DNA Microarray Virtual Lab

Biology | Biochemistry | Genetics | Microbiology

As Featured In

DNA Microarray Virtual Lab

General Aim of DNA microarray simulation

Gene expression profiling

 

Method of DNA Microarray Virtual Lab

DNA Microarray Assay hybridization: whole human genome (4*44) oligo microarray and dual-color labelling kits.

Learning Objectives (ILOs) of DNA microarray lab

  • By the end of DNA Microarray virtual lab, students will be able to:

  • Perform the steps for RNA amplification in a DNA microarray simulation.

  • Practice the laboratory protocols to synthesize cDNA, cRNA, and fragment cRNA prior to hybridization.

  • Practice the technique for dual labelling of samples for microarray hybridization.

  • Apply the skills and precautions required for microarray slide handling and sample application.

  • Identify the benefits of the positive displacement pipette.

  • Practice the process of microarray slide wash prior to detection 

Theoretical Background / Context

  •  In a DNA microarray virtual lab, the identification of differential gene expression between two samples can be easily and rapidly done by DNA microarrays procedure. 
  • This requires high-quality RNA samples, proper labeling, and hybridization.
  • A microarray is a technique used to detect the expression of thousands of genes, at the same time, on microarray slides. 
  • These small slides are originally printed with thousands of spots, each with a known DNA sequence. These sequences are probes that help detect gene expression analysis upon DNA hybridization with samples. 
  • During sample preparation in the DNA microarray virtual lab, two fluorescent dyes are added, cy3 (green fluorescence) to the ‘to be studied group’ and cy5 (red fluorescence) to the ‘reference group’. Thus; samples that contain DNA sequences complementary to array slide probes hybridize and fluoresce when scanned. 
  • Good quality arrays should produce high signals at relatively low PMT values. Massive or widely spread differential gene expression is probably non-significant. Thus; a picture of the array should look more yellow, rather than green or red. Good quality signals should also be in a dynamic range, where the signal histograms fully overlap.
  • In the DNA Microarray Virtual Lab, quality control of RNA samples applied to microarrays is important and can be detected using bioanalyzer 2100. 
  • It is worth mentioning that good quality total RNA samples should produce two major peaks corresponding to the 2 major ribosomal RNA species. Severely degraded, low quality RNA will show a broad peak or a series of peaks at low retention times, while the 2 ribosomal RNA peaks will be of very low intensity or not identifiable at all. 
  • An RNA Integrity Number (RIN) higher than 9 is preferably used. 

Other applications of DNA microarray Experiment:

  • Transcriptomes and proteomes.
  • Gene chips to diagnose several pathogenic and genetic diseases in man.
  • Species-specific probes
  • Single nucleotide polymorphism (SNP) analysis. 

Dna Microarray Experiment | Principle of Work

In this DNA Microarray virtual lab protocol, Two RNA samples were prepared: cancerous & healthy (reference).

A- Amplification and labeling of extracted RNA:

1) synthesizing cDNA:

Using T7 RNA polymerase by reverse transcription.

2) synthesizing cRNA:

cDNA is used in an in vitro transcription reaction to generate cRNA. This reaction is performed in the presence of labeled ribonucleotides, producing microgram quantities of labeled RNA for array hybridization. 

B- Microarray hybridization:

  1. the generation of fluorescently labeled RNA using Agilent's Quick Amp labeling kit.

A hybridization sample is prepared and added to the cRNA prior to array hybridization. During this stage, cRNA is fragmented and labeled. cyanine 3  (cy3-fluoresces green) is added to the ‘to-be studied’ cells and cyanine 5 (cy5-fluoresces red) is added to the reference cells.

  1. Sample upload into the array slide with positive displacement pipette. The slide is then put in the hybridization station.

C- Microarray slide wash prior to scan:

The scanner has a laser which causes the hybrid bonds to fluoresce

PraxiLabs is Recognized Worldwide

Customers Love PraxiLabs

“With the onset of the COVID-19 pandemic, we found ourselves in a situation that forced us to act quickly to find the best solution available to provide our students with a quality molecular genetics laboratory experience.”

Korri Thorlacius, B.Sc.
Biology Laboratory Instructor
Biology Department
Kwantlen Polytechnic University

'' Although there are now several vendors offering virtual reality software for physics labs, there is only one that offers a realistic, I feel like I’m in a real lab, solution: PraxiLabs.''

Dr.‌ ‌William‌ ‌H.‌ ‌Miner,‌ ‌Jr.‌ ‌
Professor‌ ‌of‌ ‌Physics‌ ‌
Palm‌ ‌Beach‌ ‌State‌ ‌College‌ ‌
Boca‌ ‌Raton,‌ ‌FL‌

" PraxiLabs offered my students a chance to actively engage with the material. Instead of watching videos on a topic, they could virtually complete labs and realize the practical applications of class topics. This is a quality alternative to in-person labs."

Crys Wright
Teaching Assistant
Texas A&M University, USA

"Great user experience and impressive interaction, I am very pleased to have tried the simulations and will continue to do so."

Dr. Khaled M Goher
Lecturer in Biomedical Engineering
Aston University, UK

The #1 Science Virtual Labs used by Educational Institutions

Explore More Interactive 3D Virtual Simulations

Designed for Safety and Engagement

Find out how PraxiLabs keeps students engaged and improves learning outcomes