Index

[suludana]

Hi,
someone had news about the launch of the indexing kit?

Thanks

[monad]

It is now officially available (see below).

Multiplexing Sample Preparation
Oligonucleotide Kit
Kitted oligonucleotides used to prepare up to
96 samples for multiplexed sequencing.
PE-400-1001

Multiplexing Sequencing Primers
and PhiX Control Kit
Kitted multiplexing sequencing primers, multiplexing
control DNA, and buffer set. Sufficient for up to
10 Genome Analyzer runs.
PE-400-1002

[ShirleyHS]

Hi,

Has anyone tried the indexing? Any success? difficulties? Will be glad to receive insights as far as sample prep / sequencing / analysis are concerned.

Shirley.

[floor121]

I try to sample prep with the index kit last month, it seems work well and the workflow is almost the same as PE library prep except PCR, however, the index libraries cannot run with normal PE libraries, it is not easy to construct 7 libraries to run at the same time.

[suludana]

I also see this problem.
Moreover the kits of sample preparation do not adjust well (in number of samples) to the kits of index…

[ShirleyHS]

Any experience with analyzing the indexed samples? Are they well-separated?

[scooterdog]

I've heard that the cost for indexing is $30 more on a per-sample basis. So to index 12 samples on a single lane, is it a one-sample library prep cost (say $370 for doing a library prep on 12 samples) or is it 12 times the single-sample library prep ($370 x 12 = $4,440) just with the index?

[huguesparri]

The library generation cost is not reduced (it's a bit higher) as you have to go through the entire library preparation protocole. The indexing is taking place in the last PCR step.
You earn money on the cluster and sequencing part: you only use 1 paired end cluster generation kit and 1 (+ part of another one to sequence the indexing tag) sequencing kit for up to 96 samples.

[scooterdog]

Thanks huguesparri for the reply.

So if I understand correctly then for 84 samples (12 x 7 lanes) the library preparation alone would be some 84 x $370 = $31,080 for the library preparation alone, and of course the per-sample cost for the cluster-generation/SBS is cut down by a factor of 84... a very expensive experiment...

[huguesparri]

You can also try the "100 RXN Paired End Oligo Only Kit" (PE-102-1003).
Illumina's price is € 4.445,16 ( like 6000 US$ or so) for our department.
I didn't calculated if it's cheaper as it's depending on the price you have for the "non-Illumina's" supplies but it can be an option...

[bioinfosm]

Any experience with analyzing the indexed samples? Are they well-separated?

Yes.. the samples are well separated. Although I would think some index would be closer to a few others, making it useful to group selective indexes in a lane if thats an option

[Aaron Cooper]

This question is in response to the above comment that index reads cannot be done mixed in with PE libraries without indexes.

I am planning on doing SE 100 sequencing, but for multiple reasons I'd like to use a PE adapter with an index. The sequencing core at our institution accepts lanes for sequencing and will batch your library with several others to fill a flow cell. Does anyone know if it is possible with regard to the GAIIx/HiSeq 2000 instruments and Illumina software to get an index read if not all of the lanes have PE adapters?