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Old 11-26-2008, 05:16 AM   #1
mja
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Post barcodes for SOLiD small RNA Expression Kit

Does anyone know precisely how the barcodes embedded within ABI / Ambion's small RNA adapters are designed to work?

The 6nt barcoded regions appear to be buried deep within the adapters such that one needs to sequence a full 25nts of the 3' adapter (through what they call the "internal adapter" in the kit manual) in order to get to the barcodes. Given a 21nt small RNA, this would require a full 49 nts of reads to get to the barcode which does not seem feasible given the 35nt read-length of SOLiD runs. In the manual, it is stated that the barcodes are not yet supported by the SOLiD software but will be in the future. But it seems logical that one could manually separate different barcoded libraries by parsing differential adapter sequences at the end of the inserts for a given library.

for reference, I am referring to the SOLiD Small RNA expression kit marketed by ABI as cat # 4397682
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Old 11-26-2008, 05:41 AM   #2
solidifier
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The barcodes are read in a separate sequencing reaction using a different primer. After the 25 nt (or 35 nt) run, everything is re-set and a new primer is added. It's similar to how mate-pair works. Then software classifies the sequence based on the barcode from the same bead. Works great.
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Old 11-26-2008, 05:54 AM   #3
mja
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thanks solidifier, quite helpful.
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Old 04-24-2009, 04:24 AM   #4
blouro
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Question SOLiD™ Whole Transcriptome Expression Kits

Hi all,

is there any difference between the SOLiD™ small RNA and the Whole Transcriptome Expression Kits, besides the 10 to 16 possibles barcodes?

Is the "SOLiD™ Whole Transcriptome Expression Kits already in the market, so we can ask opnions about either kits?

Have this questions, because I was about to advance with SuperSAGE in 454, but if this kits are as good as they advertise, the advantages are obvious in many aspects.

All feedback are much welcome!
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Old 04-25-2009, 01:30 PM   #5
Chipper
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Hi,
yes the WT kit is available and is based on the small RNA kit. I have no idea on how it compares to SuperSAGE but it should give >100M aligned strand specific reads per slide.
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Old 04-27-2009, 09:56 AM   #6
blouro
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Quote:
Originally Posted by Chipper View Post
Hi,
yes the WT kit is available and is based on the small RNA kit. I have no idea on how it compares to SuperSAGE but it should give >100M aligned strand specific reads per slide.
Thanks a lot Chipper,

by any chance have you used any of these kits? I'm really looking forward for an opnion from a end-user of these kits. Experience tells me that what they sell sometimes is quite different from reality, as it has been seen with the all NG sequence systems implementations itself.

Opnions from someone that has used index reads in Solexa multiplexed sequencing are also much appreciated.

Cheers
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