True Single Molecule Sequencing Services

BioInformatics

NGS data interpretation and the ability to re-mine that data is increasingly important to companies. SeqLL provides a complete bioinformatics solution to help maintain timelines and identify critical knowledge related to drug candidate action and effect. Our implementation for each project is specific, efficient and cost effective. SeqLL bioinformatics specialists will work with your team to define and confirm your exact requirements and deliver information that answers the questions your program is investigating. Once complete, the results are reviewed with you at a closing meeting or the next step in the program.

Interpretation - including raw reads, filtered reads, aligned reads (when applicable), sequence information and data files are provided with each sequencing project.

Basic Bioinformatics - Data interpretation starts with informed reads, quality control, Digital Gene Expression (DGE), box plots and bar graphs.

Advanced Bioinformatics - Typically this expands the report to include Differentially Expressed Gene (DEG), gene ontology and pathway analysis to gain additional insight.

Custom Bioinformatics - combine your molecule or target specific expertise with our analysis experience to gain non-intuitive insight to ADARediting, vlincRNA construction, CAGE analysis and other specific complex statistical analysis. Re-evaluate existing data for additional correlation and discovery.

DRS - Direct RNA Sequencing

Sequence RNA transcripts directly without conversion to cDNA. The technology offers direct observation of RNA and allows you to understand the true nature of normal and disease transcriptomes and pathways without adding sample preparation bias or sequencing artifacts.

DRS

• Simplified Sample Prep
• Single molecule synthesis and reads
• Authentic Transcriptome detail
• Bias free data creation or generation
• Evaluate 3’ end formation for gene expression studies
• Study transcription interference events
• Direct transcriptome investigations and expression regulation studies

Library Validation

Confirm that rare transcripts were not eliminated in the library preparation due to amplification bias. Combining high sensitivity with amplification independent single molecule sequencing tSMS is able to confidently detect and identify Differentially Expressed Genes and rare transcription modification events. Compare raw sample to the library prepared to uncover any biases.

FFPE - Formalin Fixed Paraffin Embedded

Sample degradation during processing or storage challenges other NGS systems to provide meaningful information and results. tSMS provides the coverage and sensitivity to accurately analyze and report content information from damaged and degraded FFPE samples.

cDNA based - RNA Seq -

allows investigators to design monitoring studies related to cancer, infectious diseases, age related diseases and genetic diseases. Complete detailed studies of the effect of transcriptome or phenotypes associated with disease progression and responses to standard and investigational treatment regimes. Typical applications include: • Transcript Identification revealing both dominant and rare pathogens • Splice Variant Analysis can provide the expression rate of the exons across a transcript identifying variants • Differentially Expressed Gene effect studies • Obscure correlation event studies for drug candidates or treatment regimes  

Epigenetics

is the study of DNA modification caused by environmental stresses that lead to changes in gene expression that can be passed to offspring. These changes leave the underlying DNA sequence untouched while altering gene expression, resulting in a new phenotype. These environmentally induced changes can also be transient (and potentially) reversible, creating an extremely complex situation to study and understand. The ability to understand and selectively switch faulty genes on or off through new drug development is extremely important in a variety of disease areas. Probe DNA and histone modifications at a single molecule level and correlate with sequence information to open up new areas of discovery, (see paper below).

Single-molecule decoding of combinatorially modified nucleosomes
Science 06MAY2016 Vol 352, Issue 6286
http://science.sciencemag.org/content/352/6286/717
Efrat Shema, Daniel Jones, Noam Shoresh, Laura Donohue, Oren Ram, Bradley E. Bernstein

Different combinations of histone modifications have been proposed to signal distinct gene regulatory functions, but this area is poorly addressed by existing technologies. We applied high-throughput single-molecule imaging to decode combinatorial modifications on millions of individual nucleosomes from pluripotent stem cells and lineage-committed cells.We identified definitively bivalent nucleosomes with concomitant repressive and activating marks, as well as other combinatorial modification states whose prevalence varies with developmental potency. We showed that genetic and chemical perturbations of chromatin enzymes preferentially affect nucleosomes harboring specific modification states. Last, we combined this proteomic platform with single-molecule DNA sequencing technology to simultaneously determine the modification states and genomic positions of individual nucleosomes. This single-molecule technology has the potential to address fundamental questions in chromatin biology and epigenetic regulation.