Sniffing Out the Ion Proton

chinese-crested-dogSince the completion of the human genome project in 2003, more and more research has been poured into DNA sequencing. In the past 15 years or so, we have seen the cost of genome sequencing decrease from approximately $100 million dollars to right around $1000 dollars. This dramatic price reduction is due to the rapid advancement in DNA sequencing technology, and as a result, whole-genome sequencing is no longer relegated to large sequencing facilities. Companies such as Illumina, Life Technologies, and Pacific Biosciences all offer what are known as “desktop” sequencing platforms, and thereby are able to bring whole-genome and whole-exome sequencing power to large sequencing facilities and smaller research labs alike. In Canine Genetics and Epidemiology, a research team from Swedish University of Agricultural Sciences recently published their findings concerning the efficacy of the Ion Proton system and its ability to provide sufficient coverage of the genome and exome of four Chinese Crested dogs.

Viluma et al. created a 200bp library for each dog and sequenced each library on two Ion PI chips. The research team was able to achieve 80% coverage of the genome and 77% coverage of the exome when compared to the known genetic variants. In order to validate their findings, Viluma et al. compared the detected variants by the Ion Proton system against those detected using the Illumina HD canine SNP array. With the ability to detect 90% of the variants detected by the Illumina SNP array, the Ion Proton system has proven that it has a place in laboratories looking to complete whole-exome and whole-genome studies

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chinese-crested-dogSince the completion of the human genome project in 2003, more and more research has been poured into DNA sequencing. In the past 15 years or so, we have seen the cost of genome sequencing decrease from approximately $100 million dollars to right around $1000 dollars. This dramatic price reduction is due to the rapid advancement in DNA sequencing technology, and as a result, whole-genome sequencing is no longer relegated to large sequencing facilities. Companies such as Illumina, Life Technologies, and Pacific Biosciences all offer what are known as “desktop” sequencing platforms, and thereby are able to bring whole-genome and whole-exome sequencing power to large sequencing facilities and smaller research labs alike. In Canine Genetics and Epidemiology, a research team from Swedish University of Agricultural Sciences recently published their findings concerning the efficacy of the Ion Proton system and its ability to provide sufficient coverage of the genome and exome of four Chinese Crested dogs.

Viluma et al. created a 200bp library for each dog and sequenced each library on two Ion PI chips. The research team was able to achieve 80% coverage of the genome and 77% coverage of the exome when compared to the known genetic variants. In order to validate their findings, Viluma et al. compared the detected variants by the Ion Proton system against those detected using the Illumina HD canine SNP array. With the ability to detect 90% of the variants detected by the Illumina SNP array, the Ion Proton system has proven that it has a place in laboratories looking to complete whole-exome and whole-genome studies. 

Whole Exome Sequencing

Exome sequencing is a strategy to selectively sequence the coding regions of the genome. In the human genome, exons constitute about 1% of its genome and that the protein coding regions of the human genome constitute about 85% of the disease-causing mutations. MRDNA uses TruSeq exome enrichment kit (Illumina) for the sample library preparation. Sequence data generated from exome enrichment are analyzed using a script to generate two sets of statistics; post alignment and post CASAVA (Consensus Assessment of Sequence and Variation) analysis. MRDNA routinely performs exome sequencing. Please visit www.mrdnalab.com.

Whole exome sequencing is an efficient, sensitive and …

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Nature reportswhether whole exome sequencing (WES) is a sensitive method … WES is an efficient, sensitive, specific and cost-effective method for mutation ….. and Illumina Nextera Rapid Capture Exome (Illumina-Rapid) by downloading the  ..

 

***The team of scientists at MR DNA are able to fulfill your WES needs at an affordable price to you.

 

Pricing | Biotech Center | MR DNA

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MR DNA offers cost-effective research services to Universities and … Exome Capture (Nextera Rapid Exome Capture)

 

Next Generation Sequencing

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MR DNA is capable of processing and analyzing all forms of sequencing … whole genome sequencing, custom targeted resequencing including exome  …

 

Comparison of Next-Generation Sequencing Systems

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The Journal of Biomedicine and Biotechnology compares 454, SOLiD, HiSeq 2000 is the cheapest in sequencing with …. The Nextera, TruSeq, and Illumina’s reversible terminator-based ….studies that use whole-genome or whole-exome sequencing strategies.

***Contact MR DNA to see which platform best fits your needs. We try to beat any price.***

 

Whole-exome sequencing of circulating tumor cells provides …

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Nature reports thatWhole-exome sequencing of circulating tumor cells enables accurate and … Whole-genome sequencing libraries were prepared using the Nextera DNA Sample Prep Kit …Captured DNA was sequenced using the Illumina HiSeq platform, and  …

 

ChIP-Seq (Chromatin immunoprecipitation sequencing)

chip-seq sequencing serviceChromatin immunoprecipitation (ChIP) is a powerful method for studying interactions between specific proteins and a genomic DNA region. MRDNA routinely performs ChIP-seq and provide cost effective high quality data, global binding site maps for a protein of interest and robust output. Please visit www.mrdnalab.com.

Our services – MR DNA Laboratory

MR DNA

Illumina HiSeq 2500/200, MiSeq – The HiSeq 2500/2000 sequencing systems offer the … Metagenomics and amplicon sequencing; ChIPSeq  …

 

Functional Genomics

MR DNA

MR DNA offers library prep, sequencing, and basic data analysis services for …Simple ChIPSeq … hiSeq2500, …., sequence the samples

 

High-Throughput Sequencing Center

MR DNA

We provide services for high-throughput next-generation sequencing using the … (ChIPSEQ), RNA discovery and Multiplex sequencing … Pricing forHiSeq 2500 sequencing is based on ……..sequencing run,  …

 

MR DNA Research Laboratory Services

Services. Transcriptomics. mRNA-Seq: Stranded and non-stranded, high levels of multiplexing … ChIPSeq. Transcription factor analysis; Histone modifications

 

Genome Sequencing Service

Genome sequencing is described as the process of determining the order of the nucleotide bases within a certain length strand of DNA. You can sequence a short piece, the whole genome, or parts of the genome (exomes – parts of the genome that contain genes).

The knowledgeable team at MR DNA Lab (also known as Molecular Research) have been helping hundreds of researchers from around the world get the next-generation sequencing (NGS) services they need. We are one of the most reputable NGS labs providing high-quality data, and have fast turn-around without compromising quality. Our genome sequencing services are a cost-effective solution, and we try to beat anyone’s quoted pricing.

MR DNA scientists have more than 20 years of continuous experience (not combined) developing new and novel molecular methods, systematics, microsatellite screening, MHC assays, viral assays, protozoan assays and much more. Our team’s goal is to take advantage of each new technology as it arrives and leverage it to develop unique, improved and more cost effective molecular methods and tools.

Our highly-trained scientists are ready to help you with your research goals. We always try and understand the focus of your research to best provide you with the analysis you are looking for. Your results are always confidential.

At MR DNA, we offer a wide variety of genome sequencing services. Below is a general list of the different types of services we provide:

Metagenomics

ALLinONE

Whole Genome Resequencing

Exome Sequencing

Target Region Sequencing

de novo Sequencing

Whole Genome Mapping

Genotyping

Sanger Sequencing

Oligo Synthesis

Single-cell DNA Sequencing

Epigenomics

Bisulfite Sequencing

RRBS

MeDIP-Seq

Chip-Seq

Transcriptomics

RNA-Seq (Transcriptome)

RNA-Seq (Quantification)

Whole Transcriptome Sequencing

Single-cell RNA sequencing

Here is a small sample of the organisms in our database:

Acanthostigma septoconstrictum

Acanthostigmella brevispina

Acanthosyris asipapote

Acanthosyris falcata

Acanthothecis aurantiaca

Acanthothecis peplophora

Acanthotrema brasilianum

Acanthurus guttatus

Acanthurus japonicus

Acanthurus xanthopterus

Acari

Acarichthys heckelii

Acaricomes phytoseiuli

Acaromyces ingoldii

Acaromyces sp.

Acaromyces sp. icmp 17482

Acaromyces sp. tr033

Acaronia nassa

Acarospora austroshetlandica

Acarospora badiofusca

Acarospora badiofusca subsp. badiofusca

Acarospora bullata

Acarospora canadensis

Acarospora cervina

Acarospora cf. bullata flakus 9547

Acarospora cf. dissipata

Acarospora clauzadeana

Acarospora complanata

Acarospora fulvoviridula

Acarospora fuscata

Acarospora hilaris

Acarospora laqueata

Acarospora macrospora subsp. macrospora

Acarospora moenium

Acarospora molybdina

Acarospora nitrophila

Acarospora peliscypha

Acarospora rhizobola

Acarospora rosulata

Acarospora rugulosa

Acarospora scabrida

Acarospora schleicheri

Acarospora sinopica

Acarospora smaragdula

Acarospora smaragdula var. lesdainii

Acarospora sp. hertel 39.701

Acarospora sp. nimis 23/6/1990

#DNA on Twitter

Tweet-tweet! Nowadays, Twitter is not merely a social-network. It has become a must-read source of real-time industry news and information with regular updates, news and discussions from the leading minds of today. The advent of Twitter has allowed for folks to have real-time conversations with thought leaders across the field. An upcoming researcher in genomics can now engage with genomics gurus at the swipe off a finger. Online communities such as blogs have been around for a bit, but now the micro-communities like Twitter allow for real-time discussions. Get the latest insights from across the globe as they are happening. Over 35 percent of Americans per capita are active on Twitter, a close second to the UK which has almost 40 percent.

The infographic below displays the top nations actively using Twitter per capita:

Follow @MRDNA_Lab on Twitter to get the latest content surrounding applied DNA sciences, genomics news, next-generation sequencing and more.

Don’t have a Twitter account? You can sign up for free today.

Twitter is a real-time information network that connects people to the latest stories, ideas, opinions and news that they find interesting. At the heart of Twitter are small bursts of information called Tweets. Each Tweet is 140 characters long. Tweets include photos, videos and conversations that enable followers to get the whole story at a glance, and all in one place.

Twitter connects organizations to their audiences in real time—and organizations can use Twitter to quickly share information with people interested in their products and services, gather real-time market intelligence and feedback, and build relationships with customers, partners and influencers. This is done by ‘following’ members of your target market or by communicating with twitter users who are already interested and ‘following’ you. Tweets can include live links in the form of hash tags (#) and user tags or handles (@). Twitter is all about engaging with an audience in real time, with short sharp alerts and posts, providing links to further content if necessary.

Microbial Communities: Microbiome, Metagenome, Microbiota

microbial

What consists of microbial communities analysis? Microbiome and microbiota explain the collective genomes of the microorganisms that inhabit an environmental niche or the microorganisms themselves. Microbiota are the microorganisms present within a particular environment. The approach to describe microbial diversity relies on analyzing the gene diversity 16S ribosomal RNA (16S rRNA) through next-generation sequencing. The “S” in 16S rRNA genes sequencing represents a Svedberg unit. Microbiome refers to the entire habitat; including the microorganisms, their genes, and the surrounding environmental setting. Metagenome is the collection of genomes and genes from the members of a microbiota.

MR DNA Lab offers microbial sequencing. Microbial sequencing is the focused sequencing of a single microbe or relatively small group of microbes, in contrast with metagenomics. It can assist in the discovery of genetic variations that support the designing of antimicrobial compounds, vaccines, and even engineered microbes for industrial applications. (1)

Next-Generation Sequencing Services (DNA)

Scientists are now able to elucidate the microbiome of human diseases, agricultural and other natural, environments. Especially at MR DNA Lab, scientists are dedicated to microbiome research. Their method development has opened doors to research around the world.

This initiative is one component of the MR DNA program and constitutes a major NIH effort to broaden access to rapid assay technologies. This program will fund the development and adaptation of biological assays for use in automated high throughput molecular screening (HTS). It is intended that this initiative promote the development of automated screening projects. High throughput molecular screening (HTS) is the automated, simultaneous testing of thousands of distinct molecular signatures in models of biological mechanisms. Active compounds identified through HTS can provide the starting point in the design of powerful research tools that allow pharmacological probing of basic biological mechanisms, and which can be used to establish the role of a molecular target in a disease process, or, its ability to alter the metabolism or toxicity of a therapeutic. The immense potential of HTS to impact our understanding of biological mechanisms is largely untapped because access to automated screening facilities and large compound libraries is limited in academic, government and non-profit research sectors. Many in vitro biological models are currently used to study biological pathways, the effects of genetic perturbations and to establish a disease association. These can be adapted to high throughput formats for the purpose of screening large collections of biologically active compounds. There are a number of characteristics that make an assay suitable for high throughput approaches. The assay must be robust, reproducible and have a readout that is amenable to automated analysis. In addition, it must be possible to miniaturize the assay, for example; to a 96-well plate (or higher density) format or flow-cytometric approach. Further, the assay protocol should be simple enough for automated handling. A broad range of models share many of these features, including; biochemical assays, cellular models and certain model organisms such as yeast or C. elegans. This initiative will support the development of innovative assays for use in both basic research and in therapeutics development programs, with an emphasis on novelty of assay approach and/or novel targets and mechanisms. (1)

The following list is a basic description of the sequencing services provided by Molecular Research, LP (MR DNA).

Genome Sequencing

Genome sequencing is the process through which we can elucidate the the core information (genes) of the DNA or RNA of the sample, or in the case of whole genome sequencing, the entirety of the information (genes and non-coding sequences).

Metagenomics

Metagenomics is a rapidly evolving field through which scientists can elucidate some of the previously hidden insights into the vast array of microscopic life on the planet. Every day, scientists are gaining a better understanding of ecology, evolution, diversity, and functions of the microbial universe thanks to metagenomics, which seeks to help sequence microorganisms in large groups that are often difficult to culture.

Microbial Sequencing

Microbial sequencing is the focused sequencing of a single microbe or relatively small group of microbes, in contrast with metagenomics. It can assist in the discovery of genetic variations that support the designing of antimicrobial compounds, vaccines, and even engineered microbes for industrial applications.

Genotyping

Genotyping is the technique through which the variations in an organisms DNA are determined by comparing that organisms DNA to a reference sequence. Genoptyping of an organism also reveals its alleles, the various alternative forms of genes or groups of genes. It plays a very important part in the study of diseases, and in combination with next-generation sequencing technology will help improve treatment methods.

Exome Sequencing

Selective sequencing of coding regions of the genome is an effecient and effective alternative to whole genome sequencing. Exons are the parts of coding regions which control the translation of proteins.

Transcriptome Sequencing

Transcriptome sequencing focuses on the complete array of RNA molecules, which include transfer RNA, messenger RNA, ribosomal RNA, and non-coding RNA. Transcriptome sequencing can help answer questions about gene expression, discovery of novel genes and their functions, classification of diseases, or to help identify targets for drug treatment development.

Amplicon Sequencing

Amplicon sequencing targets relatively small, specific regions of the genome usually in the hundreds of base pairs. Amplicon sequencing combined with next-generation sequencing allows for thousands of amplicons across many samples to be prepared simultaneously and indexed within hours and often within a single-run.

Bacterial/Viral Typing

Bacterial and virus typing is used in the accurate and fast identification and discrimination of strains. Enhancements in bacterial and viral typing can also assist in outbreak identification, surveillance, and in the understanding of transmission, pathogenesis, and evolutionary relationships of the target. Often specific isolates can be sequenced within a day using next-generation sequencing techniques.

De novo Sequencing

De novo is a latin expression meaning “from the beginning”. Hence, de novo sequencing is primarily focused on the sequencing of a novel genome for the first time, or genomes in which large variations are expected, such as genomes with high plasticity. It often requires specialized assembly of sequencing reads, and can be very computationally intensive, though next-generation sequencing has largely reduced the overhead associated with it.

Targeted DNA Sequencing

Targeted DNA sequencing allows the researcher to utilize the specificity of PCR in order to target the genes of their choosing. Targeted DNA sequencing provides the ability to acheive deeper sequencing coverage in order to identify those genes expressed at lower levels that may possibly have been missed by other sequencing methods.

Targeted RNA Sequencing

Targeted RNA sequencing allows the researcher to utilize the specificity of PCR in order to target the genes of their choosing. Targeted RNA sequencing provides the ability to acheive deeper sequencing coverage in order to identify those transcripts expressed at lower levels that may possibly have been missed by other sequencing methods.

Aneuploidy and CNV Analysis

Aneuploidy and Copy-umber variations (CNV) are important factors in the study of genetic disorders, disease, and phylogenetics. Next-generation sequencing has made the study and analysis of aneuploidy and CNV much easier than with previous methods.

Small RNA and miRNA Sequencing

This type of sequencing uses high-throughput methods to sequence miRNA and small RNA, which are important to tissue expression patterns, isoforms, and disease associations.

(Source)

Organic Molecules: Nucleic Acids (RNA and DNA)

Organic molecules are classified in four classes: carbs, lipids, proteins, and last but not least nucleic acids. There are two principle nucleic acids, ribonucleic acid (RNA) and deoxyribonucleic acid (DNA).

DNA is a double polymer of nucleotides, whereas RNA is only once strand. RNA strands are substantially shorter than DNA. The reason why DNA strands are longer is because they contain the code for many different proteins.

There are four nitrogeneous bases in DNA, divided into two types. The first type is a double ring structure, consisting of purine’s adenine and guanine. The second type only has a single ring structure, and includes pyrimidine’s thymine and cytosine.

The four bases in RNA are similar than in DNA, however when DNA is transcribed to RNA, all the T bases (thymine) are changed to U (uracil). RNA can be transcribed in three types:

· Messenger RNA (mRNA) – transcribed from structural genes

· Ribosomal RNA (rRNA) – transcribed from rDNA, component of the structure of ribosomes

· Transfer RNA (tRNA) – transcribed from tDNA, key player in translation

Ribosomal RNA, rRNA, is present in all cells. Consequently, rRNA genes are sequenced for the purposes like indentifying taxonomic groups, assessing related groups, and judging rates of species divergence.

Sequencing for rRNA can be processed in small subunits like 16S. 16S rRNA sequencing can be performed by labs like MR DNA Lab. To find more information on 16S rRNA and other genomic sequencing, visit MR DNA or find them on Twitter and Facebook.

DNA Gets Social

With over 200 million users, Twitter has emerged as a viable medium for determining influence in many fields – including the field of science. Scientists from all over the world are taking to Twitter to spread the ideas and information to followers.

Social media teams, like the one at MR DNA Lab, have added Twitter to their platform. Followers use @mrdna_lab as their resource to science-related news and keep their clients updated. Connecting with @mrdna_lab is useful for those interested in learning more about updates or advancements in biological sciences, such as latest discoveries in genotyping or genome sequencing. Join the conversation today by following @mrdna_lab on Twitter.

Whether it’s fungal genome or ion proton sequencing, MR DNA Lab can help with your next-generation sequencing. Need it fast? They can provide rush-orders if eligible! To learn more about the services they can offer, please visit their website.