Intro. to Genomics – Spring 2024 | Hasan Alhaddad Genetics Lab

Class time and location

Mon, Wed – 9:30-10:45 (Room: 1st floor, SCI-S-194)

Important dates:

Exam 1: Wednesday 28/2/2024 (10%)

Exam 2: Wednesday 20/3/2024 (10%)

Exam 3: Monday 8/4/2024 (10%)

Exam 4: Wednesday 8/5/2024 (10%)

Report due: Monday 15/4/2024 (10%)

Presentations due: 9/5/2024 (10%)

Final Exam: Thursday 23/5/2024 – 11:00-1:00 (40%)

Your report should be typed using Microsoft Word (no lower or upper limit to the report) and be named (YOUR NAME_485). The report should include (to the best of your ability) the following with respect to your organism:

The common and scientific.
The taxonomy.
The closest relatives.
The geographic distribution.
Physical characteristics.
Life cycle.
Any unique information that fascinated you.

Projects:

Reem Alsayegh (Tuatara, Paper).*/
Saad Almutairi (Asian vine snake, Paper)./
Omar Rashdan (Green anole lizard, Paper).*/
~~Fatmah Alsahly (Australian dragon lizard, Paper).*/~~
Dana Altaher (King cobra, Paper)./
Narjes Aleissa (Habu, Paper).*/
Nutaila Almahfudhi (Tiger Rattlesnake, Paper)./
Belqees Almutairi (Anguid lizard, Paper).*/
Duaa Shaher (Leopard gecko, Paper)./
Sara Alwohaib (Guatemalan Beaded Lizard, Paper).*/
Amna Alrashid (Burmese python, Paper)./
(Organism: Common Lizard, Paper)./

Lecture 1: General Introduction

Lecture 2: History and Review (I)

Lecture 3: History and Review (II)

Lecture 4: The genome: the word and beyond

Lecture 5: Exploring the genome: workable pieces

Lecture 5.1: 485_lec5.1_DNAExtraction

Lecture 5.2: 485_lec5.2_DNAQualityQuantity

Lecture 6: DNA sequencing: the thing to the information (485_lec6_Sequencing)

Sequencing methods videos:

– Maxam and Gilbert Sequencing

– Sanger Sequencing, V2

– Pyrosequencing, V2

– Illumina Sequencing, V2

– SOLiD Sequencing

– Ion Torrent Sequencing, V2

– Oxford Nanopore Sequencing, V2

– PacBio Sequencing, V2

Lecture 7: The sequence: Reading the reads

Sequencing strategies videos:

– Hierarchical Sequencing

– Whole-Genome Shotgun Sequencing (WGS)

– The race to the human genome

Lecture 8: Stitching the sequences: Genome assembly

– Sequence Alignment (Abdulatif Alfulaij + Hafsa Aziz)

Lecture 9: The meaning: Genome annotation

Lecture 10: Meaningful parts: coding regions

Lecture 11: Functional annotation

RNAi (Abdulatif Alfulaij, Malak Alrasabiya)

CRISPR-Cas9 (Abdulatif Alfulaij), CRISPR-Cas9 (Malak Alrasabiya)

Lecture 12 : Non-coding genomic elements

Lecture 13 : Genetic transfer

Lecture 14: Polymorphisms

Lecture 15: Population Genetics

To Do:

Make a folder on your desktop named “485 material”.

Do you know what your organism looks like?

Download a high quality photo of your organism.

Visit the wikipedia page of your organism and send a link of the page to your instructor.

14/2/23

Learn the different forms of communication in science.

Learn the different forms of printed scientific communication and their levels of scientific details.

Learn the process of publishing scientific papers.

Learn the difference between scientific journals and news journals.

Learn to do a mindful search for genome papers using keywords and search engines.

How do I know that a scientific journal is a good journal?

Can you search for the genome sequence paper of your organism?

Did you find the same article that your instructor assigned to you?

16/2/23

Download the pdf of your article into your folder.

Download the supplementary files of your paper into your folder.

Print your article and keep it with you everyday.

DO NOT print your supplementary material.

23/2/2023

Identify (1) the journal that your paper was published in, (2) the publisher, (3) year published, (4) authors, (5) volume, (6) issue, (7) doi.

How many individuals authored your paper?

Circle the name of the first author.

Circle the name of the last author.

Was your paper authored by a consortium?

Why genome papers are authored by many authors?

How many words are used in the title?

Circle the following words in the title if present: genome, sequence, organism name.

What is the common name of your organism?

Is the common name of your organism present in the title?

What is the scientific name of your organism?

Is the scientific name of your organism present in the title?

When titles include scientific names and when titles include a common name?

Does the title of your paper reveal the objective of the study?

Read the abstract and locate the objective sentence.

Does the abstract of your paper contain an introductory sentence?

Can you locate the methods sentence(s) in the abstract of your paper?

Can you locate the results sentence(s) in the abstract of your paper?

Does the abstract of your paper highlight the significance of the study?

30. Can you identify the major components of you scientific paper (Abstract, Intro, M&M, Results, Discussion, and Refs)?

31. In the introduction of your paper, locate the summary paragraph of the study and the detailed objectives (if present).

32. Can you from the introduction of your assigned paper find general information of the organism under investigation?

33. Make a list of the general information regarding your organism that you extracted from the introduction?

34. Are there any information regarding the number of chromosomes and genome architecture of your organism in the introduction?

35. What is the source of DNA used to sequence your organism?

36. What is the sequencing method(s) used in your assigned paper?

37. Make sure that you understand all sequencing methods and specifically the methods in your paper.

38. Send links of YouTube videos of the sequencing methods (your choice) to your instructor.

39. Identify the sequencing strategy used in your paper

40. Send links of YouTube videos of the sequencing strategies to your instructor

41. Identify wether the sequencing single-end or paired-end sequencing was performed in you paper.

42. What is the sequence coverage or sequence depth in your paper

43. What is the total number of reads of your genome?

44. What is the number of contigs in your genome assembly?

45. What is the number of scaffolds in your genome assembly?

46. What is the N50 contig of your genome assembly?

47. What is the N50 scaffold of your genome assembly?

48. What is the size of the largest contig?

49. What is the size of the largest scaffold?

50. Send a draft of your powerpoint presentation to your instructor.

51. What is the number of predicted genes in your organism’s genome?

52. What is the number of operons in your organism’s genome? (if reported and applicable).

53. What is the GC content of your organism’s genome?

54. What is the average gene size in your organism’s genome? (mention minimum and maximum).

55. What % of your organism’s genome is represented by genes?

56. What is the average number of exons per gene in your organism’s genome?

57. What is the average number of introns per gene in your organism’s genome?

58. What is the gene density in your organism’s genome?

59. How many rRNA genes are present in your organism’s genome?

60. How many tRNA genes are present in your organism’s genome?

61. What % of your organism’s genome is represented by repeat elements?

62. What % of your organism’s genome is represented by simple repeats?

63. What % of your organism’s genome is represented by tandem repeat elements?

64. What % of your organism’s genome is represented by psuedo-genes?

65. What % of your organism’s genome is represented by transposable elements?

66. What % of your organism’s genome is represented by LINE elements?

67. What % of your organism’s genome is represented by SINE elements?

68. Send your final summary of data collection Excel file (Fall2020_genomic_data_YourName).

Data collection (YourName_485_data)

Presentation template (PresentationTemplate_485)