The Microarray Core provides services for genome-wide analysis of gene expression, nucleotide variation, copy number variation, and chromatin protein binding sites. The core platforms include microarrays and "next generation" sequencing. Consultation on experimental design, and assistance with data analysis are also available.
The Microarray Core carries out gene expression profiling on 3' arrays and on Exon arrays; genotyping and comparative genomic hybridization both on single nucleotide polymorphism (SNP) arrays, and Chromatin ImmunoPrecipitation localization (ChIP-on-Chip). All services use oligonucleotide microarrays. Biostatistical support to assist in analyzing the data is available. The services of the Core are accessible to DFCI investigators and to investigators outside of DFCI.
Facility has 2 of these instruments.
Facility has 8 of these instruments.
Facility has 2 of these instruments.
Facility has 3 of these instruments.
SOLiD (Sequencing by Oligonucleotide Ligation and Detection) sequencer
"The consultation involves educating and helping with troubleshooting. The staff will not perform analyses for investigators."
"A number of methods have been used to compare the absolute or relative expression of genes in two or more specimens. These include S.A.G.E. (Serial Analysis of Gene Expression), differential display, cDNA and oligonucleotide microarrays, and other methods. The Microarray Core offers a gene expression profiling service that uses oligonucleotide microarrays. Using this method, the RNA of interest is converted into cDNA, then amplified and labeled with biotinylated nucleotides by in vitro transcription to produce biotinylated cRNA. The cRNA is hybridized to a microarray chip. The bound cRNA is stained with fluorescent streptavidin. The microarray chip is then scanned using a laser, and the positions and intensities of the fluorescent emissions are captured. These measurements provide the basis of subsequent biostatistical analysis."
"The Microarray Core at Dana-Farber Cancer Institute offers several SNP analysis options.
The Mapping 500K Set is comprised of two chips, Mapping Nsp and Mapping Sty, that may be analyzed together (500K) or separately (250K Nsp or 250K Sty). Each of the two arrays is designed to discriminate alleles at approximately 250,000 dimorphic positions in the human genome. These microarrays have been particularly useful in cancer research for carrying out genome-wide analysis of allelic changes (including deletions, amplifications, and gene conversions) in tumors. They are also useful in linkage analysis. At this time, only DNA from a fresh or frozen source can be analyzed on the SNP microarrays.
The SNP 6.0 array is a single array that contains probes for SNP discrimination at over 900,000 loci plus approximately 940,000 probes at non-SNP loci. It therefore provides a higher resolution analysis of both SNP genotypes and copy number variations than can be obtained with the 250K arrays either singly or in combination.
The Mouse Diversity array is a single array that contains probes for SNP discrimination at approximately 600,000 loci plus probes for approximately 900,000 non-polymorphic regions. High density genotype information can be obtained from the SNP probes; high resolution copy number data can be obtained from both the SNP and non-polymorphic probes.
The sample processing procedures for the 500K, 250K, SNP 6.0 and Mouse Diversity assay are similar in that all use restriction digestion, adapter ligation, PCR, fragmentation and biotinylation. Details of each procedure can be found below."
"Human tiling arrays are designed by dividing the non-repetitive sequence of a genomic region or regions into contiguous 35 base pair units. A 25-mer is designed from each of these units (Promoter and Whole Genome arrays) or overlapping 7 base pair (ENCODE array) or 16 base pair (Chromosome 21/22 array) units The collection of these 25-mers comprises a tiling array. The arrays are useful for the localization of the genomic binding sites of transcription factors and other chromatin associated proteins. In addition to the human arrays (ENCODE, chromosome 21/22, promoter, whole genome), mouse arrays (promoter, whole genome), whole genome arrays for c.elegans, drosophila, s.cerevisiae, s.pombe and arabidopsis are also available.
The process is as follows: an investigator performs chromatin immunoprecipitation, uses LM-PCR to amplify the DNA that has been extracted from the immunoprecipitate, fragments and biotinylates the PCR products, then submits those products to the Microarray Core for hybridization, staining and scanning."