David F. Barker

7 Questions 268 Answers 0 Followers

Questions related from David F. Barker

Has anyone used BGI Americas for an RNA-seq project and/or have a basis for comparison of different companies offering RNA-seq?

BGI Americas is offering an apparently attractive promotion for RNA-seq and Bioinformatics services. http://bgiamericas.com/rna-seq-promotion/ Any suggestions for what a buyer should beware of or...

10 October 2013 590 3 View

How concerned should I be that a commercial "18S" rRNA primer pair actually recognizes the precursor RNA and not the mature one?

I recently noticed and confirmed experimentally that the mouse 18S rRNA qPCR primers sold by a company that does not provide explicit primer sequence information actually specifically amplifies...

09 September 2013 8,232 1 View

How uniform is the microbiome of commercially sourced mice?

In experiments designed to test the effect of diet/drugs etc. on the mouse microbiome, one could assume that the initial microbial content of each mouse of one commercially-sourced set of mice is...

03 March 2013 3,404 10 View

How small of a "fold-change" in gene expression can be reliably measured by RT-qPCR?

When using Sybr green or TaqMan qPCR assays to measure gene expression changes, can differences that are less than at least two-fold be taken as credible? What minimum fold-change or percent...

02 February 2013 1,777 44 View

For metagenomic "profiling" which is more useful, DGGE or TaqMan based qPCR?

To obtain a quick, but reasonably accurate metagenomic profile or fingerprint without any deep sequencing, I have seen the use of both 16S rRNA analyzed with denaturing gradient electrophoresis...

10 October 2012 6,344 16 View

What is the advantage of expressing an shRNA vs a microRNA primary transcript in a lentiviral vector?

Is there any particular advantage, other than the smaller insert size, to expressing an shRNA rather than a microRNA primary transcript when using a lentiviral delivery system?

09 September 2012 949 8 View

How useful are spike-in controls (like ERCC1 for example) for whole transcriptome RNA-seq in mouse or human?

What refined analysis is possible and are they reliable?

07 July 2012 6,075 5 View