Next-Generation Sequencing

CD Genomics

RNA-Seq is the premier tool for mapping and quantifying transcriptomes by utilizing next-generation sequencing (NGS) technology. The transcriptome refers to the complete set of transcripts in a cell, which provides information on the transcript level for a specific developmental stage or physiological condition. Understanding the transcriptome is necessary for interpreting the functional elements of the genome and understanding development and disease. The key purpose of transcriptomics includes cataloging all species of transcripts; determining the transcriptional structure of genes; and quantifying the expression levels of each transcript under different conditions.

The Development and Workflow of RNA-seq, Learn more at https://www.cd-genomics.com/resourse-Bioinformatics-Workflow-of-RNA-Seq.html

Principle and Workflow of RNA Sequencing

As a leading provider of NGS services, CD Genomics is providing an integrated portfolio of methylation sequencing services. Whole genome bisulfite sequencing (WGBS) is an effective and reliable strategy to identify individually methylated cytosines on a genome-wide scale. With over 10 years of experience and the state-of-the-art next-generation sequencing platforms, we can totally meet your project requirements and budgets in the exploration of methylome.


https://www.cd-genomics.com/Whole-Genome-Bisulfite-Sequencing.html

Principle and Workflow of Whole Genome Bisulfite Sequencing

CD Genomics has extensive experience in providing support for the selection and design of microsatellite markers for a wide range of plant and animal species. Besides microsatellite genotyping, we also provide genotyping by sequencing (GBS) method, which saves time and resources.  https://www.cd-genomics.com/Microsatellite-Genotyping-Service.html

Microsatellite Genotyping Service  at CD Genomics

Oncotarget

Oncotarget published this trending research perspective in Volume 13, entitled, "Treasures from trash in cancer research" by researchers from Núcleo de Pesquisas em Oncologia/Universidade Federal do Pará, Belém, Pará, Brazil; Instituto Metrópole Digital/Universidade Federal do Rio Grande do Norte, Natal, Brazil; Instituto de Ciências Biológicas/Universidade Federal do Pará, Belém, Pará, Brazil.

DOI - https://doi.org/10.18632/oncotarget.28308

Correspondence to - Paulo Pimentel de Assumpção - assumpcaopp@gmail.com

Abstract

Introduction: Cancer research has significantly improved in recent years, primarily due to next-generation sequencing (NGS) technology. Consequently, an enormous amount of genomic and transcriptomic data has been generated. In most cases, the data needed for research goals are used, and unwanted reads are discarded. However, these eliminated data contain relevant information. Aiming to test this hypothesis, genomic and transcriptomic data were acquired from public datasets.

Materials and Methods: Metagenomic tools were used to explore genomic cancer data; additional annotations were used to explore differentially expressed ncRNAs from miRNA experiments, and variants in adjacent to tumor samples from RNA-seq experiments were also investigated.

Results: In all analyses, new data were obtained: from DNA-seq data, microbiome taxonomies were characterized with a similar performance of dedicated metagenomic research; from miRNA-seq data, additional differentially expressed sncRNAs were found; and in tumor and adjacent to tumor tissue data, somatic variants were found.

Conclusions: These findings indicate that unexplored data from NGS experiments could help elucidate carcinogenesis and discover putative biomarkers with clinical applications. Further investigations should be considered for experimental design, providing opportunities to optimize data, saving time and resources while granting access to multiple genomic perspectives from the same sample and experimental run.

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Keywords - cancer metagenomics, cancer sncRNA expression, RNA-Seq variant calling

About Oncotarget

Oncotarget is a primarily oncology-focused, peer-reviewed, open access journal. Papers are published continuously within yearly volumes in their final and complete form, and then quickly released to Pubmed. On September 15, 2022, Oncotarget was accepted again for indexing by MEDLINE. Oncotarget is now indexed by Medline/PubMed and PMC/PubMed.

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Treasures From Trash in Cancer Research

Oxford Nanopore Technologies

Take your sequencing to the next level with the recently released PromethION 2 devices. They enable flexible, high-yield sequencing, in a compact, accessible design. The devices are designed for users with sample processing requirements of up to four full-length sequencing runs per week / ~200 flow cells per year. Each flow cell can deliver hundreds of gigabases of nanopore sequencing data. With this sequencing capacity, you can obtain the data you need for completing large genomes, studying complex metagenomic samples, obtaining known and novel transcripts from single-cell sequencing, and much more.

[url][link]https://nanoporetech.com/resource-centre/promethion-2-brochure?utm_campaign=P2%202022&utm_source=tech_networks&utm_medium=video[/link][name]Download the PromethION 2 brochure[/name][/url]

[url][link]https://nanoporetech.com/products/promethion-2?utm_campaign=P2%202022&utm_source=tech_networks&utm_medium=video[/link][name]Browse the PromethION 2 page[/name][/url]


Flexible, high-yield nanopore sequencing for every lab

Bruker Mass Spectrometry

Join Bruker's Erica Forsberg with Sapient Founder & CEO Mohit Jain, & Co-Founder and Head of Analytical R&D, Jeramie Watrous as they take you behind the scenes of  Sapient’s  lab. Get ready to learn more about how the timsTOF Pro 2 is helping Sapient amplify their biomarker discovery. 

Live from the Lab at Sapient: How timsTOF is helping to transform the speed and scale of small molecule biomarker discovery

CD Genomics has been providing the accurate and affordable whole genome sequencing service for couple of years. We combine both Illumina (short reads) and PacBio (long reads) platforms to achieve whole genome de novo assemblies and re-sequencing for viruses, microbes, plants, animals and humans. https://www.cd-genomics.com/Whole-Genome-Sequencing.html

Methods and Workflow of Whole Genome Sequencing

CD genomics can provide microorganism quantification amplicon sequencing based on 16S external standard sequences to obtain absolute abundance data for species in the sample. The 16S amplicon library is constructed and sequenced by adding a synthetic sequence of known copy number to the sample DNA, and then a standard curve is drawn according to the number of amplicon reads and the absolute copy number of the external standard sequence. And finally the absolute copy number of the 16S rRNA gene of the corresponding species of the OTU representative sequence in the sample is calculated. More information at https://www.cd-genomics.com/absolute-quantitative-16s-18s-its-amplicon-sequencing.html

Bioinformatics Analysis of 16s rRNA Amplicon Sequencing Data

CD Genomics is offering five platforms for genome-wide epigenomics analysis, each designed to accommodate a wide range of sample types and suit your specific research needs, allowing researchers to look at epigenetic alterations easily. This information will help us not only understand the role of DNA methylation but also identify targets for therapeutic treatment. https://www.cd-genomics.com/Epigenomics.html

Next-Generation Sequencing

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