Table of contents

1. Introduction to Genetics51m
2. Mendel's Laws of Inheritance3h 37m
3. Extensions to Mendelian Inheritance2h 41m
4. Genetic Mapping and Linkage2h 28m
5. Genetics of Bacteria and Viruses1h 21m
6. Chromosomal Variation1h 48m
7. DNA and Chromosome Structure56m
8. DNA Replication1h 10m
9. Mitosis and Meiosis1h 34m
10. Transcription1h 0m
11. Translation58m
12. Gene Regulation in Prokaryotes1h 19m
13. Gene Regulation in Eukaryotes44m
14. Genetic Control of Development44m
15. Genomes and Genomics1h 50m
16. Transposable Elements47m
17. Mutation, Repair, and Recombination1h 6m
18. Molecular Genetic Tools19m
- Genetic Cloning
  9m
- Methods for Analyzing DNA
  9m
19. Cancer Genetics29m
- Overview of Cancer
  21m
- Cancer Mutations
  7m
20. Quantitative Genetics1h 26m
21. Population Genetics50m
- Hardy Weinberg
  19m
- Allelic Frequency Changes
  31m
22. Evolutionary Genetics29m

15. Genomes and Genomics

Sequencing the Genome

Genetics

15. Genomes and Genomics

Sequencing the Genome

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1:18 minutes

Problem 1d

Textbook Question

How can we correlate the genome with RNA expression data in a tissue or a single cell?

Verified step by step guidance

Step 1: Understand the relationship between the genome and RNA expression. The genome contains the complete set of DNA instructions for an organism, while RNA expression reflects the active transcription of specific genes in a tissue or cell. RNA expression data can provide insights into which genes are being actively transcribed under specific conditions.

Step 2: Use sequencing technologies to gather data. To correlate the genome with RNA expression, perform whole-genome sequencing to identify the complete DNA sequence of the organism. Then, use RNA sequencing (RNA-Seq) to measure the levels of RNA transcripts in the tissue or single cell of interest.

Step 3: Map RNA-Seq data to the genome. Align the RNA-Seq reads to the reference genome using bioinformatics tools. This step helps identify which regions of the genome are actively transcribed and provides quantitative data on gene expression levels.

Step 4: Analyze differential expression. Compare RNA expression data across different tissues, cells, or conditions to identify patterns of gene activity. Statistical methods can be used to determine which genes are upregulated or downregulated in specific contexts.

Step 5: Integrate functional genomics data. Combine RNA expression data with other genomic information, such as epigenetic modifications, transcription factor binding sites, or chromatin accessibility, to gain a deeper understanding of gene regulation and cellular function.

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Key Concepts

Here are the essential concepts you must grasp in order to answer the question correctly.

Genomics

Genomics is the study of the complete set of DNA, including all of its genes, within an organism. It involves analyzing the structure, function, evolution, and mapping of genomes. Understanding genomics is crucial for correlating genomic data with RNA expression, as it provides the foundational information about genetic sequences that can influence gene expression patterns.

Transcriptomics

Transcriptomics is the study of the transcriptome, which encompasses all RNA molecules, including mRNA, rRNA, and non-coding RNAs, produced in a cell or tissue at a specific time. By analyzing RNA expression data, researchers can determine which genes are actively being expressed and how their expression levels vary under different conditions, allowing for a correlation with genomic data.

Single-Cell Analysis

Single-cell analysis refers to techniques that allow for the examination of individual cells rather than bulk populations. This approach is essential for understanding heterogeneity in gene expression within tissues, as it reveals how different cells may express genes differently. Correlating genomic data with RNA expression at the single-cell level provides insights into cellular functions and disease mechanisms.

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Multiple Choice

Which of the following sequence techniques requires the use of vectors?

Dideoxy nucleotides (ddNTPs) are used in Sanger sequencing because they have what function?

You have discovered a new species of archaea from a hot spring in Yellowstone National Park. How would your strategy change if you were unable to grow the strain in culture?

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Textbook Question

You have discovered a new species of archaea from a hot spring in Yellowstone National Park.After growing a pure culture of this organism, what strategy might you employ to sequence its genome?

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Textbook Question

How do we know which contigs are part of the same chromosome?

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Textbook Question

Repetitive DNA poses problems for genome sequencing. What strategies can be employed to overcome these problems?