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 bias in this case?
which pyrosequencing method did u use? 454 or Illumina? Did the reads numbers drastically vary across all samples?
I used illumina. The read numbers varied a lot, but can analysis of clustered reads help in this case? Thank you
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...
09 October 2014 9,875 8 View
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
06 July 2014 8,346 10 View
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...
06 July 2014 7,523 3 View
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...
06 July 2014 8,741 4 View
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...
05 June 2014 603 14 View
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...
02 March 2014 5,312 10 View
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...
02 March 2014 9,472 11 View
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...
31 December 2013 9,636 2 View
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...
31 December 2013 8,094 9 View
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...
31 December 2013 3,461 19 View
I'm cloning a fragment of 3200 nts into plasmid. The cloning was successful, however, 02 amino acids were mutated. Now I want to fix these 02 aa by site-directed mutagenesis technique using...
08 August 2024 4,645 2 View
After performing symmetric PCR, PCR purification was performed. Afterwards, asymmetric PCR was performed using the PCR purification product as a template, but no ssDNA band was confirmed in the...
08 August 2024 1,668 3 View
A fungal strain was treated with nanoparticles. We want to do an environmental SEM analysis. So could anyone share your views on preparing the sample? Thank you.
07 August 2024 5,307 1 View
I would like to understand potential safety concerns while handling SEB in the lab. Especially while working in animal house facility. Would like to know precautions for handling. Sigma MSDS...
07 August 2024 6,034 3 View
How do soil microflora interact with plant roots and influence plant nutrition, health, and productivity?
06 August 2024 9,618 3 View
Hi, I know that low molecular weight (MW) molecules generally tend to have higher mobility, while high molecular weight molecules tend to have lower mobility. However, in my experimental...
06 August 2024 1,495 2 View
i have sorted anti-NP specific plasma cells from bone marrow of C57BL/6 mice at certain times after immunization with variable counts and isolated total RNA using TRIZOL method for RT-PCR using...
05 August 2024 8,835 1 View
I aim to be as skeptical as possible regarding whether a pair of orthologous genes results in the same phenotype in their different but related bacterial organisms under similar environmental...
05 August 2024 6,787 4 View
kindly reply me. Thanking you in advance.
05 August 2024 7,727 4 View
Is it possible to conduct a molecular dynamics simulation to see the effects of a specific carbohydrate on the structure of lipids (e.g., micelle structure)? I am a beginner in this field and plan...
03 August 2024 3,371 3 View