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Authors:
Group: UCSC BME 22L

Proper citation: 2020. Protocol 2: LAMP. protocols.io https:// Copy   

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Authors:
Group: UCSC BME 22L

Proper citation: 2020. Lab 3 Notebook. protocols.io https:// Copy   

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Proper citation: 2020. Lab 6 Notebook. protocols.io https://dx.doi.org/10.17504/protocols.io.bpzrmp56 Copy   

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Authors:
Group: UCSC BME 22L

Proper citation: 2020. Protocol 3: Antiobiotic Resistance. protocols.io https:// Copy   

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Authors:
Group: UCSC BME 22L

Proper citation: 2020. Protocol for IGV. protocols.io https:// Copy   

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Authors: Binnypreet Kaur, Drahomíra Faktorová, Julius Lukeš, ,
Group: Protist Research to Optimize Tools in Genetics (PROT-G), Julius Lukes
Summary: 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

Proper citation: 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 Copy   

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Authors: Binnypreet Kaur1, 2, Drahomíra Faktorová1, 2, , Priscila Peña-Diaz1 and Julius Lukeš1, 2
Group: Julius Lukes

Proper citation: 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 Copy   

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Authors:
Group: UCSC BME 22L

Proper citation: 2020. Gel Electrophoresis 1- Casting a gel in the Bento Lab gel box. protocols.io https:// Copy   

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Authors:
Group: UCSC BME 22L

Proper citation: 2020. Lab 5 Notebook. protocols.io https:// Copy   

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Authors:
Group: UCSC BME 22L

Proper citation: 2020. PREPARING 6X NEB LOADING BUFFER CONTAINING GELGREEN (GG) labeled ‘6XNEB+GG’. protocols.io https:// Copy   

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Authors: Binnypreet Kaur1, 2, Drahomíra Faktorová1, 2, , Priscila Peña-Diaz1 and Julius Lukeš1, 2

Proper citation: 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 Copy   

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Authors:
Summary: hMSC Basal Media

Proper citation: 2014. hMSC basal media. protocols.io https://dx.doi.org/10.17504/protocols.io.ccrsv5 Copy   

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Authors: Ainhoa Goñi-Salaverri, Jose A. Rodriguez, Nicholas Weber, Juan Pablo Unfried, Josepmaria Argemi, , David Lara Astiaso,
Group: Coronavirus Method Development Community
Summary: 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.

Proper citation: 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 Copy   

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Proper citation: 2020. Lab 7 Notebook. protocols.io https://dx.doi.org/10.17504/protocols.io.bp29mqh6 Copy   

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Proper citation: 2020. Protocol 2: CRISPR Transformation. protocols.io https://dx.doi.org/10.17504/protocols.io.bpmumk6w Copy   

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Authors:
Group: Coronavirus Method Development Community, Narwhale for XPrize

Proper citation: 2020. GM Covid-19 saliva test (v2). protocols.io https:// Copy   

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Authors:
Group: UCSC BME 22L

Proper citation: 2020. Protocol 1: Making Agar Plates. protocols.io https:// Copy   

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Authors:
Group: UCSC BME 22L

Proper citation: 2020. Introduction to PCR. protocols.io https:// Copy   

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Authors:
Group: Narwhale for XPrize, XPRIZE Rapid Covid Testing
Summary: 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.

Proper citation: 2020. GM Covid-19 saliva test (v1). protocols.io https://dx.doi.org/10.17504/protocols.io.bkgfkttn Copy   

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Authors: 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),
Summary: 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.

Proper citation: 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 Copy   

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