Question: Quantifying mRNA level
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gravatar for Natasha
19 months ago by
Natasha30
Natasha30 wrote:

Hello,

How do we quantify the mRNA level of a gene present in a tissue? I am looking for the absolute mRNA levels of certain genes present in the skeletal tissue. Any help would be highly appreciated

rna-seq chip-seq • 677 views
ADD COMMENTlink modified 19 months ago by kristoffer.vittingseerup2.2k • written 19 months ago by Natasha30
1
gravatar for kristoffer.vittingseerup
19 months ago by
European Union
kristoffer.vittingseerup2.2k wrote:

If you work with human data I would recomend the GTEx protal where you can se the gene expression across most tissues

ADD COMMENTlink written 19 months ago by kristoffer.vittingseerup2.2k
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gravatar for Hussain Ather
19 months ago by
Hussain Ather940
National Institutes of Health, Bethesda, MD
Hussain Ather940 wrote:

A very general question. Could you be more specific? Microarrays can be used in which, generally, mRNA from a tissue/cell line is used in creating samples that converted to a large number of DNA sequences that are immobilized onto a solid surface in an ordered array. (source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC444812/)

ADD COMMENTlink written 19 months ago by Hussain Ather940

I am trying to get a measure of the level of enzymes, catalyzing a set of reactions in the glycolysis pathway ,from the mRNA levels.The authors of this paper have discussed microarray provides relative levels, whereas RNAseq analysis gives absolute gene expression levels (with relevance to yeast). I would like to know if one can obtain the absolute levels for the genes present in human tissue.If yes,where can we look up for this information?

ADD REPLYlink written 19 months ago by Natasha30

RNA-Seq provides expression levels in terms of counts of expressed transcripts that can be related to transcripts per cell and thus an absolute level.

The paper you linked has this quote. It is true that you get a count value with RNAseq but I doubt that is an absolute measurement. It is a digital measurement as opposed to microarrays where you have to convert an analog (Intensity) measurement to a digital value.

Note: I suspect the word absolute is being used as an adjective, meaning not relative or comparative.

ADD REPLYlink modified 19 months ago • written 19 months ago by genomax70k

Thanks a lot for the response.By absolute I meant not comparitive/not a ratio .(for example,a diseased state vs control/normal )

ADD REPLYlink written 19 months ago by Natasha30
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gravatar for genomax
19 months ago by
genomax70k
United States
genomax70k wrote:

You can look up gene expression values for normal human tissues via Illumina body map expression atlas page. Click on the organism parts link in left column. You can then select just skeletal muscle tissue in the dialog box that opens.

ADD COMMENTlink modified 19 months ago • written 19 months ago by genomax70k

Thanks a lot for providing the link.I am also looking for the expression levels in pancreatic tissue.I couldn't find the classification in the above mentioned page.Could you please help?

ADD REPLYlink written 19 months ago by Natasha30
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