]
This is a protocol to infect and maintain Daphnia with Metschnikowia bicuspidata for use in laboratory experiments.
[STEPS] | [] |
100,118 | OT-2 Media dispensing and culture inoculation protocol | 5 | dx.doi.org/10.17504/protocols.io.q26g7yb3kgwz/v3 | https://www.protocols.io/view/ot-2-media-dispensing-and-culture-inoculation-prot-ddzw277e | Ana Mariya Anhel, Lorea Alejaldre, Ángel Goñi-Moreno | TITLE: OT-2 Media dispensing and culture inoculation protocol
AUTHORS: Ana Mariya Anhel, Lorea Alejaldre, Ángel Goñi-Moreno
[DESCRIPTION]
This protocol is meant to distribute reactive(s) (i.e bacterial culture media) into final 96-well plates with a single channel pipette and then transfer culture samples from source ... | ["[Files Preparation] Preparing Customized Template\n\nPreparing the template (a .xlsx) with the specific variables for each experiment and a .pdf that contains the instructions on how to fill the template \n\nHere we attach one Excel with several sheets:\nGeneralVariables: variables related mainly to the labware that ... |
null | null | null | dx.doi.org/10.17504/protocols.io.ix9cfr6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocol for PFA fixation of sediment or culture samples and Percoll prep of sediments. </p>
[STEPS]
SECTION: 4% PFA in PBS
?.
SECTION: Fixing sediment or culture samples (lab based)
?.
SECTION: Fixing sediment samples (shipboard)
?.
SECTION: Mini Percoll prep for microsc... | ["[4% PFA in PBS] {\"blocks\":[{\"key\":\"2thtj\",\"text\":\"Heat 33 mL MQ water to 60\\u00b0C in a 50 mL Falcon style tube.\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[]},{\"key\":\"3qkmu\",\"text\":\" \",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entity... |
47,149 | CApyOS | 5 | dx.doi.org/10.17504/protocols.io.bsamnac6 | https://www.protocols.io/view/capyos-bsamnac6 | Eric Smith | TITLE: CApyOS
AUTHORS: Eric Smith
[STEPS]
?. [HTTP]
?. [HTTP]
?. [HTTP]
?. [HTTP]
Parameter Keys to Postmark Server
?. [HTTP] | ["[HTTP]", "[HTTP]", "[HTTP]", "[HTTP]\nParameter Keys to Postmark Server", "[HTTP]"] |
85,190 | 621.1.HTC_H&E Stain (Paraffin or Cryosections) | 1 | dx.doi.org/10.17504/protocols.io.36wgqjnq3vk5/v3 | https://www.protocols.click/view/621-1-htc-h-amp-e-stain-paraffin-or-cryosections-cxfexjje | Gloria S Pryhuber, Cory Poole, Anthony Corbett | TITLE: 621.1.HTC_H&E Stain (Paraffin or Cryosections)
AUTHORS: Gloria S Pryhuber, Cory Poole, Anthony Corbett
[DESCRIPTION]
Hematoxylin and Eosin staining is the standard chemical stain used on slides to be reviewed for assessment of general histopathology and the generation of a pathology report for each donor.
... | ["[Staining Procedure] Verify that all slides are completely dry. Slides can be dried in an 55C oven for one hour or more prior to use to prevent loss of tissue.", "[Staining Procedure] If sections were from tissue block embedded in paraffin, deparaffinize slides with 3 changes of Xylene for 5 minutes each.", "[Staini... |
59,586 | Discovery proteomic (DIA) LC-MS/MS data acquisition and analysis | 1 | dx.doi.org/10.17504/protocols.io.e6nvwk1z7vmk/v1 | https://www.protocols.io/view/discovery-proteomic-dia-lc-ms-ms-data-acquisition-b6farbie | Yan Chen, Jennifer Gin, Christopher J J Petzold | TITLE: Discovery proteomic (DIA) LC-MS/MS data acquisition and analysis
AUTHORS: Yan Chen, Jennifer Gin, Christopher J J Petzold
[DESCRIPTION]
This protocol details steps in discovery proteomic data-independent acquisition with a standard-flow UHPLC-Obitrap system and a subsequent DIA-NN library-free database search... | ["[Proteomics: HPLC and Mass Spectromtery] Thaw peptide samples on ice , and transfer 30 µLof each sample to LC autosampler vials (Agilent, Cat.#5182-0567,#5182-0564) or 96-well plate (Bio-Rad, Cat.#HSP9655).", "[Proteomics: HPLC and Mass Spectromtery] Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis... |
71,468 | Fura-2 imaging of ionomycin response, with and without R568; a CaSR positive modulator | 4 | dx.doi.org/10.17504/protocols.io.kqdg39p4zg25/v1 | https://www.protocols.click/view/fura-2-imaging-of-ionomycin-response-with-and-with-ch2kt8cw | Peter Kilfeather | TITLE: Fura-2 imaging of ionomycin response, with and without R568; a CaSR positive modulator
AUTHORS: Peter Kilfeather
[DESCRIPTION]
Fura-2 imaging protocol to accompany Kilfeather, Khoo et al., 2023: Single cell spatial transcriptomic and translatomic profiling of dopaminergic neurons in health, ageing and disease
... | ["[Data Capture] Prepare Fura-2 AM to 5 mM concentration in calcium-free HBSS supplemented with 20 mM HEPES.", "[Data Capture] Dilute Fura-2 AM to the final concentration of 2.5 mM in Neurobasal medium supplemented with B27 and L-glutamine, with DMSO (0.1%) or the CaSR positive modulator R568 (10 mM).", "[Data Capture]... |
95,879 | Immunoprecipitation for Flag-tagged proteins | 0 | dx.doi.org/10.17504/protocols.io.q26g7poxqgwz/v1 | https://www.protocols.io/view/immunoprecipitation-for-flag-tagged-proteins-c9vfz63n | Jean-Louis Parmasad | TITLE: Immunoprecipitation for Flag-tagged proteins
AUTHORS: Jean-Louis Parmasad
[DESCRIPTION]
Immunoprecipitation for Flag-tagged proteins for various biomolecular analyses.
[STEPS]
SECTION: Transfection and collection
1. Transfect HEK293T cells with 2µg of plasmid expressing Flag-tagged protein of interest using en... | ["[Transfection and collection] Transfect HEK293T cells with 2µg of plasmid expressing Flag-tagged protein of interest using enhanced polyethyleneimine transfection reagent in Opti-MEM (Thermo Fisher Scientific, 31985070).", "[Transfection and collection] After 48h, collect cells and lyse with IP Lysis Buffer (25 mM Tr... |
58,926 | Adhesive Test | 4 | dx.doi.org/10.17504/protocols.io.b5snq6de | https://www.protocols.io/view/adhesive-test-b5snq6de | Haley Geertsma | TITLE: Adhesive Test
AUTHORS: Haley Geertsma
[DESCRIPTION]
This protocol is used to test mice in the Adhesive behavioural test.
[STEPS]
1. Habituate mice in the testing room for 60 minutes.
2. Remove all mice from their home cage then remove all bedding/debris from their home cage (do not clean their home cage, jus... | ["Habituate mice in the testing room for 60 minutes.", "Remove all mice from their home cage then remove all bedding/debris from their home cage (do not clean their home cage, just give a light wipe with a dry paper towel).", "Place one mouse back into its home cage for 1 minute.", "Scruff mouse and place 1cm2 adhesive... |
null | null | null | dx.doi.org/10.17504/protocols.io.q7ddzi6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Method used to derive single cell suspension from P1 mouse kidneys on ice, generating a cell suspension with greatly reduced artifact gene expresion changes and suitable for downstream analysis using 10x Chromium or DropSeq. </p>
[GUIDELINES]
<div>
<p><strong>Storage Conditi... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.gsgbwbw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div class="page" title="Page 1">
<div class="layoutArea">
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<div class="page" title="Page 2">
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<p>This protocol is intended to illustrate the process for testing a particular cell type with the IRDye 800CW EGF for ... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.nwgdfbw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This describes a method to transform a plasmid into homemade DH5α cells.</p>
[STEPS]
?.
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87,458 | In vitro LRRK2 kinase activity assay using mass-spectrometry as readout | 4 | dx.doi.org/10.17504/protocols.io.6qpvr385ovmk/v1 | https://www.protocols.io/view/in-vitro-lrrk2-kinase-activity-assay-using-mass-sp-cznax5ae | Verena Dederer, chatterjeedeep, Sebastian Mathea, Stefan Knapp | TITLE: In vitro LRRK2 kinase activity assay using mass-spectrometry as readout
AUTHORS: Verena Dederer, chatterjeedeep, Sebastian Mathea, Stefan Knapp
[DESCRIPTION]
This protocol can be used in this form or with small adjustments regarding concentration and reaction time to determine in vitro substrate phosphorylation... | ["Incubate reaction for 3 h at room temperature.\nNote: depeding on kinase this may be shorter or longer.", "[Step-by-Step Protocol] Prepare 50 µL reaction mix I: 50 nM purified LRRK2 and 5 µM Rab8 substrate in buffer containing 20 mM Hepes pH 7.4, 150 mM NaCl, 5% glycerol, 0.5 mM TCEP, 20 µM GDP, 2.5 mM MgCl2.\nAliquo... |
93,602 | Practical Guide to Live Sampling of Livestock and Wildlife for Infectious Disease Surveillance | 1 | dx.doi.org/10.17504/protocols.io.rm7vzxro8gx1/v1 | https://www.protocols.io/view/practical-guide-to-live-sampling-of-livestock-and-c7nazmae | Stefano Catalano | TITLE: Practical Guide to Live Sampling of Livestock and Wildlife for Infectious Disease Surveillance
AUTHORS: Stefano Catalano
[DESCRIPTION]
Under- or misdiagnosed cases of disease caused by especially dangerous pathogens present public health and proliferation risks. Numerous studies have demonstrated that in low-re... | [] |
69,520 | Processing of Radial K-space DW-MRI Data | 1 | dx.doi.org/10.17504/protocols.io.j8nlkkwj1l5r/v2 | https://www.protocols.io/view/processing-of-radial-k-space-dw-mri-data-cf5qtq5w | Miguelrj, Hee Kwon Song, Stephen Pickup, Mamtaaryagupta, Rong Zhou | TITLE: Processing of Radial K-space DW-MRI Data
AUTHORS: Miguelrj, Hee Kwon Song, Stephen Pickup, Mamtaaryagupta, Rong Zhou
[DESCRIPTION]
The protocol includes reconstruction of diffusion weighted images from radial k-space data and using a 3-parameter fit to derive metrics of ADC and kurtosis index.
[STEPS]
1. Image... | ["Image reconstruction\n\nRadially acquired diffusion-weighted images (DWIs) are reconstructed using the following steps:\n\nApply zero-order phase correction to each radial spoke using the average phase offset at the center slice of the lowest b-value image\nZerofill k-space by a factor of 2 to double field of view\nM... |
59,692 | LRRK1 Immunoprecipitation kinase assay | 1 | dx.doi.org/10.17504/protocols.io.kqdg3p2wpl25/v1 | https://www.protocols.io/view/lrrk1-immunoprecipitation-kinase-assay-b6ikrccw | Asad Malik, Athanasios Karapetsas, Dario R Alessi | TITLE: LRRK1 Immunoprecipitation kinase assay
AUTHORS: Asad Malik, Athanasios Karapetsas, Dario R Alessi
[DESCRIPTION]
We describe a non-radioactive assay that we deploy for analysing LRRK1 protein kinase activity in vitro using Rab7A as a substrate. This assay can be used to measure the intrinsic activity of LRRK1 i... | ["[Transient transfection of HEK293 cells for analysis of over-expressed LRRK1 activity in vitro:] Transfect HEK293 cells at around 60-70% confluency. For a 10cm dish, add 10 µg DNA (GFP-tagged LRRK1 or GFP-empty vector) and 30 µL of 1 mg/mL PEI solution to 1 mL of Opti-MEMTM Reduced Serum Medium and vortex for 20/30 s... |
44,756 | PBMC- 03 - TEFF+TREG Isolation from PBMC with “Miltenyi CD4+CD25+ Regulatory T cell Isolation Kit” | 4 | dx.doi.org/10.17504/protocols.io.bpxumpnw | https://www.protocols.io/view/pbmc-03-teff-treg-isolation-from-pbmc-with-milteny-bpxumpnw | Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino | TITLE: PBMC- 03 - TEFF+TREG Isolation from PBMC with “Miltenyi CD4+CD25+ Regulatory T cell Isolation Kit”
AUTHORS: Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">List of published ... | ["Isolate PBMCs according either to the standard protocol from fresh blood or from buffy coat (PBMC- 01a - Isolation of Human PBMC from Buffy Coat, PBMC- 01b - Isolation of Human PBMC from Whole Blood).", "Determine the cell number and viability with the microscope by staining with either Türk or Trypan blue. You can ... |
96,716 | Cylinder Test | 0 | dx.doi.org/10.17504/protocols.io.5qpvo3jmzv4o/v1 | https://www.protocols.io/view/cylinder-test-dapk2dkw | Xiaobo Mao, Ramhari Kumbhar, Hanseok Ko, Valina L. Dawson, Ted Dawson | TITLE: Cylinder Test
AUTHORS: Xiaobo Mao, Ramhari Kumbhar, Hanseok Ko, Valina L. Dawson, Ted Dawson
[DESCRIPTION]
The Cylinder test is used to evaluate locomotor asymmetry and spontaneous movement in rodent models.
[STEPS]
1. Set up small, transparent cylinder in front of video recorder.
2. Place mouse in cylinder a... | ["Set up small, transparent cylinder in front of video recorder.", "Place mouse in cylinder and record spontaneous activity for 10 min.", "Clean cylinder in between mice.", "For all recordings, view in slow motion and count the number of forepaw touches to the cylinder walls, rears, and grooming bouts."] |
57,373 | Childcare services | 1 | dx.doi.org/10.17504/protocols.io.b395qr86 | https://www.protocols.io/view/childcare-services-b395qr86 | Alex AE Alex | TITLE: Childcare services
AUTHORS: Alex AE Alex
[DESCRIPTION]
15 Festive and Fun Christmas Craft Activities for Childcare Centers
[STEPS]
SECTION: Childcare services
1. 15 Festive and Fun Christmas Craft Activities for Bright Beginnings Centers
The Holiday season gives so many fun and beautiful (and glittery!) creat... | ["[Childcare services] 15 Festive and Fun Christmas Craft Activities for Bright Beginnings Centers\n\nThe Holiday season gives so many fun and beautiful (and glittery!) create exercises for childcare focuses. Here is our rundown of 15 fun ideas that will get everybody in the Christmas soul.\n\n1. Straw and Paper Christ... |
73,056 | Aplicación de reserva de espacios y ¿Cómo reservar un asiento en la Biblioteca-sala de estudio? | 1 | dx.doi.org/10.17504/protocols.io.kxygx93dkg8j/v1 | https://www.protocols.io/view/aplicaci-n-de-reserva-de-espacios-y-c-mo-reservar-cjj8ukrw | Pedro Postigo Gimeno | TITLE: Aplicación de reserva de espacios y ¿Cómo reservar un asiento en la Biblioteca-sala de estudio?
AUTHORS: Pedro Postigo Gimeno
[DESCRIPTION]
Aplicación de reserva de espacios y como reservar un asiento en la Biblioteca/Sala de Estudio de la Universidad Católica de Murcia UCAM
[STEPS]
SECTION: Aplicación de rese... | ["[Aplicación de reserva de espacios y ¿Cómo reservar un asiento en la Biblioteca-Sala de estudio?] Aplicación reserva de espacios\n\n \nPrimeros pasos para utilizar la nueva aplicación de reserva de espacios de la universidad: \n\nInstrucction in English", "[Aplicación de reserva de espacios y ¿Cómo reservar un asien... |
34,643 | Amplification Free Paired End Library Construction Protocol | null | dx.doi.org/10.17504/protocols.io.bd3ti8nn | null | Graham J Etherington, Darren Heavens, David Baker, Ashleigh Lister, Rose McNelly, Gonzalo Garcia, Bernardo Clavijo, Iain Macaulay, Wilfried Haerty, Federica Di Palma | TITLE: Amplification Free Paired End Library Construction Protocol
AUTHORS: Graham J Etherington, Darren Heavens, David Baker, Ashleigh Lister, Rose McNelly, Gonzalo Garcia, Bernardo Clavijo, Iain Macaulay, Wilfried Haerty, Federica Di Palma
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Amplificat... | ["A total of of DNA was sheared in a volume on a Covaris S2 (Covaris, Massachusetts, USA) for 1 cycle of with a duty cycle of 5%, cycles per burst of 200 and intensity of 3.\n600 ng\n60 µl", "The fragmented molecules were then end repaired in volume using the NEB End Repair Module (NEB, Hitchin, UK) incubating the ... |
80,423 | SARS-CoV-2 Macrodomain (Mac1) TR-FRET Dose Response | 1 | null | https://www.protocols.io/view/sars-cov-2-macrodomain-mac1-tr-fret-dose-response-cssfwebn | Haim Barr, Noa Lahav | TITLE: SARS-CoV-2 Macrodomain (Mac1) TR-FRET Dose Response
AUTHORS: Haim Barr, Noa Lahav
[DESCRIPTION]
This is a HTRF-based peptide displacement assay
-------------------------------------------------------
Experiment Concentrations (From Stock to Assay)
ReagentStockLoaded into CombiFinal in assay plateUnitsHis-... | ["[Prepare 384-well Plate] PRIME Multi-Drop Combi Tube Dispensing Cassette MAC1 Buffer by selecting the PRIME button on the Combi Dispenser until the tubes are filled completely. \nNote: Be sure to cycle dispensing several times on a a clean plate lid (This confirms there are no bubbles in the Dispensing Cassette).", "... |
null | null | null | dx.doi.org/10.17504/protocols.io.gyxbxxn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<h4>Method Overview</h4>
<p>This protocol outlines a quick and simple procedure for extracting all organic compounds from a yeast culture for subsequent analysis via Liquid chromatography–mass spectrometry (LC-MS). It is suitable for quickly assessing the presence of products fr... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.h9mb946 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><span style="font-weight: 400;">The purpose of this protocol is to evaluate the significance of delta G values, as a strategy to determine the significance of secondary structure. Sequences are shuffled randomly 100x, maintaining base composition but not base order. The perce... | [] |
49,435 | Chemical Oxygen Demand Originality Test | 1 | null | https://www.protocols.io/view/chemical-oxygen-demand-originality-test-buh3nt8n | William Brigman | TITLE: Chemical Oxygen Demand Originality Test
AUTHORS: William Brigman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Version 2.0 (COD station 1</span><span style = "vertical-align:super;">st</span><span> lab and analytical trailer)</span></div><div class = "text-block"><span style = ":UNDER... | ["Fill out the COD data sheet, record the sample identification number and COD vial number.", "For samples with moderate to low COD (such as constructed wetlands) use the 1,500 mg/L COD vials.For samples with high COD (such as lagoons) use the 15,000 mg/L COD vials.", "Turn on COD block heater digester (DRB 200-HACH) (... |
100,824 | Cryo-EM sample preparation for RCKW:DARPin complex | 4 | dx.doi.org/10.17504/protocols.io.bp2l6224kgqe/v1 | https://www.protocols.io/view/cryo-em-sample-preparation-for-rckw-darpin-complex-depy3dpw | Marta Sanz Murillo | TITLE: Cryo-EM sample preparation for RCKW:DARPin complex
AUTHORS: Marta Sanz Murillo
[DESCRIPTION]
This is Leschziner's Lab protocol for making cryo-EM grids for RCKW:DARPin complex.
[BEFORE_START]
Decide which protein concentration to use, and create the proper LRRK2 buffers in order to obtain the right salt concen... | ["[Freezing Grids] Plasma clean grids.\nWe used UltrAuFoil Holey Gold 1.2/1.3 300 mesh grids and plasma cleaned them in the Solarus II (Gatan) using the QuantiFoil Au preset.", "[Freezing Grids] Apply protein to grids and plunge freeze (3-4 uL)\nWe used a Vitrobot (FEI) to blot away excess sample and plunge freeze", "[... |
23,682 | Statistical methods to analyze the persistence of threatened birds using citizen science data: A systematic review | null | dx.doi.org/10.17504/protocols.io.3dagi2e | null | Udani Wijewardhana, Denny Meyer, Madawa Weerasinghe | TITLE: Statistical methods to analyze the persistence of threatened birds using citizen science data: A systematic review
AUTHORS: Udani Wijewardhana, Denny Meyer, Madawa Weerasinghe
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left"><span style = "font-... | ["[Define the review question]\nTo identify suitable factors to explain and measure persistence or extinction risk of threatened birds using citizen science data.", "[Guideline]\nThis systematic review was reported in accordance with the preferred reporting items for systematic review and meta-analysis protocols (PRISM... |
39,071 | SARS-CoV-2 NCBI consensus submission protocol: GenBank | 1 | dx.doi.org/10.17504/protocols.io.bid7ka9n | https://www.protocols.io/view/sars-cov-2-ncbi-consensus-submission-protocol-genb-bid7ka9n | Ruth Timme, Heather Blankenship, Pavitra Roychoudhury, Erin Young, Emma Griffiths, Duncan MacCannell, Stacia Wyman, Lee Katz | TITLE: SARS-CoV-2 NCBI consensus submission protocol: GenBank
AUTHORS: Ruth Timme, Heather Blankenship, Pavitra Roychoudhury, Erin Young, Emma Griffiths, Duncan MacCannell, Stacia Wyman, Lee Katz
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">PURPOSE: </span></div>... | ["[\"Ingredients\" to have in place before starting your submissions]\n1.1: Ensure you have a working NCBI user account1.2: Identify your NCBI submission user group or establish a new one if necessary. 1.3: Bookmark the link to your submission portal1.4. BioSample + BioProject assessions in-handAfter these steps are co... |
48,418 | Processing of pediatric bronchoalveolar lavage samples for single cell analysis | 4 | dx.doi.org/10.17504/protocols.io.btiankae | https://www.protocols.io/view/processing-of-pediatric-bronchoalveolar-lavage-sam-btiankae | Shivanthan Shanthikumar, Richard Saffery, Sarath C. Ranganathan, Melanie Neeland | TITLE: Processing of pediatric bronchoalveolar lavage samples for single cell analysis
AUTHORS: Shivanthan Shanthikumar, Richard Saffery, Sarath C. Ranganathan, Melanie Neeland
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the collection, processing, cryopreservation and th... | ["[COLLECTION OF BAL.]\nAfter obtaining informed consent from family and/or patient, obtain any excess BAL fluid collected at the time of clinically indicated bronchoscopy and lavage.", "[PROCESSING OF BAL TO RECOVER SINGLE CELLS.]\nCentrifuge BAL samples at .\nCentrifuge: 300 34, 10 min, 4 10", "[PROCESSING OF BAL TO... |
null | null | null | dx.doi.org/10.17504/protocols.io.ferbjd6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Short instructions on how to allow copying and pasting to the virtual machine. </p>
[STEPS]
?.
?.
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23,002 | Evaluation of stability of balance recovery from unpredictable perturbations through the compensatory arm and leg movements (CALM) scale | null | dx.doi.org/10.17504/protocols.io.2p2gdqe | null | Marina Torres Betelli, Patrícia Sayuri Takazono, Caroline Ribeiro de Souza, Julia Ávila de Oliveira, Daniel Boari Coelho, Luis Augusto Teixeira | TITLE: Evaluation of stability of balance recovery from unpredictable perturbations through the compensatory arm and leg movements (CALM) scale
AUTHORS: Marina Torres Betelli, Patrícia Sayuri Takazono, Caroline Ribeiro de Souza, Julia Ávila de Oliveira, Daniel Boari Coelho, Luis Augusto Teixeira
[DESCRIPTION]
<div cla... | ["[Preparation]\nParticipants are warmed up for 5 min. with global movements. Given that balance perturbations are vigorous, possibly requiring fast movements of arms and legs, this is an important preparatoty step.", "[Instructions]\n(a) Firts, participants watch a video of a pearson responding to the balance perturba... |
null | null | null | dx.doi.org/10.17504/protocols.io.gvkbw4w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div class="page" title="Page 2">
<div class="layoutArea">
<div class="column">
<p>Immunoprecipitation (IP) is a valuable tool that utilizes antibody: antigen interactions to isolate a specific target protein from thousands of proteins in a complex solution. The specificity of t... | ["[Sample Preparation (Day 1)] {\"blocks\":[{\"key\":\"8uqdi\",\"text\":\" Starting with a total of 820 \\u03bcg of A431 cell lysate, transfer 200 \\u03bcg into each of 4 separate 1.5 mL microcentrifuge tubes and place the four tubes on ice.\\n \\n \",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entity... |
57,621 | Restriction Digest -- CHEM 384/584 | 1 | dx.doi.org/10.17504/protocols.io.b4hvqt66 | https://www.protocols.io/view/restriction-digest-chem-384-584-b4hvqt66 | New England Biolabs, Ken Christensen | TITLE: Restriction Digest -- CHEM 384/584
AUTHORS: New England Biolabs, Ken Christensen
[DESCRIPTION]
The following is a "typical" restriction endonuclease reaction. Please see the "guidelines" tab below for the NEB tips on optimizing restriction digests.
[GUIDELINES]
Guidelines for Optimizing Restriction Endonucle... | ["Set up the following reaction (total reaction volume 50 µl).\n \n Restriction Enzyme 10 units is sufficient, generally 1µl is used DNA 1 µg 10X NEBuffer 5 µl (1X) Total Reaction Volume 50 µl Incubation Time 1 hour* Incubation Temperature Enzyme dependent \n* Can be decreased to 5-15 minutes by using a T... |
64,375 | XP Nutrition Keto Gummies : Negative Reviews, Bad Complaints & Side Effects?Pills Advanced BHB Boost Ketogenic Supplement Exogenous Ketones for Men Women 60 Capsules 2 Bottles | 1 | dx.doi.org/10.17504/protocols.io.14egn7yo6v5d/v1 | https://www.protocols.io/view/xp-nutrition-keto-gummies-negative-reviews-bad-com-ca4xsgxn | fateh | TITLE: XP Nutrition Keto Gummies : Negative Reviews, Bad Complaints & Side Effects?Pills Advanced BHB Boost Ketogenic Supplement Exogenous Ketones for Men Women 60 Capsules 2 Bottles
AUTHORS: fateh
[DESCRIPTION]
According to the product’s official website, the XP Nutrition Keto Gummies are taking America by stor... | ["XP Nutrition Keto Gummies\nXP Nutrition Keto Gummies - According to the product’s official website, the XP Nutrition Keto Gummies are taking America by storm with the way they help people get rid of their unwanted fat. They contain Beta-Hydroxybutyrate (BHB), and BHB is getting released in the body when on the ketoge... |
50,725 | Diagnostic accuracy of pelvic imaging for acute pelvic inflammatory disease: protocol for a systematic review and meta-analysis | 1 | dx.doi.org/10.17504/protocols.io.bvsdn6a6 | https://www.protocols.io/view/diagnostic-accuracy-of-pelvic-imaging-for-acute-pe-bvsdn6a6 | Yuji Okazaki, Yasushi Tsujimoto, Kohei Yamada, Takashi Ariie, Shunsuke Taito, Masahiro Banno, Yuki Kataoka, Yoshiaki Tsukizawa | TITLE: Diagnostic accuracy of pelvic imaging for acute pelvic inflammatory disease: protocol for a systematic review and meta-analysis
AUTHORS: Yuji Okazaki, Yasushi Tsujimoto, Kohei Yamada, Takashi Ariie, Shunsuke Taito, Masahiro Banno, Yuki Kataoka, Yoshiaki Tsukizawa
[DESCRIPTION]
<div class = "text-blocks"><div ... | [] |
55,429 | Dynamin conditional knockout fibroblasts: Tamoxifen inducible Knockout method | 1 | dx.doi.org/10.17504/protocols.io.b2ddqa26 | https://www.protocols.io/view/dynamin-conditional-knockout-fibroblasts-tamoxifen-b2ddqa26 | Daehun Park, Pietro De Camilli | TITLE: Dynamin conditional knockout fibroblasts: Tamoxifen inducible Knockout method
AUTHORS: Daehun Park, Pietro De Camilli
[DESCRIPTION]
This cell line was described and characterized in the following paper: Ferguson, S.M., Raimondi, A., Paradise, S., Shen, H., Mesaki, K., Ferguson, A., Destaing, O., Ko, G., Takas... | ["[Protocol] Culture the cells at 37 °C and 5% CO2 in DMEM containing 10% FBS, 100 U/ml penicillin, 100 mg/mL streptomycin.", "[Protocol] When cells reach 80-90% confluency, detach cells from the dishes using trypsin-EDTA and split the cells 1:4 and add 2 micromolar (µM) 4-hydroxy-tamoxifen along with fresh cultur... |
null | null | null | dx.doi.org/10.17504/protocols.io.imycc7w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p> </p>
<p>Considering the potential lack of consensus regarding appropriate measure and reduced reliability values of scapular dyskinesis visual dynamic evaluation, this protocol includes the main three classification approaches by considering the methodological improvements s... | [] |
36,274 | Masson's Trichrome Staining Protocol for FFPE spheroids and microtissues | 1 | dx.doi.org/10.17504/protocols.io.rm7vz82w5vx1/v1 | https://www.protocols.io/view/masson-39-s-trichrome-staining-protocol-for-ffpe-s-bfnsjmee | Angela Denn, Zbigniew Mikulski | TITLE: Masson's Trichrome Staining Protocol for FFPE spheroids and microtissues
AUTHORS: Angela Denn, Zbigniew Mikulski
[DESCRIPTION]
The following protocol has been optimized for image analysis-based quantification of collagen within FFPE spheroid samples. It is run on a Leica ST5020 automated stainer. This pro... | ["[Deparaffinization Protocol]", "[Mordanting] For formalin fixed tissue, post-fix deparaffinized slides in Bouin’s solution for 1 hour at 56°C or at room temperature overnight. Do not leave in oven overnight. Bouin’s solution must be preheated to insure proper mordanting.\nWash in water and discard first two changes t... |
null | null | null | dx.doi.org/10.17504/protocols.io.fywbpxe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div class="page" title="Page 1">
<div class="layoutArea">
<div class="column">
<p>The SensiFAST™ Probe Lo-ROX One-Step Kit has been formulated for highly reproducible first-strand cDNA synthesis and subsequent real-time PCR in a single tube. The kit is formulated for use with p... | [] |
61,965 | Labelled Building Blocks | 6 | dx.doi.org/10.17504/protocols.io.3byl4b3rovo5/v1 | https://www.protocols.io/view/labelled-building-blocks-b8rmrv46 | BOC Sciences | TITLE: Labelled Building Blocks
AUTHORS: BOC Sciences
[DESCRIPTION]
Isotope labeled building blocks refer to replacing one or more atoms in building blocks molecular with stable isotopes. Stable isotope labeled building blocks have the advantages of high sensitivity, simple location and accurate quantification. T... | [] |
66,361 | Diaetoxyl 600 mg : Ce produit est-il légitime ou une arnaque ? | 1 | dx.doi.org/10.17504/protocols.io.dm6gpbkj8lzp/v1 | https://www.protocols.io/view/diaetoxyl-600-mg-ce-produit-est-il-l-gitime-ou-une-cc2zsyf6 | roxyuben | TITLE: Diaetoxyl 600 mg : Ce produit est-il légitime ou une arnaque ?
AUTHORS: roxyuben
[DESCRIPTION]
Qu'est-ce que le Diaetoxyl 600 mg?
Derrière le nom Diaetoxyl 600 mg se cache une préparation dite "amaigrissante". Selon le fabricant, l'objectif des gélules est de stimuler la combustion des graisses et de favoris... | ["[Diaetoxyl 600 mg] La prise de Diaetoxyl 600 mg pour perdre du poids n'est pas liée à un régime ou à l'adhésion à une salle de sport. Il n'y a donc pas de frais supplémentaires ni d'élimination d'aliments de ton garde-manger. La préparation amaigrissante peut ainsi obtenir un premier point positif en ce qui concerne ... |
32,490 | Hematoxylin and Eosin Staining Protocol | 1 | null | https://www.protocols.io/view/hematoxylin-and-eosin-staining-protocol-bbyiipue | Sierra Simpson, Olivier George | TITLE: Hematoxylin and Eosin Staining Protocol
AUTHORS: Sierra Simpson, Olivier George
[STEPS]
?. Prepare 95% ETOH in slide staining apparatus Heomtoxylin in slide staining apparatus Eosin in slide staining apparatus
?. Stain in Mayer's Hematoxylin
?. Rinse slides 3X 15 min in tap water - if tap water is acidic, prepa... | ["Prepare 95% ETOH in slide staining apparatus Heomtoxylin in slide staining apparatus Eosin in slide staining apparatus", "Stain in Mayer's Hematoxylin", "Rinse slides 3X 15 min in tap water - if tap water is acidic, prepare Scott's tap water recipe in sigma insert", "Rinse with DI water 30 Seconds", "Place slide in 9... |
75,490 | Guidance for populating GenomeTrakr metadata templates (BioSample and SRA) | 1 | dx.doi.org/10.17504/protocols.io.eq2ly3x1pgx9/v10 | https://www.protocols.io/view/guidance-for-populating-genometrakr-metadata-templ-cmyau7se | Ruth Timme, Errol Strain, Tina.Pfefer, Maria Balkey | TITLE: Guidance for populating GenomeTrakr metadata templates (BioSample and SRA)
AUTHORS: Ruth Timme, Errol Strain, Tina.Pfefer, Maria Balkey
[DESCRIPTION]
PURPOSE: Guidance on how to populate NCBI's metadata packages, maximizing interoperability for foodborne pathogen surveillance.
SCOPE: This protocol provides d... | ["[Overview] Guidance for organizing and populating the metadata templates required for direct submission to NCBI. This guidance is applicable for most enterics and/or microbial pathogens. \n\n \n\n\nTwo metadata templates are required for each NCBI submission:\n1. BioSample metadata (metadata describing the sample so... |
70,072 | HMW DNA extraction for Long Read Sequencing using CTAB | 4 | dx.doi.org/10.17504/protocols.io.bp2l694yzlqe/v1 | https://www.protocols.io/view/hmw-dna-extraction-for-long-read-sequencing-using-cgnytvfw | Benoît Vacherie, Karine Labadie, Cyril Falentin | TITLE: HMW DNA extraction for Long Read Sequencing using CTAB
AUTHORS: Benoît Vacherie, Karine Labadie, Cyril Falentin
[DESCRIPTION]
High Molecular Weight DNA extraction protocol for Long Read sequencing.
Extraction is performed from flash frozen leaves stored at -80°C.
The protocol is adapted for an extraction of 1g... | ["[preparation of reagents] Extraction Buffer : Prepare 20 mL of extraction buffer (per 1g of leaves) in a 50 mL tube", "[DNA Extraction] Add 50 µl of 2-Mercaptoethanol to 20 ml of extraction buffer and preheat to 65 °C (approx. 15 min).\n20 mL \n50 µL \n65 °C", "[DNA Extraction] Put a mortar in ice.\nCool the morta... |
44,625 | 3.2 Production of a Cleared Cell Lysate | 4 | dx.doi.org/10.17504/protocols.io.bptrmnm6 | https://www.protocols.io/view/3-2-production-of-a-cleared-cell-lysate-bptrmnm6 | Peter Simons, Virginie Bondu, Angela Wandinger-Ness, Tione Buranda | TITLE: 3.2 Production of a Cleared Cell Lysate
AUTHORS: Peter Simons, Virginie Bondu, Angela Wandinger-Ness, Tione Buranda
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Small, monomeric guanine triphosphate hydrolases (GTPases) are ubiquitous cellular integrators of signaling. A signal activ... | ["[3.2 Production of a Cleared Cell Lysate]\nTwo days before an assay seed a 48-well plate with 20,000 target cells in 100 μL of culture medium per well, resulting in about 50,000 cells the next day. The rate of cell proliferation might vary based on cell type and conditions. The critical target is 50,000 cells at the ... |
53,475 | Rapid scoping review of measures taken to maintain the provision and the use of essential services for MNCAAH (maternal, newborn, child, adolescent and older person's health) | 1 | null | https://www.protocols.io/view/rapid-scoping-review-of-measures-taken-to-maintain-bygbptsn | Lenka Benova, Elise Huysmans, Anayda Portela | TITLE: Rapid scoping review of measures taken to maintain the provision and the use of essential services for MNCAAH (maternal, newborn, child, adolescent and older person's health)
AUTHORS: Lenka Benova, Elise Huysmans, Anayda Portela
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style... | ["[Searching literature]\nSearch locations Peer reviewed article databases: a. Medline b. EMBASE c. Global Health d. Web of Science e. Lilacs (https://lilacs.bvsalud.org/en/) f. JSTOR g. Open Edition (French language literature) References of included articles/resources and searches of networks of papers (using conn... |
73,034 | NASC-seq2 Protocol | 1 | dx.doi.org/10.17504/protocols.io.6qpvr43nogmk/v1 | https://www.protocols.io/view/nasc-seq2-protocol-cjjiukke | Gert-Jan Hendriks, Daniel Ramsköld, Anton Larsson, Juliane Mayr, Christoph Ziegenhain, Michael Hagemann-Jensen, Leonard Hartmanis, rickard.sandberg | TITLE: NASC-seq2 Protocol
AUTHORS: Gert-Jan Hendriks, Daniel Ramsköld, Anton Larsson, Juliane Mayr, Christoph Ziegenhain, Michael Hagemann-Jensen, Leonard Hartmanis, rickard.sandberg
[DESCRIPTION]
Insights into transcriptional bursting kinetics and regulation have emerged from real-time nascent RNA imaging and analyse... | ["[Prepare lysis plates] Prepare the following lysis buffer on ice.\n\n\n\n \n\non ice", "[Prepare lysis plates] Use a nanodispenser to distribute 0.3 uL of freshly prepared lysis buffer to each well of vapor-lock containing 384-well PCR plate.\n\n0.3 µL \non ice", "[Prepare lysis plates] Optional: Store lysis plate.\n... |
83,150 | Transcardiac Perfusion of Mouse for Brain Tissue | 1 | null | https://www.protocols.click/view/transcardiac-perfusion-of-mouse-for-brain-tissue-cvfnw3me | Maryana Nissan, divya.darwinarulseeli | TITLE: Transcardiac Perfusion of Mouse for Brain Tissue
AUTHORS: Maryana Nissan, divya.darwinarulseeli
[DESCRIPTION]
Transcardiac perfusion is a method used for clearing blood and preserving the mouse brain for immunostaining.
[STEPS]
1. Add Neutralizing Agent to break down Paraformaldehyde [PFA] for proper disposa... | ["Add Neutralizing Agent to break down Paraformaldehyde [PFA] for proper disposal. We use Hydeaway [CAT #2201 from Decon Labs]", "Turn on perfusion apparatus and place tube into 1X Phosphate-Buffered Saline [PBS]", "Wash system for 1 round, until the tube is saturated with 1X PBS", "Saturate anesthetic chamber with Iso... |
56,423 | White Water Ranch Pollinator Enhancement Study Design | 1 | dx.doi.org/10.17504/protocols.io.b3cfqitn | https://www.protocols.io/view/white-water-ranch-pollinator-enhancement-study-des-b3cfqitn | Lauren Ponisio | TITLE: White Water Ranch Pollinator Enhancement Study Design
AUTHORS: Lauren Ponisio
[DESCRIPTION]
Field protocol for Whitewater Ranch wildflower patch enhancement study
[STEPS]
SECTION: Questions
1. Can native, flowering plants succeed (germinate and flower within 1-3 years after seeding) in clearcuts with minimal ... | ["[Questions] Can native, flowering plants succeed (germinate and flower within 1-3 years after seeding) in clearcuts with minimal site prep?\nIs there an interaction between plant success and planting inside burn piles or outside burn piles? \nDoes intraspecific competition influence success? \nIs there an effect of d... |
95,291 | Histology examination: preparation and staining of bovine tissues | 4 | dx.doi.org/10.17504/protocols.io.4r3l22wn3l1y/v1 | https://www.protocols.io/view/histology-examination-preparation-and-staining-of-c9a3z2gn | Jade Ros, Marthe Vilotte, Julie Rivière, Cecile Grohs | TITLE: Histology examination: preparation and staining of bovine tissues
AUTHORS: Jade Ros, Marthe Vilotte, Julie Rivière, Cecile Grohs
[DESCRIPTION]
Histology is a technique that makes it possible to highlight what we want to observe and to "fix" a sample at a given time, while preserving characteristics close to its... | ["[Fixing the tissue] Fixation is the most important step in the histological preparation process. Its purpose is to preserve structures and stabilise cellular material against the potentially damaging effects of certain analytical techniques such as staining and immunohistochemistry.\n\nThe fixation time depends on th... |
105,840 | AAV Injection and Tissue Preparation | 0 | dx.doi.org/10.17504/protocols.io.14egn6wkql5d/v2 | https://www.protocols.io/view/aav-injection-and-tissue-preparation-djkq4kvw | Justin T Savage | TITLE: AAV Injection and Tissue Preparation
AUTHORS: Justin T Savage
[DESCRIPTION]
This protocol provides guidelines for injection of AAVs into the cortex and striatum of young and adult mice. For post-injection tissue processing, the protocol for perfusing mice and preparing brain tissue for sectioning is also inclu... | ["[Perfusion of Animals and Tissue Processing] A) Setup/Preparation", "[Perfusion of Animals and Tissue Processing] 1. Thaw out 4% PFA at least 30mins prior to perfusion. Estimate 15-25ml/animal (P21 depending on size).", "[Perfusion of Animals and Tissue Processing] 2. Prepare TBS/Heparin solution according to the fol... |
84,826 | Embedding organoids in agarose | 4 | null | https://www.protocols.io/view/embedding-organoids-in-agarose-cw32xgqe | Gabriela Vallejo Flores, Annika Fendler | TITLE: Embedding organoids in agarose
AUTHORS: Gabriela Vallejo Flores, Annika Fendler
[DESCRIPTION]
This protocol is for embedding organoids in low melting point agarose, the protocol was adapted from Fendler, A., et al. Research Square ( 2020).
[BEFORE_START]
Before starting the protocol, prepare the following so... | ["[Organoids embedding in agarose] Remove the supernatan from the well and add 1 mL to release the organoids from the matrigel, 500 x g, 4 min, 4 °C", "[Organoids embedding in agarose] Wash the organoids with 1 mL , and 300 x g, 4 min, 4 °C and discard the supernatant.", "[Organoids embedding in agarose... |
null | null | null | dx.doi.org/10.17504/protocols.io.u3neyme | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Step-by-step description on the use of iPATH3 on Uproc-DNA outputs.
Path3.0 (http://pathways.embl.de) is a web-application for the visualization and analysis of cellular pathways. It is freely available and open to everyone. Currently it is based on four KEGG global maps, wh... | ["[Create a pathway map for a unique sample] {\"blocks\":[{\"key\":\"b7duh\",\"text\":\"Note : this protocol uses as an example set the sample SRS143565 from the HMP project. SRS143565 is a right cubital fossa WGS available here. The uproc-dna result for this sample is available in the description of this protocol. \"... |
90,403 | Preparation and shipping of mouse tibiae for multiphoton microscopy | 4 | null | https://www.protocols.io/view/preparation-and-shipping-of-mouse-tibiae-for-multi-c4ibyuan | Chad A Lerner, Sofiya Galkina, Gen Matsumae, Simon Melov, Tamara Alliston, Akos A Gerencser | TITLE: Preparation and shipping of mouse tibiae for multiphoton microscopy
AUTHORS: Chad A Lerner, Sofiya Galkina, Gen Matsumae, Simon Melov, Tamara Alliston, Akos A Gerencser
[DESCRIPTION]
Isolation and packaging of mouse tibiae for overnight shipment for bioenergetic analysis of live in situ osteocytes.
[STEPS]
SE... | ["[Consumables and Tools] Dissection tools and surfaces should be clean, free of detergents, alcohol or disinfectants. \nTool cleaning:\nDetergent wash\nAlcohol wash (ethanol or isopropanol)\nWater\nPBS", "[Cleaning of bones - lab bench] Place a 60mm dish on a dissection microscope and half-fill it with room temperatur... |
90,544 | Lifeplan Audio Recording Protocol | 1 | null | https://www.protocols.io/view/lifeplan-audio-recording-protocol-c4nqyvdw | Arielle M Farrell, Gaia Giedre Banelyte, Hanna M.K. Rogers, Petteri Lehikoinen, Deirdre Kerdraon, Bess Hardwick | TITLE: Lifeplan Audio Recording Protocol
AUTHORS: Arielle M Farrell, Gaia Giedre Banelyte, Hanna M.K. Rogers, Petteri Lehikoinen, Deirdre Kerdraon, Bess Hardwick
[DESCRIPTION]
Here we describe a protocol that is used for collecting audio recordings of birds and bats using an AudioMoth (AudioMoth | Open Acoustic Device... | ["[Site Selection and Placement] Site design\n\nThe Lifeplan equipment is deployed within a 1 hectare plot. We aim for an accuracy of 10 meters.\n\nThere are two design options to choose from depending on budget and site access. In Lifeplan, we started with Option 1 in 2021, and reduced to Option 2 in 2023 by removing ... |
null | null | null | dx.doi.org/10.17504/protocols.io.e2nbgde | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Anti-BrdU Staining Protocol using DNAse with surface and fluorescent proteins</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
81,701 | Online Survey Among Pregnant Women With Medical Indication Or Wish For Elective Caesarean Section On Second Opinions In Germany: Study Protocol | 1 | dx.doi.org/10.17504/protocols.io.j8nlkwxqwl5r/v1 | https://www.protocols.io/view/online-survey-among-pregnant-women-with-medical-in-ct2dwqa6 | Nadja Könsgen, Anke Kaulbert, Barbara Prediger | TITLE: Online Survey Among Pregnant Women With Medical Indication Or Wish For Elective Caesarean Section On Second Opinions In Germany: Study Protocol
AUTHORS: Nadja Könsgen, Anke Kaulbert, Barbara Prediger
[DESCRIPTION]
Background: Caesarean section (CS) rates have been continuously rising worldwide over the last dec... | [] |
31,981 | Case Processing SOP for Thymus | null | dx.doi.org/10.17504/protocols.io.bbgmiju6 | null | Marda Jorgensen, Jerelyn Nick | TITLE: Case Processing SOP for Thymus
AUTHORS: Marda Jorgensen, Jerelyn Nick
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The purpose of this Standard Operating Procedure (SOP) is to outline the procedures for processing and storing thymus tissue received for HuBMAP consortium assay and analysi... | ["The tissues received will be identified as follows: Thymus (TH).", "Sample prepared from tissues will be identified using the following nomenclature, abbreviations, and formats: Formalin Fixed Paraffin Embedded---FFPE (paraffin block)Formalin Fixed Frozen Embedded---Fixed OCT BlockFresh Frozen Embedded---Fresh OCT Bl... |
17,086 | CANINE HEALTH-RELATED QUALITY OF LIFE INDEX (CHQoLI) | null | dx.doi.org/10.17504/protocols.io.uw6exhe | null | Eric Troncy, Louis-Philippe de Lorimier | TITLE: CANINE HEALTH-RELATED QUALITY OF LIFE INDEX (CHQoLI)
AUTHORS: Eric Troncy, Louis-Philippe de Lorimier
[STEPS] | [] |
73,472 | Methods for paper "Deceiving appearances: anthropogenic introgressive hybridization affects phenotypically-selected hatchery broodstock used in ‘supportive breeding’ programmes of the critically endangered marble trout Salmo marmoratus, Cuvier (Osteich | 1 | dx.doi.org/10.17504/protocols.io.bp2l692mdlqe/v1 | https://www.protocols.io/view/methods-for-paper-34-deceiving-appearances-anthrop-cjy8upzw | Gianluca Polgar | TITLE: Methods for paper "Deceiving appearances: anthropogenic introgressive hybridization affects phenotypically-selected hatchery broodstock used in ‘supportive breeding’ programmes of the critically endangered marble trout Salmo marmoratus, Cuvier (Osteich
AUTHORS: Gianluca Polgar
[DESCRIPTION]
In the first sec... | ["[Study area, fish sampling, phenotypic selection, age determination] The Toce River (length 83.6 km; catchment area ~1,780 km2, average slope 2.4%; Regione Piemonte 2004) is one of the main tributaries of Lake Maggiore (Fig. 1), rising from glacier valleys at ~1,720 m above sea level (a.s.l.; Geoportale Piemonte 2021... |
51,088 | Installing Swarm of Pis | 5 | null | https://www.protocols.io/view/installing-swarm-of-pis-bv5qn85w | Olivier George | TITLE: Installing Swarm of Pis
AUTHORS: Olivier George
[DESCRIPTION]
This protocol guides you through the installation of a swarm of raspberry Pis
[GUIDELINES]
Setup only 1 Rpi at a time to be able to identify the IP address
[STEPS]
SECTION: Install Ubuntu on the Mini PC
2. Install Ubuntu:
https://itsfoss.com/inst... | ["[Install Ubuntu on the Mini PC] Install Ubuntu:\nhttps://itsfoss.com/install-ubuntu-1404-dual-boot-mode-windows-8-81-uefi/\n\nhttps://ubuntu.com/download/desktop/thank-you?version=20.04.2.0&architecture=amd64\n\nMini PC", "[Flash the SD card with the latest RPi clone] Download RPi clone: https://www.dropbox.com/sh/1a... |
39,712 | RT-LAMP SARS-CoV-2 positive control stock | 1 | null | https://www.protocols.io/view/rt-lamp-sars-cov-2-positive-control-stock-biz8kf9w | Christina Newman, Andrea Weiler, Dawn Dudley, Mitchell Ramuta, Amelia Haj, Shelby O'Connor, David O'Connor | TITLE: RT-LAMP SARS-CoV-2 positive control stock
AUTHORS: Christina Newman, Andrea Weiler, Dawn Dudley, Mitchell Ramuta, Amelia Haj, Shelby O'Connor, David O'Connor
[STEPS]
?. Using either the company-provided stock concentration or a qRT-PCR determined stock concentration, dilute virus in dH2O to create a 1e9 copies/... | ["Using either the company-provided stock concentration or a qRT-PCR determined stock concentration, dilute virus in dH2O to create a 1e9 copies/ml stock virus.", "Create a 1e6 copies/ml stock virus by diluting 1e9 copies/ml stock 1:1000 in 50% dH2O and 50% 1x PBS solution.", "Create a ready-to-use positive control sto... |
40,389 | Salmonella live attenuated vaccine preparation. | 4 | dx.doi.org/10.17504/protocols.io.bjpdkmi6 | https://www.protocols.io/view/salmonella-live-attenuated-vaccine-preparation-bjpdkmi6 | Angel Justiz-Vaillant, Suzette Curtello | TITLE: Salmonella live attenuated vaccine preparation.
AUTHORS: Angel Justiz-Vaillant, Suzette Curtello
[STEPS]
?. A Salmonella cocktail (mixture of five Salmonella strains: S. Montevideo, S. Yeerongpilly, S. Augustenborg, S. Kentucky and S.Typhimurium) is incubated at 37°C in peptone broth with combinations of natur... | ["A Salmonella cocktail (mixture of five Salmonella strains: S. Montevideo, S. Yeerongpilly, S. Augustenborg, S. Kentucky and S.Typhimurium) is incubated at 37°C in peptone broth with combinations of natural extracts.", "Preparation includes clean, sun dried onion and garlic cloves.", "After a week of drying, onion and... |
48,596 | Cell dissociation from nasal, bronchial and tracheal brushings with cold-active protease for single-cell RNA-seq | 1 | dx.doi.org/10.17504/protocols.io.btpunmnw | https://www.protocols.io/view/cell-dissociation-from-nasal-bronchial-and-trachea-btpunmnw | Kaylee Worlock, Masahiro Yoshida, Kerstin Meyer, Marko Z. Nikolić | TITLE: Cell dissociation from nasal, bronchial and tracheal brushings with cold-active protease for single-cell RNA-seq
AUTHORS: Kaylee Worlock, Masahiro Yoshida, Kerstin Meyer, Marko Z. Nikolić
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This modified protocol provides details on the cell dis... | ["[Sample Collection and processing]\nPerform nasal brush biopsy in the nasal cavity in the inferior nasal conca zone (UBERON:0005922) using cytological sampling brushes (CY1050). Tracheal and bronchial brush biopsies were collected using single-use cytology brushes (BC-202D-2010) from the tracheal mucosa (UBERON:00003... |
74,715 | Test-Luciferase-Based Cytotoxicity Assay with bispecific antibodies | 4 | dx.doi.org/10.17504/protocols.io.n2bvj8d1xgk5/v1 | https://www.protocols.io/view/test-luciferase-based-cytotoxicity-assay-with-bisp-ck73uzqn | Gülfem Öner-Ziegler, Christiane Stadler | TITLE: Test-Luciferase-Based Cytotoxicity Assay with bispecific antibodies
AUTHORS: Gülfem Öner-Ziegler, Christiane Stadler
[DESCRIPTION]
The purpose of this assay is to determine the cytotoxic potential of bispecific antibodies.
This protocol describes the preparation and analysis of an in vitro assay with human tar... | ["[Preparation] Required Supplies\n ... |
27,616 | UC Davis - Imaging CMGI | null | dx.doi.org/10.17504/protocols.io.678hhrw | null | Douglas J. Rowland | TITLE: UC Davis - Imaging CMGI
AUTHORS: Douglas J. Rowland
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">The Center for Molecular and Genomic Imaging (CMGI) provides small animal imaging services for preclinical rese... | ["Micro- PET, CT, SPECT imaging procedures1. For some radiotracers, mice or rats will be fasted (water unrestricted) for up to 20 hours to improve radiotracer uptake.\n2. Various radiotracers (see Radiotracer list below) are available for micro-PET (mPET) imaging in small animals. Trace amounts ( a. In some cases, ... |
42,744 | DNA Clean & Concentrator-5--CHEM 584 | 4 | dx.doi.org/10.17504/protocols.io.bmyyk7xw | https://www.protocols.io/view/dna-clean-amp-concentrator-5-chem-584-bmyyk7xw | Ken Christensen | TITLE: DNA Clean & Concentrator-5--CHEM 584
AUTHORS: Ken Christensen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Product Description</span></div><div class = "text-block">The DNA Clean & Concentrator™-5 (DCC™-5) provides a hassle-free method for the rapid purifi... | ["[PCR Cleanup/Cleanup after Restriction Digest]\nIn a 1.5 ml microcentrifuge tube, add 2-7 volumes of DNA Binding Buffer to each volume of DNA sample (see table below). Mix briefly by vortexing. ABC1ApplicationDNA Binding Buffer:SampleExample2Plasmid, genomic DNA (>2 kb)2:1200 ul : 100 ul3PCR product, DNA fragment5:1... |
52,663 | Isolating and growing fibroblast cells from threespine stickleback (Gasterosteus aculeatus) | 4 | null | https://www.protocols.io/view/isolating-and-growing-fibroblast-cells-from-threes-bxnxpmfn | Gabrielle Q Le, Natalie Steinel, Lauren Fuess, Maria Rodgers | TITLE: Isolating and growing fibroblast cells from threespine stickleback (Gasterosteus aculeatus)
AUTHORS: Gabrielle Q Le, Natalie Steinel, Lauren Fuess, Maria Rodgers
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol goes through the process of isolating and growing fibroblast cells f... | ["[Obtaining tissue]\nPrepare and sterile filter 30 mL of 5% FBS media.", "[Obtaining tissue]\nPrepare and sterile filter 10 mL of 20% FBS media.", "[Obtaining tissue]\nPrepare two petri dishes on ice for collecting the tissues. Fill the petri dish half of the way with the 5% FBS media.", "[Obtaining tissue]\nPrepare 2... |
76,038 | Whole genome amplification of West Nile virus lineage 2 | 1 | dx.doi.org/10.17504/protocols.io.e6nvwjopdlmk/v1 | https://www.protocols.io/view/whole-genome-amplification-of-west-nile-virus-line-cnhevb3e | Anna Nagy | TITLE: Whole genome amplification of West Nile virus lineage 2
AUTHORS: Anna Nagy
[DESCRIPTION]
West Nile virus is one of the most important endemic arbovirus in Hungary. For next-generation whole genome sequencing of West Nile virus lineage 2, a one-step reverse transcription PCR assay was developed. PCR amplicons ca... | ["[Nucleic acid extraction] Use Qiagen QIAamp Viral RNA Mini Kit (cat. no. 52904 or 52906) for nucleic acid extraction. Nucleic acid extraction should be done by following the manufacturer's instructions. The total volume of the extracted viral RNA is 60 µl.", "[One-Step Reverse transcription (RT) PCR Setup] Reagent na... |
75,775 | P5- RECONOCIMIENTOS | 1 | dx.doi.org/10.17504/protocols.io.14egn2mn6g5d/v1 | https://www.protocols.io/view/p5-reconocimientos-cm87u9zn | cgarcia | TITLE: P5- RECONOCIMIENTOS
AUTHORS: cgarcia
[DESCRIPTION]
Los alumnos matriculados en un programa de doctorado de la EIDUCAM podrán reconocer actividades formativas teniendo en cuenta el reglamento de reconocimiento de la EIDUCAM y siguiendo el siguiente procedimiento:
[STEPS]
SECTION: P5- RECONOCIMIENTOS
1. Reunión ... | ["[P5- RECONOCIMIENTOS] Reunión con su tutor para identificar y concretar las posibles actividades formativas objeto de reconocimiento, en función de su trayectoria académica, profesional y experiencia investigadora. Esta reunión deberá mantenerla en el inicio de cada curso académico.", "[P5- RECONOCIMIENTOS] El alumno... |
30,690 | HTAPP_Dissociation of human neuroblastoma tumors to a single-cell suspension for single-cell RNA-seq using Papain | 1 | dx.doi.org/10.17504/protocols.io.98ah9se | https://www.protocols.io/view/htapp-dissociation-of-human-neuroblastoma-tumors-t-98ah9se | Anand Patel, Asa Karlstrom, Brittney Gordon, Elizabeth Stewart, Michael Dyer | TITLE: HTAPP_Dissociation of human neuroblastoma tumors to a single-cell suspension for single-cell RNA-seq using Papain
AUTHORS: Anand Patel, Asa Karlstrom, Brittney Gordon, Elizabeth Stewart, Michael Dyer
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol was used for the dissocia... | ["[Reagent Preparation]\nPrepare reagents (1 set for each sample):", "[Reagent Preparation]\nAdd 5 mL of Earle's Balanced Salt Solution (vial #1) to papain (vial #2). Allow papain to dissolve for 15 min at 37° C.\n37 °C", "[Reagent Preparation]\nAdd 500 µL of Earle's Balanced Salt Solution (vial #1) to DNase I (vial #3... |
70,879 | Wastewater QC workflow in GalaxyTrakr (SSQuAWK4) | 1 | dx.doi.org/10.17504/protocols.io.kxygxzk5dv8j/v9 | https://www.protocols.io/view/wastewater-qc-workflow-in-galaxytrakr-ssquawk4-chf7t3rn | Jasmine Amirzadegan, Tunc Kayikcioglu, hugh.rand, Ruth Timme, Maria Balkey | TITLE: Wastewater QC workflow in GalaxyTrakr (SSQuAWK4)
AUTHORS: Jasmine Amirzadegan, Tunc Kayikcioglu, hugh.rand, Ruth Timme, Maria Balkey
[DESCRIPTION]
PURPOSE:
Step-by-step instructions for checking sequence quality for SARS-CoV-2 wastewater samples using SSQuAWK: SARS - CoV - 2 Sequence Quality Assurance Workf... | ["[Account set up] Create a GalaxyTrakr account here: https://account.galaxytrakr.org/Account/Register", "[Account set up] Log into your GalaxyTrakr account: https://galaxytrakr.org", "[Create a new history] Create a new history. \n\nWe recommend creating a new history for each new MiSeq sequence set with details and d... |
40,296 | Barcoded Calling Cards and Transcriptomes: Library Preparation | 1 | dx.doi.org/10.17504/protocols.io.bp2l6nqokgqe/v1 | https://www.protocols.io/view/barcoded-calling-cards-and-transcriptomes-library-bjkgkktw | Matthew Lalli, Urvashi Thopte, Arnav Moudgil, Michael N. Wilkinson, Xuhua Chen, Robi D. Mitra | TITLE: Barcoded Calling Cards and Transcriptomes: Library Preparation
AUTHORS: Matthew Lalli, Urvashi Thopte, Arnav Moudgil, Michael N. Wilkinson, Xuhua Chen, Robi D. Mitra
[DESCRIPTION]
This protocol is a modification of Moudgil et al's Bulk Calling Cards Library Preparation that uses barcoded self-reporting transpo... | ["[RNA Extraction wtih Direct-Zol RNA Miniprep] Harvest cells. Do not overload columns. If you have more than 107 cells, split cells in half and process on two columns, then merge the RNA pools.", "[RNA Extraction wtih Direct-Zol RNA Miniprep] Add TRI Reagent directly to cells in a dish. Use the following table as a g... |
null | null | null | dx.doi.org/10.17504/protocols.io.eavbae6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
For use in "<a href="https://www.protocols.io/view/PCTE-Protocol-for-VLP-enumeration-eaubaew" target="_blank">PCTE Protocol for VLP enumeration</a>"
[STEPS]
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.qwedxbe | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?. | [] |
63,892 | Tamela Mann Keto Gummies – Is This The Weight Loss Tamela Mann Keto Gummies You Need? Reviews | 1 | dx.doi.org/10.17504/protocols.io.kqdg3pympl25/v1 | https://www.protocols.io/view/tamela-mann-keto-gummies-is-this-the-weight-loss-t-camusc6w | SharonGillespiea | TITLE: Tamela Mann Keto Gummies – Is This The Weight Loss Tamela Mann Keto Gummies You Need? Reviews
AUTHORS: SharonGillespiea
[DESCRIPTION]
Tamela Mann Keto Gummiesis a dietary supplement developed to trigger Ketosis more conveniently mainly.Tamela Mann Keto Gummiesputs your body ketosis extra ...
[STEPS]
1. ➢ Pro... | ["➢ Product Name — Tamela Mann Keto Gummies\n\n➢ Composition — Natural Organic Compound\n\n➢ Side-Effects — NA\n\n➢ Availability — Online\n\n➢ Rating — ⭐⭐⭐⭐⭐\n\n➢ Official Website (Sale Is Live) — Tamela Mann Keto Gummies\n\n➢VISIT THE OFFICIAL WEBSITE TO BUY TODAY SPECIAL OFFER!!\n\n➢VISIT THE OFFICIAL WEBSITE TO BUY... |
78,446 | [Modified] Lake ABPS Protocol - University of Maine | 1 | dx.doi.org/10.17504/protocols.io.x54v9d5yzg3e/v1 | https://www.protocols.io/view/modified-lake-abps-protocol-university-of-maine-cqunvwve | Grayson Huston | TITLE: [Modified] Lake ABPS Protocol - University of Maine
AUTHORS: Grayson Huston
[DESCRIPTION]
A modified version of the Lake ABPS protocol as described in Thomson-Laing et al. 2022
Protocol successful at detecting fish sedDNA collected from lake surface sediments, as well as river sediments during an anadromous fi... | ["[Alkaline Lysis & Ethanol Precipitation] CENTRIFUGE sediment samples at 5250 x g for 5 min \n\nDISCARD pore water using a sterile pipette, so only sediment remains", "[Alkaline Lysis & Ethanol Precipitation] ADD 10 g of wet sediment to a sterile 50 mL tube\n\nADD 6 mL sodium hydroxide (NaOH, 0.33M) to the sa... |
37,124 | PEG-mediated moss protoplast transformation | null | dx.doi.org/10.17504/protocols.io.bghcjt2w | https://www.protocols.io/view/peg-mediated-moss-protoplast-transformation-bghcjt2w | Yoan Coudert, Arthur Muller | TITLE: PEG-mediated moss protoplast transformation
AUTHORS: Yoan Coudert, Arthur Muller
[STEPS]
?. [Day 1]
Turn on waterbath at 45°C and flame forceps in laminar flowhood.
?. [Day 1]
Prepare 1% driselase solution in 8% mannitol. To do so weight 100mg driselase in the cap of a 15ml falcon tube. In flow hood add 10mL ... | ["[Day 1]\nTurn on waterbath at 45°C and flame forceps in laminar flowhood.", "[Day 1]\nPrepare 1% driselase solution in 8% mannitol. To do so weight 100mg driselase in the cap of a 15ml falcon tube. In flow hood add 10mL 8% mannitol. Mix by shaking, wrap tube in foil and leave for 15 minutes at room temperature.", "[D... |
72,931 | Library pooling and quality control for Illumina sequencing | 4 | dx.doi.org/10.17504/protocols.io.q26g7yp6kgwz/v1 | https://www.protocols.io/view/library-pooling-and-quality-control-for-illumina-s-cjgbujsn | Katherine Smollett, Lily Tong, Jenna Nichols, Kirsty Kwok, Kyriaki Nomikou, Ma. Jowina Galarion, Daniel Mair, Ana Filipe | TITLE: Library pooling and quality control for Illumina sequencing
AUTHORS: Katherine Smollett, Lily Tong, Jenna Nichols, Kirsty Kwok, Kyriaki Nomikou, Ma. Jowina Galarion, Daniel Mair, Ana Filipe
[DESCRIPTION]
The ability to multiplex many samples on the same run makes Illumina sequencing a powerful and affordable to... | ["[Pooling] Before pooling the samples determine the number of samples per pool. The estimated reads per sample will depend on the required depth, genome length and expected percentage of on-target reads. The number of samples per pool will also depend on the type of Illumina sequencer/cartridge used and the read lengt... |
99,637 | Protocol preparation of bacterial cells | 0 | dx.doi.org/10.17504/protocols.io.dm6gpzb45lzp/v1 | https://www.protocols.io/view/protocol-preparation-of-bacterial-cells-ddiv24e6 | Thomas Quiroz Monnens, Alice Boulanger | TITLE: Protocol preparation of bacterial cells
AUTHORS: Thomas Quiroz Monnens, Alice Boulanger
[DESCRIPTION]
This protocol details the preparation of bacterial cells to set up LSBA.
[STEPS]
SECTION: For Xanthomonas campestris pv. campestris (Xcc)
1.
We collect bacteria in exponential phase. (OD600nm between 1 an... | ["[For Xanthomonas campestris pv. campestris (Xcc)] We collect bacteria in exponential phase. (OD600nm between 1 and 2). For our experiments, 400 mL of washed bacteria at an OD600nm of 0.1 (1 × 108 cfu/ml) are required for the lower receiver of each of the LSBAs.", "[For Xanthomonas campestris pv. campestris (Xcc)] For... |
68,283 | Student Guide | 3 | null | https://www.protocols.io/view/student-guide-cew3tfgn | Brian Teague | TITLE: Student Guide
AUTHORS: Brian Teague
[DESCRIPTION]
This is the student guide for the Yeast ORFans CURE. Associated protocols and an instructor guide are found in the Yeast ORFans CURE workspace.
[STEPS] | [] |
38,099 | Extraction of high molecular weight DNA from aphids and other sap-feeding insects for long-read sequencing. | 4 | dx.doi.org/10.17504/protocols.io.bhftj3nn | https://www.protocols.io/view/extraction-of-high-molecular-weight-dna-from-aphid-bhftj3nn | Roland Wouters, Sam Mugford, Roberto Biello, Darren Heavens, Saskia Hogenhout | TITLE: Extraction of high molecular weight DNA from aphids and other sap-feeding insects for long-read sequencing.
AUTHORS: Roland Wouters, Sam Mugford, Roberto Biello, Darren Heavens, Saskia Hogenhout
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Chromosome-scale genome assembly usually requires ... | ["Grind approx. 10mg (20 frozen aphids; originated from a single female, one froghopper) in a 1.5ml Eppendorf tube, with a plastic pestle, pre-cooled in liquid nitrogen. Ensure that tissue remains frozen throughout. When grinding the samples do not turn the pestle, but crush the aphids via an up-down movement.", "Add 6... |
19,823 | Standard Operating Procedure for Solid Phase Adsorption Toxin Testing (SPATT) Assemblage and Extraction of HAB Toxins | null | dx.doi.org/10.17504/protocols.io.xkpfkvn | null | Kendra Negrey, meredith Howard, Jayme Smith, Raphael Kudela, David Caron | TITLE: Standard Operating Procedure for Solid Phase Adsorption Toxin Testing (SPATT) Assemblage and Extraction of HAB Toxins
AUTHORS: Kendra Negrey, meredith Howard, Jayme Smith, Raphael Kudela, David Caron
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">SPATT has been developed and tested for a var... | [] |
43,300 | Top-down proteomics data analysis on the NRTDP TDPortal | 1 | dx.doi.org/10.17504/protocols.io.bnicmcaw | https://www.protocols.io/view/top-down-proteomics-data-analysis-on-the-nrtdp-tdp-bnicmcaw | Jeannie Camarillo, Neil Kelleher | TITLE: Top-down proteomics data analysis on the NRTDP TDPortal
AUTHORS: Jeannie Camarillo, Neil Kelleher
[DESCRIPTION]
This method describes how to analyze data on TD Portal, a top-down proteomics search tool from the National Resource for Translational and Developmental Proteomics.
[STEPS]
1. Top-down proteomics d... | ["Top-down proteomics data was searched on the TD Portal (portal.nrtdp.northwestern.edu)", "Raw files for analysis were selected for search using Top Down Search v. 4.0.", "Search parameters:\nOrganism: Homo Sapiens (Human) with Curated Histones: (Taxon 9606 - June 2020)\nUse Empirical P-Score: FALSE\nFilter by FDR: TR... |
66,131 | Peanut seed sterilization and germination | 4 | null | https://www.protocols.io/view/peanut-seed-sterilization-and-germination-ccttswnn | Ziliang Luo, Liping Wang | TITLE: Peanut seed sterilization and germination
AUTHORS: Ziliang Luo, Liping Wang
[DESCRIPTION]
Treatments of peanut seeds with HgCl2 and fungicide Abound
[STEPS]
1. In a Clean Bench in room 332, put
In a sterile flask, add 150 mL sterilized 0.1% Hg2Cl solution and shake occasionally for 7 min.
2. Remove t... | ["In a Clean Bench in room 332, put \n\n\n\n In a sterile flask, add 150 mL sterilized 0.1% Hg2Cl solution and shake occasionally for 7 min.", "Remove the Hg2Cl by pouring it to a specific biohazard collection container.", "Rinse the seeds 3 times with 150 mL for 5 min each with constant shaking.Collect the rinse w... |
100,911 | Simultaneous detection of miRNA and mRNA at the single-cell level in plant tissues (v2) | 4 | dx.doi.org/10.17504/protocols.io.q26g714e8gwz/v2 | https://www.protocols.io/view/simultaneous-detection-of-mirna-and-mrna-at-the-si-desp3edn | Chi-Chih Wu | TITLE: Simultaneous detection of miRNA and mRNA at the single-cell level in plant tissues (v2)
AUTHORS: Chi-Chih Wu
[DESCRIPTION]
Detecting the simultaneous presence of a microRNA (miRNA) and a mRNA in a specific tissue can provide support for the prediction that the miRNA regulates the mRNA. Ｗe develop a method that ... | ["Section permeabilization\n \n 1. The slides with sections are taken out the freezer and equilibrated to RT for 40 mins. 2. Permeabilized in 20 ug/ml proteinase k for proper duration 3. Quickly wash in DEPC-PBS 4. Quickly dehydrate the slides in EtOH (50, 70, 99 %) and then air dry 5. Mount ... |
20,752 | SYSB 3036 W05 Introduction to Hidden Markov Models | null | dx.doi.org/10.17504/protocols.io.yhqft5w | null | Frank Aylward | TITLE: SYSB 3036 W05 Introduction to Hidden Markov Models
AUTHORS: Frank Aylward
[STEPS]
?. First let's download some data from GitHub:git clone https://github.com/faylward/hmm_introductionand then cd hmm_introduction
?. There should be two files there, nifh.faa.gz and nosz.faa.gz. We will use the nifh.faa.gz file tod... | ["First let's download some data from GitHub:git clone https://github.com/faylward/hmm_introductionand then cd hmm_introduction", "There should be two files there, nifh.faa.gz and nosz.faa.gz. We will use the nifh.faa.gz file today, and the nosz.faa.gz file will be for your homework.The nifh.faa.gz file contains protei... |
101,653 | Live cell microscopy sample preparation (yeast culture) | 0 | dx.doi.org/10.17504/protocols.io.8epv5r23dg1b/v1 | https://www.protocols.io/view/live-cell-microscopy-sample-preparation-yeast-cult-dfhv3j66 | Jakub Zahumensky, Jan Malinsky | TITLE: Live cell microscopy sample preparation (yeast culture)
AUTHORS: Jakub Zahumensky, Jan Malinsky
[DESCRIPTION]
In our approach, (cell-walled) cells in thick suspensions are placed on microscopy cover glass and overlaid by a small block of 1% agarose prepared either in buffer or cultivation medium identical to th... | ["[Microscopy sample preparation] Cultivate cells under desired conditions.", "[Microscopy sample preparation] Transfer the whole culture to a 50 ml Falcon tube (if not already used for cultivation) or remove 1 mL aliquot to a 1.5 mL microcentrifuge tube.", "[Microscopy sample preparation] Centrifuge for 2 min at 1430 ... |
64,321 | Haemolymph extraction of adult Drosophila | 1 | dx.doi.org/10.17504/protocols.io.eq2lyd5elx9k/v3 | https://www.protocols.io/view/haemolymph-extraction-of-adult-drosophila-ca29sgh6 | Björn Brembs, Christine Damrau, Brembs' lab members | TITLE: Haemolymph extraction of adult Drosophila
AUTHORS: Björn Brembs, Christine Damrau, Brembs' lab members
[DESCRIPTION]
This is a very simple protocol showing how to extract haemolymph from adult Drosophila melanogaster. (Based on protocols from Sigma Aldrich).
[STEPS]
SECTION: Fly preparation
1. Punch three ho... | ["[Fly preparation] Punch three holes in a 0.5ml Eppendorf cap and put it into a 1.5ml Eppendorf cap with removed lid.", "[Fly preparation] Remove the flies’ wings, spear the fly’s thorax with a needly.", "[Fly preparation] Collect 20 speared flies in the 0.5ml Eppendorf cap with holes, on ice.", "[Fly preparation] Cen... |
44,802 | Direct nuclear tagmentation and RNA-sequencing (DNTR-seq) | 1 | null | https://www.protocols.io/view/direct-nuclear-tagmentation-and-rna-sequencing-dnt-bpzamp2e | Vasilios Zachariadis, Huaitao Cheng, Nathanael Andrews, Martin Enge | TITLE: Direct nuclear tagmentation and RNA-sequencing (DNTR-seq)
AUTHORS: Vasilios Zachariadis, Huaitao Cheng, Nathanael Andrews, Martin Enge
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Understanding how genetic variation alters gene expression - how genotype affects phenotype - is a central cha... | ["[Prepare lysis buffer plates for cell sorting]\nPrepare lysis buffer mixNOTE: Reagents are prepared on ice, working quickly. ERCC is stored in single-use aliquots at , thawed on ice and added last. ABCD1ReagentReaction conc.µL per reaction384w plate2Nuclease free H2O-1.9657863RNase Inhibitor (40u/µL)1 unit/µL0.075... |
25,207 | RNA Isolation from Plant Tissue Protocol 18: innuPREP Plant RNA Kit | null | dx.doi.org/10.17504/protocols.io.4uxgwxn | null | null | TITLE: RNA Isolation from Plant Tissue Protocol 18: innuPREP Plant RNA Kit
AUTHORS:
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Implemented by: Michael Melkonian and Barbara Surek</div><div class = "text-block"><span>A small number of algae samples were extracted using the </span><a href="https... | [] |
43,927 | Novel In Vivo Regeneration System of Tomato | 4 | dx.doi.org/10.17504/protocols.io.bn5xmg7n | https://www.protocols.io/view/novel-in-vivo-regeneration-system-of-tomato-bn5xmg7n | Huiying Cao, Xinyue Zhang, yanyeruan , Lijun Zhang, Xuxiao Li, Bing Jia, Rui Ju | TITLE: Novel In Vivo Regeneration System of Tomato
AUTHORS: Huiying Cao, Xinyue Zhang, yanyeruan , Lijun Zhang, Xuxiao Li, Bing Jia, Rui Ju
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Plant in vitro regeneration is an important constituent part of horticulture technology and modern molecular bre... | ["Tomato plantsSeeds were placed on moistened filter papers for approximately 3 to 4 d until the seeds sprouted in room temperature. The germinated seeds were seeded into a tray of 72 cells filled with a mixture of nutrient soil, matrix, vermiculite and perlite (2:2:1.5:0.5(v/v/v/v)), and grown in a culture room with t... |
95,785 | Closed-head controlled impact model in adult rats- VandeVord Lab | 0 | dx.doi.org/10.17504/protocols.io.dm6gp37z8vzp/v1 | https://www.protocols.io/view/closed-head-controlled-impact-model-in-adult-rats-c9shz6b6 | Caiti-Erin Talty, Susan Murphy, Pamela VandeVord | TITLE: Closed-head controlled impact model in adult rats- VandeVord Lab
AUTHORS: Caiti-Erin Talty, Susan Murphy, Pamela VandeVord
[DESCRIPTION]
This is a protocol to describe the materials and methods utilized to perform preclinical traumatic brain injury (TBI) using a closed-head controlled impact model in adult rats... | ["Choose impactor tip based on diameter of choice (See Note 1) and tightly screw the tip into the bottom of the actuator before mounting the actuator on the stereotaxic crossbar.", "Connect the actuator to the impactor control box and connect the control box to a power source (outlet).", "Connect the stereotaxic coordi... |
67,419 | Diaetoxil Kapseln : Aktualisieren, überprüfen, offizieller Preis hier | 1 | dx.doi.org/10.17504/protocols.io.4r3l2ow54v1y/v1 | https://www.protocols.io/view/diaetoxil-kapseln-aktualisieren-berpr-fen-offiziel-cd33s8qn | health | TITLE: Diaetoxil Kapseln : Aktualisieren, überprüfen, offizieller Preis hier
AUTHORS: health
[DESCRIPTION]
Diaetoxil Kapseln ist ein nebenwirkungsfreies Naturprodukt. Lesen Sie mehr über Betrug, Preisbewertungen und Bezugsquellen.
[STEPS]
1. Diaetoxil Nach vierwöchiger Einnahme der Kapseln wiegen Diaetoxil Kapseln ... | ["Diaetoxil Nach vierwöchiger Einnahme der Kapseln wiegen Diaetoxil Kapseln in Frankreich 93 % der Probanden, was etwa 11,3 kg oder weniger entspricht. In der Placebogruppe wogen die Teilnehmer im Durchschnitt weniger als 0,4 kg. Als die Forscher nach bestimmten Gefühlen während der Einnahme von Diaetoxil Kapseln Pille... |
34,982 | Protocol for chemiluminescence based detection of ROS production in tomato | 1 | dx.doi.org/10.17504/protocols.io.beeejbbe | https://www.protocols.io/view/protocol-for-chemiluminescence-based-detection-of-beeejbbe | Parvinderdeep S Kahlon, Remco Stam | TITLE: Protocol for chemiluminescence based detection of ROS production in tomato
AUTHORS: Parvinderdeep S Kahlon, Remco Stam
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This assay is based on luminol and horseradish peroxidase-dependent chemiluminescence detection of reactive oxygen speci... | ["Make leaf discs (8 leaf discs per genotype) with biopsy punch and incubate in 200µl of 20mM MOPS in 96- well plate overnight.", "Remove the buffer the next day and add 75µl of HRP mix to each well.", "Read the plate for detecting luminescence in 1-5 minutes intervals at the luminometer for the initial 10 minutes to a... |
31,269 | HuBMAP - Tissue Sectioning for CODEX Specimens | null | dx.doi.org/10.17504/protocols.io.basdiea6 | null | Leigh Propper, Marda Jorgensen | TITLE: HuBMAP - Tissue Sectioning for CODEX Specimens
AUTHORS: Leigh Propper, Marda Jorgensen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This method details the microtomy process for specimens that will be stained and analyzed using the Akoya CODEX® system.</div><div class = "text-block">This p... | ["[Microtome Preparation]\nFill flotation bath dish completely with de-ionized or purified water.", "[Microtome Preparation]\nTurn the flotation bath on, and set the water temperature to 42°C.\n[Flotation Bath]\nAt this step, also inspect the microtome you are planning to use; Ensure it is clean, well maintained, and ... |
78,355 | Objectives (Part 2 of "Effects of Online Exercise Intervention on Physical and Mental Conditions in Young Adults with Chronic Neck Pain") | 1 | dx.doi.org/10.17504/protocols.io.q26g7ynzkgwz/v1 | https://www.protocols.io/view/objectives-part-2-of-34-effects-of-online-exercise-cqrtvv6n | Yiting Lin | TITLE: Objectives (Part 2 of "Effects of Online Exercise Intervention on Physical and Mental Conditions in Young Adults with Chronic Neck Pain")
AUTHORS: Yiting Lin
[DESCRIPTION]
This is Part 2 of "Effects of Online Exercise Intervention on Physical and Mental Conditions in Young Adults with Chronic Neck Pain"... | [] |
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