Kiko Garcia

CD Genomics is providing PacBio Single Molecular Real-Time (SMRT) sequencing to increase your research method for bacterial whole genome sequencing. A comprehensive view of the bacterial genome, including genes, regulatory regions, IS elements, phage integration sites, and base modifications is vital to understanding key traits such as antibiotic resistance, virulence, and metabolism.

At CD Genomics, we are using the long-read PacBio Sequel platform to support researchers all over the word with bacterial de novo whole genome sequencing needs. Our bioinformatics analysis include: Genome assembly and polishing, gene prediction, genome annotation, and comparative species genomes analysis.

Currently, the complete sequence map of more than 90% bacterial strains can be constructed by making use of a combination of Illumina HiSeq and PacBio SMRT systems. Pacbio RS II system can achieve complete genome assembly even in the regions of high or low GC content, as well as repetitive sequences. The complete sequence map of the rest 10% bacterial strains can be achieved with Sanger sequencing data. CD Genomics has completed hundreds of bacterial genome assembly cases without gap.

A closed, high-quality genome sequence for C. autoethanogenum DSM10061 was generated using only using PacBio sequencing to achieve "0 Gap" assembly and without the need for manual finishing. But there are still many gaps in the genome obtained using Illumina and 454 sequencing platforms. C.autoethanogenum and C. ljungdahliiare were indistinguishable at the 16S rRNA gene level and had high scores for similarity. Through whole-genome sequencing, it was found that there were significant differences in CRISPR system, hydrogenase and other aspects between the two, which were difficult to detect through second-generation sequencing.

CD Genomics is providing PacBio SMRT sequencing to complement our NGS facility. By taking advantage of the long-read and single molecular sequencing capability developed by PacBio, we are proud to offer advanced genome de novo assembly solutions and full-length gene/transcript sequencing strategy to suit your project needs.

Single Molecular Real-Time (SMRT) sequencing employs a specialized flow cell with many thousands of individual picolitre wells with transparent bottoms -- zero-mode waveguides (ZMW). The polymerase is fixed to the bottom of the well and allows the DNA strand to progress through the ZMW. As a result, the system can focus on a single molecular. SMRT sequencing allows for real-time imaging of fluorescently tagged nucleotides that are synthesized along individual DNA template molecules. The sequencing reaction ends when the template and polymerase dissociate. The average read length from the PacBio instrument is approximately 2 kb, and some reads may be over 20 kb. Longer reads are especially useful for de novo assemblies of novel genomes that can span many more repeats and bases.

Highly repetitive elements found in both eukaryotic and prokaryotic genomes pose a challenge for genome assembly and make the detailed study of repetitive sequences difficult. Long-read sequencing delivers reads in excess of several or dozens of kilobases (kbs), which can span complex or repetitive regions with a single continuous read, allowing for the resolution of these large structural features. Besides considerably longer and highly accurate DNA sequences from individual unamplified molecules, it can also exhibit where methylated bases occur, thereby providing functional information about DNA methyltransferases encoded by the genome. PacBio SMRT sequencing has unique advantages in studies of de novo genomics, metagenomics, transcriptomics and epigenetics.

We utilize the advanced PacBio SMRT instruments (PacBio SR II and PacBio Sequel) for several research purposes including whole-genome de novo genome assembly, full-length target sequencing, metagenomics studies, full-length transcripts sequencing, and genome-wide DNA modification analysis. Our highly experienced expert team executes quality management following every procedure to ensure confident and unbiased results.

CD Genomics is providing PacBio Single Molecular Real-Time (SMRT) sequencing to increase your research method for bacterial whole genome sequencing. A comprehensive view of the bacterial genome, including genes, regulatory regions, IS elements, phage integration sites, and base modifications is vital to understanding key traits such as antibiotic resistance, virulence, and metabolism.

At CD Genomics, we are using the long-read PacBio Sequel platform to support researchers all over the word with bacterial de novo whole genome sequencing needs. Our bioinformatics analysis include: Genome assembly and polishing, gene prediction, genome annotation, and comparative species genomes analysis.

Currently, the complete sequence map of more than 90% bacterial strains can be constructed by making use of a combination of Illumina HiSeq and PacBio SMRT systems. Pacbio RS II system can achieve complete genome assembly even in the regions of high or low GC content, as well as repetitive sequences. The complete sequence map of the rest 10% bacterial strains can be achieved with Sanger sequencing data. CD Genomics has completed hundreds of bacterial genome assembly cases without gap.

A closed, high-quality genome sequence for C. autoethanogenum DSM10061 was generated using only using PacBio sequencing to achieve "0 Gap" assembly and without the need for manual finishing. But there are still many gaps in the genome obtained using Illumina and 454 sequencing platforms. C.autoethanogenum and C. ljungdahliiare were indistinguishable at the 16S rRNA gene level and had high scores for similarity. Through whole-genome sequencing, it was found that there were significant differences in CRISPR system, hydrogenase and other aspects between the two, which were difficult to detect through second-generation sequencing.

RNA-Seq delivers an unbiased and unprecedented high-resolution view of the global transcriptional landscape, which allows an affordable and accurate approach for gene expression quantification and differential gene expression analysis between multiple groups of samples. RNA-Seq can identify novel and previously-unexpected transcripts without the need for a reference genome, allowing de novo assembly of new transcriptome that is not previously studied before. It also enables the discovery of novel gene structures, alternatively spliced isoforms, gene fusions, SNPs/InDel, and allele-specific expression (ASE).

i. RNA-Seq is a sensitive tool for gene expression profiling. Compared to microarray, RNA-Seq offers a digital read that is more accurate for all gene expression.

The authors found 1089 genes differentially expressed between the CLL and normal B cells (Table 1). As was expected, the most differentially expressed genes are immunoglobulins due to the clonality of the CLL cells. Pathway analyses revealed that genes involved in metabolic pathways had higher expression in CLL, while genes related to splicesome, proteasome, and ribosome were substantially down-regulated in CLL.

Figure 1. CLL transcriptional landscape. (A) The coding potential of differentially expressed genes between the CLL and normal samples. (B) Normalized expression of transposable elements (TEs). (C) Genes with condition-specific splicing ratios. (D) Allele-specific expression of somatic mutations.

Figure 4. Major transcriptional CLL subgroups. (A) Clustering of CLL and normal samples. (B) Consensus cluster. (C) Multidimensional scaling of CLL and normal samples based on gene expression. (D&E) Enrichment score plot.

CD Genomics provides robust transcriptome research service down to single-cell input levels in high-quality samples These global gene expression patterns in single cells already have dramatically advanced cell biology.

Cells are the basic unit of life and each cell is unique. The ability to reveal complex cellular events in biological systems is critical to a better understanding of cellular contributions during development or in disease progression. Gene expression research at the single-cell resolution on samples composed of mixed cell populations allows for deep insight into c into the transcriptome complexity of diverse cell types.

The advent of cell sorting/partitioning technologies, such as flow cytometry and microfluidics, has made it possible to capture single cells, and the DNA or RNA of single cells is amplified for single-cell sequencing. The general workflow for single-cell RNA sequencing is outlined below.

Fluidigm C1 Single-Cell mRNA Workflow. With Fluidigm C1 system, We provide single-cell transcriptome profiling service at an optional scale. C1 can rapidly and reliably capture and process individual cells. The steps in Integrated C1 Single-Cell mRNA Seq workflow include fluidics circuits (IFCs) to capture cells, convert polyA+ RNA into full-length cDNA, and perform universal amplification of the cDNA. With the customizable microfluidic circuits, C1 enables seamlessly transition from identifying critical cell populations to generate sequencing libraries for transcript 3′ End Counting, full-length mRNA sequencing, DNA sequencing, epigenetic analysis, micro-RNA expression profiling and more.

CD Genomics provides accurate and reliable HLA typing service based on next-generation sequencing (NGS) technology that generates unambiguous, phase-resolved HLA sequencing results in a single assay.

The HLA (human leucocyte antigen) system encodes the major histocompatibility complex (MHC) proteins in humans. These integral cell membrane glycoproteins are responsible for the regulation of the human immune system. There are two classes of MHC, i.e., MHC class I and MHC class II. The HLA gene complex is located on a 3.6 Mb region within chromosome 6p21. They are the most polymorphic gene family found in the human genome, with more than 10,000 different HLA alleles reported to date, thus the capacity to mount an immune response can be dramatically different between individuals within a cohort selected from a single population. HLA genes have been strongly implicated in transplant rejection, autoimmune disease, vaccine pharmacogenomics, cancer, infectious diseases, and mate selection.

HLA genotyping is the identification of the HLA class I and class II gene polymorphisms for individuals, which is indispensable for transplant matching and disease association studies. Unambiguous HLA genotyping is technically challenging owing to high polymorphism in various genomic regions. The development of NGS has changed this landscape of genotyping. High-resolution HLA genotyping by using PCR and NGS is uniquely able to address limitations of traditional HLA genotyping and Sanger sequencing assays in patients. It enables robust, simple, high-quality, and high-throughput analysis of the key HLA genes, data can be phased to a minimum of 6 digits. Another advantage is that phasing problem is determined since DNA templates are derived from single molecules.

Our HLA typing service has been widely applied in organ transplantation, population evolution, gene therapy, as well as immunological disease and cancer studies.

Our highly experienced expert team executes quality management following every procedure to ensure comprehensive and accurate results. Our HLA typing workflow is outlined below, including DNA isolation, HLA gene capture, library preparation, high-throughput sequencing, and bioinformatics analysis.

16S/18S/ITS Amplicon Sequencing has now been a well-established method for microbial identification and phylogeny studies of samples from complicated microbiomes or environments. In addition to next-generation sequencing platforms, CD Genomics also provides full-length 16S/18S/ITS amplicon sequencing by using PacBio SMRT sequencing technology.

As depicted in Figure 1, the beta diversity analysis discriminated HNSCC from control samples. PCA (Principal Component Analysis) reveals that the microbial communities in HNSCC patients are significantly different from those in control samples. NMDS revealed that the microbial communities in HPV- oropharyngeal samples are significantly different from those in HPV- oral cavity patients.

The OTU network depicted in Figure 3 significantly discriminates the HNSCC samples from normal samples, and HPV negative from HPV positive samples. The total abundance of Streptococcus, Dialister, and Veillonella had a different dominance in tumor samples and control samples.

Amplicon sequencing is based on NGS technology or PacBio SMRT sequencing. The ultra-deep sequencing of amplicons (PCR products) allows efficient variant identification and characterization. This technique has a wide range of applications, including 16S/18S/ITS gene sequencing, SNP genotyping, CRISPR sequencing, somatic/complex variant discovery, antibody screening sequencing, immune repertoire sequencing, et al.

Whether you would like to detect the diversity of microbial communities or discover rare somatic mutations in complex samples. CD Genomics could provide professional, cost-efficient and high-speed amplicon sequencing services to meet your project requirements.

With decades of experience in the fields of genome sequencing, CD Genomics is devoted to providing the accurate and affordable microbial whole genome sequencing service. We combine both Illumina (short reads) and PacBio (long reads) platforms for microbial re-sequencing and complete genome de novo sequencing . Our strong expertise is enhanced by flexible sequencing strategies and professional bioinformatics pipelines.

Microbial whole genome sequencing yields tons of data enabling a comprehensive evaluation of all genetic features of an isolated microorganism. Shotgun sequencing strategy is a primary method of microbial whole genome sequencing. The sequencing steps do not need labor-intensive mapping and cloning, which saves tremendous time and money. Furthermore, high-throughput sequencing allows us to sequence hundreds of bacteria or viruses at the same time with the power of multiplexing. In whole genome shotgun sequencing, the whole genome is broken up into small fragments for sequencing, and then assembled together by computational method based on the overlapped regions, hence not requiring a reference genome. PacBio SMRT technology enables us to provide bacterial de novo whole genome sequencing and fungal de novo whole genome sequencing that generate more accurate and contiguous sequences.

Microbial whole genome sequencing is crucial for precise microbial identification, the generation of complete reference genomes (de novo sequencing), comparative genomic studies (re-sequencing), and genomic exploitation. Comparative genomic studies can identify individual genetic variations and large-scale structural variations within a population for which a reference genome is available. Evolutionary characteristics and phylogenetic relationships can be hence inferred. Microbial whole genome sequencing provides the possibility of gene finding and annotation. After multiple genes are explained, novel biochemical pathways that may be beneficial for medicine and biotechnology will likely be identified.

There are three ways to ensure the accuracy of genome assembly: (i) prior to assembly, correct sequences in the consensus sequence; (ii) correct the results of sequence assembly utilizing sequencing data; (iii) correct the results of sequence assembly utilizing high quality next generation sequencing data. After the three corrections, the accuracy of final sequence assembly can reach 99.99%.

CD Genomics is providing PacBio Single Molecular Real-Time (SMRT) sequencing to increase your research method for bacterial genome sequencing. A comprehensive view of the bacterial genome, including genes, regulatory regions, IS elements, phage integration sites, and base modifications is vital to understanding key traits such as antibiotic resistance, virulence, and metabolism.

At CD Genomics, we are using the long-read PacBio Sequel platform to support researchers all over the word with bacterial de novo whole genome sequencing needs. Our bioinformatics analysis include: Genome assembly and polishing, gene prediction, genome annotation, and comparative species genomes analysis.

Currently, the complete sequence map of more than 90% bacterial strains can be constructed by making use of a combination of Illumina HiSeq and PacBio SMRT systems. Pacbio RS II system can achieve complete genome assembly even in the regions of high or low GC content, as well as repetitive sequences. The complete sequence map of the rest 10% bacterial strains can be achieved with Sanger sequencing data. CD Genomics has completed hundreds of bacterial genome assembly cases without gap.

A closed, high-quality genome sequence for C. autoethanogenum DSM10061 was generated using only using PacBio sequencing to achieve "0 Gap" assembly and without the need for manual finishing. But there are still many gaps in the genome obtained using Illumina and 454 sequencing platforms. C.autoethanogenum and C. ljungdahliiare were indistinguishable at the 16S rRNA gene level and had high scores for similarity. Through whole-genome sequencing, it was found that there were significant differences in CRISPR system, hydrogenase and other aspects between the two, which were difficult to detect through second-generation sequencing.