Tools for Genomic Analysis

Which type of genomic analysis tools works best for answering a specific question is dependent on the nature of the question. In general, questions regarding know and well-characterized transcripts (mRNAs and miRNAs) are answered more straight forward using microarrays. Gene discovery and characterization of ChIP material is done more efficiently by sequencing. Some frequently interrogated themes are described here:

RNA

microRNA analysis

FGC provides the Affymetrix miRNA GeneChip for miRNA analysis. For over 70 organisms, a comprehensive analysis of known miRNAs is performed on a single array.

Minimal amount: 250 ng total RNA

Discovery of novel small RNAs (miRNAs, piRNAs and other types of small RNAs) is most efficiently performed by sequencing.

Minimal amount: 1000 ng total RNA

mRNA expression profiling

For over 20 organisms, we provide Affymetrix expression arrays for mRNA profiling. These arrays provide a robust and reliable tool to quantify expression of the majority of known genes.

Minimal amount: 50 ng total RNA for ST arrays, 5 ng for 3' arrays

For over 100 organisms, we provide NimbleGen expression arrays for mRNA profiling. These arrays are especially suited for small genomes since multiple samples can be analyzed on a single array, leading to cost reduction.

Minimal amount: 1000 ng total RNA

RNA seq

By nature, this is performed by sequencing. It allows characterization of alternative splicing, transcriptional start and stop sites and discovery of novel transcripts. Sample processing and data analysis are highly experimental and do not follow standard operating procedures yet.

Minimal amount: 5000 ng total RNA

DNA

DNA copy number variation (CNV analysis)

CNV analysis at a resolution of 10-100kb is performed on all organisms where expression arrays are available from Affymetrix or NimbleGen. In addition, NimbleGen provides a broad spectrum of arrays dedicated to CNV analysis for many organisms.

Minimal amount: 5000 ng genomic DNA

Especially for organisms with a smaller genome (drosophila, yeast etc.), CNV analysis is also performed by genome sequencing. Together with CNV information, many other types of genetic alterations (point mutations, InDels, translocations, inversions) are studied in the same experiment.

Minimal amount: 5000 ng genomic DNA

ChIP-Seq

Characterization of transcription factor binding sites and location of histone modifications is best performed by sequencing the ChIP material. In organisms with a complex genome like human or mouse, the optimal baseline (control antibodies, ChIP-input) is not determined yet.

Minimal amount: 10 ng ChIPed DNA

DNA methylation

Analysis of multiple loci for DNA methylation is still performed in an experimental phase. For specific projects regarding DNA methylation, please contact FGC.