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Sample Question Mid-2 Practical

The document contains instructions for three separate analyses: 1. Lookup genome sequence counts for influenza viruses in humans in Brazil and ebolaviruses of the Sudan species in humans in Africa from online databases. 2. Analyze a gene expression dataset from ArrayExpress including comparing gene expression between samples and identifying upregulated and downregulated genes. 3. Perform quality control on a FASTQ file using Galaxy and answer questions about sequence counts, lengths, GC content, per base sequence content, and overrepresented sequences.

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17 views

Sample Question Mid-2 Practical

The document contains instructions for three separate analyses: 1. Lookup genome sequence counts for influenza viruses in humans in Brazil and ebolaviruses of the Sudan species in humans in Africa from online databases. 2. Analyze a gene expression dataset from ArrayExpress including comparing gene expression between samples and identifying upregulated and downregulated genes. 3. Perform quality control on a FASTQ file using Galaxy and answer questions about sequence counts, lengths, GC content, per base sequence content, and overrepresented sequences.

Uploaded by

Labiba
Copyright
© © All Rights Reserved
Available Formats
Download as DOCX, PDF, TXT or read online on Scribd
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1. a.

Go to the genome database of #virus using the following link


https://www.ncbi.nlm.nih.gov/genomes/FLU/Database/nph-select.cgi?go=database
Find out how many sequences of influenza viruses are available for humans in Brazil.

Answer:

b. Go to the genome database of ebolaviruses using the following link


https://www.ncbi.nlm.nih.gov/genomes/VirusVariation/Database/nph-
select.cgi?taxid=186536
Find out how many sequences of ebolaviruses are available for sudan species, humans in Africa,
matrix protein from any sources

Answer:

2. Identify gene expression or other information using ArrayExpress or Expression Atlas as


instructed.
A. Go to Accession number: E-MTAB-4444 and answer the following questions
I. Name of the Experiment
II. Type of experiment
III. Organism
IV. What are the sample type?
V. How many samples
VI. What conditions?
B. Go to expression atlas of this experiment.
Compare confluent monolayer on collagen' at '7 day' vs 'freshly isolated' at '0 day'. Set log2
fold change to 8 and adjusted p value 0.01. Answer the following.
VII. How many genes upregulated?
VIII. How many genes downregulated?
IX. Name the genes that are upregulated.
X. What is the function of the gene which shows highest upragulation? Any two functions.

3. Using Galaxy do a QC test for the FASTQ file and answer the questions below.

I. How many total sequences are there in this file?


(1 mark)

II. What is the sequence length and GC%? (1 mark)


III. Is Per base sequence content for all reads bad? If
not, identify the positions which are good.
(2 marks)

IV. Average sequence length? (1 mark)

V. Do you get any Overrepresented sequences? If


yes, indicate counts and percentages of the
highest appeared sequences? (2 marks)

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