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

[JackYu]

Hi,

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

[hongbo]

hi

thanks for the information!

[islet_liang]

tnank you for the information!

[mcsol]

"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!

[mcsol]

Thanks for taking the time to explain this marvelous technology!
I have never used the SOLiD system, but I think I understand the gist of it. Just a couple of questions: How can the color space be translated into sequence, if the first position can be one out of 4 bases? Don't they have to know with what base they started with, in order to figure all downstream bases? And second question, in figure 4 (schematic), it appears as if primer n-2, -3, -4 coloring is off? It looks as if the read (for n-2) started at base +4?
Thanks so much!
And, oh, this is my first post... :-)

[ECO]

I've finally found the time to update this post for v2.0 chemistry. Enjoy.

[bogard]

You're right ! 5' last nucleotides !
I submit this question to SOLID staff. The answer : chemical cleavage/proprietary reagent.

[pmiguel]

[QUOTE=ECO;436]I couldn't tell you. I haven't come across that in my reading. I'm sure someone here (or maybe one of our ABI members? ) will chime in.



My guess would be that 'z' bases would be inosine. But that is almost pure speculation on my part.

--
Phillip

[bogard]

This is my first post..
Regarding SOLiD sequencing, I have a question : how are the three 3' last nucleotides, including the fluorophore, cleaved ? What is the cleavage agent ?

[JPC]

I think I get it now, because the n-1 reaction types the 3' base of the primer which is known, the first base of the clonal product is identified definitively, thanks DNAcowboy

[DNAcowboy]

This is my understanding, the 16 possible 2 base-combinations for the oligos are present in the mix, not only those 4 on their diagrams. Am I wrong?

[JPC]

Is there a fixed (or recommended) order for adding the oligos? I don’t understand why the first four oligos to be added would be CA CT GC GG (as suggested by the diagram) why would you not start with AA AC AG AT, hence identifying all the beads that start with an A, followed by a round of oligos starting with C etc

My suspicious mind tells me that there must be a reason for the presented order so I'm concerned there's something I'm not fully understanding?

[ECO]

SOLiD 2.0 has been released.

Basically the same as above with a few changes to the probe details...instead of 4,5 encoded probes it will use 1,2 encoded probes and a series of "bridge probes" that prevent backing up too far into the P1 primer region.

Still only 35bp reads max (7 ligations + 5 primers).

Will post more details as they become available. I've put the SOLiD data definitions in the first post.

[DNAcowboy]

Thanxx Eco. I should be visited soon by AB's representatives and should post some answers asap.

[ECO]

Thanks for the terrific explanation of the technology and the color space document. Very helpful. What are the "z" bases and how are they cleaved?

I couldn't tell you. I haven't come across that in my reading. I'm sure someone here (or maybe one of our ABI members? ) will chime in.

I have difficulties finding the SOLID instrument specs.
How long will be a run? How much data will it generate? Do we have these published somewhere?

I believe a run is on the order of ~7-8 days, depending on the application. (From www.in-sequence.com).

From ABI's website:
Read Length
--Fragment libraries - up to 35 bases
--Mate-paired libraries - 2 x 25 bases

Typical Mappable* Output/Slide
--Fragment libraries: 1-1.5GB
--Mate-paired libraries: 1.5-2 GB