BioMicroCenter:Genome Seq: Difference between revisions
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== Sample Submission Guidelines == | == Sample Submission Guidelines == | ||
'''Users are required to prepare their own libraries for sequencing''' by following the corresponding Illumina [[BioMicroCenter:Protocols| Protocols]]. If this is a service that you would like the BMC to perform in the future please visit the [[BioMicroCenter:Ideas|Ideas]] page. | '''Users are required to prepare their own libraries for sequencing''' by following the corresponding Illumina [[BioMicroCenter:Protocols| Protocols]]. If this is a service that you would like the BMC to perform in the future please visit the [[BioMicroCenter:Ideas|Ideas]] page. Illumina Paired End sample preparation kits can be purchased through the BioMicro Center for $3,600.00 plus shipping costs (10 sample preps per kit). To request an order or for more information please contact [[BioMicroCenter:People|Ali Perrotta]] | ||
Samples which are ready for sequencing should be gel-purified according to your protocol, and provided as at least 5uL of solution at a concentration of at least 10 nM in EB/ Tween 0.1%. To calculate your sample’s molar concentration, you must know the average length of your product. | Samples which are ready for sequencing should be gel-purified according to your protocol, and provided as at least 5uL of solution at a concentration of at least 10 nM in EB/ Tween 0.1%. To calculate your sample’s molar concentration, you must know the average length of your product. | ||
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When submitting a sample you must supply the BMC with the molar concentration, average length, and species of origin of all samples. | When submitting a sample you must supply the BMC with the molar concentration, average length, and species of origin of all samples. | ||
We encourage all those submitting samples to allow us to run QC | We encourage all those submitting samples to allow us to run QC to obtain/confirm concentration information. For more information on our QC methods please see the [[BioMicroCenter:Sequencing_Quality_Control|Sequencing Quality Control]] page. | ||
Samples generated using standard kits with Illumina PCR primers can be submitted without sequencing primers. Custom sample preparations using customized PCR primer sequences should be provided along with a complementary sequencing primer. | Samples generated using standard kits with Illumina PCR primers can be submitted without sequencing primers. Custom sample preparations using customized PCR primer sequences should be provided along with a complementary sequencing primer. |
Revision as of 08:37, 29 July 2009
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Genome Seq
De novo sequencing can be done using the Genome Analyzer. Read lengths have recently been increased and data associated with these long reads look very good! http://illumina.com/downloads/ch2-ILMN_ProdGuide_DNAsequencing.pdf
Sample Submission Guidelines
Users are required to prepare their own libraries for sequencing by following the corresponding Illumina Protocols. If this is a service that you would like the BMC to perform in the future please visit the Ideas page. Illumina Paired End sample preparation kits can be purchased through the BioMicro Center for $3,600.00 plus shipping costs (10 sample preps per kit). To request an order or for more information please contact Ali Perrotta
Samples which are ready for sequencing should be gel-purified according to your protocol, and provided as at least 5uL of solution at a concentration of at least 10 nM in EB/ Tween 0.1%. To calculate your sample’s molar concentration, you must know the average length of your product.
When submitting a sample you must supply the BMC with the molar concentration, average length, and species of origin of all samples.
We encourage all those submitting samples to allow us to run QC to obtain/confirm concentration information. For more information on our QC methods please see the Sequencing Quality Control page.
Samples generated using standard kits with Illumina PCR primers can be submitted without sequencing primers. Custom sample preparations using customized PCR primer sequences should be provided along with a complementary sequencing primer.
Data
Images acquired from the solexa sequencer are processed through the bundled solexa inage extraction pipeline to get the sequence and quality score for each base. The data is aligned to a reference genome, if requested, using an interative ELAND algorithm. An in-depth QC report is included in the package. Sample QC report is here.
Turnaround Time
Each Genome Analyzer processes 8 samples per run, or 7 samples plus a control. The control is typically used to improve sequence quality. Full flowcells can be run usually within two weeks of submission. Partial submissions of less than eight samples (or 7 with control) are put into a project queue, where they join existing samples or await others before processing. Wait times for partial submissions vary depending on demand from other users.
Once the run has begun approximately 10 days are required for clustering, sequencing, and data analysis for a Paired End read (36 bp read x 2).
Pricing
Illumina sequencing is currently available only for labs associated with the BioMicro Center Core departments.
ILLUMINA SEQUENCING | CORE LAB/MIT | Non-MIT | unit | Notes |
---|---|---|---|---|
Paired End (36+36nt) | $1,375 | $2,000 | per lane | Includes quality control (RT-PCR or BioAnalyzer, sequencing, genome alignment and data storage of Firecrest/IPAR files for 2 yrs. |
Add'l 36nt | $295 | $370 | per lane | |
Illumina Multiplexing | $200 | $300 | per flow cell | Uses 6nt. Cost is divided by number of lanes requiring the multiplex reads. |
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Genome Seq Literature
<biblio>
- Paper1 pmid=18677319