Difference between revisions of "Services"
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==[[PEM| Paired-end sequencing]] == | ==[[PEM| Paired-end sequencing]] == | ||
The paired-end module of the GAII system allows both ends of a DNA fragment to be sequenced. This gives more specificity to alignment algorithms, especially in highly repetitive regions. The paired-end module allows for up to 36 bases of each end to be sequenced during the same sequencing run. | The paired-end module of the GAII system allows both ends of a DNA fragment to be sequenced. This gives more specificity to alignment algorithms, especially in highly repetitive regions. The paired-end module allows for up to 36 bases of each end to be sequenced during the same sequencing run. | ||
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[[PEM| More Details...]] | [[PEM| More Details...]] | ||
Revision as of 10:55, 2 July 2010
Contents
Sequencing
The GTC has two high-throughput Solexa Genome Analyzers 2.0 (Illumina), which are currently being used for a variety of applications, including ChIP-Seq, miRNA sequencing and expression sequencing. Each next-generation sequencer can process up to 16 samples per week, with a data yield of approximately 10 million reads per sample. Read lengths are 17, 26 or 36 bases. This sequencing technology consists of binding randomly fragmented DNA to an optical flowcell .
ChIP-Seq
ChIP-Sequencing (or ChIP-Seq) combines chromatin immunoprecipitation (ChIP) with DNA sequencing, allowing researchers to identify the binding sites of DNA-associated proteins. It can be used as an alternative to promoter or whole genome microarray hybridization or qPCR. http://illumina.com/downloads/ChIP-Seq_DataSheet.pdf
Genome sequencing and resequencing
De novo sequencing can be done using the Genome Analyzer, although the short read lengths can make assembly challenging, especially in larger genomes.
Paired-end sequencing
The paired-end module of the GAII system allows both ends of a DNA fragment to be sequenced. This gives more specificity to alignment algorithms, especially in highly repetitive regions. The paired-end module allows for up to 36 bases of each end to be sequenced during the same sequencing run.
Digital gene expression or RNA-Seq
We offer a mRNA Sequencing service utilizing the Genome Analyzer System (Solexa) from Illumina. Primarily, we offer:
Digital Gene Expression Sequencing Service: Digital Gene Expression is similar to SAGE analysis.
Whole Transcriptome Analysis: Sequencing the entire transcriptome can reveal valuable information about exon boundaries and splice variants that may be missed by microarray analysis or Digital Gene Expression. Kits for whole transcriptome analysis are expected to be available from Illumina soon.
Small RNA discovery
Small RNA discovery provides identification of non-coding RNA to aid in the understanding of gene regulation. It can be helpful in identifying novel small RNA molecules.
Microarray
Expression Analysis
We offer a Expression Analysis Service utilizing the 3 Plaforms - Agilent, Affymetrix and Custom Arrays.
ChIP on Chip/Location Analysis
ChIP-Chip (Chromatin IP on Chip, also called Genome Wide Location Analysis) is a method for studying the regulation of gene expression on a genome-wide scale. We offer labeling, hybridization and prelimary analysis services for 2 platforms - Agilent and Affymetrix.
miRNA Analysis
We offer a microRNA expression profiling service utilizing a microarray detection system that was developed specifically for microRNA detection.
Array Manufacturing
The Center of Microarray Technology can assist in the design, preparation and analysis of custom microarrays.
Other Services
RT PCR
The GTC features the 7900HT Fast Real-Time PCR system from Applied Biosystems for quantitative PCR. This highly flexible system supports both 96 and 384 well plate formats as well as the TLDA (TaqMan Low Density Array) card format.
Lab Use
The GTC offers Whitehead community members the opportunity to take advantage of our equipment for a nominal monthly charge of $250 per lab.
