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Search took 0.00 seconds. Search: Posts Made By: csc
Forum: Ion Torrent 08-04-2013, 11:07 PM
Replies: 3
Views: 5,123
Posted By csc
Hi LindsayS, In my experience with a couple of...

Hi LindsayS, In my experience with a couple of panels (as well as some other groups who I have sequenced panels for) it seems to take ~2-3 weeks to have a custom panel delivered.
Forum: Illumina/Solexa 06-14-2011, 12:33 PM
Replies: 1
Views: 1,755
Posted By csc
The flow cells are different in that they have...

The flow cells are different in that they have alternative forms of grafted oligos which allow for the different types of cleavage/linearization chemistry seen in SR vs. PE.
Forum: Sample Prep / Library Generation 05-06-2011, 07:10 PM
Replies: 2
Views: 2,902
Posted By csc
One of the main differences between circligase I...

One of the main differences between circligase I and II is that circligase II is basically pre-adenylated which allows it to act more efficiently. So, to answer your question, no I don't add ATP to...
Forum: Illumina/Solexa 04-15-2011, 09:54 AM
Replies: 14
Views: 5,045
Posted By csc
Installation took about 3 days. Validation took...

Installation took about 3 days. Validation took about a week. We have had some problems with it so far but they have been mostly fluidic - I think all were clogged or broken solenoids. I don't...
Forum: Illumina/Solexa 04-07-2011, 03:26 PM
Replies: 4
Views: 2,621
Posted By csc
Hi D, You may have heard (or noticed) that...

Hi D,

You may have heard (or noticed) that there is a bit of base-bias in Solexa/Illumina based sequencing data. This tends to be of the anti-GC variety. One reason for this is library...
Forum: Sample Prep / Library Generation 03-29-2011, 12:45 PM
Replies: 11
Views: 6,252
Posted By csc
In terms of increasing concentrations leading to...

In terms of increasing concentrations leading to lower densities: Are you correctly following Illumina's recommendations for high concentration library denaturation/dilution? Excess hydroxide...
Forum: Illumina/Solexa 03-22-2011, 04:43 PM
Replies: 2
Views: 10,453
Posted By csc
I would hesitate to change the value from 0.6...

I would hesitate to change the value from 0.6 unless I had a good look at the normalized intensity values of each channel. Illumina claims that 0.6 is quite a conservative cutoff. I think changing...
Forum: Sample Prep / Library Generation 03-17-2011, 07:14 AM
Replies: 6
Views: 5,204
Posted By csc
Ok, I went and looked up the reference. I think...

Ok, I went and looked up the reference. I think I understand the confusion. Ideally, in some sort of assay, one would present the absolute amount of material used (or concentration given a fixed...
Forum: Sample Prep / Library Generation 03-17-2011, 04:20 AM
Replies: 6
Views: 5,204
Posted By csc
Just a quick observation. pM is a concentration....

Just a quick observation. pM is a concentration. pmol is an amount. Are you sure you have the units correct?
Forum: Illumina/Solexa 03-14-2011, 12:00 AM
Replies: 4
Views: 2,621
Posted By csc
Hi share, Good question. The brief answer...

Hi share,

Good question. The brief answer is: for one, not all GAs have the exact same parts in them (filters, mode scramblers are pieces I know can vary). Second, every GA is tuned/aligned by...
Forum: Illumina/Solexa 03-13-2011, 05:38 PM
Replies: 4
Views: 2,621
Posted By csc
1. Acceptable intensity ranges will vary a bit...

1. Acceptable intensity ranges will vary a bit from machine to machine and run to run.

2. 700-800K clusters/mm2 generally when using SCS2.8/RTA1.8 (or 2.9/1.9)

3. The above should apply for...
Forum: Illumina/Solexa 02-23-2011, 12:45 PM
Replies: 5
Views: 3,951
Posted By csc
I wouldn't be surprised if this was true. Since...

I wouldn't be surprised if this was true. Since the HiSeq derives its imaging system from the iScan, I would imagine that the HiScan should be capable of dual surface imaging with some minor...
Forum: SOLiD 02-14-2011, 01:50 PM
Replies: 11
Views: 3,300
Posted By csc
Mosaic Tech?

Mosaic Tech?
Forum: SOLiD 02-11-2011, 09:53 PM
Replies: 11
Views: 3,300
Posted By csc
From what I have read, Illumina does look like it...

From what I have read, Illumina does look like it actually owns some amount of bridge amp IP. Solexa and Lynx Therapeutics purchased solid phase amplification (bridge amplification) from Manteia SA...
Forum: Polonator 02-10-2011, 12:03 PM
Replies: 11
Views: 72,543
Posted By csc
I know someone who has one. The impression I get...

I know someone who has one. The impression I get is that it can't quite keep up with the throughput and read length of the major commercial platforms (just doesn't have the same R&D thrust behind...
Forum: Illumina/Solexa 01-28-2011, 09:21 PM
Replies: 3
Views: 2,329
Posted By csc
If you plan on using it a lot, it isn't an...

If you plan on using it a lot, it isn't an instrument I would try to run without a service contract. A single failed run can cost thousands of dollars in replacement reagents, let alone the cost of...
Forum: Illumina/Solexa 01-25-2011, 09:33 PM
Replies: 4
Views: 4,834
Posted By csc
That is correct, "0" means the read did not pass...

That is correct, "0" means the read did not pass filter and "1" means that it did.
Forum: Illumina/Solexa 01-16-2011, 07:44 PM
Replies: 2
Views: 3,264
Posted By csc
It will depend on how early you noticed that...

It will depend on how early you noticed that reagents ran out and what steps have occurred since they ran out. If you allow chemistry to occur without enough reagents (i.e. IMR or CLM), the phasing...
Forum: Illumina/Solexa 01-13-2011, 02:48 PM
Replies: 74
Views: 50,489
Posted By csc
Are we talking internally at Illumina or...

Are we talking internally at Illumina or commercial release? It looks like this spring it will be 600Gb officially (using 2x100bp) but it seems like all they have to do later in the year to get it...
Forum: Illumina/Solexa 01-12-2011, 11:30 PM
Replies: 74
Views: 50,489
Posted By csc
Well, not surprisingly, it looks like the most...

Well, not surprisingly, it looks like the most immediate improvement is going to be increased cluster density. Flatley says upgrades (software/reagents) this spring will give HiSeq 2000 throughput...
Forum: Illumina/Solexa 01-12-2011, 09:49 PM
Replies: 74
Views: 50,489
Posted By csc
I also think it is interesting that the MiSeq is...

I also think it is interesting that the MiSeq is apparently the progeny of the Avantome acquisition. I'm not sure what specific tech. they used from Avantome IP, perhaps the fluidics? I'm wondering...
Forum: Illumina/Solexa 01-12-2011, 02:28 PM
Replies: 13
Views: 6,701
Posted By csc
As konrad98 has said "Semi-ordered arrays" did...

As konrad98 has said "Semi-ordered arrays" did show up in some of Illumina's future higher throughput roadmaps but back then (perhaps two-ish years ago) the timeline indicated that it would be...
Forum: Illumina/Solexa 01-12-2011, 01:59 PM
Replies: 74
Views: 50,489
Posted By csc
James, I can confirm that it is a single lane...

James, I can confirm that it is a single lane system.
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