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Old 10-31-2009, 07:58 AM   #1
Xi Wang
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Default mRNA-Seq protocol

Hi all,

I am now working on RNA-seq data. I am wonderint whether the standard Illumina mRNA-Seq protocol is updated or not from Jan 2008 to Sep 2009. If updated, what's the difference?

Thanks in advance.
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Old 11-02-2009, 08:48 AM   #2
antoniou
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The latest protocol on the Icon web site is dated from Sept 2009. I don't have the 2008 protocol so I cannot comment on the differences
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Old 11-02-2009, 05:20 PM   #3
Xi Wang
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Quote:
Originally Posted by antoniou View Post
The latest protocol on the Icon web site is dated from Sept 2009. I don't have the 2008 protocol so I cannot comment on the differences
Thanks. I think the protocol before Sept 2009 was not mature, so it was not published. I am just wondering that the data generated by different labs would have different data quality, and some substaintial biases. I really appreciate it if you or others could give some comments on it.
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Old 11-05-2009, 04:32 AM   #4
huguesparri
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2008 protocole and 2009 protocole are the same.
The only difference is that in the 2009 version, Illumina gives advices on how to extract/manipulate total RNA, asks for a RNA with RIN>8 and where in the protocole you can do Cold Storage option.

I joined the 2008 version to this message.
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File Type: pdf mRNA-Seq_SamplePrep_1004898_RevA.pdf (159.1 KB, 59 views)
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Old 11-05-2009, 04:49 AM   #5
Xi Wang
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Quote:
Originally Posted by huguesparri View Post
2008 protocole and 2009 protocole are the same.
The only difference is that in the 2009 version, Illumina gives advices on how to extract/manipulate total RNA, asks for a RNA with RIN>8 and where in the protocole you can do Cold Storage option.

I joined the 2008 version to this message.
Thank you very much!
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Old 11-05-2009, 06:41 AM   #6
Xi Wang
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Hi,

Anyone knows how to explain why the read distributions of a gene from two experiments are not the same (not the expression, even only one isoform)? It's normal or abnormal? Now we can discharge the protocol difference. I have no idea since I am not an experiment man. Thanks.
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