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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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Protocol 2: LAMP Resource Report Resource Website |
UCSC BME 22L | UCSC | 1 | 2020 | 2020. Protocol 2: LAMP. protocols.io https:// | 2021-04-15 09:16:57 | ||||||
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Lab 3 Notebook Resource Report Resource Website |
UCSC BME 22L | UCSC | 1 | 2020 | 2020. Lab 3 Notebook. protocols.io https:// | 2021-04-15 09:14:30 | ||||||
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Lab 6 Notebook Resource Report Resource Website |
DOI:10.17504/protocols.io.bpzrmp56 | UCSC | 1 | 2020 | 2020. Lab 6 Notebook. protocols.io https://dx.doi.org/10.17504/protocols.io.bpzrmp56 | 2021-04-15 09:14:32 | ||||||
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Protocol 3: Antiobiotic Resistance Resource Report Resource Website |
UCSC BME 22L | UCSC | 1 | 2020 | 2020. Protocol 3: Antiobiotic Resistance. protocols.io https:// | 2021-04-15 09:14:36 | ||||||
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Protocol for IGV Resource Report Resource Website |
UCSC BME 22L | UCSC | 1 | 2020 | 2020. Protocol for IGV. protocols.io https:// | 2021-04-15 09:14:53 | ||||||
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Tranfection of sgRNA using SpCas9 containing plasmids to generate cell lines with Cas9 Resource Report Resource Website |
Binnypreet Kaur, Drahomíra Faktorová, Julius Lukeš, , | DOI:10.17504/protocols.io.x39fqr6 | Protist Research to Optimize Tools in Genetics (PROT-G), Julius Lukes | This protocol describes transfection of ribonucleoprotein (RNP) complexes that consist of purified Cas9 nuclease duplexed with synthetic guide RNA in cultured cells using the AMAXA Nucleo AMAXA Nucleofector II Electroporation system using Program X-001.RNPs complex have only transient expression inside the cell, this allows for the highest levels of editing efficiency and greatly reduces the chances of possible off target and toxic effects of integration of foreignDNA in host genome | Institute of Parasitology, Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic, Institute of Parasitology, Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic;, Institute of Parasitology, Czech Academy of Sciences, Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic;, Canadian Institute for Advanced Research, Toronto, Canada | 3 | 2019 | Binnypreet Kaur, Drahomíra Faktorová, Julius Lukeš, , 2019. Tranfection of sgRNA using SpCas9 containing plasmids to generate cell lines with Cas9. protocols.io https://dx.doi.org/10.17504/protocols.io.x39fqr6 | 2021-04-15 09:15:01 | |||
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Freezing of Diplonema papillatum Resource Report Resource Website |
Binnypreet Kaur1, 2, Drahomíra Faktorová1, 2, , Priscila Peña-Diaz1 and Julius Lukeš1, 2 | DOI:10.17504/protocols.io.hfzb3p6 | Julius Lukes | 1 Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005, České Budějovice, Czech Republic 2 Faculty of Sciences, University of South Bohemia, 37005, České Budějovice, Czech Republic, 1 Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005, České Budějovice, Czech Republic 2 Faculty of Sciences, University of South Bohemia, 37005, České Budějovice, Czech Republic, 1 Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005, České Budějovice, Czech Republic 2 Faculty of Sciences, University of South Bohemia, 37005, České Budějovice, Czech Republic, 1 Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005, České Budějovice, Czech Republic 2 Faculty of Sciences, University of South Bohemia, 37005, České Budějovice, Czech Republic, 1 Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005, České Budějovice, Czech Republic 2 Faculty of Sciences, University of South Bohemia, 37005, České Budějovice, Czech Republic, 1 Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005, České Budějovice, Czech Republic 2 Faculty of Sciences, University of South Bohemia, 37005, České Budějovice, Czech Republic, 1 Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005, České Budějovice, Czech Republic 2 Faculty of Sciences, University of South Bohemia, 37005, České Budějovice, Czech Republic | 1 | 2018 | Binnypreet Kaur1, 2, Drahomíra Faktorová1, 2, , Priscila Peña-Diaz1 and Julius Lukeš1, 2 2018. Freezing of Diplonema papillatum. protocols.io https://dx.doi.org/10.17504/protocols.io.hfzb3p6 | 2021-04-15 09:15:34 | ||||
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Gel Electrophoresis 1- Casting a gel in the Bento Lab gel box Resource Report Resource Website |
UCSC BME 22L | UCSC | 1 | 2020 | 2020. Gel Electrophoresis 1- Casting a gel in the Bento Lab gel box. protocols.io https:// | 2021-04-15 09:15:06 | ||||||
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Lab 5 Notebook Resource Report Resource Website |
UCSC BME 22L | UCSC | 1 | 2020 | 2020. Lab 5 Notebook. protocols.io https:// | 2021-04-15 09:15:11 | ||||||
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PREPARING 6X NEB LOADING BUFFER CONTAINING GELGREEN (GG) labeled ‘6XNEB+GG’ Resource Report Resource Website |
UCSC BME 22L | UCSC | 1 | 2020 | 2020. PREPARING 6X NEB LOADING BUFFER CONTAINING GELGREEN (GG) labeled ‘6XNEB+GG’. protocols.io https:// | 2021-04-15 09:15:16 | ||||||
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Media Composition for Diplonema papillatum culture Resource Report Resource Website |
Binnypreet Kaur1, 2, Drahomíra Faktorová1, 2, , Priscila Peña-Diaz1 and Julius Lukeš1, 2 | DOI:10.17504/protocols.io.hfwb3pe | 1 Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005, České Budějovice, Czech Republic 2 Faculty of Sciences, University of South Bohemia, 37005, České Budějovice, Czech Republic, 1 Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005, České Budějovice, Czech Republic 2 Faculty of Sciences, University of South Bohemia, 37005, České Budějovice, Czech Republic, 1 Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005, České Budějovice, Czech Republic 2 Faculty of Sciences, University of South Bohemia, 37005, České Budějovice, Czech Republic, 1 Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005, České Budějovice, Czech Republic 2 Faculty of Sciences, University of South Bohemia, 37005, České Budějovice, Czech Republic, 1 Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005, České Budějovice, Czech Republic 2 Faculty of Sciences, University of South Bohemia, 37005, České Budějovice, Czech Republic, 1 Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005, České Budějovice, Czech Republic 2 Faculty of Sciences, University of South Bohemia, 37005, České Budějovice, Czech Republic, 1 Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005, České Budějovice, Czech Republic 2 Faculty of Sciences, University of South Bohemia, 37005, České Budějovice, Czech Republic | 1 | 2018 | Binnypreet Kaur1, 2, Drahomíra Faktorová1, 2, , Priscila Peña-Diaz1 and Julius Lukeš1, 2 2018. Media Composition for Diplonema papillatum culture. protocols.io https://dx.doi.org/10.17504/protocols.io.hfwb3pe | 2021-04-15 09:15:18 | |||||
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hMSC basal media Resource Report Resource Website |
DOI:10.17504/protocols.io.ccrsv5 | hMSC Basal Media | 1 | 2014 | 2014. hMSC basal media. protocols.io https://dx.doi.org/10.17504/protocols.io.ccrsv5 | 2021-04-15 09:15:28 | ||||||
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Manual Silane magnetic bead-based high throughput protocol for SARS-CoV-2 RNA extraction Resource Report Resource Website |
Ainhoa Goñi-Salaverri, Jose A. Rodriguez, Nicholas Weber, Juan Pablo Unfried, Josepmaria Argemi, , David Lara Astiaso, | DOI:10.17504/protocols.io.bfmajk2e | Coronavirus Method Development Community | The COVID-19 pandemic has presented an unprecedent challenge to develop and validate testing tools for urgent disease diagnosis. Current testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) via molecular diagnostics is woefully inadequate due to myriad issues with cross-entity coordination, reagent availability, and labor- and time-intensive protocols. The bottleneck in the workflow from patient sampling to diagnosis is not in the identification of viral genetic material (RT-qPCR) but in the collection, processing, and purification of the viral genetic material (patient sampling and RNA extraction). The majority of tests performed in laboratories lacking sophisticated automation require individual sample processing that severely limits the possibilities of scale-up. Thus, throughput depends on the availability of trained operator person-hours. We have developed a protocol for SARS-CoV-2 RNA extraction based on silane ferrimagnetic beads that is easily scaled up to multiwell culture plates with the processing done using multichannel pipettes. This protocol significantly reduces the hands-on time per sample and increases throughput such that an individual operator can process 100-200 samples per hour. | Cima Universidad de Navarra, Pamplona, Spain, Cima Universidad de Navarra, Pamplona, Spain, Vivet Therapeutics SL, Pamplona, Spain, Cima Universidad de Navarra, Pamplona, Spain, Liver Unit. Internal Medicine Department. Clinica Universidad de Navarra, Pamplona, Spain, Division of Medicine - Gastroenterology and Hepatology Department, University of Pittsburgh, PA, USA, Cima Universidad de Navarra, Pamplona, Spain, Cambridge Stem Cell Institute, Cambridge, England | 2 | 2020 | Ainhoa Goñi-Salaverri, Jose A. Rodriguez, Nicholas Weber, Juan Pablo Unfried, Josepmaria Argemi, , David Lara Astiaso, 2020. Manual Silane magnetic bead-based high throughput protocol for SARS-CoV-2 RNA extraction. protocols.io https://dx.doi.org/10.17504/protocols.io.bfmajk2e | 2021-04-15 09:15:32 | |||
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Lab 7 Notebook Resource Report Resource Website |
DOI:10.17504/protocols.io.bp29mqh6 | UCSC | 1 | 2020 | 2020. Lab 7 Notebook. protocols.io https://dx.doi.org/10.17504/protocols.io.bp29mqh6 | 2021-04-15 09:15:50 | ||||||
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Protocol 2: CRISPR Transformation Resource Report Resource Website |
DOI:10.17504/protocols.io.bpmumk6w | UCSC | 1 | 2020 | 2020. Protocol 2: CRISPR Transformation. protocols.io https://dx.doi.org/10.17504/protocols.io.bpmumk6w | 2021-04-15 09:15:36 | ||||||
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GM Covid-19 saliva test (v2) Resource Report Resource Website |
Coronavirus Method Development Community, Narwhale for XPrize | GM Biosciences | 2 | 2020 | 2020. GM Covid-19 saliva test (v2). protocols.io https:// | 2021-04-15 09:15:42 | ||||||
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Protocol 1: Making Agar Plates Resource Report Resource Website |
UCSC BME 22L | UCSC | 1 | 2020 | 2020. Protocol 1: Making Agar Plates. protocols.io https:// | 2021-04-15 09:15:45 | ||||||
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Introduction to PCR Resource Report Resource Website |
UCSC BME 22L | UCSC | 1 | 2020 | 2020. Introduction to PCR. protocols.io https:// | 2021-04-15 09:15:46 | ||||||
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GM Covid-19 saliva test (v1) Resource Report Resource Website |
DOI:10.17504/protocols.io.bkgfkttn | Narwhale for XPrize, XPRIZE Rapid Covid Testing | GM Covid-19 saliva test is a RT-PCR test intended for qualitative detection of nucleic acids from SARS-CoV-2 in saliva specimen. The test is used for screening purpose under class of "research used only" (RUO). The test is not for diagnostic purpose. Positive result would be referred to an official clinical test with appropriate certification (i.e CLIA) required for clinical diagnosis. | GM Biosciences | 1 | 2020 | 2020. GM Covid-19 saliva test (v1). protocols.io https://dx.doi.org/10.17504/protocols.io.bkgfkttn | 2021-04-15 09:15:52 | ||||
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Eco-hydrology observation Cikapundung riverbank, Indonesia Resource Report Resource Website |
Dasapta Erwin Irawan(1), Endah Sulistyawati(1), Keukeu Rosada(2), Ichsan Alfan(1), Sri Aditya(1), Meli Triana(1), Tantra Rahmadia(1), Achmad Darul(3), | DOI:10.17504/protocols.io.igdcbs6 | The following protocols is submitted as part of the Cikapundung Research 2017, as can be divided in to 3 submissions:1. Identifying landuse and calculating its alteration in time2. Vegetation and zoobentos observation3. Water samplingOSF folder will be made following this protocols. | Institut Teknologi Bandung, Institut Teknologi Bandung, Institut Teknologi Bandung, Institut Teknologi Bandung, Institut Teknologi Bandung, Institut Teknologi Bandung, Institut Teknologi Bandung, Institut Teknologi Bandung, Institut Teknologi Bandung | 1 | 2017 | Dasapta Erwin Irawan(1), Endah Sulistyawati(1), Keukeu Rosada(2), Ichsan Alfan(1), Sri Aditya(1), Meli Triana(1), Tantra Rahmadia(1), Achmad Darul(3), 2017. Eco-hydrology observation Cikapundung riverbank, Indonesia. protocols.io https://dx.doi.org/10.17504/protocols.io.igdcbs6 | 2021-04-15 09:15:58 |
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