Genome Sequencing Analysis Quiz

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What is the purpose of step 1 in the chromatin immunoprecipitation experiment?

To isolate DNA after reverse cross-linking

To shear chromatin into 200–500 bp DNA fragments

To precipitate RNA polymerase II

To cross-link proteins to DNA and proteins to proteins (correct)

In the results from mouse embryonic stem cells, what does the left plot indicate about RNA polymerase II transcription?

Transcription in the antisense direction only

Transcription with no specific directionality

Transcription only in the sense direction

Transcription in both directions (correct)

What is the purpose of using an anti-RNA polymerase II antibody in step 3 of the experiment?

To isolate DNA after reverse cross-linking

To shear chromatin into fragments

To precipitate RNA polymerase II and its linked DNA (correct)

To sequence DNA using massively parallel sequencing

What is the main outcome of chromatin immunoprecipitation using an antibody to RNA polymerase II?

Identifying divergent transcription from CpG island promoters Signup and view all the answers

Which step involves reverse cross-linking and isolating DNA in the chromatin immunoprecipitation experiment?

Step 4 Signup and view all the answers

Why is the sonication step needed in the chromatin immunoprecipitation experiment?

To solubilize chromatin and shear it into fragments Signup and view all the answers

What is the purpose of chromatin immunoprecipitation (ChIP) technique?

To detect binding of specific proteins to specific DNA sequences in vivo Signup and view all the answers

In immuno-fluorescence, what is used to localize antigens in cells?

Specific antibodies coupled to fluorescent dye Signup and view all the answers

What is the main function of immuno-precipitation technique?

To isolate proteins associated with specific antibodies Signup and view all the answers

Which technique involves a combination of immuno-precipitation, PCR, and DNA sequencing?

ChIP (chromatin immunoprecipitation) Signup and view all the answers

What is the purpose of immuno-precipitation in the context of antibody production?

To hook antibodies to large beads for isolating proteins Signup and view all the answers

Which technique is specifically used to detect where a protein associates with the genome?

Chromatin immunoprecipitation (ChIP) Signup and view all the answers

What does the plot of the number of reads over each position in genome represent?

The level of synthesis of RNA over each locus of genome Signup and view all the answers

How are antibodies defined?

Proteins produced to combat invading exogenous proteins Signup and view all the answers

What is the characteristic feature of monoclonal antibodies?

Each clone produces a unique and highly specific antibody Signup and view all the answers

How can polyclonal antibodies be obtained?

By tricking animals to produce them using antigens Signup and view all the answers

In antibody production, how can highly specific antibodies against a protein of interest be obtained?

By isolating single clones of B-lymphocytes to produce monoclonal antibodies Signup and view all the answers

What is the purpose of injecting animals with antigens in antibody production?

To induce the production of multiple antibodies against the antigen Signup and view all the answers