BioMicroCenter:Illumina Sequencing: Difference between revisions
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Illumina currently provides reagents and support for a five major sequencing applications: | Illumina currently provides reagents and support for a five major sequencing applications: | ||
* [[ChIP_Seq|ChIP Seq]] | * [[BioMicroCenter:ChIP_Seq|ChIP Seq]] | ||
* [[Expression_Seq|RNA Seq]] | * [[BioMicroCenter:Expression_Seq|RNA Seq]] | ||
* [[Small_RNA_Seq|Small RNA Sequencing]] | * [[BioMicroCenter:Small_RNA_Seq|Small RNA Sequencing]] | ||
* [[Genome_Seq|Genome sequencing and resequencing ]] | * [[BioMicroCenter:Genome_Seq|Genome sequencing and resequencing ]] | ||
* [[PEM|Paired End Sequencing]] | * [[BioMicroCenter:PEM|Paired End Sequencing]] | ||
Other DNA Sequencing applications: The following applications have been published but do not yet have kits from Illumina. | Other DNA Sequencing applications: The following applications have been published but do not yet have kits from Illumina. | ||
* Genotyping: Protocols are being developed for detection of SNPs, chromosomal rearrangements and other genotyping applications. <br> | * Genotyping: Protocols are being developed for detection of SNPs, chromosomal rearrangements and other genotyping applications. <br> | ||
* [[GRO_Seq|Genome Wide Nuclear Run-on Analysis (GRO-seq)]]: This method allows for the detection of nascent transcripts directly associated with the genome. GRO-seq was developed by John Lis at Cornell University. Reference: http://www.sciencemag.org/cgi/content/abstract/1162228 | * [[BioMicroCenter:GRO_Seq|Genome Wide Nuclear Run-on Analysis (GRO-seq)]]: This method allows for the detection of nascent transcripts directly associated with the genome. GRO-seq was developed by John Lis at Cornell University. Reference: http://www.sciencemag.org/cgi/content/abstract/1162228 | ||
== Data Analysis == | == Data Analysis == | ||
Each lane of the flow cell should produce sequence from between 2 and 5 million DNA fragments. Understanding this data often requires a significant investment in informatics. This is complicated by the fact that many applications require entirely different interpretations of the data. As part of our sequencing service we provide many of the early steps of bioinformatics for different applications. Further data processing can be arranged on a collaborative basis as resources are available. For more information, check out the links below: | Each lane of the flow cell should produce sequence from between 2 and 5 million DNA fragments. Understanding this data often requires a significant investment in informatics. This is complicated by the fact that many applications require entirely different interpretations of the data. As part of our sequencing service we provide many of the early steps of bioinformatics for different applications. Further data processing can be arranged on a collaborative basis as resources are available. For more information, check out the links below: | ||
* [[IlluminaDataPipeline#Basics|Illumina pipeline - How it works!]] -- ''under construction'' | * [[BioMicroCenter:IlluminaDataPipeline#Basics|Illumina pipeline - How it works!]] -- ''under construction'' | ||
* [[IlluminaDataPipeline#Output_Files|Illumina pipeline output formats]] -- ''under construction'' | * [[BioMicroCenter:IlluminaDataPipeline#Output_Files|Illumina pipeline output formats]] -- ''under construction'' | ||
* [[BioMicroCenter:Computing#BioInformatics_Services|Bioinformatic Consulting]] | * [[BioMicroCenter:Computing#BioInformatics_Services|Bioinformatic Consulting]] | ||
== Pricing == | == Pricing == | ||
Illumina sequencing is currently available '''only''' for labs associated with the BioMicro Center [[CoreDeps|Core departments]]. Sequencing is currently available at an '''introductory''' price: | Illumina sequencing is currently available '''only''' for labs associated with the BioMicro Center [[BioMicroCenter:CoreDeps|Core departments]]. Sequencing is currently available at an '''introductory''' price: | ||
'''Single End Reads:''' '''Paired End Reads:''' | '''Single End Reads:''' '''Paired End Reads:''' | ||
Revision as of 15:34, 7 January 2009
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ILLUMINA MASSIVELY PARALLEL SEQUENCING
The MIT BioMicro Center has one high-throughput Solexa Genome Analyzers 2.0 (Illumina), which is currently being used for a variety of applications, including ChIP-Seq, miRNA sequencing and expression sequencing. The next-generation sequencer can process up to 16 samples per week, with a data yield of approximately 10 million reads per sample. Read lengths can be any length upto 36 bases. Longer runs (upto 72nt) should be available in early 2009.
Illumina sequencing works by binding randomly fragmented DNA to an optical flowcell . Templates are sequenced by incorporating fluorescently labeled nucleotides in a “Sequencing-By-Synthesis” reaction. A detailed description of this process can be found here: http://illumina.com/pages.ilmn?ID=203
The system consists of a cluster generation station, a Paired-End module, and a Genome Analyzer, all of which work in concert to generate and analyze flowcells. An overview of the Illumina Genome Analyzer system can be found at the Illumina website: http://illumina.com/pages.ilmn?ID=204
Applications
Illumina currently provides reagents and support for a five major sequencing applications:
Other DNA Sequencing applications: The following applications have been published but do not yet have kits from Illumina.
- Genotyping: Protocols are being developed for detection of SNPs, chromosomal rearrangements and other genotyping applications.
- Genome Wide Nuclear Run-on Analysis (GRO-seq): This method allows for the detection of nascent transcripts directly associated with the genome. GRO-seq was developed by John Lis at Cornell University. Reference: http://www.sciencemag.org/cgi/content/abstract/1162228
Data Analysis
Each lane of the flow cell should produce sequence from between 2 and 5 million DNA fragments. Understanding this data often requires a significant investment in informatics. This is complicated by the fact that many applications require entirely different interpretations of the data. As part of our sequencing service we provide many of the early steps of bioinformatics for different applications. Further data processing can be arranged on a collaborative basis as resources are available. For more information, check out the links below:
- Illumina pipeline - How it works! -- under construction
- Illumina pipeline output formats -- under construction
- Bioinformatic Consulting
Pricing
Illumina sequencing is currently available only for labs associated with the BioMicro Center Core departments. Sequencing is currently available at an introductory price:
Single End Reads: Paired End Reads: 7 lanes | 8 lanes 7 lanes | 8 lanes $610 | $550 per lane $1105 | $980 per lane
Protocols
Protocols for all of the supported technologies can be found by visiting the Protocols page
Initial page written by Summeet Gupta at the WI-CGT
