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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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How to Label a Gel Resource Report Resource Website |
UCSC BME 22L | UCSC | 1 | 2020 | 2020. How to Label a Gel. protocols.io https:// | 2021-04-15 09:14:25 | ||||||
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Protocol 1: PCR Resource Report Resource Website |
UCSC BME 22L | UCSC | 1 | 2020 | 2020. Protocol 1: PCR. protocols.io https:// | 2021-04-15 09:14:21 | ||||||
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Protocol to UCSC Genome Browser & BLAST Resource Report Resource Website |
UCSC BME 22L | UCSC | 1 | 2020 | 2020. Protocol to UCSC Genome Browser & BLAST . protocols.io https:// | 2021-04-15 09:14:27 | ||||||
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Lab 6 Notebook Resource Report Resource Website |
UCSC BME 22L | UCSC | 1 | 2020 | 2020. Lab 6 Notebook. protocols.io https:// | 2021-04-15 09:14:40 | ||||||
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Preparation of cell-free RNAPT7 reactions Resource Report Resource Website |
Anibal Arce Medina, | DOI:10.17504/protocols.io.iekcbcw | Laboratorio de Tecnologias Libres | This collection contains the protocols and recipes for the preparation of cell-free RNAPT7 transcription/translation coupled reactions.The crude extracts are obtained from IPTG-treated E.coli BL21 DE3 STAR cells. IPTG triggers RNAPT7 expression and accumulation in cells before collection. Reactions take place when the cell extract is mixed with a maltodextrin-based energy solution along with amino acids solution and other salts (Magnesium and Potassium). This system allows transcription/translation coupled reactions from plasmid DNA that contains T7 promoter transcriptional units. In our hands, it has been possible to express different fluorescent reporters, including deGFP which is highly efficient. Products of the reaction can be measured during the whole reaction time in a plate reader with appropriate optic filters, open hardware cameras, and microscopes. When set up correctlly, deGFP fluorescence intensity is detected as fast as ∼30 minutes after the reaction starts and it shows a rapid increase during the first ∼2.5-3.0 hours. The system presented here contains the features highlighted bellow, and is an adaptation of protocols and findings from the following listed papers: 1.- This system uses maltodextrin and Polyphosphate-based energy solution: Kim, H.-C., Kim, T.-W., Kim, D.-M., . Prolonged production of proteins in a cellfree protein synthesis system using polymeric carbohydrates (2011) Caschera, F.; Noireaux, V., A cost-effective polyphosphate-based metabolism fuels an all E. coli cell-free expression system. Metabolic engineering (2015) 2.- The S12 crude extract is prepared from E.coli cells ( expressing Pol T7 ) using bead beater. Sun, Z. Z.; Hayes, C. A.; Shin, J.; Caschera, F.; Murray, R. M.; Noireaux, V., Protocols for implementing an Escherichia coli based TX-TL cell-free expression system for synthetic biology. Journal of visualized experiments (2013) Kim, TW., Kim, HC., Oh, IS. et al. A highly efficient and economical cell-free protein synthesis system using the S12 extract of Escherichia coli. Biotechnol Bioproc E (2008) 3.- The amino acid stock solution contains each amino acid at ∼12 nM in a stable solution: Caschera, V. Noireaux Preparation of amino acid mixtures for cell-free expression systems. Benchmarks (2015) | , | 1 | 2017 | Anibal Arce Medina, 2017. Preparation of cell-free RNAPT7 reactions. protocols.io https://dx.doi.org/10.17504/protocols.io.iekcbcw | 2021-04-15 09:14:34 | |||
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Lab 4 Notebook Resource Report Resource Website |
UCSC BME 22L | UCSC | 1 | 2020 | 2020. Lab 4 Notebook. protocols.io https:// | 2021-04-15 09:14:33 | ||||||
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Introduction to Nanopore Resource Report Resource Website |
UCSC BME 22L | UCSC | 1 | 2020 | 2020. Introduction to Nanopore. protocols.io https:// | 2021-04-15 09:14:40 | ||||||
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Agarose Gel Casting Protocol Resource Report Resource Website |
UCSC BME 22L | UCSC | 1 | 2020 | 2020. Agarose Gel Casting Protocol. protocols.io https:// | 2021-04-15 09:14:59 | ||||||
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Protocol PCR Wet Lab Resource Report Resource Website |
DOI:10.17504/protocols.io.bpzpmp5n | UCSC | 1 | 2020 | 2020. Protocol PCR Wet Lab . protocols.io https://dx.doi.org/10.17504/protocols.io.bpzpmp5n | 2021-04-15 09:15:26 | ||||||
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Lab Notebook Template Resource Report Resource Website |
UCSC BME 22L | UCSC | 1 | 2020 | 2020. Lab Notebook Template. protocols.io https:// | 2021-04-15 09:15:35 | ||||||
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Protocols for CRISPR Resource Report Resource Website |
UCSC BME 22L | UCSC | 1 | 2020 | 2020. Protocols for CRISPR. protocols.io https:// | 2021-04-15 09:15:50 | ||||||
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MRM-LC-MS/MS Assay for inflammatrory associated proteins in serum Resource Report Resource Website |
DOI:10.17504/protocols.io.bm4vk8w6 | Metabolomics Protocols & Workflows, Translational Mass Spectrometry Research Group | Multiplex targeted proteomic assay to measure human proteins associated with inflammation in serum. A unique peptide is selected to represent a protein and is measured using multiple reaction monitoring (MRM) mass spectrometry. | Doykov I, Hällqvist J, Gilmour KC, Grandjean L, Mills K, Heywood WE, ‘The long tail of Covid-19’ - The detection of a prolonged inflammatory response after a SARS-CoV-2 infection in asymptomatic and mildly affected patients. F1000Research doi: 10.12688/f1000research.27287.1 | University College London, University of London | https://doi.org/10.12688/f1000research.27287.1 | 1 | 2020 | 2020. MRM-LC-MS/MS Assay for inflammatrory associated proteins in serum. protocols.io https://dx.doi.org/10.17504/protocols.io.bm4vk8w6 | 2021-04-15 09:15:43 | ||
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Protocols for Primer Design Resource Report Resource Website |
UCSC BME 22L | UCSC | 1 | 2020 | 2020. Protocols for Primer Design. protocols.io https:// | 2021-04-15 09:15:41 | ||||||
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Protocols for PCR Resource Report Resource Website |
UCSC BME 22L | UCSC | 1 | 2020 | 2020. Protocols for PCR. protocols.io https:// | 2021-04-15 09:15:45 | ||||||
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Diplonema Genomic DNA isolation Resource Report Resource Website |
Binnypreet Kaur1, 2, Drahomíra Faktorová1, 2, , Priscila Peña-Diaz1 and Julius Lukeš1, 2 | DOI:10.17504/protocols.io.hfyb3pw | Julius Lukes | E-mail: [email protected] | 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. Diplonema Genomic DNA isolation. protocols.io https://dx.doi.org/10.17504/protocols.io.hfyb3pw | 2021-04-15 09:15:58 | |||
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Protcol 1: PCR Dry Lab Resource Report Resource Website |
UCSC BME 22L | UCSC | 1 | 2020 | 2020. Protcol 1: PCR Dry Lab. protocols.io https:// | 2021-04-15 09:16:00 | ||||||
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Protocol: Know Your BentoLab Resource Report Resource Website |
UCSC | 1 | 2020 | 2020. Protocol: Know Your BentoLab. protocols.io https:// | 2021-04-15 09:16:12 | |||||||
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Lab 3 Notebook (Draft) Resource Report Resource Website |
UCSC BME 22L | UCSC | 1 | 2020 | 2020. Lab 3 Notebook (Draft). protocols.io https:// | 2021-04-15 09:16:33 | ||||||
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Reagent Safety & PPE Resource Report Resource Website |
UCSC BME 22L | UCSC | 1 | 2020 | 2020. Reagent Safety & PPE. protocols.io https:// | 2021-04-15 09:16:34 | ||||||
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Lab 1 Notebook Resource Report Resource Website |
UCSC BME 22L | UCSC | 1 | 2020 | 2020. Lab 1 Notebook. protocols.io https:// | 2021-04-15 09:16:51 |
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