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Search: Posts Made By: cmawhinney
Forum: Bioinformatics 04-05-2012, 10:44 AM
Replies: 1
Views: 1,729
Posted By cmawhinney
Question Maq error after using cutadapt

I have some small RNA data, generated with a GAIIx, and I need to trim the adapter sequence off the 3' end. I used cutadapt, which seemed easy enough, but now I can't get the trimmed sequences to...
Forum: Illumina/Solexa 08-02-2011, 03:17 PM
Replies: 0
Views: 2,178
Posted By cmawhinney
Sequencing ChIPseq samples prepped with micrococcal nuclease?

I was wondering if anyone has had any issues sequencing samples that were prepped using a micrococcal nuclease?

I ran a flow cell that contained mostly these types of samples and the T channel was...
Forum: Core Facilities 03-15-2011, 02:24 PM
Replies: 5
Views: 3,055
Posted By cmawhinney
how MUCH data do you give back?

Hi all!

We're a relatively new core running Illumina's GAIIx and I'm trying to deal with the issue of data. Typically once the customers run finishes and if they want me to do the alignment I run...
Forum: Illumina/Solexa 01-19-2011, 12:24 PM
Replies: 32
Views: 22,709
Posted By cmawhinney
I'm hoping to go gel free for all of my library...

I'm hoping to go gel free for all of my library preps (I've had some cross contamination issues that I think is coming from the gel step) and would love to try the double spri method.

I've used...
Forum: Sample Prep / Library Generation 12-10-2010, 08:18 AM
Replies: 3
Views: 2,562
Posted By cmawhinney
My primer concentration varied depending on the...

My primer concentration varied depending on the concentration of the ChIP DNA. For example, Illumina recommends 25uM primers for 10ng of DNA. If my sample was 1ng I would dilute the primers 10...
Forum: Sample Prep / Library Generation 12-10-2010, 07:23 AM
Replies: 3
Views: 2,562
Posted By cmawhinney
ChIPseq: Strange Peaks after Gel Extraction

x-posted from general: i didn't realize i posted in the wrong forum until today.

Hi,

I've been doing ChIP library preps for a good while now and never before have I seen anything like this and...
Forum: Sample Prep / Library Generation 12-09-2010, 01:16 PM
Replies: 9
Views: 4,698
Posted By cmawhinney
I try and dilute my primers a bit, especially if...

I try and dilute my primers a bit, especially if I don't have the recommended 10ng of ChIP DNA to play with, ie, if I have 2ng of DNA then I will likely dilute my primers 1:5. I then clean up my PCR...
Forum: General 12-09-2010, 01:04 PM
Replies: 1
Views: 1,916
Posted By cmawhinney
ChIPseq: Strange Peaks after Gel Extraction

Hi,

I've been doing ChIP library preps for a good while now and never before have I seen anything like this and was hoping someone maybe has?

I am seeing two peaks in my samples. One at around...
Forum: Illumina/Solexa 12-01-2010, 08:02 AM
Replies: 28
Views: 12,127
Posted By cmawhinney
Thanks for this info. Super helpful. How are...

Thanks for this info. Super helpful. How are you using the Ambion frag buffer then? Are you starting with 50 - 100ng of mRNA? Are you following Ambions protocol for 70C x 15 minutes? And in what...
Forum: Illumina/Solexa 09-08-2010, 08:29 AM
Replies: 28
Views: 12,127
Posted By cmawhinney
This is exactly what I was looking for! Thank...

This is exactly what I was looking for! Thank you so much!
Forum: Illumina/Solexa 09-07-2010, 07:48 PM
Replies: 28
Views: 12,127
Posted By cmawhinney
Hi all, I am looking at the directional...

Hi all,

I am looking at the directional protocol now and see that it requires the v1.5 sRNA 3' Adaptor. Which adaptor is this? I'm assuming it is NOT the Small RNA 3' adaptor.

Thanks!
Forum: Illumina/Solexa 08-12-2010, 09:48 AM
Replies: 17
Views: 9,200
Posted By cmawhinney
^ I have not but this was something that was just...

^ I have not but this was something that was just suggested to me and I might give it a try. For generating the matrix file, how many tiles do you think is adequate? And do you do all cycles or can...
Forum: Illumina/Solexa 08-12-2010, 08:33 AM
Replies: 17
Views: 9,200
Posted By cmawhinney
We ended up spiking with 30% PhiX (at 7.5pM)...

We ended up spiking with 30% PhiX (at 7.5pM) because we realized spiking in such a low % of PhiX wouldn't help. Doesn't look like the 30% helped much either since Pipeline is having a hard time with...
Forum: Illumina/Solexa 07-21-2010, 10:01 AM
Replies: 17
Views: 9,200
Posted By cmawhinney
When do you add your PhiX to the sample? I'm...

When do you add your PhiX to the sample? I'm assuming if it's already at a pM concentration then it's after denaturation and you're adding PhiX diluted in HT1 to your samples that are denatured and...
Forum: Sample Prep / Library Generation 03-24-2010, 07:55 AM
Replies: 3
Views: 4,027
Posted By cmawhinney
Spiking phiX into multiplexed libraries as well as barcode sequences

Hi all, I have a two part question:

I am wondering if anyone here has tried spiking phiX into their multiplexed library samples? I heard from a couple people (as well as an Illumina rep) that...
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