In biotechnology a protocol is a predefined written procedural method in the design and implementation of experiments. Protocols are written whenever it is desirable to standardize a laboratory method to ensure successful replication of results by others in the same laboratory or by other laboratories. Detailed protocols also facilitate the assessment of results through peer review. In addition to detailed procedures and lists of required equipment and instruments, protocols often include information on safety precautions, the calculation of results and reporting standards, including statistical analysis and rules for predefining and documenting excluded data to avoid bias. The biotech team will continue to revise and write new protocols and SOPs.
Please click on the gel image to print a PDF of four gel templates. Each time you run a gel you are required to have this completed and on top of the chamber. Please label wells with the sample and include the ladder, voltage, time, & buffer. |
Spectrophotometer (Spectron 20D) Podcast
|
Agar Media Protocol (including N. crassa)
This protocol is for preparing LB agar and LB broth (Miller formulation). Additionally, this document includes the Vogel's Medium recipe for culturing Neurospora crassa along with instructions for pouring slants.
This protocol is for preparing LB agar and LB broth (Miller formulation). Additionally, this document includes the Vogel's Medium recipe for culturing Neurospora crassa along with instructions for pouring slants.
Antibiotic/Arabinose Media Protocol
This document contains the protocol for sterile filtering common media additives, including the concentrations for stock and working solutions. Use this protocol to select for transformants and to induce various operons.
This document contains the protocol for sterile filtering common media additives, including the concentrations for stock and working solutions. Use this protocol to select for transformants and to induce various operons.
Aseptic Technique and Cell Culturing Protocol
Our protocol for aseptic technique and methodology for cell culturing and streaking for isolated colonies.
Our protocol for aseptic technique and methodology for cell culturing and streaking for isolated colonies.
Biotech Notebook Standard Operating Procedure (SOP)
This is our protocol for maintaining your biotech lab notebook. It is written in the form of an SOP as an exemplar for students to write new SOPs for the lab. This protocol is under constant revision to meet the needs of the students.
This is our protocol for maintaining your biotech lab notebook. It is written in the form of an SOP as an exemplar for students to write new SOPs for the lab. This protocol is under constant revision to meet the needs of the students.
Chlorophyll-a Standard Operating Procedure (SOP)
This is our student-designed protocol for collecting chlorophyll-a degradation through acidification data to calculate the primary productivity of an aquatic system.
This is our student-designed protocol for collecting chlorophyll-a degradation through acidification data to calculate the primary productivity of an aquatic system.
CRISPR Guide RNA (gRNA) Design Protocol
This is a start to a protocol for designing guide RNA for the CRISPR-Cas9 system.
This is a start to a protocol for designing guide RNA for the CRISPR-Cas9 system.
Electroporation Protocol for Neurospora crassa
This protocol details the procedure for transforming N. crassa using electroporation.
This protocol details the procedure for transforming N. crassa using electroporation.
Environmental DNA (eDNA) Protocol
This protocol used to filter and extract eDNA using the syringe technique, which is typically done in the lab and not in the field.
This protocol used to filter and extract eDNA using the syringe technique, which is typically done in the lab and not in the field.
Gel Electrophoresis Protocol (modified from Addgene)
Excellent comprehensive protocol for pouring/running gels modified from Addgene.
Excellent comprehensive protocol for pouring/running gels modified from Addgene.
Gel Electrophoresis Dyes Protocol
Protocol for making various dyes for electroporetic separation. We will usually have already prepared samples available.
Protocol for making various dyes for electroporetic separation. We will usually have already prepared samples available.
GENEWIZ Unpurified PCR Product Submission Protocol
Submission guidelines for sequencing un-purified PCR product.
Submission guidelines for sequencing un-purified PCR product.
Glycerol Bacteria Stock Protocol (Addgene)
Instructions for making glycerol stock solutions for long-term storage of bacterial strains at -20 C.
Instructions for making glycerol stock solutions for long-term storage of bacterial strains at -20 C.
Journal of Emerging Investigators Protocol
This is the document students should use as they write their manuscripts for peer-review publication.
This is the document students should use as they write their manuscripts for peer-review publication.
Neurospora crassa DNA Extraction protocol
Protocol for extraction includes conidial suspension protocol
Protocol for extraction includes conidial suspension protocol
Neurospora crassa Media Preparation Protocol
Recipes for various media including Vogel's Medium N and Synthetic Cross (SC) medium.
Recipes for various media including Vogel's Medium N and Synthetic Cross (SC) medium.
Notebook (biotech) Standard Operating Procedure (SOP)
This is our protocol for maintaining your biotech lab notebook. It is written in the form of an SOP as an exemplar for students to write new SOPs for the lab. This protocol is under constant revision to meet the needs of the students.
This is our protocol for maintaining your biotech lab notebook. It is written in the form of an SOP as an exemplar for students to write new SOPs for the lab. This protocol is under constant revision to meet the needs of the students.
Nucleotide Codes for Primers (IUPAC)
These are the IUPAC bioinformatic codes for nucleotides. Use this system when ordering oligonucleotides.
These are the IUPAC bioinformatic codes for nucleotides. Use this system when ordering oligonucleotides.
Oil Immersion Protocol 2016
Protocol for oil immersion microscopy. Use this for chapter 3 protocol 3.5
Protocol for oil immersion microscopy. Use this for chapter 3 protocol 3.5
PAGE Protogel Protocol
Protocol used to pour and cast polyacrylamide gels (completed at university by teacher)
Protocol used to pour and cast polyacrylamide gels (completed at university by teacher)
Plasmid Purification (minipreps) Protocol
This is a "generic" protocol and explanation for plasmid purification.
This is a "generic" protocol and explanation for plasmid purification.
Polymerase Chain Reaction Guide (PCR; Qiagen)
We will mostly use TopTaq master mix from Qiagen. This link will take you to Qiagen's comprehensive guide to PCR.
We will mostly use TopTaq master mix from Qiagen. This link will take you to Qiagen's comprehensive guide to PCR.
Primer Design Protocol
This protocol will guide you through the entire process of designing specific primers to amplify target DNA.
This protocol will guide you through the entire process of designing specific primers to amplify target DNA.
Primer Design Protocol (with Restriction Enzyme Sites)
This protocol will guide you through the entire process of designing specific primers to amplify target DNA to include restriction enzyme sites.
This protocol will guide you through the entire process of designing specific primers to amplify target DNA to include restriction enzyme sites.
Research Synopsis Protocol
This protocol that research students should use when composing their weekly synopses. To view an exemplar click here.
This protocol that research students should use when composing their weekly synopses. To view an exemplar click here.
Spectrophotometer Protocol (v3; 2017)
This protocol describes how to use the Spectronic 20 machine and how to choose an appropriate wavelength.
This protocol describes how to use the Spectronic 20 machine and how to choose an appropriate wavelength.
Statistical Analysis Protocol (v1; 2014)
This protocol describes how to use some basic inferential statistics and includes a dichotomous key to help students choose the appropriate test.
This protocol describes how to use some basic inferential statistics and includes a dichotomous key to help students choose the appropriate test.
Qiagen DNeasy Blood & Tissue Extraction Protocol
This is the protocol used for nearly all of our DNA extractions. There are modifications to this for environmental DNA and N. crassa conidial suspension extractions. Please see us for the adjustments that need to be made to this protocol.
This is the protocol used for nearly all of our DNA extractions. There are modifications to this for environmental DNA and N. crassa conidial suspension extractions. Please see us for the adjustments that need to be made to this protocol.
Qiagen Qiaquick Gel Extraction Protocol
Qiagen Qiaquick Gel Extraction Protocol (annotated with notes)
This is the protocol used to purify DNA from agarose gels. There are two versions. The second version is annotated with various notes that may help to clarify steps of the protocol. When in doubt, please ask one of us for guidance.
Qiagen Qiaquick Gel Extraction Protocol (annotated with notes)
This is the protocol used to purify DNA from agarose gels. There are two versions. The second version is annotated with various notes that may help to clarify steps of the protocol. When in doubt, please ask one of us for guidance.
Qiagen Qiaquick PCR Extraction Protocol
This is the protocol used to purify amplified DNA straight from a PCR sample (i.e., not from a gel).
This is the protocol used to purify amplified DNA straight from a PCR sample (i.e., not from a gel).
Qiagen TopTaq Polymerase Chain Reaction Protocol
This is the protocol used for nearly all of our PCR. Use this along with the PCR guide (click here)
This is the protocol used for nearly all of our PCR. Use this along with the PCR guide (click here)
Qubit 3.0 Fluorometer Protocol
This is the protocol used for the Qubit 3.0 fluorometers, which are used to quantify genomic and plasmid DNA.
This is the protocol used for the Qubit 3.0 fluorometers, which are used to quantify genomic and plasmid DNA.