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Forum: Sample Prep / Library Generation 02-13-2015, 02:17 PM
Replies: 2
Views: 2,921
Posted By VanessaS
Is anyone else still experiencing issues with...

Is anyone else still experiencing issues with these kits?
Forum: Sample Prep / Library Generation 12-04-2012, 10:02 AM
Replies: 4
Views: 2,431
Posted By VanessaS
I'm also curious about this. We are being...

I'm also curious about this. We are being strongly encouraged to use nextera over Truseq for exome sequencing and I'd like to get some feedback before we jump in. My understanding is that the...
Forum: Sample Prep / Library Generation 02-07-2012, 12:27 PM
Replies: 3
Views: 2,653
Posted By VanessaS
Quantitate your libraries by qPCR, not BioA.

Quantitate your libraries by qPCR, not BioA.
Forum: SOLiD 10-04-2011, 03:06 PM
Replies: 3
Views: 2,263
Posted By VanessaS
There might be an issue with sequencing a 5500...

There might be an issue with sequencing a 5500 library on the solid 4?
Forum: SOLiD 10-04-2011, 02:48 PM
Replies: 5
Views: 1,989
Posted By VanessaS
How about in the waste bottle? If I recall...

How about in the waste bottle? If I recall correctly, if your filter is bad or if it is breached, they can go to waste. I've not heard of this happening on an E20 but we have had it happen on...
Forum: SOLiD 07-25-2011, 04:13 PM
Replies: 1
Views: 2,116
Posted By VanessaS
I have access, but have not ordered any yet. My...

I have access, but have not ordered any yet. My understanding is they will have to come do something nifty to the instrument and I've not had time to deal with it. Soon!
Forum: SOLiD 07-09-2011, 05:35 AM
Replies: 16
Views: 6,315
Posted By VanessaS
Two runs are done, the quality of the reads looks...

Two runs are done, the quality of the reads looks really good. From what I can tell. Its kind of hard to tell, other than the floaty dot and the green bars were together and up high. Who thought...
Forum: SOLiD 06-30-2011, 05:53 AM
Replies: 16
Views: 6,315
Posted By VanessaS
We are in the middle of our first two runs. ...

We are in the middle of our first two runs. Deposition is a breeze, tho we are having a harder time hitting the beads per panel we want. Getting the flowchip on is easy as pie, and its basically ...
Forum: SOLiD 06-18-2011, 04:34 AM
Replies: 15
Views: 4,838
Posted By VanessaS
I'll be doing one library soon, I look forward to...

I'll be doing one library soon, I look forward to hearing how you have optimized the protocol. Have you run any of the libraries on the instrument yet?
Forum: SOLiD 06-07-2011, 03:46 PM
Replies: 16
Views: 6,315
Posted By VanessaS
Our first 5500xl is due in the lab on June 13th....

Our first 5500xl is due in the lab on June 13th. Has anyone completed any runs yet? Especially paired end?
Forum: SOLiD 05-31-2011, 10:19 AM
Replies: 2
Views: 1,428
Posted By VanessaS
I believe we have had this, or something similar....

I believe we have had this, or something similar. We called the Bioinformatics FAS and he logged in and did his wizardry and fixed it.
Forum: SOLiD 05-17-2011, 07:57 PM
Replies: 1
Views: 1,793
Posted By VanessaS
Heck, I'd like to hear anything about any...

Heck, I'd like to hear anything about any completed runs done on the 5500 or 5500xl.
Forum: SOLiD 05-05-2011, 06:28 AM
Replies: 1
Views: 2,468
Posted By VanessaS
No idea if the NEB kits work, but for ChIPSeq on...

No idea if the NEB kits work, but for ChIPSeq on the SOLiD we use the regular fragment library kit, not the ChIPSeq kit, since we only process the ChIPped DNA and don't create it.
This kit is...
Forum: SOLiD 04-29-2011, 06:15 AM
Replies: 11
Views: 3,560
Posted By VanessaS
I think what you are looking for is on the WFA,...

I think what you are looking for is on the WFA, the p2#/p1# ratio.
Forum: RNA Sequencing 03-06-2011, 09:45 PM
Replies: 23
Views: 18,593
Posted By VanessaS
I'm not qualified to say anything is definite,...

I'm not qualified to say anything is definite, other than its not from shearing the cDNA. Maybe someone can comment on the kinds of biases, if any, introduced from enzymatic shearing of the RNA? We...
Forum: RNA Sequencing 03-05-2011, 06:13 AM
Replies: 23
Views: 18,593
Posted By VanessaS
In our protocol, the cDNA isn't fragmented, the...

In our protocol, the cDNA isn't fragmented, the RNA is.
Forum: SOLiD 02-18-2011, 07:57 AM
Replies: 45
Views: 9,479
Posted By VanessaS
Woohoo, Goldilocks and the three Bears, NGS style!

Woohoo, Goldilocks and the three Bears, NGS style!
Forum: SOLiD 02-18-2011, 05:59 AM
Replies: 45
Views: 9,479
Posted By VanessaS
Ok, now I'm going to be paranoid about the...

Ok, now I'm going to be paranoid about the Enricher doors, as well as the syringe. Not that I've had issues with the doors but now I'll worry just for good measure.:( The incorrect times are a pet...
Forum: SOLiD 02-09-2011, 10:10 AM
Replies: 8
Views: 2,371
Posted By VanessaS
Amen Brotha, testify! This run... was actually a...

Amen Brotha, testify! This run... was actually a re-run from when the flowcell on the other instrument died. On the same samples. Twice.( it didnt really die, turns out it was the thingamajig that...
Forum: SOLiD 02-09-2011, 08:37 AM
Replies: 8
Views: 2,371
Posted By VanessaS
Yes this was with v4 chem. Our syringe bit the...

Yes this was with v4 chem. Our syringe bit the dust......
Forum: SOLiD 02-09-2011, 04:36 AM
Replies: 8
Views: 2,371
Posted By VanessaS
We had a similar occurrence. When I saw the...

We had a similar occurrence. When I saw the bubble, I panicked thinking everything was ruined! Apparently, according to my FAS, the flowcell maintains moisture and humidity so even though a large...
Forum: Sample Prep / Library Generation 02-02-2011, 04:21 AM
Replies: 6
Views: 4,991
Posted By VanessaS
Eww. Looks very degraded to me. I don't...

Eww. Looks very degraded to me.
I don't have any experience prepping PFA samples, nor with prokaryote samples, but if this is to judge the quality of your Total RNA, before library prep I'd...
Forum: SOLiD 02-02-2011, 04:12 AM
Replies: 45
Views: 9,479
Posted By VanessaS
Hmmm. So you gotta make the oil, that takes 15...

Hmmm. So you gotta make the oil, that takes 15 min or so, and have to let that degas for 30 min. You have to defrost your ePCR stuff, which can be going at the same time. You need to dilute your...
Forum: Sample Prep / Library Generation 01-25-2011, 02:31 PM
Replies: 1
Views: 2,641
Posted By VanessaS
Sure Select on Illumina....

I just had a little chat with the sales rep for Illumina and he was telling me some pretty fantastic things about the HiSeq, with regards to exon capture and sample throughput. I'd like to know...
Forum: SOLiD 01-25-2011, 02:15 PM
Replies: 40
Views: 9,716
Posted By VanessaS
At the Sequencing at the Tipping Point...

At the Sequencing at the Tipping Point Conference, back in December, they were saying the new file format would be .xqs (or maybe it was .xsq?)
Its a binary file format, with one file per lane. ...
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