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Total: 120 points

I. Multiple Choices (3 points for each question)

  1. Approximately what’s the percentage of mRNA in total RNA?
    A. 5% C. 25%
    B. 15% D. 35%
  2. Which of the following is NOT interspersed repeats in eukaryotic genome?
  3. Which of the following is NOT a human disease database?
    A. OMIM
    B. SRA
    C. HGMD
    D. GeneCards
  4. Which of the following sequencing platform is NOT based on Sequencing by Synthesis (SBS)?
    A. Roche 454 C. Illumina/Solexa
    B. ABi SOLiD D. LifeTech Ion Torrent
  5. The yeast two-hybrid method is used to
    A. determine if two genes are turned on together
    B. make hybrid proteins for in vitro isolation
    C. identify protein-protein interactions
    D. identify protein-DNA interactions
  6. Which of the following is a criterion for selection of genome for sequencing?
    A. Relevance to human disease
    B. Relevance to basic biological questions
    C. Genome size
    D. All of the above

II. True/False (3 points for each question)

If the statement is True, place a “T” in front of the number. If it is false, place an “F” in front of the number and explain why it is false.

  1. DNA amplification is not required for most of Next Generation Sequencing technologies, such as 454, Illumina and SOLiD.
  2. Both RNA-Seq and Exome-Seq can detect gene expression levels.
  3. Next Generation Sequencing can detect SNPs, point mutations, chromosomal rearrangements, chromosomal duplications, DNA methylations, gene expression levels, novel transcripts and alternative splicing.
  4. 45% of the human genome or more consists of repeats derived from transposons.

III. Short Answers (your answers should be concise and to the point)

  1. In Illumina/Solexa sequencing technology, what unique design ensures that one and only one dNTP is incorporated into the newly synthesized DNA and is able to be detected in each chemistry cycle? (5 points)
  2. You are planning on hiking to the top of Mount Everest. This hike will take you to an unknown climate of decreased oxygen and atmospheric pressure. You are interested in how this hike might affect your muscle cell transcriptome.
    a. Describe how you might use next-gen sequencing (NGS) to determine this. Include all possible steps. (5 points)

b. What technique(s) might you use, other than NGS and microarray, to verify your results? (2 points)

  1. What are the 8 model organisms for functional genomics? Why were they chosen? (4 points)
  2. Mutations in Htt cause Huntington Disease (HD). What is the phenotype of the disease? Which chromosome is Htt localized? (4 points)
  3. What are the significant difference between structural genomics and classical structural biology? (4 points)
  4. What’s difference between reverse and forward genetics? (4 points)
  5. What’s the general workflow of CRISPR/Cas9 gene editing approach? What’s the critical step to target the specific gene? (4 points)

IV. NGS data analysis

  1. In this experiment, a transcription factor (TF) was studied using ChIP-Seq. The chromatin DNA associated with TF was immunoprecipitated by the antibody against TF, and subjected to high-throughput sequencing. This is the “ChIP” data. Meanwhile, the genomic DNA without immunoprecipitation was also sequenced, called “input”, which is regarded as background. The dataset is listed below:

Your task is to analyze the dataset to identify the binding sites using Galaxy. During the analysis, use human “hg19” (Human Feb. 2009 (GRCh37/hg19 (hg19)) as reference genome assembly, and tag size of 60bp when appropriate.

Note: Due to the long analysis and waiting time, do it as early as possible!

1) Report how many binding sites (regions) are identified. Also take a screenshot to show the number of regions. (15 points)

2) Report how many regions for each chromosome. Do not include the contigs with names “random”, “hap” or “chrUn”, just report “chr1 to chr22”, “chrX”, and “chrY”. (5 points)

3) Report the top 10 regions (without “random”, “hap” or chrUn” in chromosome names) of strongest binding. (5 points)

4) Visualize the strongest binding site in chr3 in UCSC Genome Browser. Take a screenshot. Report which gene(s) are closest to this binding site and briefly describe the gene(s) (limit 1 sentence). (8 points)

5) Find the closest peak (binding site) of gene “BRAF” that is in upstream promoter region (not in intron region), report the coordinates of this peak and take a screenshot of this peak along with RefSeq track. (5 points)

6) Design a set of primers to detect this binding site. Report the DNA sequence you are using for primer design and give the primer set of your design. (5 points)

7) Visualize the primers obtained from step b) in UCSC Genome Browser. (5 points)

8) Briefly describe this gene “BRAF”. (5 points)

9) With the identification of a binding site of BRAF gene promoter, a qPCR experiment was conducted to verify. The qPCR data were listed below. Plot the data into a bar graph with error bars. (5 points)

BRAF Ct Conc.(ng/ul)
IgG 33.02 0.060
34.56 0.023
33.86 0.036
CREB ChIP 30.30 0.340
30.83 0.243
30.32 0.337

Sample Answer

Compelling correspondence is essential to the achievement all things considered but since of the changing idea of the present working environments, successful correspondence turns out to be more troublesome, and because of the numerous impediments that will permit beneficiaries to acknowledge the plan of the sender It is restricted. Misguided judgments.In spite of the fact that correspondence inside the association is rarely completely open, numerous straightforward arrangements can be executed to advance the effect of these hindrances.

Concerning specific contextual analysis, two significant correspondence standards, correspondence channel determination and commotion are self-evident. This course presents the standards of correspondence, the act of general correspondence, and different speculations to all the more likely comprehend the correspondence exchanges experienced in regular daily existence. The standards and practices that you learn in this course give the premise to additionally learning and correspondence.

This course starts with an outline of the correspondence cycle, the method of reasoning and hypothesis. In resulting modules of the course, we will look at explicit use of relational connections in close to home and expert life. These incorporate relational correspondence, bunch correspondence and dynamic, authoritative correspondence in the work environment or relational correspondence. Rule of Business Communication In request to make correspondence viable, it is important to follow a few rules and standards. Seven of them are fundamental and applicable, and these are clear, finished, brief, obliging, right, thought to be, concrete. These standards are frequently called 7C for business correspondence. The subtleties of these correspondence standards are examined underneath: Politeness Principle: When conveying, we should build up a cordial relationship with every individual who sends data to us.

To be inviting and polite is indistinguishable, and politeness requires an insightful and amicable activity against others. Axioms are notable that gracious “pay of graciousness is the main thing to win everything”. Correspondence staff ought to consistently remember this. The accompanying standards may assist with improving courtesy:Preliminary considering correspondence with family All glad families have the mystery of progress. This achievement originates from a strong establishment of closeness and closeness. Indeed, through private correspondence these cozy family connections become all the more intently. Correspondence is the foundation of different affiliations, building solid partners of obedient devotion, improving family way of life, and assisting with accomplishing satisfaction (Gosche, p. 1). In any case, so as to keep up an amicable relationship, a few families experienced tumultuous encounters. Correspondence in the family is an intricate and alluring marvel. Correspondence between families isn’t restricted to single messages between families or verbal correspondence.

It is a unique cycle that oversees force, closeness and limits, cohesiveness and flexibility of route frameworks, and makes pictures, topics, stories, ceremonies, rules, jobs, making implications, making a feeling of family life An intelligent cycle that makes a model. This model has passed ages. Notwithstanding the view as a family and family automatic framework, one of the greatest exploration establishments in between family correspondence centers around a family correspondence model. Family correspondence model (FCP) hypothesis clarifies why families impart in their own specific manner dependent on one another ‘s psychological direction. Early FCP research established in media research is keen on how families handle broad communications data. Family correspondence was perceived as an exceptional scholastic exploration field by the National Communications Association in 1989. Family correspondence researchers were at first impacted by family research, social brain science, and relational hypothesis, before long built up the hypothesis and began research in a family framework zeroed in on a significant job. Until 2001, the primary issue of the Family Communication Research Journal, Family Communication Magazine, was given. Family correspondence is more than the field of correspondence analysts in the family. Examination on family correspondence is normally done by individuals in brain science, humanism, and family research, to give some examples models. However, as the popular family correspondence researcher Leslie Baxter stated, it is the focal point of this intelligent semantic creation measure making the grant of family correspondence special. In the field of in-home correspondence, correspondence is normally not founded on autonomous messages from one sender to one beneficiary, yet dependent on the dynamic interdependency of data shared among families It is conceptualized. The focal point of this methodology is on the shared trait of semantic development inside family frameworks. As such, producing doesn’t happen in vacuum, however it happens in a wide scope of ages and social exchange.

Standards are rules end up being followed when performing work to agree to a given objective. Hierarchical achievement relies significantly upon compelling correspondence. So as to successfully impart, it is important to follow a few standards and rules. Coming up next are rules to guarantee powerful correspondence: clearness: lucidity of data is a significant guideline of correspondence. For beneficiaries to know the message plainly, the messages ought to be sorted out in a basic language. To guarantee that beneficiaries can without much of a stretch comprehend the importance of the message, the sender needs to impart unmistakably and unhesitatingly so the beneficiary can plainly and unquestionably comprehend the data.>

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