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Forum: Illumina/Solexa 09-28-2011, 07:53 AM
Replies: 12
Views: 3,134
Posted By gogreen
I also would recommend against investing on a...

I also would recommend against investing on a GAIIx at this point. The Hiseq has been around for a couple of years already, so the GAIIs sound ancient in terms of the data generated and costs...
Forum: Sample Prep / Library Generation 09-27-2011, 01:09 PM
Replies: 26
Views: 29,471
Posted By gogreen
I've never isolated RNA from silkworm, but my...

I've never isolated RNA from silkworm, but my best guess is that it might be similar to the drosophila RNA. I'm sorry that I don't have any RNA profiles in my current lab. But a google search got me...
Forum: Sample Prep / Library Generation 05-12-2011, 02:10 AM
Replies: 6
Views: 3,572
Posted By gogreen
I have the same questions as pmiguel too, What do...

I have the same questions as pmiguel too, What do you mean by 'totally degraded' in the context? . I've sequenced libraries which were stored for over 3 months and everything was fine. I've seen a...
Forum: Sample Prep / Library Generation 05-12-2011, 02:01 AM
Replies: 5
Views: 2,954
Posted By gogreen
Hi Joe, I don't work on Roche library preps,...

Hi Joe,
I don't work on Roche library preps, but the problem sounds familiar! In my experience, the Ampure beads are very effective in recovering most of the stuff in the reaction, but when one lets...
Forum: Sample Prep / Library Generation 05-09-2011, 02:09 PM
Replies: 5
Views: 3,855
Posted By gogreen
hi Emongs, IMHO, the invitrogen magnet doesn't...

hi Emongs, IMHO, the invitrogen magnet doesn't work any better than other ones. I totally quit using invitrogen magnets and now use magnets which costs nothing compared to the terribly expensive...
Forum: Sample Prep / Library Generation 05-09-2011, 02:01 PM
Replies: 6
Views: 3,985
Posted By gogreen
When you say 612 bp, is it the mean insert size...

When you say 612 bp, is it the mean insert size or the size that was gel selected? If it was the selected size, you'd lose around 120 bp for the adapters on both ends which would explain why you get...
Forum: Sample Prep / Library Generation 05-09-2011, 10:35 AM
Replies: 5
Views: 3,855
Posted By gogreen
hi bunnymac, Probably you've figured out the...

hi bunnymac,
Probably you've figured out the issue already, but I just saw the bioanalyzer profile now and realized that it was a RNA Nano. When you say 4/6/8 ug, do you mean total RNA or mRNA? (I...
Forum: Sample Prep / Library Generation 05-08-2011, 07:05 AM
Replies: 1
Views: 1,599
Posted By gogreen
Hi Heidi, I would recommend a cleanup of gDNA...

Hi Heidi, I would recommend a cleanup of gDNA (columns, beads or phenol ChCl3) before you do library prep. If I got it right, you want to use the DNA for sequence capture before actual sequencing....
Forum: Sample Prep / Library Generation 05-08-2011, 06:57 AM
Replies: 6
Views: 3,985
Posted By gogreen
hi delphi_ote, Krobison was right with the point....

hi delphi_ote, Krobison was right with the point. If one uses Gel selection or other automated size selection methods, the size selected fragments are mostly in X±30 bp where X is the selected size. ...
Forum: Illumina/Solexa 10-04-2010, 02:20 AM
Replies: 16
Views: 8,279
Posted By gogreen
We are currently using the NEB master mix kit for...

We are currently using the NEB master mix kit for the illumina sample prep kit, I've prepared quite a lot of libraries with the kit and satisfied with the quality and ease of usage because it saves a...
Forum: 454 Pyrosequencing 04-12-2010, 08:30 AM
Replies: 10
Views: 4,296
Posted By gogreen
Hi Nickloman, I use the NEBnext sample prep kit...

Hi Nickloman, I use the NEBnext sample prep kit for the Illumina library prep. This works quite well for me and Its much cheaper than the Illumina reagents. I don't know about the Roche sample prep...
Forum: Illumina/Solexa 04-06-2010, 02:05 AM
Replies: 21
Views: 14,958
Posted By gogreen
I've no clue of why this happens. I tried the...

I've no clue of why this happens. I tried the enzyme again. This time with a longer enzyme inactivation step. I didnt clean up my reaction. But I still have difference between the gel and bioanalyzer...
Forum: Illumina/Solexa 03-30-2010, 01:24 AM
Replies: 32
Views: 22,865
Posted By gogreen
I think the cost of the library prep is quite...

I think the cost of the library prep is quite high for the SPRiworks. It would save a lot of hands on time for sure, but I wonder if the throughput that you get for that money is worth it!! The Broad...
Forum: Illumina/Solexa 03-12-2010, 01:39 AM
Replies: 21
Views: 14,958
Posted By gogreen
I used the enzyme for just testing the...

I used the enzyme for just testing the fragmentation and was pretty impressed with the fragment size on the gel. It was a focussed smear at 100-600 bp. But when I ran the samples on the bioanalyzer...
Forum: Sample Prep / Library Generation 03-10-2010, 06:24 AM
Replies: 23
Views: 17,216
Posted By gogreen
Hi Greigite, I see a similar band at 130 bp...

Hi Greigite,

I see a similar band at 130 bp in my sequencing library too! Did you figure out why this happens and any way to get rid of this? I tried going down on the adaptor concentration. But...
Forum: Sample Prep / Library Generation 03-09-2010, 11:48 PM
Replies: 26
Views: 29,471
Posted By gogreen
Hi Xi wang, I'm sorry if my question was...

Hi Xi wang, I'm sorry if my question was confusing. I meant about the 3 large rRNA subunits. Normally you see 2 of them for mammals and bacteria (In case of drosophila, 2 close peaks at the 18 S and...
Forum: Sample Prep / Library Generation 03-09-2010, 12:24 AM
Replies: 26
Views: 29,471
Posted By gogreen
Hi peromhc, Just got curious about the 3 peaks...

Hi peromhc,
Just got curious about the 3 peaks that you see in the profile. What is this organism??
Forum: Introductions 03-09-2010, 12:14 AM
Replies: 373
Views: 123,842
Posted By gogreen
Hi all, I am a technician in Heidelberg...

Hi all,
I am a technician in Heidelberg working on solexa single end & PE and RNA seq
gg
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