Next Gen Sequencing FAQs

1. Why are you using the Illumina Platform?

a. After gathering feedback from our customers and reviewing all Next Generation Sequencing platforms, we found that the Illumina platform is the current leader in Next Generation Sequencing. It offers the best combination of data quality and quantity, and is proved to be versatile for a wide variety of genomic applications. However, our goal is to serve your Next Gen Sequencing Needs with the leading technologies available. We are committed to continuously evaluating and adopting the most cutting-edge technologies as they become available.

2. What kind of projects can I do using NGS Illumina platform?

a. Please click here to explore the versatility of the Illumina Platform.

3. What’s the turn around time for Next Generation Sequencing samples?

a. Elim offers the fastest turn around for Next Gen Sequencing. The specific time requirement varies depending on the type of the run and length of the read that you require. It can take anywhere from a few days to two weeks. Generally, single-read 36bp runs require a week for data delivery.

4. Do I have to fill all 8 lanes of the Illumina flow cell to be eligible for an illumina run?

a. No. We charge you per lane, and keep in mind that you can have multiple samples run simultaneously in the same lane through multiplexing.

5. How do I order an Illumina Run?

a. Please "contact us" with your specific project needs so that we can design the run with you from the beginning stages.

b. Also, we like to run one of the lanes as a control to ensure that we are providing you with high quality data, so one full flow cell will have the capability to run 7 lanes of samples

6. Do you do library constructions as well?

a. Yes! Please "contact us" to discuss your specific project's needs!

7. What NGS applications can you support?

Our highly trained staffs have expertise in many NGS applications, including,

De novo Sequencing
Assemble contigs from millions of reads without a reference sequence.

Whole-Genome Resequencing
Discovery of genome-wide changes—copy number variations, chromosomal rearrangements (deletions, insertions, translocations, etc.), and single-nucleotide variations.

Targeted Sequencing (e.g., Exome Sequencing)
Isolation of specific targeted regions of the genome (all coding exons, immunoglobulin switching regions, regions identified by association studies) by long PCR or hybridization to oligonucleotide synthesized on arrays.

Whole-Transcriptome Profiling (e.g., mRNAseq, Tag Profiling)
Sequencing of random-primed cDNA libraries from RNA fractions (nuclear, cytoplasmic, polyA, capped, or small RNA) provides a high-resolution map of all RNA species. Sequencing of tags created by restriction digestion of cDNA generates gene expression profiles with an absolute count (from one to a few million) of the RNA in the sample.

Protein-DNA or Protein-RNA Interactions (e.g., ChIP sequencing)
Discovery of functional transcription factor binding sites across the whole genome and determination of patterns of DNA occupancy by nucleosomes, polymerases, etc. via immunoprecipitation of proteins bound to nucleic acids and the subsequent sequencing of the associated DNA or RNA (ChIP sequencing); selective isolation of DNA via enzyme trapping methods such as trapping of methyltransferases by DNA labeled with aza-nucleotides.

Determination of DNA methylation variation across the whole genome via bisulfite sequencing or sequencing of fragments generated by methylation restriction polymorphisms, purification of methylated fragments by antibody affinity, or methyltransferase trapping.

And Many More….

8. How NGS works on Illumina® Sequence-by-Synthesis

Your sample libraries are prepared and annealed to a flow cell. Each flow cell has 8 lanes, so you have the opportunity to run different templates for each lane. The prepared libraries are amplified into millions of clonal clusters, which are then sequenced one base at a time, in parallel, for each of the millions of clusters.

The base calling (sequencing data gathering) steps include incorporation of fluorophore-labeled nucleotides, fluorescence capture of the incorporated nucleotide, and cleavage of the fluorescence molecule. Each of these cycles are run 36, 50, 75, or 100 times, depending on your experimental requirements.

There is also the option to run either single read (only one end of the template clonal clusters will be sequenced) or paired-end read (both ends of the template clonal clusters will be sequenced). A Real Time Analysis program actively interprets the raw data to determine each base being incorporated as the sequence-by-synthesis occurs.
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