We need to find biomarkers for prognostic, diagnostic and personalised treatment development. Notably to fight cancers that affect tissues. Since biopsies are invasive, it’s better to look for biomarkers in body fluids. Indeed, a simple blood sample becomes a kind of ‘liquid biopsy’ to reveal tissues affections. For 13 years, increasing interest has been shown for miRNA as biomarkers and it will last for sure. The 2 main reasons are that they are major regulators of cell processes and they are released from tissues into the blood. They are major biomarker candidates in serum and plasma. Thus, these circulating miRNA (cmiRNA) are the best hope for modern medicine. Still, a lot of research has to be done to determine the specific signature for each pathology, and also depending on the patient background. Obviously, cmiRNA profiling is a key step and requires sensitive and reproducible method. Sequencing, qRT-PCR, several kind of microarrays… Let’s explore together what the best approach could be. [Read more…]
Whole-genome Pol II transcription profiling by NET-Seq
Accurate monitoring of genome transcription activities is of crucial interest for deciphering gene expression and for a better understanding of RNA biology. Over the past years, various experimental methods for RNA Pol II mapping density across the whole genome have been designed. Here, I’d like to offer a brief introduction to the human Native Elongating Transcript-Sequencing (NET-Seq) method.
New: CleanTag Ligation Kit for Small RNA Library Prep
As detailed in a previous post, chemically-modifying oligonucleotide adapters is an effective means to prevent adapter dimer formation during small RNA library prep. Just as primer dimers form when very little template DNA is used for PCR, adapter dimers can form with low starting concentrations of RNA. The CleanTag™ Ligation Kit for Small RNA Library Prep is a complete kit which is compatible with Illumina® technology that makes use of such modified adapters in optimized buffer conditions. The kit includes CleanTag™ chemically modified adapters that greatly reduce adapter dimer formation and is optimized for total RNA input from 1-1000 ng. [Read more…]
A look inside the new Otogenetics NGS library prep kits
More than a month ago we wrote a post about the new DNASeq library prep kits from Otogenetics, a U.S. based sequencing service provider who created their own kits to reduce costs. Now, we’ve had a chance to see what the kits and their contents look like… [Read more…]
High quality, low cost DNASeq kits and gene enrichment panels
Otogenetics Corporation, a DNASeq and RNASeq next generation sequencing service provider has processed over 11,000 samples and is now producing their own DNASeq kits. In order to reduce costs and improve results, Otogenetics developed and validated kits in-house and has now made these high quality, low cost kits available to other researchers.
Buccal swab DNA Collection with no cold chain required
For years tebu-bio has been selling Epicentre-Illumina’s BuccalAmp™ system for non-invasive DNA sampling from inner cheek buccal cells. For many research studies, we find that researchers need two important things from a swab-based DNA collection system. First, the system must yield high quality DNA suitable for Next Generation Sequencing applications. Secondly, the system must instantly stabilize the sample to allow for at-home or remote location sampling (no cold chain required). In this post, I will introduce you to the iSWAB™-DNA Collection Kits.
Prevent adapter dimer formation during NGS library prep
![from: Shore et al. Improved Small RNA Library Preparation Workflows for Next Generation Sequencing [Poster]](https://beingbioreactive.files.wordpress.com/2014/10/screen-shot-2014-10-26-at-11-13-23-am.png)
Sources: Shore et al. “Improved Small RNA Library Preparation Workflows for Next Generation Sequencing” [Poster]
In a poster presented at the recent ASHG 2014 meeting in San Diego, researchers from TriLink Biotechnologies described their innovative technology solving the adapter dimer problem in Next Generation Sequencing library prep.
Similar to the primer dimer problem observed when performing PCR (i.e. low molecular weight PCR by-products of primer-primer hybridization), adapter dimerization generates by products of NGS library prep that will greatly decrease the number of informative sequencing reads. This is particularly a problem for low-input studies and when working with small RNAs (e.g. miRNA).
TriLink’s expertise in chemistry-based solutions for biological problems has previously led to the creation of the CleanAmp™ product line. CleanAmp™ Primers, CleanAmp™ dNTPs and 2X PCR Master Mix employ heat labile modifications, similar to those on hot-start polymerases, to prevent primer dimerization or premature polymerase activity prior to a high-temperature activation step.
CleanAmp™ 7-deaza-dGTP is a chemistry-based solution allowing for the amplification of difficult GC-rich PCR products.
Interested in learning more about TriLink’s products and services (including GMP production of modified oligonucleotides for Phase I human trials)? Contact tebu-bio experts who are representing TriLink in Europe.
The empirical approach to rRNA depletion for NGS
Ribosomal RNA (rRNA) depletion is a must for Next Generation Sequencing (NGS) studies to reduce the number of irrelevant reads. While commercially-available kits such as the Ribo-zero or the BioMag® SelectaPure mRNA System are popular for rRNA depletion, there are some experimental situations in which another approach is required.