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Old 09-19-2012
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Default Gene expression in pancreatic ca. - which method used?

A study is undertaken to assess gene expression in pancreatic adenocarinoma to better understand its pathophysiology. Total RNA and mRNA from 10 specimens are labeled and hybridized with 5000 human genes. This reveals 150 genes with differential expression: 90 genes are upregulated, and 60 genes are downregulated; 15 genes are previously undescribed. What method was most likely used to obtain these results?

a) Array-based comparative genome hybridization (CGH)
b) Microarray gene expression analysis
c) Northern blotting
d) Reverse-transcriptase polymerase chain reaction (RT-PCR)
e) Serial analysis of gene expression (SAGE)
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Quote:
Originally Posted by Casandra View Post
A study is undertaken to assess gene expression in pancreatic adenocarinoma to better understand its pathophysiology. Total RNA and mRNA from 10 specimens are labeled and hybridized with 5000 human genes. This reveals 150 genes with differential expression: 90 genes are upregulated, and 60 genes are downregulated; 15 genes are previously undescribed. What method was most likely used to obtain these results?

a) Array-based comparative genome hybridization (CGH)
b) Microarray gene expression analysis
c) Northern blotting
d) Reverse-transcriptase polymerase chain reaction (RT-PCR)
e) Serial analysis of gene expression (SAGE)

really tough and nice question.....many of the options are not known to me at all...

i'm answering with pure guess.......C) northern blotting.....
but thinking of SAGE too...

waiting for your valuable explanation...please also post briefly abt the remaining options too
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up regulation and down regulation... hmmm

Just a wild guess a) CGH though i dont know what it is

or I would go with d) RT-PCR

what is the ans???/
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A study is undertaken to assess gene expression in pancreatic adenocarinoma to better understand its pathophysiology. Total RNA and mRNA from 10 specimens are labeled and hybridized with 5000 human genes. This reveals 150 genes with differential expression: 90 genes are upregulated, and 60 genes are downregulated; 15 genes are previously undescribed. What method was most likely used to obtain these results?

a) Array-based comparative genome hybridization (CGH)
b) Microarray gene expression analysis
c) Northern blotting
d) Reverse-transcriptase polymerase chain reaction (RT-PCR)
e) Serial analysis of gene expression (SAGE)
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I would go with "Microarray gene expression analysis
Plz don't ask me why because i also don't know why
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experimental part of exam questions
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A study is undertaken to assess gene expression in pancreatic adenocarinoma to better understand its pathophysiology. Total RNA and mRNA from 10 specimens are labeled and hybridized with 5000 human genes. This reveals 150 genes with differential expression: 90 genes are upregulated, and 60 genes are downregulated; 15 genes are previously undescribed. What method was most likely used to obtain these results?


c) Northern blotting
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Default C is the answer

Quote:
Originally Posted by Casandra View Post
A study is undertaken to assess gene expression in pancreatic adenocarinoma to better understand its pathophysiology. Total RNA and mRNA from 10 specimens are labeled and hybridized with 5000 human genes. This reveals 150 genes with differential expression: 90 genes are upregulated, and 60 genes are downregulated; 15 genes are previously undescribed. What method was most likely used to obtain these results?

a) Array-based comparative genome hybridization (CGH)
b) Microarray gene expression analysis
c) Northern blotting
d) Reverse-transcriptase polymerase chain reaction (RT-PCR)
e) Serial analysis of gene expression (SAGE)
C is the answer
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Arrow C

I will go with Northern blotting, since the questions says, RNA samples are being used to access gene expression.
The only others I can exclude is RT-PCR and Microarray
not sure about the other options
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Default correct answer :)

The answer is b) Microarray gene expression analysis

Microarray gene expression analysis uses multiplex hybridization assays to measure the relative abundance of thousands of gene transcripts simultaneously.

as for C) - Northern blotting provides a measure of the transcription level of a specific gene by hybridizing a gene or a cDNA probe to RNA prepared from a specific tissue or cell line. The RNA is size-fractionated on a gel, allowing the specific size of the RNA transcript to be estimated. It does not examine the expression pattern of multiple genes simultaneously.
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Quote:
Originally Posted by Casandra View Post
The answer is b) Microarray gene expression analysis

Microarray gene expression analysis uses multiplex hybridization assays to measure the relative abundance of thousands of gene transcripts simultaneously.

as for C) - Northern blotting provides a measure of the transcription level of a specific gene by hybridizing a gene or a cDNA probe to RNA prepared from a specific tissue or cell line. The RNA is size-fractionated on a gel, allowing the specific size of the RNA transcript to be estimated. It does not examine the expression pattern of multiple genes simultaneously.
thanks for the question and explanation.....
but can you give little explanation:sorry: of A,D,E options as well.....
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Cassandra, can we say that by measuring the relative abundance of thousands of genes in Microarray gene expression, we are measuring the rate of expression? Since we know from your explanation that Northern blot would measure transcription level?
Just asking so I can get a better concept about their difference. So far, I am sure about a major difference between the two, which is the sheer amount of gene transcripts (in thousands) which Microarray can simulataneously evaluate, and the transcription level of a single gene evaluated by Northern Blot.

Quote:
Originally Posted by Casandra View Post
The answer is b) Microarray gene expression analysis

Microarray gene expression analysis uses multiplex hybridization assays to measure the relative abundance of thousands of gene transcripts simultaneously.

as for C) - Northern blotting provides a measure of the transcription level of a specific gene by hybridizing a gene or a cDNA probe to RNA prepared from a specific tissue or cell line. The RNA is size-fractionated on a gel, allowing the specific size of the RNA transcript to be estimated. It does not examine the expression pattern of multiple genes simultaneously.
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Quote:
Originally Posted by dockhi View Post
Cassandra, can we say that by measuring the relative abundance of thousands of genes in Microarray gene expression, we are measuring the rate of expression? Since we know from your explanation that Northern blot would measure transcription level?
Just asking so I can get a better concept about their difference. So far, I am sure about a major difference between the two, which is the sheer amount of gene transcripts (in thousands) which Microarray can simulataneously evaluate, and the transcription level of a single gene evaluated by Northern Blot.
hmm..I'm sorry but I'm not sure if understand what you mean by "rate of the expression"...? you mean upregulated/downregulated?
the main idea of this question was simultaneous hibridization - we don't have it in Northern blotting (where we use hibrids for 1 particular gene).
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Quote:
Originally Posted by Casandra View Post
hmm..I'm sorry but I'm not sure if understand what you mean by "rate of the expression"...? you mean upregulated/downregulated?
the main idea of this question was simultaneous hibridization - we don't have it in Northern blotting (where we use hibrids for 1 particular gene).
Yes, yes. That's what I was asking. Northern blot won't measure upregulation/downregulation of a gene right? Just wanted to reinforce their difference, that's why I asked. No matter how much I do, it sounds alien to me at some sad point! Thank you for the questions!
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