Philip Lyons

12 Questions 34 Answers 0 Followers

Questions related from Philip Lyons

What is an acceptable sequencing depth for microbiome analysis?

I am undertaking 16S amplicon microbiome characterization of fish gut using MiSeq. Just wondering if anybody has any similar experience in figuring out a required sequencing depth to achieve this...

10 October 2014 9,809 8 View

Are QIAamp and QIAquick Spin Columns Interchangeable?

I know that the two columns are silica-membrane based, but perhaps they bind different sizes of DNA? I am extracting DNA from intestinal content samples for microbial community analyses, and the...

07 July 2014 8,689 4 View

Can anyone help with inhibitex tablets for PCR inhibitor removal?

Does anybody have the Inhibitex tablets (Qiagen) for removal of PCR inhibitors from DNA extraction preps? I have a sampling coming up and really need them. Thank you

07 July 2014 8,305 10 View

Does anyone have a QIAamp DNA Stool Mini Kit?

Long shot here I know, but does anybody have this kit, or even the Inhibitex tablets for it? I have a sampling coming up shortly and Qiagen are not stocking this kit until end August. I've tried...

07 July 2014 7,465 3 View

Has anyone used the InhibitEx Buffer in new Qiagen Fast DNA Stool Mini Kit?

I have always used Qiagen's DNA Stool Mini Kit for extraction of community DNA from environmental samples. However, the manufacturer has no replaced this kit with "Fast DNA Stool Mini Kit", which...

06 June 2014 538 14 View

Can analyzing sequence clusters, as opposed to raw reads help to eliminate bias when samples return different numbers of total reads?

I am analyzing microbiome data from a pyroseq run. My analysis returned different numbers of reads for each sample. Can clustering of sequences belonging to different genera help to eliminate any...

03 March 2014 2,371 2 View

What is the difference between 'genus read counts' and 'genus read clusters' in bioinformatics?

I am interpreting microbiome data output from illumina miseq. The genus read counts are significantly higher than genus read clusters, and I am trying to understand the difference between them. A...

03 March 2014 9,433 11 View

What is the typical number of reads from a illumina MiSeq 16S microbial community profile from an environmental sample?

I ran 10 samples altogether, yielding a total of 10,289,176 reads before quality filtering. After removal of chimeras and denoising (up to OTU assignment), the total was 4,560,861. I then quality...

03 March 2014 5,258 10 View

How many cycles in 16S illumina sequencing once adapters added?

I am performing a 16S microbiome study, and have sent my samples to a lab for NGS using illumina MiSeq, until our own MiSeq here is up and running. I have received pictures of the preliminary...

01 January 2014 8,178 2 View

When sampling small amounts of intestinal contents (approx. 150mg), is it preferable to perform DNA extractions right away?

Or to immediately snap freeze in liquid N or at -80CIf storage is in option, can the samples be stored in a sterile eppendorf only, or does the eppendorf have to contain a stabilizing buffer...

01 January 2014 9,586 2 View

How much starting material is needed for DNA extraction and subsequent microbiome analysis using pyrosequencing?

I am performing a microbiome analysis of the fish gut using next gen sequencing. I am wondering how much starting material I should be using for my DNA extractions. The Qiagen kit that I use for...

01 January 2014 8,050 9 View

What could explain the low species evenness in 16S metagenomics?

A recent experiment examining the fish gut microbiome returned results showing quite a low level of species evenness but high level of species diversity. One gut microbe in particular was very...

01 January 2014 3,413 19 View