Genomics Sequencing Services
Sanger
Custom Sequencing
For custom sequencing submissions (≤24 samples) are supplied as purified DNA in 1.5ml eppendorf tubes. The procedure for custom sequencing analysis is for the customer to fill out a customer submission sheet located in the Principle Investigator folder and submit their samples in a sample box contained in a small refrigerator outside the entrance to our lab, S-18 in the basement of the Plant Biology Building.
High Throughput Sequencing
For large sequencing projects (≤24 sequences to whole genomes), samples can be supplied as either purified DNA or bacterial cultures in a 96 well format. DNA from bacterial cultures are purified at RTSF using Qiagen 3000 robots. Once the fluorescently labeled sequencing products are generated by PCR amplification, the products are separated by capillary electrophoresis on an ABI 3730 Genetic Analyzer. All sequence data and chromatograms are made available to researchers via the Internet through our Geospiza Finch server web interface.
Pricing
Custom Sequencing
Service |
Price/ Sample |
|---|---|
1-24 samples |
$10.50 |
|
$11.50 |
|
$12.50 |
|
$13.50 |
High Throughput Sequencing
Service |
Price/ Sample |
|---|---|
|
$4.85 |
|
$4.70 |
|
$3.50 |
|
$3.35 |
Overview
- We accept either purified plasmid DNA or PCR amplified DNA.
- Ten standard primers are offered by RTSF at no extra charge, or alternatively you can provide you own custom-designed primer.
- All samples for high throughput sequencing should be submitted to the RTSF facility at S18 Plant Biology Building (submission form). Purified DNA should be aliquoted into 96-well PCR plates sealed with foil tape (both available at RTSF). If submitting less than 96 samples, please arrange by column (i.e., A1-H1, A2-H2, etc) as opposed to rows. This allows us to use our equipment most efficiently. Sequences from purified DNA are often available within 48 hrs.
- Sequences can be obtained accessed and downloaded from our local Geospiza Finch server.
- Typically sequences from purified DNA can be obtained in as few as 2 working days. The times are best estimates and may be longer if demand exceeds capacity, or in the case of equipment failure. Inquire at the time of submittal. Using recommended plasmid vectors and bacterial strains, we typically obtain >80% usable sequences, although the efficiency of sequencing from some commonly used plasmid vectors and bacterial strains can be considerably less.
Next Gen - Illumnia
GAII and Hi Seq 2000
This ultra high-throughput sequencing systems support a wide range of genetic analysis applications from resequencing to de novo assembly, transcriptome profiling to the study of regulatory mechanisms. Powered by Illumina Sequencing technology, the Genome Analyzers can generate gigabases of data per run with the highest percentage of perfect reads.
The Genome Analyzer system are powered by Illumina Sequencing technology, which uses a massively parallel sequencing-by-synthesis four-dye approach to generate billions of bases of high-quality DNA sequence per run. Randomly fragmneted genomic DNA is attached to an optically transparent surface, a flow cell. These atteched fragments are extended and bridge amplified to create an ultra-high density flow cell generating up to 1.5 billion clusters. Each of these clusters contain ~1,000 copies of the same template and are sequenced using a propietary reversible terminator-based chemistry. The sequence reads are mapped against a reference genome and genetic difference called using a data analysis pipeline.
The Genome Analyzers have the flexibility to enable a wide range of genome-scale applications that differ only in sample preparation and downstream data analysis.
• whole-genome sequencing and resequencing, de novo sequencing, structural variation and CNV analysis
Transcriptome Analysis
Characterization of transcriptional activity, coding and non-coding in any organism. mRNA-Seq uses the mRNA-Seq protocol where full sequence is generated form any poly-A tailed RNA to analyze novel and rare transcripts, novel isoforms,alternative splice zones, and cSNPs in one experiment.
- dna methylation analysis
- protein-nucleic acid interaction analysis
Our Genome Analyzer II is equipped with a paired end module enabling researchers to sequence from both ends of a defined insert size fragmnet. This instrument can generate up to 95Gb of data, 30 million reads/lane and 60 million paired-end reads per lane.
Pricing
Sample Prep |
Price/ Sample |
|---|---|
Genomic 1-3 Samples |
$485.00 |
Genomic 4-7 Samples |
$425.00 |
Genomic Paired End 1-3 Samples |
$580.00 |
Genomic Paired End 4-7 Samples |
$520.00 |
mRNA Seq 1-3 Samples |
$555.00 |
mRNA Seq 4-7 Samples |
$470.00 |
ChIP 1-3 Samples |
$485.00 |
ChIP 4-7 Samples |
$425.00 |
Sequencing Run |
Price/ Flow Cell |
1 x 35nt |
$5,800.00 |
1 x 55nt |
$6,950.00 |
1 x 75nt |
$7,545.00 |
2 x 35nt (paired end) |
$10,020.00 |
2 x 55nt (paired end) |
$12,700.00 |
2 x 75nt (paired end) |
$13,890.00 |
Total Pricing will be the Sample Price multiplied by the # of samples plus the cost of the sequencing run. Sequencing run price depends on the number of cycles desired.
The HiSeq 2000 has the capacity to run 2 flow cells at one time increasing throughput. One flow cell can generate up to 300Gb of data and 187 million reads per lane or 370 million paired-end reads per lane.
Illumina HiSeq Pricing
Library preparation
mRNAseq |
|
$200 |
|
Genomic |
|
$175 |
|
Final Cost Per Sequencing run
|
Single read |
Paired end |
||
50 cycle |
100 cycle |
2x50 cycle |
2x100 cycle |
|
Per flow cell |
$8,810 |
$11,950 |
$14,030 |
$19,440 |
Per lane |
$1,101 |
$1,494 |
$1,754 |
$2,430 |
Bioinformatics
Contact Kevin Carr at carrk@msu.edu
Next Gen Roche 454
The 454 GSFLX Titanium Sequencer can obtain more than 100 million bases per run. No libraries, cloning and colony picking are needed, so there is no cloning bias. A typical bacterial genome can be sequenced in days very cost-effectively. The 454 sequencer uses pyro-sequencing instead of Sanger dideoxy-termination sequencing. It can be used for a wide range of applications including de novo sequencing of microbial genomes and BACs, high-throughput sequencing of small DNA fragments for expression profiling (SAGE or CAGE libraries), transcription analyses, identification of transcription factor binding sites (ChIP libraries), genome-wide miRNA analysis, and metagenomic analysis of complex biological samples.
Prices
Prices vary depending on the type and size of project, number of runs and other variables. The cost is in the range of $8800-$13,000 for each large titanium run with 1 sample. We would be glad to provide a quote for your project. A single large format (70×75) sequencing run (>400 Mb) is less than $14K which equates to about 20¢ per kb.
Bioinformatics
Contact Kevin Carr at carrk@msu.edu
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