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Authors:
Group: UCSC BME 22L

Proper citation: 2020. How to Label a Gel. protocols.io https:// Copy   

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Authors:
Group: UCSC BME 22L

Proper citation: 2020. Protocol 1: PCR. protocols.io https:// Copy   

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Authors:
Group: UCSC BME 22L

Proper citation: 2020. Protocol to UCSC Genome Browser & BLAST . protocols.io https:// Copy   

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Authors:
Group: UCSC BME 22L

Proper citation: 2020. Lab 6 Notebook. protocols.io https:// Copy   

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Authors: Anibal Arce Medina,
Group: Laboratorio de Tecnologias Libres
Summary: 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)

Proper citation: Anibal Arce Medina, 2017. Preparation of cell-free RNAPT7 reactions. protocols.io https://dx.doi.org/10.17504/protocols.io.iekcbcw Copy   

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Authors:
Group: UCSC BME 22L

Proper citation: 2020. Lab 4 Notebook. protocols.io https:// Copy   

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Authors:
Group: UCSC BME 22L

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

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Authors:
Group: UCSC BME 22L

Proper citation: 2020. Agarose Gel Casting Protocol. protocols.io https:// Copy   

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Proper citation: 2020. Protocol PCR Wet Lab . protocols.io https://dx.doi.org/10.17504/protocols.io.bpzpmp5n Copy   

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Authors:
Group: UCSC BME 22L

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

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Authors:
Group: UCSC BME 22L

Proper citation: 2020. Protocols for CRISPR. protocols.io https:// Copy   

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Authors:
Group: Metabolomics Protocols & Workflows, Translational Mass Spectrometry Research Group
Summary: 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.

Proper citation: 2020. MRM-LC-MS/MS Assay for inflammatrory associated proteins in serum. protocols.io https://dx.doi.org/10.17504/protocols.io.bm4vk8w6 Copy   

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Authors:
Group: UCSC BME 22L

Proper citation: 2020. Protocols for Primer Design. protocols.io https:// Copy   

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Authors:
Group: UCSC BME 22L

Proper citation: 2020. Protocols for PCR. protocols.io https:// Copy   

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Authors: Binnypreet Kaur1, 2, Drahomíra Faktorová1, 2, , Priscila Peña-Diaz1 and Julius Lukeš1, 2
Group: Julius Lukes
Summary: E-mail: [email protected]

Proper citation: 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 Copy   

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Authors:
Group: UCSC BME 22L

Proper citation: 2020. Protcol 1: PCR Dry Lab. protocols.io https:// Copy   

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Proper citation: 2020. Protocol: Know Your BentoLab. protocols.io https:// Copy   

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Authors:
Group: UCSC BME 22L

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

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Authors:
Group: UCSC BME 22L

Proper citation: 2020. Reagent Safety & PPE. protocols.io https:// Copy   

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Authors:
Group: UCSC BME 22L

Proper citation: 2020. Lab 1 Notebook. protocols.io https:// Copy   

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