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Forum: Academic/Non-Profit Jobs 05-09-2017, 06:03 AM
Replies: 0
Views: 721
Posted By zhengz
Postdocs in Functional Genomics using Single-cell CRISPR and Computational Approaches

Postdoctoral Researcher in Functional Genomics using Single-cell CRISPR and Computational Approaches

Karolinska Institutet

Last application date: 18.May.2017 11:59 PM CET

Please see details...
Forum: Sample Prep / Library Generation 09-15-2016, 09:42 PM
Replies: 15
Views: 20,323
Posted By zhengz
The original paper combining several steps into...

The original paper combining several steps into one:

http://nar.oxfordjournals.org/content/38/13/e137.full
Forum: 454 Pyrosequencing 05-13-2012, 07:49 AM
Replies: 6
Views: 2,156
Posted By zhengz
Awesome! Congrats!

Awesome! Congrats!
Forum: Sample Prep / Library Generation 03-14-2012, 09:40 AM
Replies: 2
Views: 5,458
Posted By zhengz
RNA-DNA binging is stronger than DNA-DNA. The rG...

RNA-DNA binging is stronger than DNA-DNA. The rG TSO would anneal better than a dG one to the short stretch of 2-5 cytosines.
Forum: 454 Pyrosequencing 11-27-2011, 01:33 PM
Replies: 9
Views: 4,151
Posted By zhengz
Hi audioPL, There is a protocol...

Hi audioPL,

There is a protocol "Titration-free 454 sequencing using Y adapters". http://www.nature.com/nprot/journal/v6/n9/abs/nprot.2011.369.html

Not exactly as the Roche adapter, but might...
Forum: Sample Prep / Library Generation 10-23-2011, 07:47 AM
Replies: 12
Views: 8,363
Posted By zhengz
I think it is a single Y adapter, not two...

I think it is a single Y adapter, not two different Y adapters, in the reaction.
Forum: 454 Pyrosequencing 08-30-2011, 05:54 AM
Replies: 7
Views: 4,562
Posted By zhengz
Hi andylai, Have you solved this problem?...

Hi andylai,

Have you solved this problem? The problem seems to persist in v2.6.
Forum: Sample Prep / Library Generation 08-01-2011, 12:56 PM
Replies: 1
Views: 2,337
Posted By zhengz
Just my personal views. Are the inosines,...

Just my personal views.

Are the inosines, really necessary?
-- Not necessary with the short stem.

Are the phosphorothioates necessary on the adapter tails? We don't have them on our Illumina...
Forum: Sample Prep / Library Generation 06-16-2011, 12:41 AM
Replies: 12
Views: 7,998
Posted By zhengz
Thank you very much for sharing the tips, ECO!

Thank you very much for sharing the tips, ECO!
Forum: General 05-30-2011, 05:46 AM
Replies: 2
Views: 1,627
Posted By zhengz
Hi, To answer a little part of your Q1, one...

Hi,

To answer a little part of your Q1, one nanogram after fragmentation was enough for 10 454 Titanium runs.

To just test what was in a mixed sample, sub-picogram DNA was used for a mini-454...
Forum: Ion Torrent 05-23-2011, 10:51 PM
Replies: 18
Views: 10,180
Posted By zhengz
As Ion prioritizes quick turnaround time,...

As Ion prioritizes quick turnaround time, amplicon length has been sacrificed. The advertisement says read length is going to be double in 201x. It has been quite long time since 454 advertised 1000...
Forum: 454 Pyrosequencing 04-22-2011, 11:07 PM
Replies: 18
Views: 7,168
Posted By zhengz
Hi ali, I guess the sfffile looks for the...

Hi ali,

I guess the sfffile looks for the barcode set which you define in your barcode file and the name you specify in the command line after -s. If no match, it continues to look for gsMID and...
Forum: 454 Pyrosequencing 04-21-2011, 12:23 AM
Replies: 18
Views: 7,168
Posted By zhengz
Hi aligenie, Since you define the name for...

Hi aligenie,

Since you define the name for the set of barcodes as 'barcode', which is the line above {, would the following command work?

sfffile -mcf barcode.txt -s barcode read.sff


In...
Forum: Ion Torrent 02-26-2011, 11:36 AM
Replies: 0
Views: 2,711
Posted By zhengz
read length limits sample prep time?

It seems very critical to increase PCR time to generate less biased long amplicons such as >200, >400, >1kb? Trying to reduce sample prep time including emPCR might, at least currently, be limited by...
Forum: RNA Sequencing 11-04-2010, 12:34 PM
Replies: 15
Views: 17,636
Posted By zhengz
It was microbiota composition data - histograms...

It was microbiota composition data - histograms of each OTU (suppose this is the same as what you referred to as each gene) for groups of tens of samples. (OK, not RNA-seq data) But I think for...
Forum: RNA Sequencing 11-04-2010, 12:53 AM
Replies: 15
Views: 17,636
Posted By zhengz
It would be nice to see some references...

It would be nice to see some references addressing when to use zero-inflated NB and when ordinary NB.

UCLA Statistical Computing is a very nice stitistics source...
Forum: RNA Sequencing 11-03-2010, 04:06 PM
Replies: 15
Views: 17,636
Posted By zhengz
What about zero-inflated count models? I...

What about zero-inflated count models?

I once checked the histograms of many variables and many did not look like follow Poisson distribution or negative binomial distribution, as there were...
Forum: 454 Pyrosequencing 10-20-2010, 11:41 AM
Replies: 7
Views: 3,068
Posted By zhengz
At the first look at the result that gave 711...

At the first look at the result that gave 711 million bases (1.7 M passFilter reads, median read length ~430 bases, mode read length ~500 bases), I doubted I had made something seriously wrong and...
Forum: 454 Pyrosequencing 10-19-2010, 11:14 AM
Replies: 7
Views: 3,068
Posted By zhengz
Sorry for confusing...I use the two words quite...

Sorry for confusing...I use the two words quite often recently and mixed them from time to time.

Thanks Philip. I did not know that before.
Forum: 454 Pyrosequencing 10-19-2010, 10:31 AM
Replies: 7
Views: 3,068
Posted By zhengz
My guess is that using inosines to prevent...

My guess is that using inosines to prevent supressive PCR.

Inosines allow forming of Y adaptors initially, but after the sencond cycle of amplification, it's sequence on the newly formed strand...
Forum: Sample Prep / Library Generation 09-17-2010, 07:30 AM
Replies: 5
Views: 2,175
Posted By zhengz
No, I don't know the concentration. As I said,...

No, I don't know the concentration. As I said, they were not able to be quatified by Qubit High Senstivity, meaning that the amount were less than 1 nanogram.

I am interested in this thread...
Forum: Sample Prep / Library Generation 09-16-2010, 12:00 PM
Replies: 5
Views: 2,175
Posted By zhengz
Good that your results have been improved. I...

Good that your results have been improved.

I have no experience with the Roche Rapid Kit. I only use home-made Y adaptors and qPCR quantification. In my hand, the amount of DNA is not a problem -...
Forum: Sample Prep / Library Generation 08-05-2010, 01:03 AM
Replies: 5
Views: 2,175
Posted By zhengz
Hi kisand, I feel it unlikely to be related...

Hi kisand,

I feel it unlikely to be related with the amount of DNA. Rather, as you already indicated, the preferential amplification of shorter fragments during emulsion PCR.

The amount of PCR...
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