Tools for genomic and transcripomic analysis

RNA

For RNA analysis, FGC provides a broad range of tools allowing answering basically every question of transcriptomic analysis at every level of resolution. We can provide you for example with accurate expression profiles from as few as ten cells or we can provide you with the complete information of expression including all classes of transcripts from miRNAs to standard mRNAs, non-polyadenylated transcripts, unknown transcripts and all variants of splicing. FGC helps researchers to identify the optimal tool to answer your scientific question. Below you find some of the tools and technologies for RNA analysis.

Pico Profiling

This method that was developed by us (Gonzalez Roca et al., 2010) allows generating expression profiles from as few as 10 cells. It is based on a combination of optimized RNA isolation, amplification and labeling. Pico Profiling generates expression profiles equally accurate as other methods do it from millions of cells. The expression profiles are currently generated using microarrays.
mRNA expression profiling
Transcriptome analysis is performed at various levels of resolution, dependent on your needs. We provide you with measurements of one value per gene, or per exon, whatever you prefer. We can focus on well known transcripts or discover new transcripts, and analysis can include or exclude non-polyadenylated transcripts. Starting material is usually between 25 and 100 ng total RNA. Alternative protocols for low input are available.

Our expression profiling platforms are

• RNA-Seq
• Microarray expression profiling

Small RNA (miRNA) analysis

The FGC provides the Affymetrix and Agilent miRNA microarrays for quantification of well characterized small RNAs and miRNAs of over 70 organisms. Minimal amount is 120 ng total RNA.
For discovery of novel small RNAs (miRNAs, piRNAs and other types of small RNAs) and quantification, FGC offers small RNA sequencing. Minimal amount is 100 ng total RNA .

DNA

For DNA analysis, FGC provides a broad range of tools allowing answering basically every question of genomic analysis at every level of resolution. As a rule of thumb, large amplifications and deletions are often most efficiently analyzed on microarrays, while small InDels and point mutations are best detected by massive parallel sequencing (NGS, Next Generation Sequencing, Illumina).

DNA copy number variation (CNV analysis, CGH)

CNV analysis at a resolution of 10-100kb is performed on all organisms for which expression arrays are available from Affymetrix. This is made possible through a method developed in our lab (Auer et al., 2007), which hybridizes genomic DNA to expression arrays and quantifies DNA copy numbers from the hybridization signals. In addition, Agilent provides a broad spectrum of arrays dedicated to CNV analysis for many organisms. Minimal amount: 500 ng genomic DNA.

CNV analysis is also performed by genome sequencing, especially for organisms with a smaller genome (Drosophila, yeast etc.). Together with CNV information, many other types of genetic alterations (point mutations, InDels, translocations, inversions) are studied in the same experiment. Minimal amount: 200 ng genomic DNA.

ChIP-Seq

Characterisation of transcription factor binding sites and location of histone modifications is best performed by sequencing ChIP material. In organisms with a complex genome like the human or mouse, the optimal baseline (control antibodies, ChIP-input) has not yet been determined. Minimal amount: 10 ng ChIPed DNA.

DNA methylation

Analysis of multiple loci for DNA methylation can be performed from methylated DNA immunoprecipitation material (MeDIP) using microarrays or sequencing. For specific projects regarding DNA methylation, please contact the facility. Minimal amount: 10 ng MeDIPed DNA.

Genomic DNA sequencing, Exome sequencing, targeted regions sequencing

To study genetic alterations down to the level of individual nucleotides, Next Generation Sequencing (NGS) is the method of choice. Sequencing of genomic DNA provides at the same time accurate quantification of CNVs. Information on CNVs is less accurate for Exome and targeted regions sequencing. Minimal amount: 200 ng genomic DNA.

Alteration of gene expression

These services are available only for researchers of IRB Barcelona and IBMB (CSIC).

Human & mouse shRNAs

shRNA clones come in lentiviral vectors for efficient infection of many cell types, including non-dividing ones. On average, we provide our internal users with 4-5 different clones per gene. In many cases, the clones targeting the same gene provide different knock-down efficiencies and help to control off-target effects. Approximately 75% of all human and mouse refseq genes are targeted. The complete list of shRNA clones is available on www.dnaarrays.org. Detailed information about the TRC1 clones is available on Sigma Aldrich’s website.

Human ORF clones

The Open Biosystems ORF library provides researchers with approximately 13,000 clones for expression of one ORF per gene. These clones are most frequently used for over-expression of genes but can also be used as probes. ORF clones contain the Gateway system for hassle-free transfer into any kind of expression vector.

The list of available ORF clones can be consulted on www.dnaarrays.org. Detailed information about the ORF clones is available on Open Biosystem's ORF webpage.