Bioinformatics Mastery: Genome Engineering using CRISPR Cas9 from Udemy

Genome engineering or gene editing is a way of making specific changes to the DNA of a cell or organism in a controlled way. It is a type of genetic engineering in which DNA is inserted, deleted, modified, or replaced in the genome of a living organism.

During the genome editing process, a type of enzyme called “engineered nuclease” cuts the genome in a specific place. When this is repaired by the cell, a change or an edit is made at the sequence, leading to a change in characteristics of a cell or an organism.

There are 3 generations of nucleases for genome editing: (1) Zing Finger Nucleases (ZFNs), (2) TALENs (Transcription activator-like effector nuclease), (3) CRISPR/Cas9.

CRISPR/Cas9 is simpler, faster, cheaper, and more accurate than older genome editing methods and thus, it is most commonly used in the genome engineering process. CRISPR stands for Cluster Random Interspaced Short Palindromic Repeats. It is the DNA-targeting part of the system which consists of an RNA molecule, or ‘guide’ designed to bind to specific DNA bases through complementary base-paring. Cas9 is the CRISPR-associated protein 9 and is the nuclease part that cuts the DNA.

The CRISPR/Cas9 system was initially identified as the RNA-based adaptive immune system in bacteria and archaea. The native CRISPR system confers resistance to viruses by incorporating “short repeats” of the viral DNA into the bacterial genome.

CRISPR Cas9 technique can be used to treat many hereditary disorders by modifying the mutated genotypes to a normal phenotype. Other applications include the creation of cellular and animal models of human disease, Improvements in biotechnology and food production, the study of the functions of genes and gene regulatory elements, and many others.

This course introduces you to the world of genome engineering and CRISPR/Cas9. Throughout the course, we will cover essential theory knowledge to understand the genome engineering process and then will start with various bioinformatics tools like guide RNA design tools, off-target prediction tools and many others used during CRISPR/Cas9 mediated gene editing.

The detailed course structure includes;

Genome Editing
NHEJ Pathway
HDR Pathway
Restriction Enzymes
Zinc Finger Nucleases
TALENs
CRISPR/Cas9
Genome Engineering using CRISPR Cas9
Retrieval of mRNA of a Gene
CRISPRdirect
Retrieval of Exon Sequence
WU-CRISPR
CAS designer
GT-Scan
Off-Spotter
Guides
GPP sg RNA designer
CRISPR Cas9 gRNA design checker
CHOP CHOP
CRISPOR

This course is a unique blend of theory and practical, where you will learn basic theory and then perform practical analysis of Genome engineering and CRISPR/Cas9 concepts. We assure you that after taking this course, your perspective will be very different for Gene editing. So, sign up for the course and see how fun, exciting, and rewarding the genome engineering tools are. We hope this course will be worth your money and time.

What's inside

Learning objectives

Introduction to genome engineering
Nhej pathway
Hdr pathway
Various genome engineering techniques like zfns and talens
Crispr/cas9

Crispr for gene & genome editing
Gene knock-in & knock-out
Gene mutagenesis
Guide rna design
Off-target analysis

Introduction to genome engineering
Nhej pathway
Hdr pathway
Various genome engineering techniques like zfns and talens
Crispr/cas9
Crispr for gene & genome editing
Gene knock-in & knock-out
Gene mutagenesis
Guide rna design
Off-target analysis

Syllabus

Genome Engineering using CRISPR Cas9

Genome Editing

NHEJ pathway

HDR pathway

Traffic lights

Read about what's good

what should give you pause

and possible dealbreakers

Covers CRISPR/Cas9, which is currently the most widely used genome editing method due to its simplicity, speed, and accuracy compared to older techniques like ZFNs and TALENs

Explores the applications of CRISPR Cas9 technology, including treating hereditary disorders, creating disease models, and improving biotechnology and food production

Includes practical analysis using bioinformatics tools for guide RNA design and off-target prediction, which are essential for effective CRISPR/Cas9 mediated gene editing

Requires learners to understand the NHEJ and HDR pathways, which are essential DNA repair mechanisms that are fundamental to understanding genome editing outcomes

Covers multiple tools such as CRISPRdirect, WU-CRISPR, and CHOPCHOP, which may require learners to install and configure software on their local machines

Reviews summary

Crispr cas9 theory and tools introduction

According to learners, this course provides a solid theoretical foundation in genome engineering techniques, particularly focusing on CRISPR/Cas9. Many appreciate the introduction to various bioinformatics tools used in the process, finding it a useful starting point for understanding guide RNA design and off-target analysis. While the theory is generally well-explained, some students note that the course could benefit from more in-depth practical exercises or updated guidance on software installation, which they found to be a challenging aspect. Overall, it's seen as a valuable resource for grasping the core concepts and tools, particularly for those new to the field or seeking a theoretical overview.

Some found the pace inconsistent or depth insufficient.

"Some sections felt rushed, especially when demonstrating the tools."

"I think it gives a broad overview but lacks the deep dive needed for actual lab work."

"Could use more in-depth coverage on complex topics or optimization techniques."

"While good for basics, it doesn't go into the nuances needed for advanced applications."

Useful for newcomers to the field.

"This course is a perfect introduction if you are new to CRISPR and genome editing."

"It gives a comprehensive overview without being overwhelming for beginners."

"A great place to start learning about this complex topic."

"For someone like me with limited prior knowledge, it was a very accessible entry point."

Covers key software for guide RNA design and analysis.

"Introducing various online tools for guide RNA design and off-target prediction was very beneficial."

"Learning about specific tools like CRISPOR and CHOP CHOP gave me practical insights."

"I appreciated the overview of multiple options available for practical application."

"The course showed me different platforms I can use for my own research projects."

Provides a clear foundation in CRISPR/Cas9 principles.

"The course laid out the theoretical background of genome editing and CRISPR very clearly."

"I found the explanations of NHEJ, HDR, and the history of nucleases really helpful."

"Excellent coverage of the fundamental concepts before diving into the tools."

"It gave me a solid understanding of how CRISPR works at a fundamental level."

Students face difficulties with hands-on tool usage.

"While tools are shown, I wished there were more step-by-step practical exercises to follow."

"Getting the software and pipelines to work as shown in the course was quite challenging for me."

"The course is more theoretical explanation with tool introductions, less about real hands-on practice."

"I struggled a bit translating the tool overview into actual experiments or data analysis."

Activities

Be better prepared before your course. Deepen your understanding during and after it. Supplement your coursework and achieve mastery of the topics covered in Bioinformatics Mastery: Genome Engineering using CRISPR Cas9 with these activities:

Review Basic Molecular Biology

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Strengthen your understanding of fundamental molecular biology concepts, which are essential for grasping the mechanisms of CRISPR-Cas9 and genome engineering.

Browse courses on Molecular Biology

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Review DNA structure and replication.
Study transcription and translation processes.
Familiarize yourself with basic genetic concepts.

Read 'A Crack in Creation: Gene Editing and the Unthinkable Power to Control Evolution'

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Gain a deeper understanding of the history, science, and ethical considerations surrounding CRISPR-Cas9 technology.

View A Crack in Creation on Amazon

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Read the book, taking notes on key concepts and ethical considerations.
Reflect on the potential societal impacts of CRISPR technology.

Practice Guide RNA Design

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Reinforce your understanding of guide RNA design principles by practicing with different target sequences and online tools.

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Select several gene sequences from a database.
Use online tools to design guide RNAs for each sequence.
Evaluate the specificity and potential off-target effects of each guide RNA.

Four other activities

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Show all seven activities

Explore 'Genome Editing: Engineering Life'

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Expand your knowledge of genome editing technologies beyond CRISPR-Cas9 and explore their diverse applications.

View Putting Knowledge to Work on Amazon

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Read the book, focusing on the technical details of different genome editing technologies.
Compare and contrast CRISPR-Cas9 with other genome editing methods.

Create a Presentation on CRISPR Applications

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Solidify your knowledge of CRISPR-Cas9 by researching and presenting on its diverse applications in medicine, agriculture, and biotechnology.

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Choose a specific application of CRISPR-Cas9.
Research the application and gather relevant information.
Create a presentation summarizing the application and its impact.

Contribute to CRISPR Analysis Tools

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Deepen your understanding of CRISPR-Cas9 by contributing to open-source bioinformatics tools used for guide RNA design or off-target analysis.

Browse courses on CRISPR

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Identify an open-source CRISPR analysis tool on platforms like GitHub.
Explore the codebase and identify areas for improvement or bug fixes.
Contribute code, documentation, or bug reports to the project.

Design a CRISPR-Based Therapy

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Apply your knowledge of CRISPR-Cas9 to design a hypothetical gene therapy for a specific genetic disease.

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Choose a genetic disease with a known genetic cause.
Design a CRISPR-Cas9 strategy to correct the disease-causing mutation.
Outline the steps involved in delivering the CRISPR-Cas9 system to the target cells.
Address potential ethical and safety concerns associated with the therapy.

Career center

Learners who complete Bioinformatics Mastery: Genome Engineering using CRISPR Cas9 will develop knowledge and skills that may be useful to these careers:

Genetic Engineer

A genetic engineer manipulates the genetic material of organisms to produce desired outcomes, and this course is highly relevant to this work. This course directly addresses core concepts in genome engineering, especially using CRISPR Cas9 technology. The practical training in guide RNA design and off-target analysis that is included in the course provides a hands-on approach to this work, which is part of the day-to-day tasks of a genetic engineer. The course helps build a crucial understanding of various gene editing techniques, extending to how methods like ZFNs and TALENs work. Therefore, those who wish to become genetic engineers should find this course particularly beneficial.

See salaries and explore the career path for Genetic Engineer

Biotechnology Researcher

Biotechnology researchers work on developing new technologies using biological systems, and this course helps build a foundation in key genome engineering techniques. The course introduces various aspects of genome editing, particularly focusing on CRISPR Cas9, a popular technology with many applications in biotechnology. The training in designing guide RNA and analyzing off-target effects, which are vital components of gene editing, is beneficial to this role. Instruction on the use of bioinformatics tools like CRISPRdirect and WU-CRISPR also prepares individuals for the kind of work a biotechnology researcher often performs. Therefore, those who wish to embark on a career in biotechnology research should find this course to be beneficial.

See salaries and explore the career path for Biotechnology Researcher

Bioinformatics Scientist

A bioinformatics scientist uses computational tools and methods to analyze biological data, including genomic data. This course focusing on genome engineering and CRISPR Cas9 directly aligns with the work of a bioinformatics scientist, particularly one working in gene editing. The course's coverage of guide RNA design, off-target analysis, and specific bioinformatics tools like CRISPRdirect and WU-CRISPR provides practical skills necessary for this kind of research. The knowledge of different genome editing techniques ZFNs and TALENs also provides an important theoretical background. Furthermore, understanding of the CRISPR-Cas9 system, which is a cornerstone of gene editing, is essential for a bioinformatics scientist working in this field.

See salaries and explore the career path for Bioinformatics Scientist

Genomics Data Analyst

A genomics data analyst interprets complex genomic data to derive insights helpful for medical or scientific advancement, and the course offers valuable training for this role. This course provides hands-on experience with bioinformatics tools used in gene editing, such as CRISPRdirect and WU-CRISPR, and helps develop the ability to analyze genome data. The course also covers fundamental concepts of genome engineering which are important to understand the context of the data. The course's focus on CRISPR Cas9, guide RNA design, and off-target analysis are all directly relevant to the work of someone in genomics data analysis.

See salaries and explore the career path for Genomics Data Analyst

Research Scientist

A research scientist often conducts experiments and analyzes data to advance a specific scientific field, such as genome research, where this course is applicable. The course material on CRISPR Cas9 methodology, along with the use of guide RNA design tools and practical analysis, provides the kind of hands-on experience a research scientist needs. The course also gives an important overview of genome editing techniques, including older methods like ZFNs and TALENs, which are beneficial to understand the state of the field. This course is useful for someone who wishes to perform research in the area of genome engineering.

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Molecular Biologist

A molecular biologist studies the structure and function of molecules essential to life, and this course is relevant because it focuses on molecular techniques used for genome modification. This course covers core topics like the CRISPR Cas9 system, guide RNA design, and off-target analysis, all of which are heavily used in molecular biology research. It is relevant for those who study gene expression and regulation, and the practical training in bioinformatics tools like CRISPRdirect and WU-CRISPR is very helpful. The course also introduces older gene editing techniques such as ZFNs and TALENs, which serve as a useful background when taking a broad view of the field.

See salaries and explore the career path for Molecular Biologist

Laboratory Technician

A laboratory technician assists scientists with experiments and research, and this course provides relevant knowledge and skills for working in a molecular biology lab. This course introduces essential concepts of genome engineering, with a particular focus on CRISPR Cas9 technology, which often forms part of experiment design. The course's practical training in using bioinformatics tools for guide RNA design and off-target analysis helps develop the kind of experience relevant for this role. An understanding of gene editing techniques like ZFNs and TALENs also enhances the technician's ability to understand lab procedures with better context. This course may be useful for any lab technician involved in molecular work.

See salaries and explore the career path for Laboratory Technician

Pharmaceutical Scientist

A pharmaceutical scientist works on drug discovery and development, and this course may be useful for those working on gene therapies. The course focuses on CRISPR Cas9, a gene editing technology relevant to drug development. Practical training in guide RNA design and off-target analysis, provided by the course, is useful to anyone developing therapeutics using genetic manipulation. Furthermore, the course's overview of genome engineering and gene editing offers a theoretical background useful in pharmaceutical research. This course may be useful to the pharmaceutical scientist who wishes to work with gene therapy focused drug development.

See salaries and explore the career path for Pharmaceutical Scientist

Biochemist

A biochemist studies chemical processes in living organisms, and this course may be relevant if their work involves genetic manipulation. The course helps develop an understanding of fundamental concepts in genome engineering, particularly using CRISPR Cas9 technology. Moreover, practical experience with designing guide RNA sequences and understanding off-target effects helps a biochemist who works with DNA. The course may also be useful for one who wishes to understand how gene editing works, especially as it applies to biological systems at the molecular level.

See salaries and explore the career path for Biochemist

Biomedical Engineer

Biomedical engineers develop solutions for healthcare using engineering principles, and the genome editing skills covered in this course are relevant to some areas of this field. Biomedical engineering is a very diverse field, where some subfields may utilize genome engineering or gene editing. The course provides training in concepts such as CRISPR-Cas9, which has applications in areas such as gene therapy. Also, the course's training in guide RNA design and off-target analysis provides hands-on knowledge for those interested in applied and translational applications of gene editing. The course may be useful to the biomedical engineer who wishes to work in this niche area.

See salaries and explore the career path for Biomedical Engineer

Agricultural Scientist

An agricultural scientist focuses on improving agricultural practices, and this course may be helpful for one who wishes to work with plant genomics. This course introduces various genome engineering techniques, with a special focus on CRISPR Cas9, which has applications in plant breeding. The course covers guide RNA design and off-target analysis which are important for gene editing in plants. This course may be useful for the agricultural scientist working in plant genomics and gene editing.

See salaries and explore the career path for Agricultural Scientist

Science Educator

A science educator teaches scientific concepts, and this course may be useful to improve the educator's knowledge of genome engineering. This course offers a comprehensive overview of genome editing, specifically through CRISPR Cas9 technology and its applications. The course may be useful for a science educator who seeks to deepen their knowledge of the principles of gene editing and the details of the CRISPR system. An understanding of bioinformatics tools like CRISPRdirect and WU-CRISPR, which are also covered in the course, helps build a more robust understanding of the subject. This can allow the science educator to teach the topic of genome engineering and gene editing more thoroughly.

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Science Writer

A science writer communicates complex scientific topics to the general public, and this course may be helpful for improving the writer's understanding of genome engineering. This course includes essential concepts of genome editing, particularly CRISPR Cas9. The course may be useful to a science writer who wants to understand the concepts of gene editing and its impact on modern science. Knowledge of techniques used in gene editing and bioinformatics from the course will allow a more thorough and accurate explanation of genome engineering.

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Patent Attorney

A patent attorney handles legal aspects of scientific discoveries, and this course may be beneficial for an attorney specializing in biotechnology. This course introduces concepts around genome engineering and gene editing, especially CRISPR Cas9. The course may be beneficial for the patent attorney handling intellectual property within the biotechnology field. A deep understanding of the science behind gene editing and the use of techniques in gene editing may assist a patent attorney focused in this field.

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Clinical Geneticist

A clinical geneticist diagnoses and manages genetic disorders, and while the course does not focus on diagnosis, it helps build knowledge of the technologies used in gene editing, which is relevant to the field. This course teaches core concepts in genome engineering, especially the CRISPR Cas9 system, that may be useful for a clinical geneticist who wishes to have an understanding of the gene editing technology. The course’s overview of guide RNA design and off-target analysis are particularly helpful to understand how genome editing is performed. The course may be useful for the clinical geneticist who seeks a deeper understanding of techniques that may be used in the development of future therapeutic interventions for genetic diseases.

See salaries and explore the career path for Clinical Geneticist

Bioinformatics Mastery

Genome Engineering using CRISPR Cas9

What's inside

Learning objectives

Syllabus

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Reviews summary

Crispr cas9 theory and tools introduction

Activities

Career center

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