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Forum: Sample Prep / Library Generation 04-29-2014, 07:04 PM
Replies: 1
Views: 1,543
Posted By Gina_P
Illumina Nextera Mate Pair libraries.

I am curious about the directions for the Zymo Genomic DNA Clean & Concentrator recommended by the Illumina kit. It says to add 2 volumes of the DNA Binding Buffer to the tagmentation reaction and...
Forum: Sample Prep / Library Generation 05-07-2013, 05:58 AM
Replies: 3
Views: 1,708
Posted By Gina_P
We carried the libraries through despite the odd...

We carried the libraries through despite the odd appearance of the beads which seems to be not unusual after all, and got less than 99.5% rRNA contamination with Oryza sativa using the plant leaf...
Forum: Sample Prep / Library Generation 03-28-2013, 10:09 AM
Replies: 3
Views: 1,708
Posted By Gina_P
Beads sticking to tube during Ribo-Zero protocol

Hi all. I noticed that the Ribo-Zero magnetic beads tend to stick to the sides of the tube after you add your RNA sample and mix with pipetting and vortexing, and that this effect carries on through...
Forum: Sample Prep / Library Generation 01-11-2013, 12:35 PM
Replies: 4
Views: 1,227
Posted By Gina_P
Ah I see. Thanks!

Ah I see. Thanks!
Forum: Sample Prep / Library Generation 01-11-2013, 12:22 PM
Replies: 4
Views: 1,227
Posted By Gina_P
Hm. That could be it. It says the previous wells...

Hm. That could be it. It says the previous wells are around 200 pg/uL, so I'm not sure, unless some of that sample didn't even get measured and just went into the empty wells. Would it be bunched...
Forum: Sample Prep / Library Generation 01-11-2013, 10:06 AM
Replies: 4
Views: 1,227
Posted By Gina_P
Anyone know what this peak is on my BA trace?

This is an RNA pico chip and the well is supposed to be empty.
Forum: Sample Prep / Library Generation 01-03-2013, 05:52 AM
Replies: 4
Views: 2,209
Posted By Gina_P
Hi Phillip, thanks for your answer. I used...

Hi Phillip, thanks for your answer. I used RNAClean Ampure beads to recover my RNA - my experiences in the past with these beads has been good so I'm not sure if this step is the problem. I am in...
Forum: Sample Prep / Library Generation 01-02-2013, 07:19 AM
Replies: 4
Views: 2,209
Posted By Gina_P
Getting enough mRNA after RiboZero

Happy new year, everyone. I am posting to receive any advice you have for me regarding an issue I'm having with RiboZero plant leaf! I am using the kit for RNA extracted from Oryza sativa. I've...
Forum: Sample Prep / Library Generation 01-16-2012, 12:25 PM
Replies: 3
Views: 4,702
Posted By Gina_P
I have used SYBR gold with great success, mixed...

I have used SYBR gold with great success, mixed into the gel as Illumina suggests. I used Benchtop ladder, which was also suggested in the manual, which does resolve quite clearly. It could be that...
Forum: Illumina/Solexa 01-12-2012, 12:12 PM
Replies: 1
Views: 10,841
Posted By Gina_P
Length of P5 and P7 adapters from Illumina

Hi all,
I'm wondering how long the adapters are from the Illumina TruSeq kit. I am having a really hard time finding this number! Thanks.
Forum: Sample Prep / Library Generation 01-06-2012, 03:04 PM
Replies: 11
Views: 4,053
Posted By Gina_P
Here's the new BA result with smaller fragment...

Here's the new BA result with smaller fragment size. There's still some problem with sample 9. For now, I'm not going to put it on the sequencer. It looks like the DNA is dragging along some...
Forum: Sample Prep / Library Generation 01-06-2012, 09:12 AM
Replies: 11
Views: 4,053
Posted By Gina_P
Hm, good point about the concentration. Thanks...

Hm, good point about the concentration. Thanks for your help. I'm going to prep the other cuts today.
Forum: Sample Prep / Library Generation 01-06-2012, 08:56 AM
Replies: 11
Views: 4,053
Posted By Gina_P
I cut from about 500 - 600, which was by...

I cut from about 500 - 600, which was by accident. I meant to cut from 400 - 500. I have additional gel slices from 400 - 500 range saved in my fridge.
Forum: Sample Prep / Library Generation 01-06-2012, 08:51 AM
Replies: 11
Views: 4,053
Posted By Gina_P
I used the whole-genome resequencing protocol for...

I used the whole-genome resequencing protocol for Covaris:
40 seconds, 10% duty cycle, 5.0 intensity, 200 bursts per second, frequency sweeping mode, 6 degree temperature.

I started with 1 ug...
Forum: Sample Prep / Library Generation 01-06-2012, 07:53 AM
Replies: 11
Views: 4,053
Posted By Gina_P
Unfortunately I don't... For now, I have recut...

Unfortunately I don't... For now, I have recut the gels below my original extractions. I used the same shearing protocol on Covaris that I have used in the past, with good results, and I have never...
Forum: Sample Prep / Library Generation 01-06-2012, 05:42 AM
Replies: 11
Views: 4,053
Posted By Gina_P
Hi DMO, Thanks for answering me. I have a...

Hi DMO,

Thanks for answering me. I have a BioA QC. There are a few libraries that need to be cleaned up.

Also, apologies for being vague - this is for Illumina 2x50 sequencing!
Forum: Sample Prep / Library Generation 01-05-2012, 11:05 AM
Replies: 11
Views: 4,053
Posted By Gina_P
Fragment size limit

Hi all, I have some libraries with fragments that look a bit on the large side (650 - 700 bp including adaptors) for re-sequencing. Should I just use these libraries anyway? Or possibly redo gel...
Forum: Sample Prep / Library Generation 12-26-2011, 04:18 PM
Replies: 5
Views: 7,853
Posted By Gina_P
Hi, it could be pipetting errors, but more likely...

Hi, it could be pipetting errors, but more likely you simply have a bit of batch variation from Sigma so that it's not exactly 400 ng/uL. However, I don't have any experience with these stocks so...
Forum: Sample Prep / Library Generation 12-26-2011, 01:50 PM
Replies: 49
Views: 73,008
Posted By Gina_P
I use 80% ethanol, and also, I have let my beads...

I use 80% ethanol, and also, I have let my beads dry to the point of cracking (15 minutes) and have seen no ill results from that. I always have gobs of library for sequencing. However, it's good...
Forum: Introductions 12-06-2011, 05:24 AM
Replies: 0
Views: 720
Posted By Gina_P
Hello from New York!

Hi everyone! I'm a technician working with Chlamydomonas reinhardtii (and getting started with Oryza sativa, though having some early setbacks in growth techniques... :P).

I started using the...
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