NASA finally has proved there is life on Mars and brought back a newly identifie
ID: 99535 • Letter: N
Question
NASA finally has proved there is life on Mars and brought back a newly identified animal, named Mars 1254. Our university has been very successful in breeding Mars 1254, meaning now we have a population that we can do research with. Your work involves characterizing the gene expression profile of Mars 1254. We don’t have any prior knowledge of its genome information. Because Mars 1254 is a split hoofed, non-rumen animal and is able to digest feed provided from our swine farm, you wonder if its metabolic system is closer to pigs than it is to cattle. You hypothesize that genes involved in Mars 1254 metabolism are similar to those of pigs. You want to use gene expression experiments to prove your hypothesis. Make sure to include the platform you are going to use, why you chose that particular system, and a brief description of the experimental design (times, control, samples, etc.), analysis, and data interpretation.
Explanation / Answer
The gene expression systems study the global expression of genes of a particular organism.
The expression profiling of the Mars 1254 can be studied by devising the experiments used for pig genomes It will involve the following 39 steps
Experimental design
1. Objectives articulation 2. Resources allocation 3. Study design 4. Power and confidence 5. Pilot collection 6. Statistical design validation 7. Data collection
Gene collection
8. Gene coverage 9. Probe selection 10. Resources annotation 11. Confidence metrics 12. Probe synthesis and purification 13. Quality controls and metrics • Sample collection 14. Sample selection 15. Resources cataloguing 16. Sample preparation 17. Quality controls and metrics
Array preparation
18. Instruments calibration 19. Slides printing and treatment 20. Quality controls (QC) • Target synthesis 21. Spike RNA controls 22. Biochemical reactions 23. Quality controls and metrics • Hybridization 24. Hybridization and mixing 25. Washing and drying 26. Quality controls (QC) • Data transformation 27. Image acquisition 28. Image segmentation 29. Data subtraction and filtering 30. Data normalization 31. Data reduction (replicates) 32. QC metrics, descriptive statistics of the measures
Knowledge extraction
33. Ratio- or intensity-statistics 34. Genes modules identification (clustering and classification) 35. Functional annotation 36. Networks definition 37. ‘Omics’ integration (inter-disciplinary validations)
Data storage
38. Data warehouse (proprietary or public repositories) 39. Data integrity and standards maintenance
There are three types of platforms that can be employed for expression profiling of Mars1254 genome namely
a) Long oligonucleotide platform
b) short oligonucleotide platform
c) cDNA platforms
Out of these three, the long oligonucleotide platform has been found to be highly suitable for expression profiling.
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