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Forum: Sample Prep / Library Generation 06-14-2018, 09:17 AM
Replies: 5
Views: 1,153
Posted By RickC7
Here is what my ATAC libraries look like. I agree...

Here is what my ATAC libraries look like. I agree that optimization of tagmentation enzyme amount or time should be considered.

What is you input amount? Are you starting with <50,000 cells?...
Forum: Sample Prep / Library Generation 06-13-2018, 11:14 AM
Replies: 5
Views: 1,272
Posted By RickC7
I haven't yet tried bead based normalization, but...

I haven't yet tried bead based normalization, but I have tried some plate normalization methods like SequalPrep. It did not work well in our hands. For larger sample numbers, like when we are doing...
Forum: Academic/Non-Profit Jobs 01-11-2018, 05:11 AM
Replies: 0
Views: 368
Posted By RickC7
Pbrc - research associate bioinformatics

A Research Associate position in Computational Biology is available in the COBRE Laboratory for Bioinformatics under the direction of Prof. Sujoy Ghosh at the Pennington Biomedical Research Center in...
Forum: Sample Prep / Library Generation 10-04-2017, 01:35 PM
Replies: 2
Views: 1,218
Posted By RickC7
We have successfully sequenced ATAC-Seq libraries...

We have successfully sequenced ATAC-Seq libraries on the Next-Seq. I need to look back at my notes, but we did not use the custom primers. Loosely based off Pamela Milani (Fraenkel Lab) We used the...
Forum: Sample Prep / Library Generation 09-27-2017, 02:47 PM
Replies: 5
Views: 1,272
Posted By RickC7
Thanks, I get that and have no problem when...

Thanks, I get that and have no problem when loading a sequencer for optimal cluster density. I'm also not going to quantify 192 16s libraries via qPCR for multiple projects. I more looking to get...
Forum: Academic/Non-Profit Jobs 09-27-2017, 07:51 AM
Replies: 0
Views: 15,701
Posted By RickC7
BioInformatics

https://lsu.wd1.myworkdayjobs.com/en-US/LSU/job/Research-Associate-Bioinformatics_R00005529

A Research Associate position in Computational Biology is available in the COBRE Laboratory for...
Forum: Sample Prep / Library Generation 09-27-2017, 07:01 AM
Replies: 5
Views: 1,272
Posted By RickC7
Index Read distribution

Hello,

I'm looking for advice, help, thoughts, etc on how to achieve more balanced read output when multiplexing. Typically I run all libraries on Agilent Bioanalyzer and pool according to the...
Forum: Sample Prep / Library Generation 06-07-2017, 11:16 AM
Replies: 5
Views: 1,264
Posted By RickC7
Did you ever figure out what the peak was? I have...

Did you ever figure out what the peak was? I have a similar issue...
Forum: RNA Sequencing 05-17-2017, 06:01 AM
Replies: 2
Views: 906
Posted By RickC7
Yes, I found a couple of caveats and...

Yes, I found a couple of caveats and work-arounds, but thankfully I won't need to employ any customization as Illumina gratefully offered to send me extra barcodes for this instance.
Thanks!
Forum: RNA Sequencing 05-16-2017, 09:19 AM
Replies: 2
Views: 906
Posted By RickC7
TruSeq Stranded Total RNA + NEB Barcodes??

Looking to get more index possibilities out of a TruSeq Stranded Total RNA LT kit. NEB Ultra directional workflow looks the same and NEB will sell the extra barcode kit alone. As far as I can tell,...
Forum: Illumina/Solexa 02-17-2017, 08:07 AM
Replies: 27
Views: 6,160
Posted By RickC7
The primer with LNA bases added to cartridge like...

The primer with LNA bases added to cartridge like custom primer fixed our issue. Thanks for the help!
Forum: Illumina/Solexa 01-19-2017, 12:36 PM
Replies: 27
Views: 6,160
Posted By RickC7
So you did something like this? Thanks so much...

So you did something like this? Thanks so much for your help!

ACAGGTTCAGAG+TTC+TAC+AGTCCGACGATC
Forum: Illumina/Solexa 01-19-2017, 10:16 AM
Replies: 27
Views: 6,160
Posted By RickC7
Thanks, I will give it a try. Where did you...

Thanks, I will give it a try.

Where did you have your primer synthesized?
Forum: Illumina/Solexa 01-04-2017, 01:42 PM
Replies: 27
Views: 6,160
Posted By RickC7
Thanks for the info. I am not using a custom...

Thanks for the info. I am not using a custom primer, but using custom SAGE libraries. I've modified a SuperSAGE protocol from Matsumura which incorporates Illumina adapters, so just load the library...
Forum: Illumina/Solexa 12-01-2016, 01:20 PM
Replies: 27
Views: 6,160
Posted By RickC7
Similar but different issue on Next-Seq. I...

Similar but different issue on Next-Seq.

I am of course screwed b/c I'm using a custom Tag-sequencing protocol, no custom primers as we have Gex adapters. Lanes 1 and 3 look great, but lanes 2 and...
Forum: Introductions 12-01-2016, 10:10 AM
Replies: 3
Views: 3,158
Posted By RickC7
For LPA try gelcompany.com

For LPA try gelcompany.com
Forum: Sample Prep / Library Generation 10-19-2016, 01:55 PM
Replies: 8
Views: 1,694
Posted By RickC7
Did you check concentration on qubit? May be...

Did you check concentration on qubit? May be outside of upper range? Have seen similar, not so pronounced, but diluting helped in our case.
Forum: Academic/Non-Profit Jobs 10-04-2016, 12:28 PM
Replies: 0
Views: 456
Posted By RickC7
Research Associate - Genomics Core Facility - PBRC Baton Rouge, Louisiana USA

Description:
The Pennington Biomedical Research Center, a facility of Louisiana State University System, is seeking to hire a Research Associate to assist in the Genomic Core Facility operations....
Forum: Academic/Non-Profit Jobs 09-19-2016, 07:05 AM
Replies: 0
Views: 493
Posted By RickC7
Research Associate Bioinformatics - Pennington Biomedical Research Center (LSU)

Job Posting Title:
Research Associate Bioinformatics

Position Type:
Other Academic

Department:
LSUPBRC Basic - Regulation of Gene Expression (Johannes M Salbaum (00010045))

Work...
Forum: SOLiD 06-30-2016, 12:40 PM
Replies: 15
Views: 5,808
Posted By RickC7
Reagent support for SOLiD until May2017 or sooner...

Reagent support for SOLiD until May2017 or sooner per demand.

We use/used SOLiD for SAGE, great for short reads but more expensive than Illumina runs. Converting everything over to Illumina...
Forum: Metagenomics 09-04-2015, 10:22 AM
Replies: 19
Views: 5,930
Posted By RickC7
strange

hi fanli,

hmmm, the run summary you posted on 5-11-2015 shows read 1 intensity at 17 and read 4 intensity at 53. The other run summary from the OP also shows low intensity 1st cycle. This also...
Forum: Metagenomics 09-04-2015, 05:53 AM
Replies: 19
Views: 5,930
Posted By RickC7
Not meaning to hijack the thread, but can anyone...

Not meaning to hijack the thread, but can anyone explain why we see such low 1st cycle intensities with 16s libraries? I see this in both v3-v4 and v4 only libaries, perhaps due to low diversity? If...
Forum: Vendor Forum 09-19-2013, 07:01 AM
Replies: 45
Views: 18,722
Posted By RickC7
RNA-Seq and 5S

I am working on an RNA-Seq project and on epibio website under species compatibility it states for Mycobacterium tuberculosis "will not remove 5S". Looking at Agilent results I have to agree b/c we...
Forum: SOLiD 04-11-2012, 06:54 PM
Replies: 4
Views: 2,690
Posted By RickC7
No sorry, I wrote directly to Hitachi several...

No sorry, I wrote directly to Hitachi several times but never got an answer back.

I took the old one apart and the lamp itself looks to be identical to the SOLiD4 lamps, just the housing is...
Forum: SOLiD 02-01-2012, 12:45 PM
Replies: 16
Views: 5,874
Posted By RickC7
Not sure if everyone realized this. I did not....

Not sure if everyone realized this. I did not. The FlowChip Manifolds should be replaced every 3 months, it is somewhere in the USB stick manuals. We are learning the hard way with leaking manifolds...
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