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Tech Summary: ABI's SOLiD (Seq. by Oligo Ligation/Detection), UPDATED for v2.0

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  • #16
    Originally posted by genseq
    "How can the color space be translated into sequence, if the first position be one out of 4 bases?"

    Look at position 0 (primer n-1)!
    Thanks!

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    • #17
      tnank you for the information!

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      • #18
        hi

        thanks for the information!

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        • #19
          Hi,

          I'm new to SOLiD technology. Can it be used to sequence transcriptom?

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          • #20
            Yes, why not?

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            • #21
              Because I can only see examples for genomic DNA sequencing in the flowchart on the previous page.

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              • #22
                Ok, I guess this thread should be updated... Of course anything that can be converted into DNA can be sequenced, I am not sure if they have the kits already but you can read more here:
                http://www3.appliedbiosystems.com/AB...ysis/index.htm

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                • #23
                  Thank you very much, Chipper! It's just released. Great!

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                  • #24
                    Great explanations of the color-space and dibase sequencing.
                    There is an error though in both Fig.5 of the sticky and Fig.2 of the accompanying SOLiD_Dibase_Sequencing_and_Color_Space_Analysis.pdf - which makes the understanding of the logic difficult.
                    For the red color, the 4 dinucleotides interrogated by it are listed as "TA CG GC TA" - where the first TA should be AT.
                    (it just happens that the example in Fig.5/2 starts with AT and it has a red circle associated with it - which makes no sense when you look it in the table above it).
                    I just thought I might mention this, to make it easier for others to understand the decoding process.

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                    • #25
                      Hello.
                      I am studying Biotechnolgy and currently doing a coursework about -Modern Methods of DNA-sequencing-.
                      Thanks for this helpful explanation, Eco. It realy helped me.
                      Unfortunately I have problems to understand step 3 in figure 4. Is a Phosphate added to prevent that a Ligation continues?If yes, why? Does it mean that only strangs that start with TA are sequenced in this example. I thought that all 16 combinations have been added.
                      Or is it just for the case that nothing bound to the bead (seems very unplausible too me)?
                      Thanks a lot
                      Last edited by Svenno; 06-13-2009, 12:13 AM.

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                      • #26
                        Hello, nice to come here to obtain an access to new sequencing technology

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                        • #27
                          I'm pretty sure it hasn't been mentioned and it's definitely not anywhere on the website but I found out that the barcode is sequenced separately. Turns out there is another universal sequence in between the sequence of interest and the barcode. Another set of universal primers are used to sequence just the barcode. I asked the guy at my campus's nucleic acid facility and he had a manual which illustrated it very well. If anyone finds an online version please post.

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                          • #28
                            Perhaps this 4 page article by LifeTech/ABI is what you want. It shows the barcode and mentions that there are two sequencing steps for single runs and three steps for paired runs.

                            http://www3.appliedbiosystems.com/cm...cms_057554.pdf

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                            • #29
                              Originally posted by westerman View Post
                              Perhaps this 4 page article by LifeTech/ABI is what you want. It shows the barcode and mentions that there are two sequencing steps for single runs and three steps for paired runs.

                              http://www3.appliedbiosystems.com/cm...cms_057554.pdf
                              Hi Rick,
                              That is a new feature. Previously there was no bar coding for mate pair runs for the SOLiD--only fragment. But the marketing bulletin you reference above clearly shows a bar-coded mate pair amplicon.

                              Even more bizarre, the bar code is being read from the P2 primer. This makes no sense within the standard SOLiD amplicon paradigm because P2 is one of the ePCR primers. Nothing can be outside P2 if you amplify with P1 and P2.

                              Will have to ask our FAS what is up with that.

                              --
                              Phillip

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                              • #30
                                Thanks, this information was really helpful! We have been learning about next generation sequencing technologies in class, but our professor's explanations were very vague. I have also read the protocol for illumina/solexa on this forum which was very helpful was well.

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